Wayne State University

AIM HIGHER

Wayne State University

High Performance Computing Services

Publications

This space provides an area to showcase publications that have some relation to the Grid.
If you have published material that is in some way related to the Grid and you would like to have it displayed on this site then please write to Aragorn Steiger at aragorn@wayne.edu.

Barnholtz-Sloan Group

2007
Racial/Ethnic Differences in Survival Among Elderly Patients with a Primary Glioblastoma
Published in J Neurooncol (2007) 85:171–180 [Abstract]
Jill S. Barnholtz-Sloan1, John L. Maldonado2, Vonetta L. Williams3, William T. Curry4, Elizabeth A. Rodkey5, Frederick G. Barker II6, Andrew E. Sloan7
1. Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, OH 44106-5065, USA
2. H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
3. H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA; Department of Epidemiology and Biostatistics, University of South Florida College of Public Health, Tampa, Florida, USA
4. Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
5. H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
6. Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
7. Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, OH 44106-5065, USA
2008
Patterns of Care and Outcomes Among Elderly Individuals with Primary Malignant Astrocytoma
Published in J Neurosurg 108:642–648, 2008 [Abstract]
Jill S. Barnholtz-Sloan, Ph.D.1,2,3, Vonetta L. Williams, M.P.H.1,4, John L. Maldonado, B.S.1, Dilip Shahani1, Heather G. Stockwell, SC.D.4, Marc Chamberlain, M.D.1,2, and Andrew E. Sloan, M.D.1,3,5
1. H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
2. Department of Interdisciplinary Oncology, College of Medicine, Tampa, Florida
3. Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine
4. Department of Epidemiology and Biostatistics, College of Public Health, University of South Florida, Tampa, Florida
5. Department of Neurosurgery, University Hospitals–Case Medical Center, Cleveland, Ohio

Chen Group

2014
Large-Scale Deep Belief Nets With MapReduce
Published in IEEE Access, 2014 (2), 395-403 [Abstract]
Kunlei Zhang, Xue-Wen Chen
Dept. of Comput. Sci., Wayne State Univ., Detroit, MI, USA

Cheng Group

2007
A Complex Sum Method of Quantifying Susceptibilities in Cylindrical Objects: The First Step Toward Quantitative Diagnosis of Small Objects in MRI
Published in Magnetic Resonance Imaging 25 (2007) 1171–1180 [Abstract]
Yu-Chung N. Cheng1, Ching-Yi Hsieh2, Jaladhar Neelavalli3, Qiang Liu2, Muhammad S. Dawood3, E. Mark Haacke1
1. Department of Radiology, Wayne State University, Detroit, MI 48201, USA
2. Medical Physics Program, Wayne State University, Detroit, MI 48201, USA
3. Department of Biomedical Engineering, Wayne State University, Detroit, MI 48201, USA
2009
Quantifying effective magnetic moments of narrow cylindrical objects in MRI
Published in Phys Med Biol. 2009 Nov 21;54(22):7025-44 [Abstract]
Yu-Chung N. Cheng1, Ching-Yi Hsieh2, Jaladhar Neelavalli3 and E. Mark Haacke1
1. Department of Radiology, Wayne State University, Detroit, MI 48201, USA
2. Medical Physics Program, Wayne State University, Detroit, MI 48201, USA
3. Department of Biomedical Engineering, Wayne State University, Detroit, MI 48201, USA
2015
An improved method for susceptibility and radius quantification of cylindrical objects from MRI
Published in Magnetic Resonance Imaging 33 (2015) 420-436 [Abstract]
Ching-Yi Hsieh1, Yu-Chung N. Cheng1, Jaladhar Neelavalli2, E. Mark Haacke2, R. Jason Stafford3
1. Medical Physics Program, Wayne State University, Detroit, MI 48201
2. Department of Radiology, Wayne State University, Detroit, MI 48201
3. Department of Imaging Physics, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030
Magnetic moment quantifications of small spherical objects in MRI
Published in Magnetic Resonance Imaging 33 (2015) 829 – 839 [Abstract]
Yu-Chung N. Cheng1, Ching-Yi Hsieh2, Ronald Tackett3, Paul Kokeny4, Rajesh Kumar Regmi3, Gavin Lawes3
1. Department of Radiology, Wayne State University, Detroit, MI 48201
2. Medical Physics Program, Wayne State University, Detroit, MI 48201
3. Department of Physics, Wayne State University, Detroit, MI 48201
4. Department of Biomedical Engineering, Wayne State University, Detroit, MI 48201
Susceptibility and size quantification of small human veins from an MRI method
Published in Magnetic Resonance Imaging 33 (2015) 1191 – 1204 [Abstract]
Ching-Yi Hsieh1, Yu-Chung N. Cheng2, He Xie3, E. Mark Haacke2, Jaladhar Neelavalli2
1. Medical Physics Program, Wayne State University, Detroit, MI 48201
2. Department of Radiology, Wayne State University, Detroit, MI 48201
3. Department of Physics, Wayne State University, Detroit, MI, 48201

Chernyak Group

2006
Exciton Scattering and Localization in Branched Dendrimeric Structures
Published in Nature Physics, 2006, 2(9), 631 - 635 [Abstract]
Chao Wu1, Sergey V. Malinin1, Sergei Tretiak2 and Vladimir Y. Chernyak1
1. Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202, USA
2. Theoretical Division, Center for Nonlinear Studies, and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
2007
Excited States and Optical Response of a Donor–Acceptor Substituted Polyene: A td-DFT Study
Published in Chemical Physics Letters 433 (2007) 305–311 [Abstract]
Chao Wu1, Sergei Tretiak2, Vladimir Y. Chernyak1
1. Department of Chemistry, Wayne State University, 5101 Cass Avenue Detroit, MI 48202, USA
2. Theoretical Division, Center for Nonlinear Studies, and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Mail Stop B268, Los Alamos, NM 87545, USA
2008
Exciton Scattering Approach for Branched Conjugated Molecules and Complexes Series III-Applications
Published in J. Chem. Phys., 129, 174113 (2008) [Abstract]
Chao Wu1, Sergey V. Malinin1, Sergei Tretiak2, and Vladimir Y. Chernyak1
1. Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA
2. Theoretical Division, Center for Nonlinear Studies, and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
Exciton Scattering Approach for Branched Conjugated Molecules and Complexes Series II-Retrieving Exciton Scattering Parameter
Published in J. Chem. Phys., 129, 174112 (2008) [Abstract]
Chao Wu1, Sergey V. Malinin1, Sergei Tretiak2, and Vladimir Y. Chernyak1
1. Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA
2. Theoretical Division, Center for Nonlinear Studies, and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
Exciton Scattering Approach for Branched Conjugated Molecules and Complexes Series I-Formalism
Published in J. Chem. Phys., 129, 174111 (2008) [Abstract]
Chao Wu1, Sergey V. Malinin1, Sergei Tretiak2, and Vladimir Y. Chernyak1
1. Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA
2. Theoretical Division, Center for Nonlinear Studies, and Center for Integrated Nanotechnologies,Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
Multiscale Modeling of Electronic Excitations in Branched Conjugated Molecules Using an Exciton Scattering Approach
Published in PRL 100, 057405 (2008) [Abstract]
Chao Wu1, Sergey V. Malinin1, Sergei Tretiak2, and Vladimir Y. Chernyak1
1. Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA
2. Theoretical Division, Center for Nonlinear Studies, and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA

Chinnam Group

2014
Assortment planning of automotive products with considerations for economic and environmental impacts of technology selection
Published in Journal of Cleaner Production 70 (2014) 132-144 [Abstract]
Ali Taghavi, Ratna Babu Chinnam
Department of Industrial and Systems Engineering, Wayne State University, 4815 Fourth Street, Detroit, MI 48202, USA
2016
Hierarchical Time-Dependent Shortest Path Algorithms for Vehicle Routing under ITS
Published in IIE Transactions. Vol. 48, Issue 2, pp. 158-169, 2016[Abstract]
Mark Mahyar Nejad1, Lena Mashayekhy2, Ratna Babu Chinnam3, and Anthony Phillips4
1. School of Industrial and Systems Engineering, University of Oklahoma
2. Department of Computer and Information Sciences, University of Delaware
3. Department of Industrial and Systems Engineering, Wayne State University
4. Research and Advanced Engineering, Ford Motor Company.

Cisneros Group

2010
DFT study of a model system for the dealkylation step catalyzed by AlkB
Published in Interdiscip. Sci.: Comput. Life Sci., 2, 70-77 [Abstract]
G. Andres Cisneros
Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
2011
Unraveling Low-Barrier Hydrogen Bonds in Complex Systems with a Simple Quantum Topological Criterion
Published in Chem. Eur. J., 2011, 17, pp 2833-2837 [Abstract]
Robin Chaudret1,2, Dr. G. Andrés Cisneros3, Dr. Olivier Parisel1,2, Dr. Jean-Philip Piquemal1,2
1. UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique case courrier 137, 4 place Jussieu, 75005, Paris (France)
2. CNRS, UMR 7616, Laboratoire de Chimie Théorique case courrier 137, 4 place Jussieu, 75005, Paris (France)
3. Wayne State University, Department of Chemistry, 5101 Cass Ave., Detroit, MI 48202 (USA)
Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations
Published in Phys. Chem. Chem. Phys, 2011, 13, pp 11239-11247 [Abstract]
Robin Chaudret1, Jean-Philip Piquemal1,2 and G. Andrés Cisneros3
1. UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique case courrier 137, 4 place Jussieu, 75005, Paris (France)
2. CNRS, UMR 7616, Laboratoire de Chimie Théorique case courrier 137, 4 place Jussieu, 75005, Paris (France)
3. Wayne State University, Department of Chemistry, 5101 Cass Ave., Detroit, MI 48202 (USA)
2012
The Kinase Activity of the Helicobacter pylori Asp-tRNAAsn/Glu-tRNAGln Amidotransferase Is Sensitive to Distal Mutations in Its Putative Ammonia Tunnel
Published in Biochemistry, 2012, 51 (1), pp 273–285 [Abstract]
Liangjun Zhao, Sajeewa W. Dewage, Michael J. Bell, Keng-Ming Chang, Shirin Fatma, Nilesh Joshi, Gayathri Silva, G. Andrés Cisneros, and Tamara L. Hendrickson
Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
Computational Prediction of Residues Involved in Fidelity Checking for DNA Synthesis in DNA Polymerase I
Published in Biochemistry, 2012, 51 (12), pp 2569–2578[Abstract]
S.E. Graham, FS. Syeda, G.A. Cisneros
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Conformational Analysis of Clostridium difficile Toxin B and its Implications for Substrate Recognition
Published in PLoS ONE, 2012, 7 (7) , e41518 [Abstract]
Rebecca Swett, G. Andrés Cisneros, Andrew L. Feig
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Concentration-independent pH detection with a luminescent dimetallic Eu(III)-based probe
Published in J. Am. Chem. Soc., 2012, 134, pp 17372-17375 [Abstract]
Jeremiah D. Moore, Richard L. Lord, G. Andrés Cisneros, and Matthew J. Allen
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Application of Gaussian Electrostatic Model (GEM) distributed multipoles in the AMOEBA force field
Published in J. Chem. Theo. Comp., 2012, 12, pp 5072-5080 [Abstract]
G.A. Cisneros
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
2013
Classical Electrostatics for Biomolecular Simulations
Published in Chem. Rev., 114, 779-814, 2013 [Abstract]
G.A. Cisneros1, Mikko Karttunen2, Pengyu Ren3, and Celeste Sagui4
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
2. Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, Canada N2L 3G1
3. Department of Biomedical Engineering, BME 5.202M, The University of Texas at Austin, 1 University Station, C0800, Austin, Texas 78712-1062, United States
4. Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, United States
Novel Alkoxide Cluster Topologies Featuring Rare Seesaw Geometry at Transition Metal Centers
Published in Chem. Eur. J., 19, 12225-12228, 2013 [Abstract]
James A. Bellow1, Dong Fang1, Natalija Kovacevic1, Philip D. Martin1, Jason Shearer2, G. Andrés Cisneros1, Stanislav Groysman1
1. Wayne State University, Detroit, MI 48202 (USA)
2. Department of Chemistry, University of Nevada, Reno, NV 89557 (USA)
Hypothesis Driven Single Nucleotide Polymorphism Search (HyDn-SNP-S)
Published in DNA Repair, 12, 733-740, 2013 [Abstract]
Rebecca J. Swett1, Angela Elias1, Jeffrey A. Miller2, Gregory E. Dyson3, G. Andrés Cisneros1
1. Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202, USA
2. Department of Computer Science, Eastern Michigan University, Ypsilanti, MI 48197, USA
3. Karmanos Cancer Institute, Wayne State University, Detroit, MI 48203, USA
Efficient Optimization of van der Waals Parameters based on Bulk Properties
Published in J. Comp. Chem., 34, 2313-2319, 2013 [Abstract]
Steven K. Burger, G. Andrés Cisneros
Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202, USA
Disruption of intrinsic motions as a mechanism for enzyme inhibition
Published in Biophys J., 105, 494-501, 2013 [Abstract]
Rebecca J. Swett, G. Andrés Cisneros, Andrew L. Feig
Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202, USA
Ab Initio QM/MM Calculations Show an Intersystem Crossing in the Hydrogen Abstraction Step in Dealkylation Catalyzed by AlkB
Published in J. Phys. Chem. B, 117, 6410-6420, 2013 [Abstract]
Dong Fang1, Richard L. Lord2, and G. Andrés Cisneros1
1. Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202, USA
2. Department of Chemistry, Grand Valley State University, Allendale, Michigan 49401, United States
Toward a Deeper Understanding of Enzyme Reactions using the coupled ELF/NCI Analysis: Application to DNA repair enzymes
Published in J. Phys. Chem. B, 117, 6410-6420, 2013 [Abstract]
Dong Fang1, Robin Chaudret2,3, Jean-Philip Piquemal2,3 and G. Andrés Cisneros1
1. Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202, USA
2. UPMC Univ Paris 06, UMR 7616 Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005, Paris, France
3. CNRS, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005, Paris, France
Further refinements of next-generation force-fields: non empirical localization of off-centered-points in molecules
Published in Can. J. Chem., 99, 1-7, 2013 [Abstract]
Robin Chaudret1,2, Nohad Gresh3, G. Andrés Cisneros4, Anthony Scemam1,5, Jean-Philip Piquemal1,2
1. UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France.
2. CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France.
3. Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, UFR Biomédicale, Université Paris Descartes, 45 rue des Saint-Pères, 75006 Paris, France.
4. Laboratoire de Chimie et Physique Quantiques, CNRS-IRSAMC, Université de Toulouse, France.
Electrostatics Interactions in Classical Simulations
Published in Biomolecular Simulations: Methods and Protocols, Methods in Molecular Biology, 924, 243-270, 2013 [Abstract]
G. Andrés Cisneros, Volodymyr Babin, Celeste Sagui
Exploring the structural determinants of selective phosphopeptide recognition using bivalent metal-coordination complexes
Published in Chem. Med. Comm., 4, 289-292, 2013 [Abstract]
Dziyana Kraskouskaya1, Joel A. Drewry1, Eugenia Duodu1, Steven Burger2, James Eaton1, G. Andrés Cisneros2 and Patrick T. Gunning1
1. Department of Chemical and Physical Sciences, University of Toronto, 3359 Mississauga Road North, Mississauga, Canada
2. Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, USA
2014
Classical Electrostatics for Biomolecular Simulations
Published inChem. Rev., 2014, 114 (1), pp 779–814[Abstract]
G. Andrés Cisneros1, Mikko Karttunen2, Pengyu Ren3, and Celeste Sagui4
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
2. Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, Canada N2L 3G1
3. Department of Biomedical Engineering, BME 5.202M, The University of Texas at Austin, 1 University Station, C0800, Austin, Texas 78712-1062, United States
4. Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, United States
GEM*: A Molecular Electronic Density--Based Force Field for Molecular Dynamics Simulations
Published in J. Chem. Theory Comput., 2014, 10 (4), pp 1361–1365[Abstract]
Robert E. Duke1, Oleg N. Starovoytov1, Jean-Philip Piquemal2,3, and G. Andrés Cisneros1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
2. Sorbonne Universités, UPMC Univ Paris 06, UMR 7616 Laboratoire de Chimie Théorique case courrier 137, 4 place Jussieu 75005, Paris, France
3. CNRS, UMR 7616 Laboratoire de Chimie Théorique case courrier 137, 4 place Jussieu 75005, Paris, France
DFT steric based energy decomposition analysis of intermolecular interactions
Published in Theo. Chem. Acc., 2014, 133, 1484:1-14[Abstract]
Dong Fang, Jean-Philip Piquemal, Shubin Liu ,G. Andrés Cisneros
Status of the Gaussian Electrostatic Model, a Density Based Polarizable Force Field
To be published in Many-body effects and electrostatics in multi-scale computations of Biomolecules, Eds. Qiang Cui, Pengyu Ren and Markus Meuwly, in press, Pan Stanford Publishing, 2014.
Jean-Philip Piquemal1, G. Andrés Cisneros2
1. Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
2. Wayne State University, Department of Chemistry, 5101 Cass Ave., Detroit, Michigan 48202, United States
Computational Study of Putative Residues Involved in, DNA Synthesis Fidelity Checking in Thermus aquaticus DNA Polymerase I
Published in J. Phys. Chem. A, 2014, 118, 7598-7612 [Abstract]
Angela A. Elias, G. Andrés Cisneros
Wayne State University, Department of Chemistry, 5101 Cass Ave., Detroit, Michigan 48202, United States
S/G-1: An Ab Initio Force-field Blending Frozen Hermite Gaussian Densities and Distributed Multipoles. Proof of Concept and First Applications to Metal Cations
Published in J. Phys. Chem. A, 2014, 118, 7598-7612 [Abstract]
Robin Chaudret1,2, Nohad Gresh3, Christophe Narth1,2, Louis Lagardère1,2,4, Thomas A. Darden5, G. Andrés Cisneros6, and Jean-Philip Piquemal1,2
1. Sorbonne Universités, UPMC, Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
2. CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
3. Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Unité de Formation et de Recherche Biomédicale, Université Paris Descartes, 45 rue des Saint-Pères, 75006 Paris, France
4. Sorbonne Universités, UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005 Paris, France
5. OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States
6. Wayne State University, Department of Chemistry, 5101 Cass Ave., Detroit, Michigan 48202, United States
S/G-1: An Ab Initio Force-field Blending Frozen Hermite Gaussian Densities and Distributed Multipoles. Proof of Concept and First Applications to Metal Cations
Published in Phys. Chem. B, 2014 118, 7156-7166[Abstract]
Robin Chaudret1,2, Nohad Gresh3, Christophe Narth1,2, Louis Lagardère1,2,4, Thomas A. Darden5, G. Andrés Cisneros6, and Jean-Philip Piquemal1,2
1. Sorbonne Universités, UPMC, Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
2. CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
3. Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Unité de Formation et de Recherche Biomédicale, Université Paris Descartes, 45 rue des Saint-Pères, 75006 Paris, France
4. Sorbonne Universités, UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005 Paris, France
5. OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States
6. Wayne State University, Department of Chemistry, 5101 Cass Ave., Detroit, Michigan 48202, United States
Development of AMOEBA Force Field for 1, 3-Dimethylimidazolium Based Ionic Liquids
Published in Phys. Chem. B, 2014, 118, 7156-7166 [Abstract]
Oleg N. Starovoytov, Hedieh Torabifard, and G. Andrés Cisneros
Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
Alternative Pathway for the Reaction Catalyzed by DNA Dealkylase AlkB from Ab Initio QM/MM Calculations
Published in J. Mol. Graph., Model., 54, 123-130, 2014 [Abstract]
Dong Fang and G. Andrés Cisneros
Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
Homology modeling, molecular dynamics, and site-directed mutagenesis study of AlkB human homolog 1 (ALKBH1)
Published in J. Mol. Graph., Model., 2014, 54, 123-130[Abstract]
Pavel Silvestrov1, Tina A. Müller2, Kristen N. Clark2, Robert P. Hausinger2, G. Andrés Cisneros1
1. Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
2. Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, United States
2015
Computational Analysis of Ammonia Transfer along Two Intra-molecular Tunnels in Staphylococcus aureus Glutamine-dependent Amidotransferase (GatCAB)
Published in J. Phys. Chem. B, 2015, 119, 3669−3677[Abstract]
Sajeewa Walimuni Dewage and G. Andres Cisneros
Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
Synthesis and Reactions of 3d Metal Complexes with the Bulky Alkoxide Ligand [OCtBu2Ph]
Published in Inorg. Chem., 2015, 54 (12), pp 5624–5633[Abstract]
James A. Bellow1, Maryam Yousif1, Dong Fang1,2, Eric G. Kratz1, G. Andrés Cisneros1, and Stanislav Groysman1
1. Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
2. Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations
Published in The Journal of Chemical Physics, 2015, 143 , 044103[Abstract]
Dong Fang1,2, Robert E. Duke1, and G. Andrés Cisneros1
1. Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
2. Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
Development of an AMOEBA water model using GEM distributed multipoles
Published in Theo. Chem. Acc., 2015, 134, 101:1-10[Abstract]
Hedieh Torabifard1, Oleg N. Starovoytov2, Pengyu Ren3, G. Andrés Cisneros1
1. Department of Chemistry, Wayne State University
2. Department of Physics, University of Houston
3. Department of Biomedical Engineering, The University of Texas at Austin
Development of an AMOEBA water model using GEM distributed multipoles
Published in Theo. Chem. Acc., 2015, 134, 101:1-10[Abstract]
Hedieh Torabifard1, Oleg N. Starovoytov2, Pengyu Ren3, G. Andrés Cisneros1
1. Department of Chemistry, Wayne State University
2. Department of Physics, University of Houston
3. Department of Biomedical Engineering, The University of Texas at Austin
Novel Histone Deacetylase Class IIa Selective Substrate Radiotracers for PET Imaging of Epigenetic Regulation in the Brain
Published in PLoS ONE, 10(8) e0133512, 2015.[Abstract]
Robin Bonomi1, Uday Mukhopadhyay5, Aleksandr Shavrin1, Hsien-Hsien Yeh6,7, Anjoy Majhi1, Sajeewa W. Dewage3, Amer Najjar4, Xin Lu1, G. Andrés Cisneros3, William P. Tong4, Mian M. Alauddin4, Ren-Shuan Liu6,7, Thomas J. Mangner2, Nashaat Turkman1, Juri G. Gelovani1
1. Department of Biomedical Engineering, Wayne State University, Detroit, MI 48202, United States of America
2. Positron Emission Tomography Center, Wayne State University, Detroit, MI 48202, United States of America
3. Department of Chemistry, Wayne State University, Detroit, MI 48202, United States of America
4. Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America
5. Center for Advanced Biomedical Imaging, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America
6. National Cyclotron and Radiochemistry Center, National Yang Ming University, Taipei, Taiwan
7. Department of Biomedical Imaging and Radiological Sciences, National Yang Ming University, Taipei, Taiwan
Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis
Published in Journal of Structural Biology, 2015, 192, 76–87[Abstract]
Andrew C. Pratt2, Sajeewa W. Dewage3, Allan H. Pang1, Tapan Biswas4, Sandra Barnard-Britson5, G. Andrés Cisneros3, Oleg V. Tsodikov1
1. Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
2. Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
3. Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
4. Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
5. Food and Drug Administration, Center for Drug Evaluation and Research, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
2016
LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields
Published in J. Comput. Chem. 2016 [Abstract]
Eric G. Kratz1, Alice R. Walker1, Louis Lagarde2,3, Filippo Lipparini4, Jean-Philip Piquemal2, and G. Andres Cisneros1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202
2. Laboratoire De Chimie Theorique, UPMC Univ. Paris 06, UMR 7617, Paris F-75005, France
3. Institut Du Calcul Et De La Simulation, UPMC Univ. Paris 06, Paris F-75005, France
4. Institut Fur Physikalische Chemie, Universitat Mainz, Duesbergweg 10-14, Mainz D-55128, Germany

Fan Group

2013
Divergent Evolutionary and Expression Patterns between Lineage Specific New Duplicate Genes and Their Parental Paralogs in Arabidopsis thaliana
Published in PLoS One. 2013 Aug 29;8(8)[Abstract]
Jun Wang, Nicholas C. Marowsky, Chuanzhu Fan
Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA

Finley Group

2010
A Stochastic Approach to Candidate Disease Gene Subnetwork Extraction
Published in Proceedings of ACM International Symposium on Applied Computing, 2010. Sierre, Switzerland, March 22-26, 2010 [Abstract]
Mohammad Shafkat Amin, Anupam Bhattacharjee, Russell L. Finley, Hasan Jamil
Wayne State University
2011
DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila
Published in Nucleic Acids Res. Jan 2011; 39(Database issue): D736–D743. [Abstract]
Thilakam Murali1, Svetlana Pacifico1, Jingkai Yu2, Stephen Guest1, George G. Roberts, III1, and Russell L. Finley, Jr1,3
1. Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
2. National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
3. Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, USA
2013
Identification of New Protein Interactions between Dengue Fever Virus and Its Hosts, Human and Mosquito
Published in PLoS One. 2013;8(1):e53535 [Abstract]
Dumrong Mairiang1, Huamei Zhang1, Ann Sodja2, Thilakam Murali1, Prapat Suriyaphol3, Prida Malasit4,5, Thawornchai Limjindaporn6, and Russell L. Finley, Jr1,7
1. Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
2. Department of Biology, Wayne State University, Detroit, Michigan, United States of America
3. Bioinformatics and Data Management for Research Unit, Faculty of Medicine Siriraj Hospital, and Center for Emerging and Neglected Infectious Diseases, Mahidol University, Bangkok, Thailand 4. Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
5. Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok, Thailand
6. Department of Anatomy, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand 7. Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, USA
2014
Integrating the interactome and the transcriptome of Drosophila
Published in BMC Bioinformatics 2014, 15:177 [Abstract]
Thilakam Murali1, Svetlana Pacifico1, and Russell L Finley1,2
1. Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201, USA 2. Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201, USA

Friedrich Group

2011
New insights from hemichordate genomes: prebilaterian origin and parallel modifications in the paired domain of the Pax gene eyegone
Published in J. Exp. Zool. (Mol. Dev. Evol.) 316:387–392, 2011[Abstract]
Markus Friedrich1,2, and Jason Caravas1
1. Department of Biological Sciences, Wayne State University, Detroit, Michigan 2. Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, Detroit, Michigan
2013
Shaking the Diptera tree of life: performance analysis of nuclear and mitochondrial sequence data partitions
Published in Systematic Entomology (2013), 38, 93–103[Abstract]
Jason Caravas1 and Markus Friedrich1,2
1. Department of Biological Sciences, Wayne State University, Detroit, Michigan 2. Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, Detroit, Michigan

Goldfield Group

2008
Quantum Mechanical Capture/Phase Space Theory Calculation of the Rate Constants for the Complex-Forming CH + H2 Reaction
Published in J. Phys. Chem. A, 2008, 112 (49), 12588-12596 [Abstract]
Amaia Saracibar1, 2, Evelyn M. Goldfield1 and Stephen K. Gray3
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
2. Departamento de Química Física, Universidad del País Vasco 01006, Vitoria, Spain
3. Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
Classical Trajectory Studies of the D + H2 → HD + H Reaction Confined in Carbon Nanotubes: Parallel Trajectories
Published in J. Phys. Chem. C, 2008, 112 (39), 15260-15266 [Abstract]
Tun Lu1, Evelyn M. Goldfield1, and Stephen K. Gray2
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
2. Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
Chemical Reactivity within Carbon Nanotubes: A Quantum Mechanical Study of the D + H2 → HD + H Reaction
Published in J. Phys. Chem. C, 2008, 112 (7), 2654-2659 [Abstract]
Tun Lu1, Evelyn M. Goldfield1, and Stephen K. Gray2
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
2. Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, USA

Grosu Group

2004
Performance Considerations for Network Switch Fabrics on Linux Clusters
Published in Proceedings of the 16th IASTED International Conference on Parallel and Distributed Computing and Systems. November 9 - 11, 2004. MIT, Cambridge, USA. [Abstract]
Philip J. Sokolowski and Daniel Grosu
Department of Electrical and Computer Engineering, Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA
Performance of the NAS Parallel Benchmarks on Grid Enabled Clusters
Published in Proceedings of 3rd IEEE International Symposium on Network Computing and Applications. 30 August - 1 September 2004. Cambridge, Massachusetts, USA. [Abstract]
Philip J. Sokolowski and Daniel Grosu
Department of Electrical and Computer Engineering, Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA
2008
Computing Equilibria in Bimatrix Games by Parallel Support Enumeration
Published in Proceedings of the 7th International Symposium on Parallel and Distributed Computing (ISPDC 2008), IEEE Computer Society Press, July 1-5, 2008, Krakow, Poland, 250-256 [Abstract]
Jon Widger and Daniel Grosu
Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA
2009
Computing Equilibria in Bimatrix Games by Parallel Vertex Enumeration
Published in Proceedings of the 38th International Conference on Parallel Processing (ICPP 2009), IEEE Computer Society Press, September 22-25, 2009, Vienna, Austria. [Abstract]
Jon Widger and Daniel Grosu
Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA
2012
A Parallel Algorithm for EDF-Schedulability Analysis of Multi-modal Real-Time Systems
Published in Proc. of the 18th IEEE International Conference on Embedded and Real-Time Computing Systems and Applications (RTCSA 2012), pp. 154-163 [Abstract]
Masud Ahmed, Nathan Fisher, and Daniel Grosu
Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA
Computing Nash Equilibria in Bimatrix Games: GPU-based Parallel Support Enumeration
Published in Proc. of the 31st IEEE International Performance Computing and Communications Conference (IPCCC'12), December 1-3, 2012, pp. 332-341, Austin, USA [Abstract]
S. Rampersaud, L. Mashayekhy and D. Grosu
Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA
2013
A Truthful Approximation Mechanism for Autonomic Virtual Machine Provisioning and Allocation in Clouds
Published in Proc. of the ACM Cloud and Autonomic Computing Conference (CAC 2013), August 5-8, 2013, Miami, Florida, USA[Abstract]
L. Mashayekhy, M. M. Nejad and D. Grosu
Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA
GPU-Based Parallel EDF-Schedulability Analysis of Multi-Modal Real-Time Systems
Published in Proc. of 15th IEEE International Conference on High Performance Computing and Communications (HPCC 2013), November 13-15, 2013, pp. 254-263, Zhangjiajie, China.[Abstract]
M. Ahmed, S. Rampersaud, N. Fisher, D. Grosu and L. Schwiebert
Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA
2014
Incentive-Compatible Online Mechanisms for Resource Provisioning and Allocation in Clouds
Published in Proc. of the 7th IEEE International Conference on Cloud Computing (CLOUD 2014) - Research Track, June 27 - July 2, 2014, pp. 312-319, Anchorage, Alaska, USA. [Abstract]
L. Mashayekhy, M. M. Nejad, D. Grosu, and A. V. Vasilakos
Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA
Computing Nash Equilibria in Bimatrix Games: GPU-based Parallel Support Enumeration
Published in IEEE Transactions on Parallel and Distributed Systems, Vol. 25, No. 12, December 2014, pp. 3111-3123 [Abstract]
S. Rampersaud, L. Mashayekhy and D. Grosu
Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA
2015
Truthful Greedy Mechanisms for Dynamic Virtual Machine Provisioning and Allocation in Clouds
Published in IEEE Transactions on Parallel and Distributed Systems, Vol. 26, No. 2, February 2015, pp. 594 - 603 [Abstract]
M. M. Nejad, L. Mashayekhy and D. Grosu
Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA
A PTAS Mechanism for Provisioning and Allocation of Heterogeneous Cloud Resources
Published in IEEE Transactions on Parallel and Distributed Systems, Vol. 26, No. 9, September 2015, pp. 2386 - 2399 [Abstract]
Lena Mashayekhy, Mahyar Movahed Nejad, and Daniel Grosu
Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA
Cloud Federations in the Sky: Formation Game and Mechanism
Published in IEEE Transactions on Parallel and Distributed Systems, Vol. 26, No. 9, September 2015, pp. 2386 - 2399 [Abstract]
Lena Mashayekhy, Mahyar Movahed Nejad, and Daniel Grosu
Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA

Hao Group

2013
Homologous recombination drives both sequence diversity and gene content variation in Neisseria meningitidis
Published in Genome Biol Evol (2013) 5 (9): 1611-1627. [Abstract]
Ying Kong1, Jennifer H. Ma2, Keisha Warren2,3, Raymond S.W. Tsang4, Donald E. Low2,3,5, Frances B. Jamieson2,3,5, David C. Alexander2,3,5 and Weilong Hao1
1. Department of Biological Sciences, Wayne State University
2. Public Health Laboratories, Public Health Ontario, Toronto, Ontario, Canada
3. Mount Sinai Hospital, Toronto, Ontario, Canada
4. National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
5. Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
2014
Horizontal transfer and gene conversion as an important driving force in shaping the landscape of mitochondrial introns
Published in G3 (Bethesda). 2014, 4(4), 605–612[Abstract]
Baojun Wu and Weilong Hao
Department of Biological Sciences, Wayne State University, Detroit, Michigan
DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood
Published in BMC Bioinformatics, 2014,15, 320[Abstract]
Tane Kim1,2 and Weilong Hao1
1. Department of Biological Sciences, Wayne State University, 48202 Detroit, USA
2. Mathematics Undergraduate Program, Wayne State University, 48202 Detroit, USA
2015
A dynamic mobile DNA family in the yeast mitochondrial genome
Published in G3, 2015, 5(6), 1273-1282 [Abstract]
Baojun Wu and Weilong Hao
Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
Extensive horizontal transfer and homologous recombination generate highly chimeric mitochondrial genomes in yeast
Published in Molecular Biology and Evolution, 2015, 32, 2559-2570[Abstract]
Baojun Wu, Adnan Buljic and Weilong Hao
Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202

Herrera Group

2011
Oil Price Shocks and Industrial Production: Is the Relationship Linear?
Published in Macroeconomic Dynamics (2011), 15 : pp 472-497 [Abstract]
Ana María Herrera,, Latika Gupta Lagalo, and Tatsuma Wada
Wayne State University, Detroit, Michigan

Huang Group

2008
Mesoscopic and Microscopic Modeling of Island Formation in Strained Film Epitaxy
Published in Phys. Rev. Lett., 2008, 101, 158701 [Abstract]
Zhi-Feng Huang1 and K. R. Elder2
1. Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, USA
2. Department of Physics, Oakland University, Rochester, Michigan 48309, USA
2010
Morphological instability, evolution, and scaling in strained epitaxial films: An amplitude-equation analysis of the phase-field-crystal model
Published in Phys. Rev. B 81, 165421 (2010).[Abstract]
Zhi-Feng Huang1 and K. R. Elder2
1. Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, USA
2. Department of Physics, Oakland University, Rochester, Michigan 48309, USA
Phase-field-crystal dynamics for binary systems: Derivation from dynamical density functional theory, amplitude equation formalism, and applications to alloy heterostructures
Published in Phys. Rev. E 82, 021605 (2010).[Abstract]
Z.-F. Huang1, K. R. Elder2, and N. Provatas3
1. Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, USA
2. Department of Physics, Oakland University, Rochester, Michigan 48309, USA
3. Department of Materials Science and Engineering and Brockhouse Institute for Materials Research, McMaster University, Hamilton, Ontario, Canada L8S-4L7
2011
Exploring spiral defect chaos in generalized Swift-Hohenberg models with mean flow
Published in Phys. Rev. E 84, 046215 (2011)[Abstract]
A. Karimi1, Zhi-Feng Huang2, M. R. Paul3
1. Department of Engineering Science and Mechanics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
2. Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, USA
3. Department of Mechanical Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
2013
Scale-coupling and interface-pinning effects in the phase-field-crystal model
Published in Phys. Rev. E 87, 012401 (2013) [Abstract]
Zhi-Feng Huang
Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, USA
Nonlinear dynamics of island coarsening and stabilization during strained film heteroepitaxy
Published in Phys. Rev. E 87, 022408 (2013) [Abstract]
Champika G. Gamage and Zhi-Feng Huang
Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, USA
Microphase separation in comblike liquid-crystalline diblock copolymers
Published in Phys. Rev. E 88, 042602 (2013) [Abstract]
S. K. Mkhonta1,2 K. R. Elder3, Zhi-Feng Huang1, and Martin Grant4
1. Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, USA
2. Department of Physics, University of Swaziland, Private Bag 4, Kwaluseni M201, Swaziland
3. Department of Physics, Oakland University, Rochester, Michigan 48309, USA
4. Department of Physics, McGill University, Montréal, Québec, Canada H3A 2T8
Exploring the complex world of two-dimensional ordering with three modes
Published in Phys. Rev. Lett. 111, 035501 (2013) [Abstract]
S. K. Mkhonta1,2 K. R. Elder3, and Zhi-Feng Huang1
1. Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, USA
2. Department of Physics, University of Swaziland, Private Bag 4, Kwaluseni M201, Swaziland
3. Department of Physics, Oakland University, Rochester, Michigan 48309, USA

Lai Group

2016
Simulation of Dual-Fuel-CI and Single-Fuel-SI Engine Combustion Fueled with CNG
Proceedings from SAE 2016-01-0789, SAE 2016 World Congress and Exhibition, Detroit, April 12~14, 2016[Abstract]
Apoorv P. Talekar, Ming-Chia Lai, Ke Zeng, Bo Yang, Marcis Jansons

Lipovich Group

2010
Genome-wide computational identification and manual annotation of human long noncoding RNA genes
Published in RNA 16 (8), 1478-1487, 2010.[Abstract]
Hui Jia1, Maureen Osak2, Gireesh K. Bogu3, Lawrence W. Stanton3, Rory Johnson3, and Leonard Lipovich1
1. Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48202, USA
2. Lee and Roland Witte Natural Sciences Division, Hillsdale College, Hillsdale, Michigan 49242, USA
3. Stem Cell and Developmental Biology Group, Genome Institute of Singapore, 138672 Singapore

Liu Group

2007
Effect of Atmospheric Turbulence on Packet Detection in Optical Communications
Published in Proceedings of the IEEE Military Communications Conference, Orlando, FL, USA ,Oct. 29-31, 2007.[Abstract]
Jacob C. Brandenburg1, John Q. Liu1, and Michael P. Polis2
1. Wayne State University, Detroit, Michigan 48202, USA
2. Oakland University, Rochester, Michigan 48309, USA
2008
Signal Detection in Optical Communications through the Atmospheric Turbulence Channel
Published in Proceedings of the IEEE Global Communications Conference, New Orleans, LA, Nov. 30 - Dec. 4, 2008 [Abstract]
Jacob C. Brandenburg and John Q. Liu
Department of Electrical and Computer Engineering, Wayne State University, Detroit, MI 48202, USA
2009
Optical Signal Detection in the Turbulent Atmosphere using p-i-n Photodiodes
Published in IEEE Journal on Selected Areas in Communications. 2009, 27 (9), 1564-1571 [Abstract]
Jacob C. Brandenburg and John Q. Liu
Department of Electrical and Computer Engineering, Wayne State University, Detroit, MI 48202, USA

Loeb Group

2010
A human systems biology approach to discover new drug targets in epilepsy
Published in Epilepsia, 51(Suppl. 3):171–177, 2010.[Abstract]
Jeffery A. Loeb
Center for Molecular Medicine and Genetics and Department of Neurology, Wayne State University School of Medicine, Detroit, Michigan, U.S.A.

Lu Group

2008
Service-Oriented Architecture for VIEW: a Visual Scientific Workflow Management System
Published in Proceedings of the IEEE 2008 International Conference on Services Computing (SCC 2008), Honolulu, Hawaii, USA, July 2008, 335-342.[Abstract]
Cui Lin, Shiyong Lu, Zhaoqiang Lai, Artem Chebotko, Xubo Fei, Jing Hua and Farshad Fotouhi
Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA
Cloud Computing and Grid Computing 360-Degree Compared
Published in IEEE Grid Computing Environments, pp.1-10, in conjunction with IEEE/ACM Supercomputing, Austin, Texas, 2008.[Abstract]
Ian Foster1,2,3, Yong Zhao4, Ioan Raicu1, Shiyong Lu5
1. Department of Computer Science, University of Chicago, Chicago, Illinois, USA
2. Computation Institute, University of Chicago, Chicago, Illinois, USA
3. Math & Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
4. Microsoft Corporation, Redmond, Washington, USA
5. Department of Computer Science, Wayne State University, Detroit, Michigan, USA
2009
RECOMBFLOW: A scientific workflow environment for intragenomic gene conversion analysis in bacterial genomes, including the pathogen Streptococcus pyogenes
Published in International Journal of Bioinformatics Research and Applications. 2009, 5 (1), 1-19.[Abstract]
Jamal Alhiyafi1, Cavitha Sabesan1, Shiyong Lu1, Jeffrey L. Ram2
1. Department of Computer Science, Wayne State University, 430 State Hall, 5143 Cass Avenue, Detroit, Michigan 48202, USA
2. Department of Physiology, Wayne State University, Detroit, Michigan 48202, USA

Luca Group

2015
QuASAR: quantitative allele-specific analysis of reads. Bioinformatics
See more information under this publication: Info.
Cross-Population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation
See more information under this publication: Info.
Bacterial infection remodels the DNA methylation landscape of human dendritic cells
See more information under this publication: Info.
A high-throughput RNA-seq approach to profile transcriptional responses
See more information under this publication: Info.
2016
Which Genetics Variants in DNase-Seq Footprints Are More Likely to Alter Binding?
See more information under this publication: Info.

Ofen Group

2015
A Reliable and Valid Method for Manual Demarcation of Hippocampal Head, Body and Tail
To be published in International Journal of Development Neuroscience
Daugherty, A.M., Yu, Q.J., Flinn, R., Ofen, N.

Pile Group

2016
Genome-wide studies reveal novel and distinct biological pathways regulated by SIN3 isoforms.
Published in BMC Genomics, 2016, 17(1), 111. [Abstract]
Nirmalya Saha, Mengying Liu, Ambikai Gajan and Lori A. Pile
Department of Biological Sciences, Wayne State University
The histone demethylase dKDM5/LID interacts with the SIN3 histone deacetylase complex and shares functional similarities with SIN3
Published in Epigenetics Chromatin, 2016; 9(4). [Abstract]
Ambikai Gajan, Valerie L. Barnes, Mengying Liu, Nirmalya Saha and Lori A. Pile
Department of Biological Sciences, Wayne State University

Pique-Regi Group

2015
QuASAR: quantitative allele-specific analysis of reads. Bioinformatics
Published in Bioinformatics (2015) 31 (8): 1235-1242 [Abstract]
Chris T. Harvey1, Gregory A. Moyerbrailean1, Gordon O. Davis1, Xiaoquan Wen2, Francesca Luca1, and Roger Pique-Regi1
1. Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University, 540 E Canfield, Scott Hall, Detroit, MI 48201, USA
2. Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
Cross-Population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation
Published in PLoS Genet, 2015, 11(4): e1005176 [Abstract]
Xiaoquan Wen1, Francesca Luca2,3, Roger Pique-Regi2,4
1. Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
2. Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
3. Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
4. Department of Clinical and Translational Sciences, Wayne State University, Detroit, MI, USA
Bacterial infection remodels the DNA methylation landscape of human dendritic cells
Published in Genome Res., 2015, 25(12):1801-11[Abstract]
Alain Pacis1,2, Ludovic Tailleux3, Alexander M Morin4, John Lambourne5, Julia L Maclsaac4, Vania Yotova1, Anne Dumaine1, Anne Danckaert6, Francesca Luca7, Jean-Christophe Grenier1, Kasper D Hansen8, Brigitte Gicquel3, Miao Yu9, Athma Pai10, Chuan He9, Jenny Tung11, Tomi Pastinen5, Michael S Kobor4, Roger Pique-Regi7, Yoav Gilad12 and Luis B Barreiro1,13
1. CHU Sainte-Justine Research Center, Department of Genetics, Montreal, H3T1C5, Canada
2. University of Montreal, Department of Biochemistry, Montreal, H3T1J4, Canada
3. Institut Pasteur, Mycobacterial Genetics Unit, Paris, 75015, France
4. Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia 5. Génome Québec, Innovation Centre, Department of Human Genetics, McGill University, Montréal, H3A0G1, Canada
6. Institut Pasteur, Imagopole, Paris, 75015, Franc
7. Wayne State University, Center for Molecular Medicine and Genetics and Department of Obstetrics and Gynecology, Detroit, MI, 48202
8. Johns Hopkins Bloomberg School of Public Health, Department of Biostatistics and McKusick-Nathans Institute for Genetic Medicine, Baltimore, MD, 21205 9. University of Chicago, Department of Chemistry and Institute for Biophysical Dynamics, Chicago, IL, 60637
10. Department of Biology, Massachusetts Institute of Technology, United States
11. Duke University, Departments of Evolutionary Anthropology and Biology and Duke Population Research Institute, Durham, NC, USA 2770
12. University of Chicago, Department of Human Genetics, Chicago, IL, 60637 13. University of Montreal, Department of Pediatrics, Montreal, H3T1J4, Canada
A high-throughput RNA-seq approach to profile transcriptional responses
Published in Sci Rep., 2015,5:14976[Abstract]
G. A. Moyerbrailean1, G. O. Davis1, C. T. Harvey1, D. Watza1, X. Wen2, R. Pique-Regi1,3,and F. Luca1,3
1. Center for Molecular Medicine and Genetics, Wayne State University
2. Department of Biostatistics, University of Michigan
3. Department of Obstetrics and Gynecology, Wayne State University
2016
Which Genetics Variants in DNase-Seq Footprints Are More Likely to Alter Binding?
Published in PLoS Genet, 2016, 12(2): e1005875[Abstract]
Gregory A. Moyerbrailean1, Cynthia A. Kalita1, Chris T. Harvey1, Xiaoquan Wen2, Francesca Luca1,3, Roger Pique-Regi1,3
1. Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
2. Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
3. Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, United States of America

Potoff Group

2004
An Improved Force Field for the Prediction of the Vapor-Liquid Equilibria for Carboxylic Acids
Published in J. Phys. Chem. B 2004, 108, 14130-14136 [Abstract]
Ganesh Kamath, Feng Cao, and Jeffrey J. Potoff
Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202
2005
Effect of Partial Charge Parametrization on the Fluid Phase Behavior of Hydrogen Sulfide
Published in J. Chem. Phys. 123, 124505 (2005) [Abstract]
Ganesh Kamath, Nusrat Lubna, and Jeffrey J. Potoff
Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202
Molecular Modeling of Phase Behavior and Microstructure of Acetone-Chloroform-Methanol Binary Mixtures
Published in J. Phys. Chem. B 2005, 109, 19463-19473 [Abstract
Ganesh Kamath, Grigor Georgiev, and Jeffrey J. Potoff
Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202
Transferable Potentials for Phase Equilibria. 8. United-Atom Description for Thiols, Sulfides, Disulfides, and Thiophene
Published in J. Phys. Chem. B 2005, 109, 24100-24107 [Abstract]
Nusrat Lubna1, Ganesh Kamath1, Jeffrey J. Potoff1, Neeraj Rai2, and J. Ilja Siepmann2
Department of Chemical Engineering and Materials Science, Wayne State University, 5050 Anthony Wayne Drive, Detroit, Michigan 48202, USA
Departments of Chemistry and of Chemical Engineering and Materials Science, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431
2006
Monte Carlo predictions for the phase behavior of H2S + n-alkane, H2S + CO2, CO2 + CH4 and H2S + CO2 + CH4 mixtures
Published in Fluid Phase Equilibria 246 (2006) 71–78 [Abstract]
Ganesh Kamath, Jeffrey J. Potoff
Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202, United States
Application of TraPPE-UA Force Field for Determination of Vapor–Liquid Equilibria of Carboxylate Esters
Published in Fluid Phase Equilibria 240 (2006) 46–55 [Abstract]
Ganesh Kamath, Jason Robinson, Jeffrey J. Potoff
Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202, USA
2007
Vapor-Liquid Equilibria of Diethylamine + Methanol, Diethylamine + Acetone and Diethylamine + Acetonitrile: Predictions of Atomistic Computer Simulations
Published in J. Phys. Chem. C 2007, 111, 1451-1458 [Abstract]
Ganesh Kamath and Jeffrey J. Potoff
Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202
2009
All-Atom Force Field for the Prediction of Vapor−Liquid Equilibria and Interfacial Properties of HFA134a
See more information under this publication: Info.
Extension of the Transferable Potentials for Phase Equilibria Force Field to Dimethylmethyl Phosphonate, Sarin, and Soman
Published in J. Phys. Chem. B 2009, 113, 10292–10297 [Abstract]
Nandhini Sokkalingam, Ganesh Kamath, Maria Coscione and Jeffrey J. Potoff
Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202
Effect of torsional potential on the predicted phase behavior of n-alkanes
Published in Fluid Phase Equilibria 279 (2009) 100–104 [Abstract]
Damien A. Bernard-Brunela and Jeffrey J. Potoff
Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
2010
Ca2+ Bridging of Apposed Phospholipid Bilayers
Published in J. Phys. Chem. B 2010, 114, 13249–13254 [Abstract]
Zeena K. Issa1, Charles W. Manke1, Bhanu P. Jena1,2, and Jeffrey J. Potoff1
1. Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
2. Department of Physiology, School of Medicine, Wayne State UniVersity, Detroit, Michigan 48202
2011
Development of an Optimized Intermolecular Potential for Sulfur Dioxide
Published in J. Phys. Chem. B 2011, 115, 4949-4954 [Abstract]
MaryBeth H. Ketko1, Ganesh Kamath2 and Jeffrey J. Potoff1
1. Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
2. Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
2012
Monte Carlo Predictions of Phase Equilibria and Structure for Dimethyl Ether + Sulfur Dixoide and Dimethyl Ether + Carbon Dioxide
Published in J. Chem. Phys. 136, 044514 (2012) [Abstract]
Ganesh Kamath1, MaryBeth Ketko2, Gary A. Baker1, and Jeffrey J. Potoff2
1. Department of Chemistry, University of Missouri, Columbia, Missouri 65211, USA
2. Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
Computational Prediction of Ionic Liquid 1-Octanol/Water Partition Coefficients
Published in J. Chem. Phys. 136, 044514 (2012) [Abstract]
Ganesh Kamath1, Navendu Bhatnagar2, Gary A. Baker1, Sheila N. Baker1 and Jeffrey J. Potoff2
1. Department of Chemistry, University of Missouri, Columbia, Missouri 65211, USA
2. Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
Direct Calculation of Octanol-Water Partition Coefficients from Adaptive Biasing Force Molecular Dynamics Simulations
Published in J. Chem. Phys. 137, 014502 (2012) [Abstract]
Navendu Bhatnagar1, Ganesh Kamath2, Isaac Chelst1, and Jeffrey J. Potoff1
1. Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
2. Department of Chemistry, University of Missouri, Columbia, Missouri 65211, USA
Study on Interfacial Interaction between Polymer and Nanoparticle in a Nanocoating Matrix: A MARTINI Coarse-Graining Method
Published in Ind. Eng. Chem. Res. 51, 73-82 (2012) [Abstract]
Rohan G. Uttarwar, Jeffrey J. Potoff and Yinlun Huang
Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
2013
Prediction of 1-Octanol-Water and Air-Water Partition Coefficients for Nitro-Aromatic Compounds from Molecular Dynamics Simulations
Published in Phys. Chem. Chem. Phys., 15, 6467-6474 (2013) [Abstract]
Navendu Bhatnagar1, Ganesh Kamath2, and Jeffrey J. Potoff1
1. Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
2. Department of Chemistry, University of Missouri−Columbia, Columbia, Missouri 65211-7600, United States
Biomolecular Simulations with the Transferable Potentials for Phase Equilibria: Extension to Phospholipids
Published in J. Phys. Chem. B, 117 (34), 9910–9921 (2013) [Abstract]
Navendu Bhatnagar1, Ganesh Kamath2, and Jeffrey J. Potoff1
1. Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
2. Department of Chemistry, University of Missouri−Columbia, Columbia, Missouri 65211-7600, United States

Ram Group

2014
Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity
Published in PLoS ONE, 2014, 9(9): e107534[Abstract]
Masanori Fujimoto1, Gregory A. Moyerbrailean1,2, Sifat Noman1, Jason P. Gizicki1, Michal L. Ram1, Phyllis A. Green3, Jeffrey L. Ram1
1. Department of Physiology, School of Medicine, Wayne State University, Detroit, Michigan, United States of America
2. Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, Michigan, United States of America
3. Isle Royale National Park, National Park Service, Houghton, Michigan, United States of America

Reynolds Group

2010
Networks Do Matter: The Socially Motivated Design of a 3D Race Controller Using Cultural Algorithms
Published in International Journal of Swarm Intelligence Research, January, 2010[Abstract]
Robert G. Reynolds and Leonard Christian Kinnaird-Heether
Wayne State University
2013
The Turing Test Track of the 2012 Mario AI Championship: Entries and Evaluation
Published in International Journal of Swarm Intelligence Research, January, 2010[Abstract]
Noor Shaker1,Julian Togelius1, Georgios N. Yannakakis2, Likith Poovanna3, Vinay S. Ethiraj3, Stefan J. Johansson3, Robert G. Reynolds4, Leonard K. Heether4, Tom Schumann5, Marcus Gallagher5
1. Cennter for Computer Games Research,IT University of Copenhagen, Denmark
2. Department of Digital Games, University of Malta, Malta
3. Blekinge Institute of Technology, Sweden
4. Department of Computer Science, Wayne State University, USA
5. University of Queensland, Australia
Optimization Problem Solving with Auctions in Cultural Algorithms
Published in Memetic Computing, June 2013, Volume 5, Issue 2, pp 83-94[Abstract]
Robert G. Reynolds and Leonard Christian Kinnaird-Heether
Wayne State University
2015
Using Cultural Algorithms to Improve Wearable Device Gesture Recognition Performance
Published in Proceeding of the IEEE Symposium in Computational Intelligence, South Africa, December 8-10, 2015 [Abstract]
Faisal Waris and Robert G. Reynolds
Department of Computer Science, Wayne State University, USA

da Rocha Group

Robson P. S. Peguin and Sandro R. P. da Rocha. Ab Initio: Relating Surfactant Tail Chemistry and Solubility in Hydrofluoralkanes (to be submitted).
Parthiban Selvam, Udayan Chokshi, Robson P. S. Peguin and Sandro R. P. da Rocha. In situ Tensiometric Study of the Surfactant-modified HFA-134a|Water Interface (to be submitted).
2006
Surfactant Design for the 1,1,1,2-Tetrafluoroethane-Water Interface: ab initio Calculations and in situ High-Pressure Tensiometry
Published in Langmuir; 2006; 22(21); 8675-8683 [Abstract]
Parthiban Selvam, Robson P. S. Peguin, Udayan Chokshi, and Sandro R. P. da Rocha
Wayne State University, 5050 Anthony Wayne Drive, Detroit, Michigan 48202
Microscopic and Thermodynamic Properties of the HFA134a-Water Interface: Atomistic Computer Simulations and Tensiometry under Pressure
Published in Langmuir; 2006; 22(21); 8826-8830 [Abstract]
Robson P. S. Peguin, Parthiban Selvam, and Sandro R. P. da Rocha
Wayne State University, 5050 Anthony Wayne Drive, Detroit, Michigan 48202
2007
Archetypical Modeling and Amphiphilic Behavior of Cobalt(II)-Containing Soft-Materials with Asymmetric Tridentate Ligands
See more information under this publication: Info.
Amphiphilic and Magnetic Properties of a New Class of Cluster-Bearing [L2Cu44-O)(μ2-carboxylato)4] Soft Materials
See more information under this publication: Info.
The Ester Group: How Hydrofluoroalkane-philic Is It?
Published in Langmuir 2007, 23, 8291-8294 [Abstract]
Robson P. S. Peguin, Libo Wu, and Sandro R. P. da Rocha
Wayne State University, 5050 Anthony Wayne Drive, Detroit, Michigan 48202
Understanding Solvation in Hydrofluoroalkanes: Ab Initio Calculations and Chemical Force Microscopy
Published in J. Phys. Chem. B 2007, 111, 8096-8104 [Abstract]
Libo Wu, Robson P. S. Peguin, and Sandro R. P. da Rocha
Wayne State University, 5050 Anthony Wayne Drive, Detroit, Michigan 48202
2008
Solvent−Solute Interactions in Hydrofluoroalkane Propellants
Published in J. Phys. Chem. B, 2008, 112 (27), 8084-8094 [Abstract]
Robson P. S. Peguin and Sandro R. P. da Rocha
Department of Chemical Engineering and Materials Science, Wayne State University, 5050 Anthony Wayne Drive, Detroit, Michigan 48202
Synthesis, Redox, and Amphiphilic Properties of Responsive Salycilaldimine-Copper(II) Soft Materials
See more information under this publication: Info.
Interfacial Behavior and Film Patterning of Redox-Active Cationic Copper(II)-Containing Surfactants
See more information under this publication: Info.
2009
All-Atom Force Field for the Prediction of Vapor−Liquid Equilibria and Interfacial Properties of HFA134a
Published in J. Phys. Chem. B, 2009, 113 (1), 178-187 [Abstract]
Robson P. S. Peguin, Ganesh Kamath, Jeffrey J. Potoff and Sandro R. P. da Rocha
Department of Chemical Engineering and Materials Science, Wayne State University, 5050 Anthony Wayne Drive, Detroit, Michigan 48202
2014
PEGylated, NH2-Terminated PAMAM Dendrimers: A Microscopic View from Atomistic Computer Simulations
Published in Mol. Pharmaceutics, 2014, 11 (5), pp 1459–1470 [Abstract]
Lin Yang and Sandro R. P. da Rocha
Department of Chemical Engineering and Materials Science, Wayne State University, 5050 Anthony Wayne Drive, Detroit, Michigan 48202
Understanding Solvation in the Low Global Warming Hydrofluoroolefin HFO-1234ze Propellant
Published in J. Phys. Chem. B, 2014, 118 (36), pp 10675–10687 [Abstract]
Lin Yang and Sandro R. P. da Rocha
Department of Chemical Engineering and Materials Science, Wayne State University, 5050 Anthony Wayne Drive, Detroit, Michigan 48202

Rodgers Group

2008
Dipole Effects on Cation−π Interactions: Absolute Bond Dissociation Energies of Complexes of Alkali Metal Cations to N-methylaniline and N,N-dimethylaniline
Published in J. Phys. Chem. A 2008, 112, 7996-8008 [Abstract]
Nuwan Hallowita1, Damon R. Carl2, P. B. Armentrout2 and M. T. Rodgers1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202
2. Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
Synthesis, Redox, and Amphiphilic Properties of Responsive Salycilaldimine-Copper(II) Soft Materials
See more information under this publication: Info.
2009
Noncovalent Interactions of Ni+ with N-donor Ligands (Pyridine, 4,4'-Dipyridyl, 2,2'-Dipyridyl, and 1,10-Phenanthroline): Collision-Induced Dissociation and Theoretical Studies
Published in J. Phys. Chem. A, 2009, 113 (16), pp 4534–4548 [Abstract]
N. S. Rannulu and M. T. Rodgers
Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202.
Modeling Metal Cation-Phosphate Interactions in Nucleic Acids: Activated Dissociation of Mg+, Al+, Cu+, and Zn+ Complexes of Triethyl Phosphate
Published in J. Am. Chem. Soc., 2009, 131 (31), pp 10918–10928 [Abstract]
Chunhai Ruan and M. T. Rodgers
Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202
Inductive Effects on Cation-π Interactions: Structures and bond Dissociation energies of Alkali metal Cation-Halobenzene Complexes
Published in Int. J. Mass Spectrom, 2009, 283 (1-3), 35–47 [Abstract]
Nuwan Hallowita, Esitima Udonkang, Chunhai Ruan, C. E. Frieler, and M. T. Rodgers
Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan, 48202
2010
Infrared Multiple Photon Dissociation Spectroscopy of Protonated Uracil and Thiouracils: Effects of Thio-keto Substitution on Gas-Phase Conformation
Published in Int. J. Mass Spectrom, 2010, 297, 139-151 [Abstract]
Y.-w. Nei1, T. E. Akinyemi1, J. D. Steill2, J. Oomens2,3, and M. T. Rodgers1
1. Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
2. FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuweigein, The Netherlands
3. Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
2011
Infrared Multiple Photon Dissociation Action Spectroscopy and Theoretical Studies of Diethyl Phosphate Complexes: Effects of Protonation and Sodium Cationization on Structure
Published in J. Am. Soc. Spectrom. (2011) 22, 1862-1871 [Abstract]
B. S. Fales1, N. O. Fujamade1, Y.-w. Nei1, J. Oomens2,3 and M. T. Rodgers1
1. Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
2. FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuweigein, The Netherlands
3. Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
Infrared Multiple Photon Dissociation Action Spectroscopy of Sodiated Uracil and Thiouracils: Effects of Thioketo-substitution on Gas-Phase Conformation
Published in Int. J. Mass Spectrom. (2011) 308, 191-202 [Abstract]
Y.-w. Nei1, T.E. Akinyemi1, C.M. Kaczan1, J.D. Steill2, G. Berdenb2, J. Oomens2,3, M.T. Rodgers1,
1. Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
2. FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuweigein, The Netherlands
3. Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
2012
Noncovalent Interactions of Zn+ with N-Donor Ligands (Pyridine, 4,4′-Dipyridyl, 2,2′-Dipyridyl, and 1,10-Phenanthroline): Collision-Induced Dissociation and Theoretical Studies
Published in J. Phys. Chem. A, 2012, 116 (5), pp 1319–1332 [Abstract]
N. S. Rannulu and M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
Structural and Energetic Effects in the Molecular Recognition of Protonated Peptidomimetic Bases by 18-Crown-6
Published in J. Am. Chem. Soc., 2012, 134 (4), pp 2313–2324 [Abstract]
Yu Chen and M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
Sodium Cation Affinities of Commonly Used MALDI Matrices Determined by Guided Ion Beam Tandem Mass Spectrometry
Published in J. Am. Soc. Mass Spectrom, 2012, 23, pp 676-689[Abstract]
S. D. M. Chinthaka and M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
Tautomerization in the Formation and Collision-Induced Dissociation of Alkali Metal Cation-Cytosine Complexes
Published in Phys. Chem. Chem. Phys., 2012,14, 4517-4526 [Abstract]
Zhibo Yang and M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
Structural and Energetic Effects in the Molecular Recognition of Amino Acids by 18-Crown-6
Published in J. Am. Chem. Soc., 2012, 134, 5863–5875 [Abstract]
Yu Chen and M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
Protonation Preferentially Stabilizes Minor Tautomers of the Halouracils: IRMPD Action Spectroscopy and theoretical Studies
Published in J. Am. Soc. Mass Spectrom., 2012, 23, 1469-1478 [Abstract]
K. T. Crampton1, A. I. Rathur1, Y.-w. Nei1, G. Berden2, J. Oomens2,3, and M. T. Rodgers1
1. Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
2. FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN, Nieuwegein, The Netherlands
3. van‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
Alkali Metal Cation Interactions with 12-Crown-4 in the Gas Phase: Revisited
Published in Int. J. Mass Spectrom., 2012, 330-332, 16-26 (Peter B. Armentrout Honor Issue) [Abstract]
P. B. Armentrout1, C. A. Austin2, and M. T. Rodgers2
1. Department of Chemistry, University of Utah, Salt Lake City, UT 84112, United States
2. Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
Re-evaluation of the Proton Affinity of 18-Crown-6 using Competitive Threshold Collision-Induced Dissociation Techniques
Published in Int. J. Mass Spectrom., 2012, 330-332, 16-26 (Peter B. Armentrout Honor Issue) [Abstract]
Yu Chen and M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
Structural and Energetic Effects in the Molecular Recognition of Acetylated Amino Acids by 18-Crown-6
Published in J. Am. Soc. Mass Spectrom., 2012, 23, 2020-2030 [Abstract]
Yu Chen and M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
Alkali Metal Cation-Cyclen Complexes: Effects of Alkali Metal Cation Size on the Structure and Binding Energy
Published in Int. J. Mass Spectrom, 2012, 330-332, 27-34 (Peter B. Armentrout Honor Issue) [Abstract]
C. A. Austin, Y. Chen, and M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
2013
Infrared Multiple Photon Dissociation Action Spectroscopy of Deprotonated DNA Mononucleotides: Gas-Phase Conformations and Energetics
Published in J. Phys. Chem. A, 2013, 117 (6), pp 1319–1335 [Abstract]
Y.-w. Nei1, N. Hallowita1, J. D. Steill2, J. Oomens2,3, and M. T. Rodgers1
1. Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
2. FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
3. van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
Metal Cation Dependence of Interactions with Amino Acids: Bond Energies of Rb+ and Cs+ to Met, Phe, Tyr, and Trp
Published in J. Phys. Chem. B, 2013, 117 (14), pp 3771–3781 [Abstract]
P. B. Armentrout1, Bo Yang2, and M. T. Rodgers2
1. Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah 84112, United States
2. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Thermochemistry of Non-Covalent Ion-Molecule Interactions
Published in Mass Spectrometry, 2013, 2, S0011 [Abstract]
P. B. Armentrout1 and M. T. Rodgers2
1. Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah 84112, United States
2. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Energy-Resolved Collision-Induced Dissociation Studies of 1,10-Phenanthroline Complexes of the Late First-Row Divalent Transition Metal Cations: Determination of the Third Sequential Binding Energy
Published in Mass Spectrometry, 2013, 2, S0011 [Abstract]
Holliness Nose, Yu Chen, and M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Infrared Multiple Photon Dissociation Action Spectroscopy of Alkali Metal Cation-Cytosine Complexes: Effects of Alkali Metal Cation Size on Gas Phase Conformation
Published in J. Am. Soc. Mass Spectrom. (2013) 24:1523-1533 [Abstract]
Bo Yang, R. R. Wu, N. C. Polfer, G. Berden, J. Oomens, M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Energy-Resolved Collision-Induced Dissociation Studies of 2,2'-Bipyridine Complexes of the Late First-Row Divalent Transition Metal Cations: Determination of the Third Sequential Binding Energy
Published in ChemPlusChem 2013, 78, 1109–1123 [Abstract]
Holliness Nose and M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Infrared Multiple Photon Dissociation Action Spectroscopy of Alkali Metal Cation-Cyclen Complexes: Effects of Alkali Metal Cation Size on Gas-Phase Conformation
Published in ChemPlusChem 2013, 78, 1109–1123 [Abstract]
C.A. Austin1, Y. Chen1, C.M. Kaczan1, G. Berden2, J. Oomens2,3, M.T. Rodgers1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
2. Radboud University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
3. Van‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
Silver Cation Affinities of Monomeric Building Blocks of Polyethers and Polyphenols Determined by Guided Ion Beam Tandem Mass Spectrometry
Published in J. Phys. Chem. A, 2013, 117 (34), pp 8274–8284 [Abstract]
Y. Chen , S. D. M. Chinthaka , and M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Infrared Multiple Photon Dissociation Action Spectroscopy of Deprotonated RNA Mononucleotides: Gas-Phase Conformations and Energetics
Published in J. Phys. Chem. A, 2013, 117 (41), pp 10634–10649 [Abstract]
Y.-w. Nei1, K. T. Crampton1, G. Berden2, J. Oomens2,3, and M. T. Rodgers1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
2. Radboud University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
3. van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
Base-Pairing Energies of Proton Bound Homodimers Determined by Guided Ion Beam Tandem Mass Spectrometry: Application to Cytosine and 5-Substituted Cytosines
Published in Anal. Chem., 2013, 85 (22), pp 11000–11006 [Abstract]
Bo Yang , R. R. Wu , and M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Infrared Multiple Photon Dissociation Action Spectroscopy of Proton-Bound Dimers of Cytosine and Modified Cytosines: Effects of Modifications on Base-Pairing Interactions
Published in J. Phys. Chem. B, 2013, 117 (46), pp 14191–14201 [Abstract]
Bo Yang1, R. R. Wu1, G. Berden2, J. Oomens2,3, and M. T. Rodgers1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
2. Radboud University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
3. van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
2014
Base-Pairing Energies of Proton-Bound Heterodimers of Cytosine and Modified Cytosines: Implications for the Stability of DNA I-Motif Conformations
Published in J. Am. Chem. Soc., 2014, 136 (1), pp 282–290 [Abstract]
Bo Yang and M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Metal Cation Dependence of Interactions with Amino Acids: Bond Dissociation Energies of Rb+ and Cs+ to the Acidic Amino Acids and Their Amide Derivatives
Published in J. Phys. Chem. B, 2014, 118 (16), pp 4300–4314 [Abstract]
P. B. Armentrout1, Bo Yang2, and M. T. Rodgers2
1. Department of Chemistry, University of Utah, 315 South 1400 E, Room 2020, Salt Lake City, Utah 84112, United States
2. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Alkali Metal Cation Interactions with 15-Crown-5 in the Gas Phase: Revisited
Published in J. Phys. Chem. A, 2014, 118 (37), pp 8088–8097 [Abstract]
P. B. Armentrout1, C. A. Austin2, and M. T. Rodgers2
1. Department of Chemistry, University of Utah, 315 South 1400 E, Room 2020, Salt Lake City, Utah 84112, United States
2. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Theoretical Studies of Pyridine Complexes of the Late First-Row Divalent Transition Metal Cations: Determination of the Structure and Sequential Binding Energies
Published in J. Phys. Chem. A, 2014, 118 (37), pp 8129–8140 [Abstract]
Holliness Nose and M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Alkali Metal Cation Binding Affinities of Cytosine in the Gas Phase: Revisited
Published in Phys. Chem. Chem. Phys., 2014,16, 16110-16120 [Abstract]
Bo Yang and M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Alkali Metal Cation-Hexacyclen Complexes: Effects of Alkali Metal Cation Size on the Structure and Binding Energy
Published in J. Phys. Chem. A, 2014, 118 (29), pp 5488–5500 [Abstract]
C. A. Austin and M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Intrinsic Affinities of Alkali Metal Cations for Diaza-18-Crown-6: Effects of Alkali Metal Cation Size and Donor Atoms on the Structure and Binding Energies
Published in Int. J. Mass Spectrom. Epub (2014), History of Mass Spectrometry Special Issue [Abstract]
C. A. Austin and M. T. Rodgers
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Infrared Multiple Photon Dissociation Action Spectroscopy of Sodium Cationized Halouracils: Effects of Halogenation on Gas-Phase Conformation
Published in Int. J. Mass Spectrom. Epub (2014), History of Mass Spectrometry Special Issue [Abstract]
C.M. Kaczan1, A.I. Rathur1, R.R. Wu1,Y. Chen1, C.A. Austin1, G. Berden2, J. Oomens2,3, M.T. Rodgers1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
2. Radboud University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
3. van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
Gas-Phase Conformations and Energetics of Protonated 2′-Deoxyguanosine and Guanosine: IRMPD Action Spectroscopy and Theoretical Studies
Published in J. Phys. Chem. B, 2014, 118 (51), pp 14774–14784 [Abstract]
R. R. Wu1, Bo Yang1, G. Berden2, J. Oomens2,3, and M. T. Rodgers1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
2. Institute for Molecules and Materials, Radbound University Nijmegen, FELIX Facility, Toernooiveld 7, 6525 ED, Nijmegen, The Netherlands
3. van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
2015
Base-Pairing Energies of Proton-Bound Dimers of Cytosine and Modified Cytosines: Implications for the Effects of Methylation on the Stability of DNA i-Motif Conformations
To be published in J. Phys. Chem. B [Abstract]
Bo Yang1, Aaron. R. Moehlig2, C. E. Frieler1, and M. T. Rodgers1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
2. Department of Chemistry, Adams State University, Alamosa, Colorado 81101, United States
Gas-Phase Conformations and Energetics of Protonated 2′-Deoxyadenosine and Adenosine: IRMPD Action Spectroscopy and Theoretical Studies
To be published in J. Phys. Chem. B
R. R. Wu1, Bo Yang1, G. Berden2, J. Oomens2,3, and M. T. Rodgers1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
2. Institute for Molecules and Materials, Radbound University Nijmegen, FELIX Facility, Toernooiveld 7, 6525 ED, Nijmegen, The Netherlands
3. van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands

Ruden Group

2011
CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping
Published in BMC Research Notes 2011, 4:171 [Abstract]
Tung Nguyen1, Weisong Shi1 and Douglas Ruden2
1. Computer Science Department, Wayne State University, US
2. Institute of Environmental Health Sciences, Wayne State University, US
2013
Intronic Non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees
Published in BMC Genomics 2013, 14:666[Abstract]
Pablo Cingolani1,2, Xiaoyi Cao3, Radhika S Khetani3, Chieh-Chun Chen3, Melissa Coon1, Alya’a Sammak1, Aliccia Bollig-Fischer5, Susan Land1, Yun Huang6, Matthew E Hudson3,4, Mark D Garfinkel7, Sheng Zhong3, Gene E Robinson3,8,9 and Douglas M Ruden1,10
1. Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA
2. School of Computer Science & Genome Quebec Innovation Centre, McGill University, Montreal, QC, Canada
3. Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
4. Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
5. Department of Oncology, Wayne State University, Detroit, MI 48201, USA
6. La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
7. Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
8. Department of Entomology, University of Illinois, Urbana, IL 61801, USA
9. Neuroscience Program, University of Illinois, Urbana, IL 61801, USA
10. Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA
2014
Lead Exposure Disrupts Global DNA Methylation in Human Embryonic Stem Cells and Alters Their Neuronal Differentiation
Published in Toxicol. Sci. (May 2014) 139 (1): 142-161[Abstract]
Marie-Claude Senut1,2, Arko Sen1,2, Pablo Cingolani1,2,3, Asra Shaik1,2, Susan J. Land1,2 and Douglas M. Ruden1,2,3
1. Institute of Environmental Health Sciences, C.S. Mott Center for Human Health and Development, Detroit, Michigan 48201
2. Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201
3. School of Computer Science and Genome Quebec Innovation Centre, McGill University, Montreal, Canada

SantaLucia Group

2007
Physical Principles and Visual-OMP Software for Optimal PCR Design
Published in Methods in Molecular Biology: PCR Primer Design. 2007, 402, 3-33.[Abstract]
John SantaLucia, Jr., Department of Chemistry
Wayne State University, Detroit, Michigan 48202, USA
AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA
Published in J. Chem. Theory Comput. 2007, 3, 1464-1475[Abstract]
Raviprasad Aduri, Brian T. Psciuk, Pirro Saro, Hariprakash Taniga, H. Bernhard Schlegel, and John SantaLucia, Jr.
Department of Chemistry, Wayne State University, Detroit, Michigan 48202
2008
Pseudouridines in rRNA helix 69 play a role in loop stacking interactions
Published in Org. Biomol. Chem., 2008, 6, 3892 - 3895 [Abstract]
Jean-Paul Desaulniers, Yu-Cheng Chang, Raviprasad Aduri, Sanjaya C. Abeysirigunawardena, John SantaLucia, Jr., Christine S. Chow
Department of Chemistry, Wayne State University, Detroit, Michigan, 48202, USA
Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA
Published in J. Mol. Biol. 2008, 376, 645-657 [Abstract]
Ashesh A. Saraiya1, Tek N. Lamichhane1, 2, Christine S. Chow2, John SantaLucia Jr2 and Philip R. Cunningham1
1. Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
2. Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
2011
Solution structure of RNase P RNA
Published in RNA. Jun 2011; 17(6): 1159–1171 [Abstract]
Alexei V. Kazantsev1 Robert P. Rambo2 Sina Karimpour1 John SantaLucia, Jr.3 John A. Tainer4 and Norman R. Pace1
1. Department of MCD Biology, University of Colorado, Boulder, Colorado 80309, USA
2. Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
3. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
4. Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
2012
Comparison of Solution Conformations and Stabilities of Modified Helix 69 rRNA Analogues from Bacteria and Human
Published in Biopolymers. Feb 2012; 97(2): 94–106 [Abstract]
Minako Sumita1 Jun Jiang2, John SantaLucia, Jr.2, and Christine S. Chow2
1. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
2. Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure
Published in RNA. Apr 2012; 18(4): 610–625. [Abstract]
José Almeida Cruz1, Marc-Frédérick Blanchet2, Michal Boniecki3, Janusz M. Bujnicki3,4, Shi-Jie Chen5, Song Cao5, Rhiju Das6,7, Feng Ding8, Nikolay V. Dokholyan8, Samuel Coulbourn Flores9, Lili Huang10, Christopher A. Lavender11, Véronique Lisi2, François Major2, Katarzyna Mikolajczak3, Dinshaw J. Patel10, Anna Philips3,4, Tomasz Puton4, John Santalucia12,13, Fredrick Sijenyi13, Thomas Hermann14, Kristian Rother4, Magdalena Rother4, Alexander Serganov10, Marcin Skorupski4, Tomasz Soltysinski3, Parin Sripakdeevong6,7, Irina Tuszynska3, Kevin M. Weeks11, Christina Waldsich15, Michael Wildauer15, Neocles B. Leontis16, and Eric Westhof1
1. Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
2. Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec H3C 3J7, Canada
3. Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
4. Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
5. Department of Physics and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
6. Department of Biochemistry
7. Department of Physics, Stanford University, Stanford, California 94305, USA
8. Department of Biochemistry and Biophysics, University of North Carolina, School of Medicine, Chapel Hill, North Carolina 27599, USA
9. Computational & Systems Biology Program, Institute for Cell and Molecular Biology, Uppsala University, 751 05 Uppsala, Sweden
10. Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
11. Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
12. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
13. DNA Software, Ann Arbor, Michigan 48104, USA
14. Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA
15. Max F. Perutz Laboratories, Department of Biochemistry, University of Vienna, Vienna 1030, Austria
16. Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
2013
Structure Modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations
Published in Nucleic Acids Res. Apr 2014; 42(6): 3971–3981[Abstract]
Jun Jiang, Raviprasad Aduri, Christine S. Chow, and John SantaLucia, Jr
Department of Chemistry, Wayne State University, Detroit, MI 48202, USA

Sarhan Group

2006
Towards Scalable Delivery of Video Streams to Heterogeneous Receivers
Published in Proceedings of ACM Multimedia, 347-356. Santa Barbra, California, USA. October 2006. [Abstract]
Bashar Qudah and Nabil J. Sarhan
Department of Electrical and Computer Engineering, Wayne State University, Detroit, Michigan 48202
Analysis of Resource Sharing and Cache Management in Scalable Video-on-Demand
Published in Proceedings of the 14th IEEE International Symposium on Modeling, Analysis, and Simulation of Computer and Telecommunication Systems (MASCOTS 2006), 327-334. Monterey, California, USA. September 2006. [Abstract]
Bashar Qudah and Nabil J. Sarhan
Department of Electrical and Computer Engineering, Wayne State University, Detroit, Michigan 48202
2007
Efficient Cost-Based Scheduling for Scalable Media Streaming
Published in Proceedings of the SPIE/ACM Multimedia Computing and Networking Conference (MMCN 2007). San Jose, California, USA. January/February 2007. July 2-5 2007. [Abstract]
Nabil J. Sarhan and Bashar Qudah
Department of Electrical & Computer Engineering, Wayne State University, Detroit, Michigan 48202, USA
Towards Enhanced Resource Sharing in Video Streaming with Generalized Access Patterns
Published in Proceedings of the IEEE International Conference on Multimedia & Expo (ICME 2007), 1219-1222. Beijing, China. July 2-5 2007. [Abstract]
Bashar Qudah and Nabil J. Sarhan
Department of Electrical and Computer Engineering, Wayne State University, Detroit, MI 48202, USA
2008
Predictive cost-based scheduling for scalable media streaming
Published in Proceedings of the IEEE International Conference on Multimedia & Expo (ICME 2008), 857 - 860. Hannover, Germany, June 2008. [Abstract]
Mohammad Alsmirat and Nabil J. Sarhan
Department of Electrical and Computer Engineering, Wayne State University Detroit, MI 48202, USA
A Scalable Delivery Framework and a Pricing Model for Streaming Media with Advertisements
Published in Proceedings of SPIE/ACM Multimedia Computing and Networking (MMCN), San Jose, California, USA, January/February 2008. [Abstract]
Musab Al-Hadrusi and Nabil J. Sarhan
Department of Electrical and Computer Engineering, Wayne State University Detroit, MI 48202, USA
2009
Workload-Aware Resource Sharing and Cache Management for Scalable Video Streaming
Published in IEEE Transactions on Circuits and Systems for Video Technology, 2009, 19(3), 386-396. [Abstract]
Bashar Qudah and Nabil J. Sarhan
Department of Electrical and Computer Engineering, Wayne State University, Detroit, MI 48202, USA
Performance and Waiting-Time Predictability Analysis of Design Options in Cost-Based Scheduling for Scalable Media Streaming
Published in Proceedings of the International Multimedia Modeling Conference (MMM 2009), pages 150-162, Antipolis, France, January 2009. [Abstract]
Mohammad Alsmirat and Nabil J. Sarhan
Department of Electrical and Computer Engineering, Wayne State University, Detroit, MI 48202, USA
2010
Waiting-Time Prediction in Scalable On-Demand Video Streaming
Published in ACM Transactions on Multimedia Computing, Communications, and Applications (ACM TOMCCAP), 2010, 6(2). [Abstract]
Nabil J. Sarhan, Mohammad A. Alsmirat, and Musab Al-Hadrusi
Department of Electrical and Computer Engineering, Wayne State University, Detroit, MI 48202, USA
Efficient Delivery of On-Demand Video Streams to Heterogeneous Receivers
Published in ACM Transactions on Multimedia Computing, Communications, and Applications (ACM TOMCCAP), 2010, 6(3). [Abstract]
Bashar Qudah and Nabil J. Sarhan
Department of Electrical and Computer Engineering, Wayne State University, Detroit, MI 48202, USA
Detailed Performance and Waiting-Time Predictability Analysis of Scheduling Options in On-Demand Video Streaming
Published in EURASIP Journal on Image and Video Processing, 2010, 2010. [Abstract]
Mohammad Alsmirat and Nabil J. Sarhan
Department of Electrical and Computer Engineering, Wayne State University, Detroit, MI 48202, USA
Waiting-Time Prediction and QoS-based Pricing for Video Streaming with Advertisements
Published in Proceedings of the IEEE International Symposium on Multimedia (ISM 2010). Taichung, Taiwan December 13-December 15 [Abstract]
Nabil J. Sarhan and Musab Al-Hadrusi
2011
Client-Driven Price Selection for Scalable Video Streaming with Advertisements
Published in Proceedings of the International Multimedia Modeling Conference (MMM 2012), pages 429-439, Klagenfurt, Austria, January 4-6, 2012. [Abstract]
Musab Al-Hadrusi and Nabil J. Sarhan.
2012
Efficient Control of PTZ Cameras in Automated Video Surveillance Systems
Published in Proceedings of the IEEE International Symposium on Multimedia (ISM 2012), pages 356 - 359, Irvine, California, December 2012. [Abstract]
Musab Al-Hadrusiand Nabil J. Sarhan.
2013
Design and Analysis of Scalable and Interactive Near Video-on-Demand Systems
Published in Proceedings of the IEEE International Conference on Multimedia and Expo, San Jose, California, July 2013[Abstract]
Kamal Nayfeh and Nabil J. Sarhan
A Scalable Delivery Solution and a Pricing Model for Commercial Video-on-Demand Systems with Video Advertisements
Published in Multimedia Tools and Applications Journal, Springer US, August 2013[Abstract]
Musab Al-Hadrusi and Nabil J. Sarhan.
2015
A Scalable Solution for Interactive Near Video-on-Demand Systems
Published in Multimedia Tools and Applications Journal, Springer US, August 2013[Abstract]
Kamal K. Nayfeh and Nabil J. Sarhan
Department of Electrical and Computer Engineering, Wayne State University, Detroit, MI, 48202 USA

Schlegel Group

2005
Dissociation of Benzene Dication [C6H6]²+: Exploring the Potential Energy Surface
Published in J. Phys. Chem. A 2005, 109, 11551-11559 [Abstract]
Smriti Anand and H. Bernhard Schlegel
Department of Chemistry and Institute for Scientific Computing, Wayne State University, Detroit, Michigan 48202
Numerical Simulation of Nonadiabatic Electron Excitation in the Strong Field Regime. 2. Linear Polyene Cations
Published in J. Phys. Chem. A 2005, 109, 10527-10534 [Abstract]
Stanley M. Smith1, Xiaosong Li2, Alexei N. Markevitch3, Dmitri A. Romanov4, Robert J. Levis3, and H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
2. Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
3. Departments of Chemistry, Center for Advanced Photonics Research, Temple University, Philadelphia, Pennsylvania 19122, USA
4. Department of Physics, Center for Advanced Photonics Research, Temple University, Philadelphia, Pennsylvania 19122, USA
Influence of Ligand Rigidity and Ring Substitution on the Structural and Electronic Behavior of Trivalent Iron and Gallium Complexes with Asymmetric Tridentate Ligands
See more information under this publication: Info.
Ab Initio QM/MM Study of Class A β-Lactamase Acylation: Dual Participation of Glu166 and Lys73 in a Concerted Base Promotion of Ser70
Published in J. AM. CHEM. SOC. 2005, 127, 15397-15407 [Abstract]
Samy O. Meroueh1, Jed F. Fisher1, H. Bernhard Schlegel2, and Shahriar Mobashery1
1. Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
2. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
Theoretical Investigation of Uranyl Dihydroxide: Oxo Ligand Exchange, Water Catalysis, and Vibrational Spectra
Published in J. Phys. Chem. A 2005, 109, 8579-8586 [Abstract]
Hrant P. Hratchian1, Jason L. Sonnenberg2,3, P. Jeffrey Hay3, Richard L. Martin3, Bruce E. Bursten2, and H. Bernhard Schlegel1
1. Department of Chemistry and Institute of Scientific Computing, Wayne State University, Detroit, Michigan 48202, USA
2. Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
3. Theoretical Division, Los Alamos National Laboratory, Mail Stop B268, Los Alamos, New Mexico 87545, USA
Ab initio Ehrenfest dynamics
Published in J. Chem. Phys. 123, 084106 (2005) [Abstract]
Xiaosong Li1, John C. Tully2, H. Bernhard Schlegel3, and Michael J. Frisch4
1. Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
2. Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
3. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
4. Gaussian, Inc., Wallingford, Connecticut 06492, USA
Comment on “Curvy-steps approach to constraint-free extended-Lagrangian ab initio molecular dynamics, using atom-centered basis functions: Convergence toward Born–Oppenheimer trajectories” [J. Chem. Phys. 121, 11542 (2004)]
Published in J. Chem. Phys. 123, 027101 (2005) [Abstract]
Srinivasan S. Iyengara1, H. Bernhard Schlegel2, Gustavo E. Scuseria3, John M. Millam4, and Michael J. Frisch5
1. Department of Chemistry and Department of Physics, Indiana University, Bloomington, Indiana-47405, USA
2. Department of Chemistry, Wayne State University, Detroit, Michigan 48202-3489, USA
3. Department of Chemistry, Rice University, Houston, Texas 77005-1892, USA
4. Semichem, Inc., Mission, Kansas 66222-0649, USA
5. Gaussian, Inc., Wallingford, Connecticut 06492, USA
Weak Carbon-Hydrogen-Nitrogen Interactions Affect the Heterocyclic Ligand Bonding Modes in Barium Complexes Containing η²-Tetrazolato and η²-Pentazolato Ligands
Published in Inorg. Chem. 2005, 44, 4894-4896 [Abstract]
Issam Kobrsi, John E. Knox, Mary Jane Heeg, H. Bernhard Schlegel, and Charles H. Winter
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
A Numerical Simulation of Nonadiabatic Electron Excitation in the Strong Field Regime: Linear Polyenes
Published in J. Phys. Chem. A 2005, 109, 5176-5185 [Abstract]
Stanley M. Smith1, Xiaosong Li2, Alexei N. Markevitch3, Dmitri A. Romanov4, Robert J. Levis3, and H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
2. Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
3. Department of Chemistry, Center for Advanced Photonics Research, Temple University, Philadelphia, Pennsylvania 19122, USA
4. Department of Physics, Center for Advanced Photonics Research, Temple University, Philadelphia, Pennsylvania 19122, USA
Lysine Carboxylation in Proteins: OXA-10 β-Lactamase
Published in PROTEINS: Structure, Function, and Bioinformatics 61:246–257 (2005) [Abstract]
Jie Li1, Jason B. Cross1, Thom Vreven3, Samy O. Meroueh2, Shahriar Mobashery2, and H. Bernhard Schlegel1,3
1. Department of Chemistry and Institute for Scientific Computing, Wayne State University, Detroit, Michigan 48202, USA
2. Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
3. Gaussian, Inc., 340 Quinnipiac St Bldg 40, Wallingford, Connecticut, USA
Computational Investigation of Irreversible Inactivation of the Zinc-Dependent Protease Carboxypeptidase A
Published in J. Phys. Chem. B 2005, 109, 4761-4769 [Abstract]
Jason B. Cross1, Thom Vreven2, Samy O. Meroueh3, Shahriar Mobashery3, and H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
2. Gaussian, Inc., 340 Quinnipiac Street, Bldg 40, Wallingford, Connecticut 06492, USA
3. Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
Finding Minima, Transition States, and Following Reaction Paths on Ab Initio Potential Energy Sources
Published in Theory and Applications of Computational Chemistry: The First Forty Years, 2005 [Abstract]
H. P. Hratchian and H. B. Schlegel
Department of Chemistry and Institute for Scientific Computing, Wayne State University, Detroit, Michigan 48202
Using Hessian Updating To Increase the Efficiency of a Hessian Based Predictor-Corrector Reaction Path Following Method
Published in J. Chem. Theory Comput. 2005, 1, 61-69 [Abstract]
H. P. Hratchian and H. B. Schlegel
Department of Chemistry and Institute for Scientific Computing, Wayne State University, Detroit, Michigan 48202
A Time-Dependent Hartree–Fock Approach for Studying the Electronic Optical Response of Molecules in Intense Fields
Published in Phys. Chem. Chem. Phys., 2005 , 7 , 233 – 239 [Abstract]
Xiaosong Li1, Stanley M. Smith1, Alexei N. Markevitch2,4, Dmitri A. Romanov3,4, Robert J. Levis2,4 and H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
2. Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
3. Department of Physics, Temple University, Philadelphia, PA 19122, USA
4. Center for Advanced Photonics Research, Temple University, Philadelphia, PA 19122, USA
Synthesis, Characterization, and Hydrolysis Products of (η²-tBu2pz)AlH(µ:η¹,η¹-tBu22pz)2AlH2 - Structural Characterization of a Complex Containing η¹-, η²-, and µ:η¹,η¹-Pyrazolato Ligands and a Complex Containing a Terminal Hydroxo Ligand
Published in Eur. J. Inorg. Chem. 2005, 330-337 [Abstract]
Zhengkun Yu1,2, John E. Knox1, Andrey V. Korolev1,3, Mary Jane Heeg1, H. Bernhard Schlegel1, and Charles H. Winter1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
2. Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, P. R. China
3. Sigma Aldrich Corporation, 485 County Rd. V, Sheboygan, Wisconsin 53085, USA
2006
Experimental and Theoretical Study of the Coordination of 1,2,4-Triazolato, Tetrazolato, and Pentazolato Ligands to the [K(18-crown-6)]+ Fragment
Published in Inorg. Chem. 2006, 45, 8700-8710[Abstract]
Issam Kobrsi, Wenjun Zheng, John E. Knox, Mary Jane Heeg, H. Bernhard Schlegel, and Charles H. Winter
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
Structural, Spectroscopic, and Electrochemical Behavior of Trans-Phenolato Cobalt(III) Complexes of Asymmetric NN'O Ligands as Archetypes for Metallomesogens
See more information under this publication: Info.
Empirical Valence-Bond Models for Reactive Potential Energy Surfaces Using Distributed Gaussians
Published in J. Chem. Theory Comput. 2006, 2, 905-911 [Abstract]
H. Bernhard Schlegel and Jason L. Sonnenberg
Department of Chemistry, Wayne State University, Detroit, Michigan 48202
Guest Species/Discrete Carbon Nanotube Inner Phase Charge Transfer and ExternalIonization
Published in J. Comput. Theor. Nanosci. 2006, 3(3) [Abstract]
John E. Knox, Mathew D. Halls, and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
Geometry Optimization with QM/MM Methods II: Explicit Quadratic Coupling
Published in Molecular Physics, 2006, 104(5-7), 701–714[Abstract]
T. Vreven1, M. J. Frisch1, K. N. Kudin2, H. B. Schlegel3 and K. Morokuma4
1. Gaussian, Inc., USA
2. Princeton University, USA
3. Wayne State University, USA
4. Emory University, USA
Electronic Excitations in Anti-aromatic Dehydro[12]- and Aromatic Dehydro[18]Annulenes: A Time-dependent Density Functional Theory Study
Published in Molecular Physics, 2006, 104(5-7), 933–941[Abstract]
Smriti Anand1,2 and H. Bernhard Schlegel1
1. Department of Chemistry and Institute for Scientific Computing, Wayne State University, Detroit, Michigan 48202, USA
2. Department of Biology, Chemistry and Environmental Science, Christopher Newport University, 1 University Place, Newport News, Virginia 23606, USA
Molecular Orbital Studies of Zinc Oxide Chemical Vapor Deposition: Gas-Phase Radical Reactions
Published in Chem. Mater. 2006, 18, 1878-1884[Abstract]
Barbara H. Munk and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan, 48202, USA
Chemical Failure Modes of AlQ3-based OLEDs: AlQ3 Hydrolysis
Published in Phys. Chem. Chem. Phys., 2006, 8, 1371–1377[Abstract]
John E. Knox, Mathew D. Halls, Hrant P. Hratchian, and H. Bernhard Schlegel
Department of Chemistry and Institute for Scientific Computing, Wayne State University, Detroit MI, 48202, USA
A Computational Exploration of Some Transnitrosation and Thiolation Reactions Involving CH3SNO, CH3ONO and CH3NHNO
Published in Org. Biomol. Chem., 2006, 4, 1352–1364[Abstract]
Jie Li1, G. Peng Wang2 and H. Bernhard Schlegel1
1. Department of Chemistry and Institute for Scientific Computing, Wayne State University, Detroit, MI 48202, USA
2. Department of Biochemistry, Ohio State University, Columbus, OH 43210, USA
Single Transition State Serves Two Mechanisms. The Branching Ratio for CH2 •- + CH3Cl on Improved Potential Energy Surfaces
Published in J. Phys. Chem. A 2006, 110, 2801-2806[Abstract]
Jie Li1, Xiasong Li1,2, Sason Shaik3, and H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
2. Department of Organic Chemistry, Yale University, New Haven, Connecticut 06520, USA
3. Lise Meitner-Minerva Center of Computational Chemistry, Hebrew University, Jerusalem 91904, Israel
Structural and Electronic Behavior of Unprecedented Five-Coordinate Iron(III) and Gallium(III) Complexes with a New Phenol-Rich Electroactive Ligand
See more information under this publication: Info.
Optical Excitations in Carbon Architectures Based on Dodecadehydrotribenzo[18]annulene
Published in J. Phys. Chem. A 2006, 110, 1305-1318[Abstract]
Smriti Anand1, Oleg Varnavski2, Jeremiah A. Marsden3, Michael M. Haley3, H. Bernhard Schlegel1, and Theodore Goodson, III2
1. Department of Chemistry and Institute for Scientific Computing, Wayne State University, Detroit, Michigan 48202, USA
2. Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
3. Department of Chemistry and Material Science Institute, University of Oregon, Eugene, Oregon 97403, USA
2007
Empirical valence bond models for reactive potential energy surfaces. II. Intramolecular proton transfer in pyridone and the Claisen reaction of allyl vinyl ether
Published in Mol. Phys. 2007, 105, 2719-2729[Abstract]
Jason L. Sonnenberg and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
Electronic optical response of molecules in intense fields: Comparison of td-HF, td-CIS, and td-CIS(D) approaches
Published in J. Chem. Phys. 126, 244110 (2007)[Abstract]
H. Bernhard Schlegel1, Stanley M. Smith2, Xiaosong Li3
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202
2. Center for Advanced Photonics Research, Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
3. Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
Numerical Simulation of Nonadiabatic Electron Excitation in the Strong-Field Regime. 3. Polyacene Neutrals and Cations
Published in J. Phys. Chem. A 2007, 111, 6920-6932[Abstract]
Stanley M. Smith1, Xiaosong Li2, Alexei Markevitch3,5, Dmitri Romanov4,5, Robert J. Levis3,5, and H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
2. Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
3. Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
4. Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
5. Center for Advanced Photonics Research, Temple University, Philadelphia, Pennsylvania 19122, USA
AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA
See more information under this publication: Info.
A Definitive Example of a Geometric “Entatic State” Effect: Electron-Transfer Kinetics for a Copper(II/I) Complex Involving A Quinquedentate Macrocyclic Trithiaether-Bipyridine Ligand
Published in J. AM. CHEM. SOC. 2007, 129, 5217-5227[Abstract]
Gezahegn Chaka1, Jason L. Sonnenberg1, H. Bernhard Schlegel1, Mary Jane Heeg1, Gregory Jaeger2, Timothy J. Nelson2, L. A. Ochrymowycz2, and D. B. Rorabacher1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
2. University of Wisconsin at Eau Claire, Eau Claire, Wisconsin 54701, USA
Exploration of Mechanisms for the Transformation of 8-Hydroxy Guanine Radical to FAPyG by Density Functional Theory
Published in Chem. Res. Toxicol. 2007, 20, 432-444[Abstract]
Barbara H. Munk1, Cynthia J. Burrows2, and H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, Detroit, Michigan, 48202, USA
2. Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
Protonated Acetylene Revisited
Published in Theor Chem Acc (2007) 118:75–80 [Abstract]
Brian T Psciuk1, Victor A. Benderskii2, H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
2. Institute of Problems of Chemical Physics, RAS, 142432 Moscow Region, Chernogolovka, Russia
2008
Calculation of pKa Values of Nucleobases and the Guanine Oxidation Products Guanidinohydantoin and Spiroiminodihydantoin using Density Functional Theory and a Polarizable Continuum Model
Published in J. Phys. Chem. A 2008, 112, 16860–16873 [Abstract]
Vincenzo Verdolino1, Roberto Cammi1, Barbara H. Munk2, and H. Bernhard Schlegel2
1. Department o di Chimica Generale ed Inorganica, Universit di Parma, Parco Area della Scienze 1, 43100 Parma, Italy
2. Department of Chemistry, Wayne State University, Detroit, Michigan, 48202, USA
Dissociation of acetone radical cation (CH3COH3+. -> CH3CO+ + .CH3): An ab initio direct classical trajectory study of the energy dependence of the branching ratio
Published in J. Phys. Chem. A 2008, 112, 13121–13127 [Abstract]
Jia Zhou, and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
An Exploration of Mechanisms for the Transformation of 8-Oxoguanine to Guanidinohydantoin and Spiroiminodihydantoin by Density Functional Theory
Published in J. Am Chem. Soc. 2008, 130, 5245-5256 [Abstract]
Barbara H. Munk1, Cynthia J. Burrows2, and H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, Detroit, Michigan, 48202, USA
2. Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850
2009
The Energy Landscape of 3-Deoxy-d-manno-octulosonate 8-Phosphate Synthase
Published in Biochemistry, 2009, 48 (49), pp 11706–11714 [Abstract]
Peng Tao1,2,, Domenico L. Gatti1 and H. Bernhard Schlegel2
1. Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
2. , Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202
Matrix Metalloproteinase 2 Inhibition: Combined Quantum Mechanics and Molecular Mechanics Studies of the Inhibition Mechanism of(4-Phenoxyphenylsulfonyl)methylthiirane and Its Oxirane Analogue
Published in Biochemistry, 2009, 48 (41), pp 9839–9847 [Abstract]
Peng Tao1, Jed F. Fisher2, Qicun Shi2, Thom Vreven3, Shahriar Mobashery2 and H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA
2. Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
3. Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, USA
Ab Initio Classical Trajectory Study of the Dissociation of Neutral and Positively Charged Methanimine (CH2NHn+, n=0-2)
Published in J. Phys. Chem. A, 2009, 113 (37), pp 9958–9964 [Abstract]
Jia Zhou and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
DFT Studies of the Ring-Opening Mechanism of SB-3CT, a Potent Inhibitor of Matrix Metalloproteinase 2
Published in Org. Lett., 2009, 11 (12), pp 2559–2562 [Abstract]
Peng Tao1, Jed F. Fisher2, Shahriar Mobashery2 and H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA
2. Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
Distributed Gaussian Valence Bond Surface Derived from Ab Initio Calculations
Published in J. Chem. Theory Comput., 2009, 5 (4), pp 949–961 [Abstract]
Jason L. Sonnenberg1, Kim F. Wong2, Gregory A. Voth2 and H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202
2. Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
Spin Contamination in Inorganic Chemistry Calculations
Published in Computational Inorganic and Bioinorganic Chemistry, Wiley, Chichester, 2009, 173-186, Edward I. Solomon (Editor), Robert A. Scott (Co-Editor), R Bruce King (Co-Editor) [Description]
Jason L. Sonnerberg, H. Bernhard Schlegel and Hrant P. Hratchian
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
Large Nonstatistical Branching Ratio in the Dissociation of Pentane-2,4-dione Radical Cation: An Ab Initio Direct Classical Trajectory Study
Published in J. Phys. Chem. A, 2009, 113 (8), 1453–1458 [Abstract]
Jia Zhou and H. Bernhard Schlegel
Department of Chemistry Wayne State University, Detroit, Michigan 48202, USA
Mechanistic Aspects of the Formation of Guanidinohydantoin from Spiroiminodihydantoin under Acidic Conditions
Published in Chem. Res. Toxicol., 2009, 22 (3), 526–535 [Abstract]
Yu Ye2, Barbara H. Munk1, James G. Muller2, Alexander Cogbill2, Cynthia J. Burrows2 and H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, Detroit, Michigan, 48202, USA
2. Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, USA
2010
Numerical Bound State Electron Dynamics of Carbon Dioxide in the Strong-Field Regime
Published in J. Phys. Chem. A, 2010, 114, 2576–2587 [Abstract]
Stanley M. Smith1,2, Dmitri A. Romanov2,3, Xiaosong Li4, Jason A. Sonk5, H. Bernhard Schlegel5 and Robert J. Levis1,2
1. Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
2. Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
3. Center for Advanced Photonics Research, Temple University, Philadelphia, Pennsylvania 19122, USA
4. Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
5. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
Photodissociation Dynamics of Methylamine Cation and its Relevance to Titan’s Ionosphere
Published in Astrophys. J. 2010, 710(1), 112-116 [Abstract]
Prashant Chandra Singh, Lei Shen, Jia Zhou, H. Bernhard Schlegel and Arthur G. Suits
Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
Matrix Metalloproteinase 2 (MMP2) Inhibition: DFT and QM/MM Studies of the Deprotonation-Initialized Ring-Opening Reaction of the Sulfoxide Analogue of SB-3CT
Published in J. Phys. Chem. B, 2010, 114 (2), 1030–1037 [Abstract]
Peng Tao1, Jed F. Fisher2, Qicun Shi2, Shahriar Mobashery2 and H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA
2. Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
Observing the Transition from Stark-Shifted, Strong-Field Resonance to Nonadiabatic Excitation
Published in J. Phys. Chem. C, 2010, 114 (12), 5645–5651 [Abstract]
Stanley M. Smith1,3, Dmitri A. Romanov2,3, George Heck2,3, H. Bernhard Schlegel4 and Robert J. Levis1,3
1. Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
2. Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
3. Center for Advanced Photonics Research, Temple University, Philadelphia, Pennsylvania 19122, USA
4. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
A Toolkit to Assist ONIOM Calculations
Published in J. Comput. Chem., 2010, 31, 2363-2369 [Abstract]
Peng Tao and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
Ab initio molecular dynamics study of the reaction between Th+ and H2O
Published in J. Phys. Chem. A, 2010, 114 (33), 8613–8617 [Abstract]
Jia Zhou and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
Effects of Electronic Mixing in Ruthenium(II) Complexes with Two Equivalent Acceptor Ligands. Spectroscopic, Electrochemical and Computational Studies
Published in Inorg. Chem., 2010, 49 (15), 6840–6852 [Abstract]
Marco M. Allard1, Onduru. S. Odongo1, Mandy M. Lee2, Yuan-Jang Chen2, John F. Endicott1 and H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
2. Department of Chemistry, Fu Jen Catholic University, Taipei Hsien 24205, Taiwan, R. O. C.
Synthesis, Characterization and Theoretical Studies of the Metal Complexes Derived from the Chiral Tripyridyldiamine Ligand Bn-CDPy3
Published in Inorg. Chem., 2010, 49 (11), 5202–5211 [Abstract]
Ahmed I. Abouelatta, Jason A. Sonk, Mirvat M. Hammoud, Danielle M. Zurcher, Joshua J. McKamie, H. Bernhard Schlegel and Jeremy J. Kodanko
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
Theoretical Studies of AnII2(C8H8)2 (An = Th, Pa, U, and Np) Complexes: The Search for Double-stuffed Actinide Metallocenes
Published in Inorg. Chem., 2010, 49 (14), 6545–6551 [Abstract]
Jia Zhou, Jason L. Sonnenberg and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
Ab initio classical trajectory study of the fragmentation of C3H4 dications on the singlet and triplet surfaces
Published in J. Phys. Chem. A, 2010, 114 (29), pp 7653–7660 [Abstract]
Brian T. Psciuk, Peng Tao and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
QM/MM Studies of the Matrix Metalloproteinase 2 (MMP2) Inhibition Mechanism of (S)-SB-3CT and its Oxirane Analogue
Published in J. Chem. Theory Comput., 2010, 6 (11), pp 3580–3587 [Abstract]
Jia Zhou1, Peng Tao1, Jed F. Fisher2, Qicun Shi2, Shahriar Mobashery2, and H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202, United States
2. Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
Observations on the Low Energy Limits for MLCT Excited State Energies of Ru(II)-polypyridyl Complexes
Published in Inorg. Chem., 2010, 49 (20), pp 9095–9097 [Abstract]
Onduru S. Odongo, Marco M. Allard, H. Bernhard Schlegel, and John F. Endicott
Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202, United States
Common basis for the mechanism of metallo and non-metallo KDO8P synthases
Published in Inorg. Chem., 2010, 49 (20), pp 9095–9097 [Abstract]
Peng Tao1, H. Bernhard Schlegel2, Domenico L. Gattia1
1. Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201, United States
2. Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202, United States
2011
Investigation of the Electronic, Photosubstitution, Redox, and Surface Properties of New Ruthenium(II)-Containing Amphiphiles
See more information under this publication: Info.
TD-CI Simulation of the Electronic Optical Response of Molecules in Intense Fields: Comparison of RPA, CIS, CIS(D) and EOM-CCSD
Published in J. Phys. Chem. A, 2011, 115 (18), pp 4678–4690 [Abstract]
Jason A. Sonk1, Marco Caricato2, and H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202, United States
2. Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
Dissociation of H2NCH Dication in a Strong Laser Field
Published in J. Phys. Chem. A, 2011, 115 (30), pp 8375–8379 [Abstract]
Jia Zhou and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202, United States
TD-CI Simulation of the Electronic Optical Response of Molecules in Intense Fields II: Comparison of DFT Functionals and EOM-CCSD
Published in J. Phys. Chem. A, 2011, 115 (42), pp 11832–11840 [Abstract]
Jason A. Sonk and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202, United States
Characterization of Low Energy Charge Transfer Transitions in (terpyridine)(bipyridine)Ruthenium(II) Complexes and their Cyanide-Bridged Bi- and Tri-Metallic Analogues
Published in Inorg. Chem., 2011, 50 (23), pp 11965–11977 [Abstract]
Chia-Nung Tsai2, Marco M. Allard1, Richard L. Lord1, Dao-Wen Luo3, Yuan-Jang Chen2, H. Bernhard Schlegel1, and John F. Endicott1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
2. Department of Chemistry, Fu Jen Catholic University, 510 Chung Cheng Rd Hsinchuang, New Taipei City 24205, Taiwan, R. O. C.
3. Instruments Center and Department of Chemistry, National Chung-Hsing University, Taichung 402, Taiwan, R. O. C.
2012
Bioinspired Five-Coordinate Iron(III) Complexes for Stabilization of Phenoxyl Radicals
Published in Angew. Chem., Int. Ed. 2012, 51, 3178-3182 [Abstract]
Marco M. Allard1, Jason A. Sonk1, Dr. Mary Jane Heeg1, Bruce R. McGarvey2, Prof. H. Bernhard Schlegel1, Prof. Cláudio N. Verani1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
2.Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4 (Canada)
Unexpected Formation of a Cobalt(III) Phenoxazinylate Electron Reservoir
Published in Eur. J. Inorg. Chem. 2012, 463-466 [Abstract]
Frank D. Lesh, Richard L. Lord, Mary Jane Heeg, H. Bernhard Schlegel, Cláudio N. Verani
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Ab Initio Classical Trajectory Calculations of 1,3-cyclobutanedione Radical Cation Dissociation
Published in Theor. Chem. Acc. 2012, 131, 1126 [Abstract]
Jia Zhou and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Coordinate Reduction for Exploring Chemical Reaction Paths
Published in Theor. Chem. Acc. 2012, 131, 1170 [Abstract]
Adam B. Birkholz and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
HCO+ dissociation in a strong laser field: An ab initio classical trajectory study
Published in Chem. Phys. Lett. 2012, 536, 14-18 [Abstract]
Suk Kyoung Lee, Wen Li, H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
TD-CI Simulation of the Strong-Field Ionization of Polyenes
Published in J. Phys. Chem. A 2012, 116, 7161-7168 [Abstract]
Jason A. Sonk and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Metallapyrimidines and Metallapyrimidiniums From Oxidative Addition of Pyrazolate N-N Bonds to Niobium(III), Niobium(IV), and Tantalum(IV) Metal Centers and Assessment of Their Aromatic Character
Published in Organomet. 2012, 31, 5971–5974 [Abstract]
T. Hiran Perera, Richard L. Lord, Mary Jane Heeg, H. Bernhard Schlegel, and Charles H. Winter
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
A Reaction Accelerator: Mid-Infrared Strong Field Dissociation Yields Mode Selective Chemistry
Published in J. Phys. Chem. Lett. 2012, 3, 2541-2547 [Abstract]
Suk Kyoung Lee, Arthur G. Suits, H. Bernhard Schlegel, and Wen Li
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Theoretical Determination of One-Electron Oxidation Potentials for Nucleic Acid Bases
Published in J. Chem. Theory Comput. 2012, 8, 5107−5123 [Abstract]
Brian T. Psciuk, Richard L. Lord, Barbara H. Munk, and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Can Metallapyrimidines Be Aromatic? A Computational Study into a New Class of Metallacycles
Published in J. Chem. Theory Comput. 2012, 8, 4950−4959 [Abstract]
Brian T. Psciuk, Richard L. Lord , Charles H. Winter, and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
2013
Computational Modeling of the Triplet Metal-to-Ligand Charge-Transfer Excited-State Structures of Mono-Bipyridine-Ruthenium(II) Complexes and Comparisons to their 77 K Emission Band Shapes
Published in Inorg. Chem. 2013, 52, 1185-98 [Abstract]
Richard L. Lord1, Marco M. Allard1, Ryan A. Thomas1, Onduro S. Odongo1, H. Bernhard Schlegel1, Yuan-Jang Chen2, and John F. Endicott1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States 2. Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan, Republic of China
Molecular dynamics in strong laser fields: a new algorithm for ab initio classical trajectories
Published in J. Chem. Theory Comput. 2013, 9, 3293–98 [Abstract]
H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Computational Prediction of One-Electron Reduction Potentials and Acid Dissociation Constants for Guanine Oxidation Intermediates and Products
Published in J. Phys. Chem. B 2013, 117, 9518–31 [Abstract]
Brian T. Psciuk and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Experimental and DFT Characterization of Metal-to-Ligand Charge Transfer Excited States of (Rutheniumammine)-(Mono-dentate Aromatic Ligand) Chromophores
Published in Inorg. Chem. 2013, 52, 9774-90 [Abstract]
Chia Nung Tsai1,2, Yi-Han Tian1, Xuetao Shi2, Richard L. Lord2, H. Bernhard Schlegel2, Yuan Jang Chen1,2, and John F. Endicott2
1. Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan, Republic of China 2. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Bond Selective Dissociation of Polyatomic Ions in Mid-Infrared Strong Fields
Published in J. Phys. Chem. A 2013, 117, 11202-9 [Abstract]
Suk Kyoung Lee, H. Bernhard Schlegel, and Wen Li
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
2014
Molecular Dynamics of Methanol Monocation (CH3OH+) in Strong Laser Fields
Published in J. Phys. Chem. A 2014, 118, 1769-76 [Abstract]
Bishnu Thapa and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
Strong field ionization rates simulated with TDCIS and an absorbing potential
Published in J. Chem. Phys. 2014, 140, 174113 [Abstract]
Pascal Krause1 and H. Bernhard Schlegel1
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
A Density Functional Theory and Spectroscopic Study of Intramolecular Quenching of Metal-to-Ligand-Charge-Transfer Excited States in Some Mono-Bipyridine Ruthenium(II) Complexes
Published in Can. J. Chem. 2014, 92, 996-1009[Abstract]
Shivnath Mazumder1, Ryan A. Thomas1, Richard L. Lord2, H. Bernhard Schlegel1. John F. Endicott1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
2. Grand Valley State University, 1 Campus Dr., Allendale, MI 49401-9403, USA.
Molecular Dynamics of Methanol Monocation CH3OH(+) in Strong Fields: Comparison of 800 nm and 7 micron Laser Fields
Published in Chem. Phys. Lett. 2014, 610-611, 219-222[Abstract]
Bishnu Thapa, H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
Molecular Dynamics of Methylamine, Methanol, and Methyl Fluoride Cations in Intense 7 Micron Laser Fields
Published in J. Phys. Chem. A 2014, 118, 10067-72[Abstract]
Bishnu Thapa, H. Bernhard Schlegel
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
The Mechanisms of Rectification in Au|molecule|Au Devices Based on Langmuir-Blodgett Monolayers of Iron(III) and Copper(II) Surfactants.
Published in Angew. Chem., Int. Ed. 2014, 53, 14462-67 [Abstract]
Lanka D. Wickramasinghe1, Dr. Shivnath Mazumder1, Sunalee Gonawala1, Meeghage Madusanka Perera2, Habib Baydoun1, Bishnu Thapa1, Li Li3, Lingxiao Xie3, Guangzhao Mao3, Zhixian Zhou2, H. Bernhard Schlegel1, Cláudio N. Verani1
1. Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202 (USA)
2. Department of Physics & Astronomy, Wayne State University, 666 W. Hancock, Detroit, MI 48201 (USA)
3. Department of Chemical Engineering & Materials Science, Wayne State University, 5050 Antony Wayne Dr., Detroit, MI 48202 (USA)
Strong field ionization rates of linear polyenes simulated with TDCIS and an absorbing potential
Published in J. Chem. Phys. 2014, 41, 174104 [Abstract]
Pascal Krause and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202 (USA)
2015
Ligand transformations and efficient proton/water reduction with cobalt catalysts based on pentadentate pyridine-rich environments
Published in Angew. Chem., Int. Ed. 2015, 54, 2105-10 [Abstract]
Debashis Basu, Shivnath Mazumder, Xuetao Shi, Habib Baydoun, Jens Niklas, Oleg Poluektov, H. Bernhard Schlegel, and Claudio N. Verani
Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202 (USA)
Calculations of pKa’s and Redox Potentials of Nucleobases with Explicit Waters and Polarizable Continuum Solvation
Published in J. Phys. Chem. A 2015, 119, 5134-44 [Abstract]
Bishnu Thapa and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202 (USA)
Modulation of electronic and redox properties in phenolate-rich cobalt(III) complexes and their implications for catalytic proton reduction
Published in Dalton Trans., 2015, 44, 3454 [Abstract]
Debashis Basu, Marco M. Allard, Fernando R. Xavier, Mary Jane Heeg, H. Bernhard Schlegel and Claudio N. Verani
Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202 (USA)
Energy dependence of the ruthenium(II)-bipyridine metal-to-ligand-charge-transfer excited state radiative lifetimes: Effects of ππ*(bipyridine) mixing
Published in J. Phys. Chem. B, 2015, 119, 7393–7406 [Abstract]
Ryan A. Thomas!, Chia Nung Tsai2, Shivnath Mazumder1, I Chen Lu2, Richard L. Lord3, H. Bernhard Schlegel1, Yuan Jang Chen2, and John F. Endicott 1
1. Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202 (USA)
2. Department of Chemistry, Fu-Jen Catholic University, New Taipei City 24205, Taiwan, R.O.C.
3. Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401-9403, United States
Using Bonding to Guide Transition State Optimization
Published in J. Comput. Chem. 2015, 36, 1157–1166 [Abstract]
Adam B. Birkholz, and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202 (USA)
Distinct Proton and Water Reduction Behavior with a Cobalt(III) Electrocatalyst Based on Pentadentate Oximes
Published in Angew. Chem., Int. Ed. 2015, 54, 7139-43 [Abstract]
Debashis Basu1, Shivnath Mazumder1, Xuetao Shi1, Richard J. Staples2, H. Bernhard Schlegel1, and Claudio N. Verani1
1. Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202 (USA)
2. Department of Chemistry, Michigan State University, Lansing, MI 48824 (USA)
Angle-dependent ionization of small molecules by time-dependent configuration interaction and an absorbing potential
Published in J. Phys. Chem. Lett. 2015, 6, 2140-46 [Abstract]
Pascal Krause and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202 (USA)
Metal-to-Ligand Charge-Transfer Emissions of Ruthenium(II) Pentaammine Complexes with Monodentate Aromatic Acceptor Ligands and Distortion Patterns of their Lowest Energy Triplet Excited States
Published in Inorg. Chem. 2015, 54, 8495–8508 [Abstract]
Chia Nung Tsai1, Shivnath Mazumder2, Xiu Zhu Zhang1, H. Bernhard Schlegel2, Yuan Jang Chen1, and John F. Endicott 2
1. Department of Chemistry, Fu-Jen Catholic University, New Taipei City 24205, Taiwan, R.O.C.
2. Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202 (USA)
Selective Photodissociation of Acetonitrile Ligands in Ruthenium Polypyridyl Complexes Studied by Density Functional Theory
Published in Inorg. Chem. 2015, 54, 8003–11 [Abstract]
Yi-Jung Tu1, Shivnath Mazumder1, John F. Endicott1, Claudia Turro2, Jeremy J. Kodanko1, and H. Bernhard Schlegel1
1. Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
2. Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
Angle-Dependent Ionization of Hydrides AHn Calculated by Time-Dependent Configuration Interaction with an Absorbing Potential
Published in J. Phys. Chem. A 2015, 119, 10212-20 [Abstract]
Pascal Krause and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202 (USA)
Relativistic and Solvation Effects on the Stability of Gold(III) Halides in Aqueous Solution
Published in J. Phys. Chem. A 2015, 119, 10212-20 [Abstract]
Kolja Theilacker1, H. Bernhard Schlegel2, Martin Kaupp1, and Peter Schwerdtfeger3
1. Technische Universität Berlin, Institut für Chemie, Theoretische Chemie, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
2.Department of Chemistry, Wayne State University, 5101 Cass Av., Detroit, Michigan 48202-3489, United States
3. New Zealand Institute for Advanced Study, Massey University Auckland, Private Bag 102 904, North Shore MSC, 0745 Auckland, New Zealand
Path Optimization by a Variational Reaction Coordinate Method I. Development of Formalism and Algorithms
Published in J. Chem. Phys. 2015, 143, 244101[Abstract]
Adam B. Birkholz and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, 5101 Cass Av., Detroit, Michigan 48202, USA
2016
Selective Release of Aromatic Heterocycles from Ruthenium Tris(2-pyridylmethyl) amine with Visible Light
Published in Inorg. Chem., 2016, 55 (1), pp 10–12 [Abstract]
Ao Li1, Jessica K. White2, Karan Arora1, Mackenzie K. Herroon3, Philip D. Martin1, H. Bernhard Schlegel1, Izabela Podgorski3,4, Claudia Turro2, and Jeremy J. Kodanko1,4
1. Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
2. Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
3. Department of Pharmacology, School of Medicine, Wayne State University, Detroit, Michigan 48201, United States
4. Barbara Ann Karmanos Cancer Institute, Detroit, Michigan 48201, United States
Evaluation of the Coordination Preferences and Catalytic Pathways of Heteroaxial Cobalt Oximes towards Hydrogen Generation
To be published in Chem. Sci., 2016 (accepted), [Abstract]
Debashis Basu1, Shivnath Mazumder1, Jens Niklas2, Habib Baydoun1, Dakshika Wanniarachchi1, Xuetao Shi1, Richard J. Staples3, O. G. Poluektov2, H. Bernhard Schlegel1, and Claudio Verani1
1. Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202
2. Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL 60439
3. Department of Chemistry, Michigan State University, Lansing, MI 48824
Controlling Chemical Reactions by Short, Intense Mid-Infrared Laser Pulses: Comparison of Linear and Circularly Polarized Light in Simulations of ClCHO+ Fragmentation
To be published in J. Phys. Chem. A (accepted), [Abstract]
Xuetao Shi, Bishnu Thapa, Wen Li, and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202
Exploration of Some Refinements to Geometry Optimization Methods
Submitted to Theor. Chem. Acc.
Adam B. Birkholz and H. Bernhard Schlegel
Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202
Investigation into 9(S)-HPODE-derived allene oxide to cyclopentenone cyclization mechanism via diradical oxyallyl intermediates
Submitted to Org. Biomol. Chem.
Hebert, S.; Cha, J. K.; Brash, A. R.; Schlegel, H. B
Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202

Schwiebert Group

2015
Evaluation of Hybrid Parallel Cell List Algorithms for Monte Carlo Simulation
Proceedings of the 7th IEEE International Workshop on Multicore and Multithreaded Architectures and Algorithms (M2A2 2015), August 2015.[Abstract]
Kamel Rushaidat1, Loren Schwiebert1, Brock Jackman1, Jason Mick2, Jeffrey Potoff2
1. Department of Computer Science, Wayne State University, Detroit, Michigan
2. Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan
Efficient Parallel Cell List Algorithms for Monte Carlo Simulations
Proceedings of 2015 The Summer Simulation Multi-Conference (SummerSim'15), Chicago, IL, July 2015. [Abstract]
Kamel Rushaidat1, Loren Schwiebert1, Brock Jackman1, Jason Mick2, Jeffrey Potoff2
1. Department of Computer Science, Wayne State University, Detroit, Michigan
2. Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan

Thomason Group

2011
Resting-state fMRI can reliably map neural networks in children
Published in NeuroImage, 55 (1), 165–175 (2011)[Abstract]
Moriah E. Thomason1,6, Emily L. Dennis2, Anand A. Joshi2,3, Shantanu H. Joshib3, Ivo D. Dinov2,3, Catie Chang4, Melissa L. Henry5, Rebecca F. Johnson5, Paul M. Thompson2,3, Arthur W. Toga2,3, Gary H. Glover4, John D. Van Horn2,3, Ian H. Gotlib5
1. Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA
2. Laboratory of Neuro Imaging (LONI), Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
3. Center for Computational Biology at UCLA, Los Angeles, CA, USA
4. Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
5. Department of Psychology, Stanford University, Stanford, CA, USA
6. Merrill Palmer Skillman Institute on Child and Family Development, Wayne State University, Detroit, MI, USA
Default-Mode and Task-Positive Network Activity in Major Depressive Disorder: Implications for Adaptive and Maladaptive Rumination
Published in NeuroImage, 55 (1), 165–175 (2011)[Abstract]
J. Paul Hamilton1, Daniella J. Furman1, Catie Chang2, Moriah E. Thomason1, Emily Dennis1, Ian H. Gotlib1
1. Department of Psychology, Stanford University, Stanford, California
2. Department of Radiology, Stanford University, Stanford, California
Evaluation of connectivity measures and anatomical features for statistical brain networks
Published in Proceeds from IEEE International Symposium on Biomedical Imaging, 2011.[Abstract]
Anand A. Joshi, Shantanu H. Joshi, Moriah E. Thomason, Ivo Dinov, and Arthur W. Toga
Laboratory of Neuro Imaging, University of California, Los Angeles, CA 90095, USA
Stress-induced activation of the HPA axis predicts connectivity between subgenual cingulate and salience network during rest in adolescents
Published in Journal of Child Psychology and Psychiatry 52 (10), 1026–1034 (2011)[Abstract]
Moriah E. Thomason1,2, J. Paul Hamilton3, Ian H. Gotlib3
1. Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI
2. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit, MI
3. Department of Psychology, Stanford University, Stanford, CA, USA
Vector autoregression, structural equation modeling, and their synthesis in neuroimaging data analysis
Published in Computers in Biology and Medicine, 41 (12), 1142–1155 (2011)[Abstract]
Gang Chen1, Daniel R. Glen1, Ziad S. Saad1, J. Paul Hamilton2, Moriah E. Thomason2, Ian H. Gotlib2, Robert W. Cox1
1. Scientific and Statistical Computing Core, NIMH/NIH/HHS, USA
2. Mood and Anxiety Disorders Laboratory, Department of Psychology, Stanford University, Stanford, CA 94305-2130, USA
Anxiety modulates insula recruitment in resting-state fMRI in youth and adults
Published in Brain Connectivity, 1(3):245-54 (2011)[Abstract]
Emily L. Dennis1, Ian H. Gotlib2, Paul M. Thompson1, and Moriah E. Thomason3, 4
1. Laboratory of Neuro Imaging, Department of Neurology, UCLA School of Medicine, Los Angeles, California.
2. Mood and Anxiety Disorders Laboratory, Department of Psychology, Stanford University, Stanford, California.
3. Merrill Palmer Skillman Institute, Wayne State University, Detroit, Michigan.
4. Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan.
Fetal magnetic resonance imaging at 3Tesla
Published in Topics in Magnetic Resonance Imaging, 22(3), 119-131 (2011)[Abstract]
Robert C. Welsh, Ursula Nemec, Moriah E. Thomason
2012
Functional and structural differences in the hippocampus associated with memory deficits in adult survivors of Acute Lymphoblastic Leukemia
Published in Topics in Pediatric Blood & Cancer, 60(2), 293-300 (2012)[Abstract]
Michelle Monje1, Moriah E. Thomason2,3, Laura Rigolo4, Yalin Wang5, Deborah P. Waber6, Stephen E. Sallan7, Alexandra J. Golby4
1. Department of Neurology, Stanford University, Stanford, California
2. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit, Michigan
3. Department of Pediatrics, Wayne State University, Detroit, Michigan
4. Department of Neurosurgery and Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
5. School of Computing, Informatics, and Decision Systems engineering, Arizona State University, Arizona
6. Department of Psychiatry, Children's Hospital Boston, Boston, Massachusetts
7. Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
Differences in resting corticolimbic functional connectivity in bipolar I euthymia
Published in Bipolar Disorders, 15, 156-166 (2012)[Abstract]
Salvatore Torrisi1, Teena D Moody2, Nathalie Vizueta1, Moriah E Thomason3, Martin M Monti4, Jennifer D Townsend1, Susan Y Bookheimer2, Lori L Altshuler1
1. Department of Psychiatry, Semel Institute for Neuroscience and Human Behavior
2. Center for Cognitive Neuroscience, University of California at Los Angeles, Los Angeles, CA
3. Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI
4. Department of Psychology, University of California at Los Angeles, Los Angeles, CA, USA
2013
Cross-Hemispheric Functional Connectivity in the Human Fetal Brain
Published in Science Translational Medicine, 5, 173ra24 (2013)[Abstract]
Moriah E. Thomason1,2,3, Maya T. Dassanayake4, Stephen Shen5, Yashwanth Katkuri6, Mitchell Alexis4, Amy L. Anderson1,3, Lami Yeo3,7, Swati Mody6, Edgar Hernandez-Andrade3,7, Sonia S. Hassan3,7, Colin Studholme8,9, Jeong-Won Jeong2,10 and Roberto Romero3,11
1. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit, MI 48202, USA.
2. Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI 48202, USA.
3. Perinatology Research Branch, National Institute of Child Health and Human Development (NICHD)/National Institutes of Health (NIH)/Department of Health and Human Services (DHHS), Detroit, MI 48202, USA.
4. Basic Medical Sciences Program, Wayne State University School of Medicine, Detroit, MI 48202, USA.
5. Wayne State University School of Medicine, Detroit, MI 48202, USA.
6. Department of Radiology, Wayne State University School of Medicine, Detroit, MI 48202, USA.
7. Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48202, USA.
8. Department of Pediatrics and Neonatology, University of Washington, Seattle, WA 98105, USA.
9. Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
10. Department of Neurology, Wayne State University School of Medicine, Detroit, MI 48202, USA.
11. Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD 20814, USA.
Functional plasticity before the cradle: A review of neural functional imaging in the human fetus
Published in Neuroscience & Biobehavioral Reviews, 37(9) Part B, 2220-2232 (2013)[Abstract]
Amy L. Anderson1,2, Moriah E. Thomason1,2,3
1. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit, MI, USA
2. Perinatology Research Branch, NICHD/NIH/DHHS, Detroit, MI, USA
3. Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA
Idle behaviors of the hippocampus reflect endogenous cortisol levels in youth
Published in Journal of the American Academy of Child & Adolescent Psychiatry, 52(6), 642-652 (2013)[Abstract]
Moriah E. Thomason1,3,4, Maria A. Tocco1, Kelly A. Quednau1, Andrea R. Bedway2, Justin M. Carré3
1. Merrill Palmer Skillman Institute for Child and Family Development at Wayne State University (WSU)
2. Michigan State University College of Human Medicine
3. Department of Psychology at WSU
4. Department of Pediatrics in the WSU School of Medicine and with the Perinatology Research Branch of the National Institute of Child Health and Human Development (NICHD), National Institutes of Health
The stimuli drive the response: an fMRI study of youth processing adult or child emotional face stimuli
Published in NeuroImage, 83, 679-689 (2013)[Abstract]
Hilary A. Marusak1,2, Justin M. Carré3, Moriah E. Thomason2, 4
1. Department of Psychiatry and Behavioral Neurosciences, Wayne State University, Detroit, MI 48202, USA
2. Merrill Palmer Skillman Institute, Wayne State University, Detroit, MI 48202, USA
3. Department of Psychology, Wayne State University, Detroit, MI 48202, USA
4. Department of Pediatrics, Wayne State University, Detroit, MI 48202, USA
Age-related changes in the structure and function of prefrontal cortex-amygdala circuitry in children and adolescents: A multi-modal imaging approach
Published in NeuroImage, 83, 679-689 (2013)[Abstract]
Johnna R. Swartz1, Melisa Carrasco2, Jillian Lee Wiggins1, Moriah E. Thomason3, 4, Christopher S. Monka2,5,6
1. Department of Psychology, University of Michigan, Ann Arbor, MI 48104, USA
2. Neuroscience Program, University of Michigan, Ann Arbor, MI 48104, USA
3. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit, MI 48202, USA
4. Department of Pediatrics, Wayne State University, Detroit, MI 48202, USA
5. Department of Psychiatry, University of Michigan, Ann Arbor, MI 48104, USA
6. Center for Human Growth and Development, University of Michigan, Ann Arbor, MI 48104, USA
Magnetic resonance venography of the fetal brain using susceptibility weighted imaging
To be published in Journal of Magnetic Resonance Imaging[Abstract]
Jaladhar Neelavalli1,Swati Mody2,Lami Yeo3,4, Pavan Kumar Jella1, Steven J. Korzeniewski3,4, Sheena Saleem2, Yashwanth Katkuri1, Ray O. Bahado-Singh3, Sonia S. Hassan3,4, E. Mark Haacke1, Roberto Romero4,5,6, Moriah E. Thomason 4,7
1. Department of Radiology, Wayne State University, Detroit, Michigan, USA
2. Department of Pediatric Imaging, Children's Hospital of Michigan, Detroit, Michigan, USA
3. Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
4. Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maryland, and Detroit, Michigan, USA
5. Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, USA
6. Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
7. Merrill Palmer Skillman Institute for Child and Family Development, Department of Pediatrics, Wayne State University, Detroit, Michigan, USA
What is a representative brain? Neuroscience meets population science
Published in Proceedings of the National Academy of Sciences of the United States of America [Abstract]
Emily B. Falk1,2,3, Luke W. Hyded5,6, Colter Mitchell5,7, Jessica Faul5, Richard Gonzalez2,4,8, Mary M. Heitzeg9, Daniel P. Keating4,5,9,10, Kenneth M. Langa5,11,12, Meghan E. Martz4, Julie Maslowsky13, Frederick J. Morrison4, Douglas C. Noll14, Megan E. Patrick5, Fabian T. Pfeffer5,7, Patricia A. Reuter-Lorenz4,5,15, Moriah E. Thomason16, 17, 18, Pamela Davis-Kean2,4,5,6, Christopher S. Monk4,5,6,9,15, and John Schulenberg4,5,6
1. Department of Communication Studies, University of Michigan, Ann Arbor, MI 48109
2. Department of Research Center for Group Dynamics, University of Michigan, Ann Arbor, MI 48109
3. Annenberg School for Communication, University of Pennsylvania, Philadephia, PA, 19104
4. Department of Psychology, University of Michigan, Ann Arbor, MI 48109
5. Department of Survey Research Center, University of Michigan, Ann Arbor, MI 48109
6. Center for Human Growth and Development, University of Michigan, Ann Arbor, MI 48109
7. Department of Population Studies Center of the Institute for Social Research, University of Michigan, Ann Arbor, MI 48109 8. Department of Statistics, University of Michigan, Ann Arbor, MI 48109
9. Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109
10. Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109
11. Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
12. Veterans Affairs Center for Clinical Management Research, Ann Arbor, MI 48105,
13. Robert Wood Johnson Foundation Health and Society Scholars Program, Population Health Sciences, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53706
14. Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109 15. Department of Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109
16. School of Medicine Pediatrics, Wayne State University, Detroit, MI 48202
17. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit, MI 48202 18. Perinatology Research Branch, National Institutes of Health, Detroit, MI 48202
2014
Age-related changes in the structure and function of prefrontal cortex-amygdala circuitry in children and adolescents: A multi-modal imaging approach
Published in Neuroimage, 2014, 86, 212-220[Abstract]
Johnna R. Swartz1, Melisa Carrasco2, Jillian Lee Wiggins1, Moriah E. Thomason3,4, Christopher S. Monk1,2,5,6
1. Department of Psychology, University of Michigan, Ann Arbor, MI 48104, USA
2. Neuroscience Program, University of Michigan, Ann Arbor, MI 48104, USA
3.Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit, MI 48202, USA
4. Department of Pediatrics, Wayne State University, Detroit, MI 48202, USA
5. Department of Psychiatry, University of Michigan, Ann Arbor, MI 48104, USA
6. Center for Human Growth and Development, University of Michigan, Ann Arbor, MI 48104, USA
MR venography of the fetal brain using susceptibility weighted imaging
Published in Journal of Magnetic Resonance Imaging, 2014, 40, 949–957[Abstract]
Jaladhar Neelavalli1, Swati Mody2, Lami Yeo3,4, Pavan Kumar Jella1, Steven J. Korzeniewski3,4, Sheena Saleem2, Yashwanth Katkuri1, Ray O. Bahado-Singh3, Sonia S. Hassan3,4, E. Mark Haacke1, Roberto Romero4,5,6, and Moriah E. Thomason4,7
1. Department of Radiology, Wayne State University, Detroit, Michigan, USA
2. Department of Pediatric Imaging, Children’s Hospital of Michigan, Detroit, Michigan, USA
3.Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA.
4. Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, and Detroit, Michigan, USA
5. Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, USA
6. Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
7. Merrill Palmer Skillman Institute for Child and Family Development, Department of Pediatrics, Wayne State University, Detroit, Michigan, USA
Method for handling intensity inhomogenieties in fMRI sequences of moving anatomy of the early developing brain
Published in J Magn Reson Imaging, 2014, 39(4), 998–1006[Abstract]
Sharmishtaa Seshamani1, Xi Cheng1, Mads Fogtmann1, Moriah E. Thomason2,3,4, Colin Studholme1
1. Biomedical Image Computing Group, Departments of Pediatrics, Bioengineering, and Radiology, University of Washington, Seattle, WA 98195, USA
2. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit, MI, USA
3. Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA
4. Perinatology Research Branch, NICHD/NIH/DHHS, Detroit, MI, USA
Measuring venous blood oxygenation in fetal brain using susceptibility-weighted imaging
Published in Medical Image Analysis 18 (2014) 285–300[Abstract]
Jaladhar Neelavalli1, Pavan Kumar Jella1, Udaybhaskar Krishnamurthy1, Sagar Buch2, E. Mark Haacke1, Lami Yeo3,4, Swati Mody5, Yashwanth Katkuri1, Ray Bahado-Singh3, Sonia S Hassan3,4, Roberto Romero4, and Moriah E Thomason4,6
1. Biomedical Image Computing Group, Departments of Pediatrics, Bioengineering, and Radiology, University of Washington, Seattle, WA 98195, USA
2. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit, MI, USA
3.Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA
4. Perinatology Research Branch, NICHD/NIH/DHHS, Detroit, MI, USA
5. Department of Pediatric Imaging, Children’s Hospital of Michigan, Detroit, Michigan, USA
6. Merrill Palmer Skillman Institute for Child and Family Development, Department of Pediatrics, Wayne State University, Detroit, Michigan, USA
Testosterone Rapidly Increases Neural Reactivity to Threat in Healthy Men: A Novel Two-Step Pharmacological Challenge Paradigm
Published in Biological Psychiatry, 2014, 76:324–331[Abstract]
Stefan M.M. Goetz1, Lingfei Tang1, Moriah E. Thomason2, 3, Michael P. Diamond4, Ahmad R. Haririe5, 6, and Justin M. Carré1,7
1. Department of Psychology, Wayne State University, Detroit, MI, USA, 48202
2. Merrill Palmer Skillman Institute, Wayne State University, Detroit, MI, USA, 48202
3. Department of Pediatrics, Wayne State University, Detroit, MI, USA, 48202
4. Department of Obstetrics and Gynecology, Georgia Regents University, Augusta, GA, USA, 30912
5. Department of Psychology and Neuroscience, Duke University, Durham, NC, USA, 27708
6. Institute for Genome Sciences & Policy, Duke University, Durham, NC, USA, 27708
7. Department of Psychology, Nipissing University, North Bay, Ontario, Canada, P1B8L7
Intrinsic Functional Brain Architecture Derived from Graph Theoretical Analysis in the Human Fetus
Published in PLoS ONE, 2014, 9(5), e94423[Abstract]
Moriah E. Thomason1,2,3, Jesse A. Brown4, Maya T. Dassanayake5, Rupal Shastri5, Hilary A. Marusak1,6, Edgar Hernandez-Andrade3,7, Lami Yeo3,7, Swati Mody2,8, Susan Berman7, Sonia S. Hassan3,7, Roberto Romero3
1. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit, Michigan, United States of America
2. Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
3. Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland and Detroit, Michigan, United States of America
4. Department of Neurology, University of California at San Francisco School of Medicine, San Francisco, California, United States of America
5. Basic Medical Sciences Program, Wayne State University School of Medicine, Detroit, Michigan, United States of America
6. Department of Psychiatry and Behavioral Neurosciences, Wayne State University, Detroit, Michigan, United States of America
7. Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America 8. Department of Radiology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
An fMRI study of cerebrovascular reactivity and perfusion in obstructive sleep apnea patients before and after CPAP treatment
Published in Sleep Medicine, 2014, 15 (8), 892–898[Abstract]
Olga Prilipko1, Nelly Huynh1, Moriah E. Thomason2, 3, Clete A. Kushida1, Christian Guilleminault1
1. Stanford University Sleep Clinic and Center for Human Sleep Research, Redwood City, CA, USA
2. Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA
3. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit, MI, USA
Unraveling the miswired connectome: a developmental perspective
Published in Neuron, 2014, 83, 1335-1353 [Abstract]
Adriana Di Martino1, Damien A. Fair2, Clare Kelly1, Theodore D. Satterthwaite3, F. Xavier Castellanos1,4, Moriah E. Thomason5,6, R. Cameron Craddock4,7, Beatriz Luna8, Bennett L. Leventhal9, Xi-Nian Zuo10,11, Michael P. Milham4, 7
1. Department of Child and Adolescent Psychiatry, Child Study Center at NYU Langone Medical Center, New York, NY 10016, USA
2. Behavioral Neuroscience and Psychiatry Departments and Advanced Imaging Research Center, Oregon Health and Science University, Portland, OR 97329, USA
3. Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
4. Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
5. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit, MI 48202, USA
6. Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI 48201, USA
7. Center for the Developing Brain, Child Mind Institute, New York, NY 10022, USA
8. Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
9. Department of Psychiatry, Langley Porter Psychiatric Institute, University of California San Francisco, San Francisco, CA 94143, USA
10. Key Laboratory of Behavioral Science and Magnetic Resonance Imaging Research Center, Institute of Psychology, Chinese Academy of Sciences, Beijing, 100101, China
11. Faculty of Psychology, Southwest University, Beibei, Chongqing 100101, China
Age-related increases in long-range connectivity in fetal functional neural connectivity networks in utero
Published in Developmental Cognitive Neuroscience, 2015, 11, 96–104 [Abstract]
Moriah E. Thomason1,2,4, Lauren E. Grove1,4, Tim A. Lozon Jr.5, Angela M. Vila1, Yongquan Ye6, Matthew J. Nye7, Janessa H. Manning1, d, Athina Pappas2,4, Edgar Hernandez-Andrade4,8, Lami Yeod8, Swati Mody5, Susan Berman8, Sonia S. Hassan4,8, Roberto Romero3,4
1. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit, MI 48202, USA
2. Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI 48202, USA
3. Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, USA
4. Perinatology Research Branch, NICHD/NIH/DHHS, Detroit, MI 48202, USA
5. Michigan State University School of Medicine, East Lansing, MI, 48824 USA
6. Department of Radiology, Wayne State University School of Medicine, Detroit, MI 48202, USA
7. University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
8. Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48202, USA
2015
Childhood trauma exposure disrupts the automatic regulation of emotional processing
Published in Neuropsychopharmacology (2015) 40, 1250–1258 [Abstract]
Hilary A Marusak1,2, Kayla R Martin3, Amit Etkin4,5 and Moriah E Thomason2,6
1. Department of Psychiatry and Behavioral Neurosciences, Wayne State University School of Medicine, Detroit, MI, USA
2. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit, MI, USA
3. Wayne State University School of Medicine, Detroit, MI, USA
4. Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
5. Sierra-Pacific Mental Illness Research, Education, and Clinical Center (MIRECC) Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
6. Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA
Altered amygdala connectivity in urban youth exposed to trauma
Published in Soc Cogn Affect Neurosci (2015) 10 (11): 1460-1468 [Abstract]
Moriah E. Thomason1,2,3, Hilary A. Marusak1,4, Maria A. Tocco5, Angela M. Vila1; Olivia McGarragle4, David R. Rosenberg4
1. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University
2. Department of Pediatrics, Wayne State University School of Medicine
3. Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD
4. Department of Psychiatry and Behavioral Neurosciences, Wayne State University School of Medicine
5. Wayne State University School of Medicine
Disrupted insula-based connectome organization and conflict interference in trauma-exposed youth
Published in NeuroImage: Clinical, 8 (2015) 516–52[Abstract]
Hilary A. Marusak1,2, Amit Etkin3,4, Moriah E. Thomason2,5
1. Department of Psychiatry and Behavioral Neurosciences, Wayne State University School of Medicine, Detroit, MI, USA
2. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit, MI, USA
3. Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
4. Sierra-Pacific Mental Illness Research, Education and Clinical Center (MIRECC), Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
5. Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA
A Neural Substrate for Behavioral Inhibition in the Risk for Major Depressive Disorder
Published in Journal of the American Academy of Child & Adolescent Psychiatry, 2015, 54(10), 841–848[Abstract]
Julie Frost Bellgowan1, Peter Molfese4, Michael Marx5, Moriah Thomason6, Daniel Glen7, Jessica Santiago1, Ian H. Gotlib5, Wayne C. Drevets1,2, J. Paul Hamilton1,3
1. Laureate Institute for Brain Research, Tulsa, OK
2. Janssen Pharmaceuticals, Beerse, Belgium
3. Center for Social and Affective Neuroscience, Linköping University, Linköping, Sweden
4. Haskins Laboratories, New Haven, CT
5. Stanford University, Stanford, CA
6. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit
7. Scientific and Statistical Computing Core, National Institute of Mental Health, Bethesda, MD
Enhancing Cognitive Abilities with Comprehensive Training: A Large, Online, Randomized, Active-Controlled Trial
Published in PLoS ONE, 2015, 10(9): e0134467[Abstract]
Joseph L. Hardy1, Rolf A. Nelson2, Moriah E. Thomason3,4, Daniel A. Sternberg1, Kiefer Katovich1, Faraz Farzin1, Michael Scanlon1
1. Department of Research and Development, Lumos Labs, San Francisco, California, United States of America
2. Department of Psychology, Wheaton College, Norton, Massachusetts, United States of America
3. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit, Michigan, United States of America
4. Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
Interactive effects of BDNF Val66Met genotype and trauma on limbic brain anatomy in childhood
Published in European Child & Adolescent Psychiatry, 2015[Abstract]
Hilary A. Marusak1,2, Nisha Kuruvadi3, Angela M. Vila1, David W. Shattuck4, Shantanu H. Joshi4, Anand A. Joshi5,6, Pavan K. Jella7, Moriah E. Thomason1,8,9
1. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, 71 E. Ferry Street, Detroit, MI 48202, USA
2. Department of Psychiatry and Behavioral Neurosciences, Wayne State University School of Medicine, Detroit, MI, USA
3. Liberty University College of Osteopathic Medicine, Lynchburg, VA, USA
4. Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
5. Brain and Creativity Institute, University of Southern California, Los Angeles, CA, USA
6. Signal and Image Processing Institute, University of Southern California, Los Angeles, CA, USA
7. Department of Radiology, Wayne State University, Detroit, MI, USA
8. Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA
9. Perinatology Research Branch, NICHD/NIH/DHSS, Detroit, MI, USA
Amygdala responses to salient social cues vary with oxytocin receptor genotype in youth
Published in Neuropsychologia, 2015, 79, Part A, 1–9[Abstract]
Hilary A. Marusak1,2, Daniella J. Furman3, Nisha Kuruvadi4, David W. Shattuck5, Shantanu H. Joshi5, Anand A. Joshi6,7, Amit Etkin8,9, Moriah E. Thomason2,10
1. Department of Psychiatry and Behavioral Neurosciences, Wayne State University School of Medicine, USA
2. Merill Palmer Skillman Institute for Child and Family Development, Wayne State University, 71 E Ferry Street, Dertroit, MI 48202, USA
3. Helen Wills Neuroscience Institute, University of California, Berkeley, USA
4. Liberty University College of Osteopathic Medicine, USA
5. Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, USA
6. Brain and Creativity Institute, University of Southern California, USA
7. Signal and Image Processing Institute, University of Southern California, USA
8. Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, USA
9. Sierra-Pacific Mental Illness Research, Education and Clinical Center (MIRECC), Veterans Affairs Palo Alto Health Care System, USA
10. Department of Pediatrics, Wayne State University School of Medicine, USA
2016
Toward understanding the impact of trauma on the early developing human brain
To be Published in Neuroscience[Abstract]
Moriah E. Thomason1,2,3 and Hilary A. Marusak1,4
1. Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, United States
2. Department of Pediatrics, Wayne State University School of Medicine, United States
3. Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, United States
4. Department of Psychiatry and Behavioral Neurosciences, Wayne State University School of Medicine, United States

Verani Group

2005
Influence of Ligand Rigidity and Ring Substitution on the Structural and Electronic Behavior of Trivalent Iron and Gallium Complexes with Asymmetric Tridentate Ligands
Published in Inorg. Chem. 2005, 44, 7414-7422 [Abstract]
Camille Imbert1, Hrant P. Hratchian1, Mauricio Lanznaster1, Mary Jane Heeg1, Lew M. Hryhorczuk1, Bruce R. McGarvey2, H. Bernhard Schlegel1, and Claudio N. Verani1
1. Department of Chemistry, Wayne State University, 5101 Cass AVe. Detroit, Michigan 48202, USA
2. Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Ave., Windsor, Ontario N9B 1P4, Canada
2006
Structural, Spectroscopic, and Electrochemical Behavior of Trans-Phenolato Cobalt(III) Complexes of Asymmetric NN'O Ligands as Archetypes for Metallomesogens
Published in Dalton Trans., 2006, 2517–2525[Abstract]
Rajendra Shakya1, Camille Imbert1, Hrant P. Hratchian1, Mauricio Lanznaster1, Mary Jane Heeg1, Bruce R. McGarvey2, Marco Allard1, H. Bernhard Schlegel1 and Claudio N. Verani1
1. Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, Michigan 48202, USA
2. Department of Chemistry and Biochemistry, University of Windsor-401 Sunset Ave., Windsor, Ontario N9B 1P4, Canada
Structural and Electronic Behavior of Unprecedented Five-Coordinate Iron(III) and Gallium(III) Complexes with a New Phenol-Rich Electroactive Ligand
Published in Inorg. Chem. 2006, 45, 955-957[Abstract]
Mauricio Lanznaster1, Hrant P. Hratchian1, Mary Jane Heeg1, Lew M. Hryhorczuk1, Bruce R. McGarvey2, H. Bernhard Schlegel1, and Claudio N. Verani1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
2. Department of Chemistry, University of Windsor, Windsor, Ontario N9B 1P4, Canada
2007
Archetypical Modeling and Amphiphilic Behavior of Cobalt(II)-Containing Soft-Materials with Asymmetric Tridentate Ligands
Published in Inorganic Chemistry 2007, 46, 9808-9818 [Abstract]
Rajendra Shakya1, Sarmad Sahiel Hindo1, Libo Wu2, Marco M. Allard1, Mary Jane Heeg1, Hrant P. Hratchian3, Bruce R. McGarvey4, Sandro R. P. da Rocha2, and Cláudio N. Verani1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
2. Department of Chemical Engineering, Wayne State University, Detroit, Michigan 48202, USA
3. Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
4. Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 1P4, Canada
Amphiphilic and Magnetic Properties of a New Class of Cluster-Bearing [L2Cu44-O)(μ2-carboxylato)4] Soft Materials
Published in Chem. Eur. J. 2007, 13 (35), 9948-8856 [Abstract]
Rajendra Shakya1, Sarmad Sahiel Hindo1, Libo Wu3, Suolong Ni4, Marco Allard1, Mary Jane Heeg1, Sandro R.P. da Rocha3, Gordon T. Yee4, Hrant P. Hratchian2, and Cláudio N. Verani1
1. Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
2. Department of Chemistry, Indiana University Bloomington, Indiana 47405, USA
3. Department of Chemical Engineering, Wayne State University Detroit, Michigan 48202, USA
4. Department of Chemistry, Virginia Polytechnic Institute and State University Blacksburg, Virginia 24061, USA
2008
Synthesis, Redox, and Amphiphilic Properties of Responsive Salycilaldimine-Copper(II) Soft Materials
Published in Inorg. Chem., 2008, 47 (8), pp 3119–3127[Abstract]
Sarmad Sahiel Hindo, Rajendra Shakya, N. S. Rannulu, Marco M. Allard†, Mary Jane; Heeg, M. T. Rodgers, Sandro R. P. da Rocha and Claudio N. Verani
Department of Chemistry and Department of Chemical Engineering, Wayne State University, Detroit, Michigan 48202
Interfacial Behavior and Film Patterning of Redox-Active Cationic Copper(II)-Containing Surfactants
Published in Chem. Eur. J. 2008, 14 (31), 9665-9674 [Abstract]
Jeffery A. Driscoll1,Marco M. Allard1, Libo Wu2, Mary Jane Heeg1, Sandro R. P. da Rocha2, and Cláudio N. Verani1
1. Department of Chemistry Wayne State University Detroit Michigan 48202, USA
2. Department of Chemical Engineering, Wayne State University, Detroit, Michigan 48201, USA
2009
On the Effect of Coordination and Protonation Preferences in the Amphiphilic Behavior of Metallosurfactants with Asymmetric Headgroups
Published in Eur. J. Inorg. Chem. 2009 (3), 345–356 [Abstract]
Frank D. Lesh, Sarmad Sahiel Hindo, Mary Jane Heeg, Marco M. Allard, Prateek Jain, Bo Peng, Lew Hryhorczuk, Cláudio N. Verani
Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI 48202, USA
Comparative Activities of Nickel(II) and Zinc(II) Complexes of Asymmetric [NN′O] Ligands as 26S Proteasome Inhibitors
Published in Inorg. Chem. 2009, 48 (13), 5928-5937 [Abstract]
Michael Frezza1, Sarmad Sahiel Hindo2, Dajena Tomco2, Marco M. Allard2, Qiuzhi Cindy Cui1, Mary Jane Heeg2, Di Chen1, Q. Ping Dou1 and Cláudio N. Verani2
1. The Prevention Program, Barbara Ann Karmanos Cancer Institute, and Department of Pathology, School of Medicine, Wayne State University, Detroit, Michigan 48201, USA
2. Department of Chemistry, Wayne State University, 5101 Cass Ave. Detroit, Michigan 48202
2011
Investigation of the Electronic, Photosubstitution, Redox, and Surface Properties of New Ruthenium(II)-Containing Amphiphiles
Published in Inorg. Chem., 2011, 50 (3), pp 969–977 [Abstract]
Frank D. Lesh, Marco M. Allard, Rama Shanmugam, Lew M. Hryhorczuk, John F. Endicott, H. Bernhard Schlegel, and Cláudio N. Verani
Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States

Wada Group

2011
The Real Exchange Rate and Real Interest Differentials: The Role of the Trend-Cycle Decomposition
Published in Economic Inquiry, 2011, 50 (4), 968-987 [Abstract]
Tatsuma Wada
Department of Economics, Wayne State University
2012
On the Correlations of Trend-Cycle Errors
Published in Economics Letters, 2012, 116 (3), 396-400 [Abstract]
Tatsuma Wada
Department of Economics, Wayne State University
The Role of Transitory and Persistent Shocks in the Consumption Correlation and International Comovement Puzzles
Published in Macroeconomic Dynamics, 2013. [Abstract]
Tatsuma Wada
Department of Economics, Wayne State University

Xu Group

2007
Exploring Event Correlation for Failure Prediction in Coalitions of Clusters
Published in SC’07, November 10-16, 2007, Reno, Nevada, USA [Abstract]
Song Fu and Cheng-Zhong Xu
Wayne State University
Quantifying Temporal and Spatial Correlation of Failure Events for Proactive Management
Published in SRDS'07, Beijing, China, October, 2007 [Abstract]
Song Fu and Cheng-Zhong Xu
Wayne State University
2009
VCONF: A reinforcement learning approach to virtual machines auto-configuration
Published in Proceedings of International Conference on Autonomic Computing and Communications (ICAC), 2009. 137-146. Barcelona, Spain. June 15–19, 2009. [Abstract]
Jia Rao, Xiangping Bu, Cheng-Zhong Xu, Leyi Wang, George Yin
Dept. of Electrical and Computer Engineering, Dept. of Mathematics, Wayne State University, Detroit, Michigan 48202, USA
A Reinforcement Learning Approach to Online Web Systems Auto-configuration
Published in Proceedings of IEEE International Conference on Distributed Computing Systems (ICDCS), 2009. Montreal, Quebec, Canada June 22-June 26 2009. [Abstract]
Xiangping Bu, Jia Rao, Cheng-Zhong Xu
Department of Electrical and Computer Engineering, Department of Mathematics, Wayne State University, Detroit, Michigan 48202, USA

H. Zhang Group

2011
Towards Predictable Real-Time Routing for Wireless Networked Sensing and Control
Published in Proceedings of Cyber-Physical-Systems (CPS) Week Workshop on Real-Time Wireless for Industrial Applications (RealWin), 2011[Information]
Xiaohui Liu, Hongwei Zhang, Qiao Xiang
The Case for Addressing the Limiting Impact of Interference on Wireless Scheduling
Published in Proceedings of 2011 19th IEEE International Conference on Network Protocols (ICNP) [Abstract]
Xin Che, Xi Ju, Hongwei Zhang
Department of Computer Science, Wayne State Univ., Detroit, MI, USA
2012
Taming Uncertainties in Real-Time Routing for Wireless Networked Sensing and Control
Published in Proceeding of 13th ACM International Symposium on Mobile Ad Hoc Networking and Computing (MobiHoc), Hilton Head Island, SC, USA, June 11–14, 2012 [Abstract]
Xiaohui Liu, Hongwei Zhang, Qiao Xiang, Xin Che, Xi Ju
2013
Taming Uncertainties in Real-Time Routing for Wireless Networked Sensing and Control
Published in IEEE Transactions on Smart Grid (TSG), special issue on "Smart Grid Communication Systems", 4(1):288-301, March 2013 [Abstract]
Xiaohui Liu, Hongwei Zhang, Qiao Xiang, Xin Che, Xi Ju
Department of Computer Science, Wayne State Univ., Detroit, MI, USA
2014
The Case for Addressing the Ordering Effect in Interference-Limited Wireless Scheduling
Published in IEEE Transactions on Wireless Communications (TWC), 13(9), September 2014[Abstract]
Xin Che, Hongwei Zhang, Xi Ju
Department of Computer Science, Wayne State Univ., Detroit, MI, USA
The Case for Addressing the Ordering Effect in Interference-Limited Wireless Scheduling
Published in ACM Transactions on Sensor Networks (TOSN), 10(2), January 2014 [Abstract]
Hongwei Zhang, Xin Che, Xiaohui Liu, Xi Ju
Department of Computer Science, Wayne State Univ., Detroit, MI, USA
A Remainder-Based Contention Avoidance Scheme for Saturated Wireless CSMA Networks
Published in IEEE Transactions on Vehicular Technology (TVT), 62(2):772-782, February 2013 [Abstract]
Wenfeng Du, Zhong Ming, Wei Nie, Hongwei Zhang
Department of Computer Science, Wayne State Univ., Detroit, MI, USA
2015
On Optimal Diversity in Network-Coding-Based Routing in Wireless Networks
To Be Published in 34th IEEE International Conference on Computer Communications (INFOCOM), 2015
Qiao Xiang, Hongwei Zhang, Jianping Wang, Guoliang Xing, Shan Lin, Xue Liu
Heterogeneous Vehicular Wireless Networking: A Theoretical Perspective
To Be Published
Hongwei Zhang, Fan Bai, Xi Ju

Z. Zhang Group

2014
Superconvergent Two-grid Methods For Elliptic Eigenvalue Problems
To Be Published[Information]
Hailong Guo, Zhimin Zhang, and Ren Zhao
Department of Mathematics, Wayne State University, Detroit, MI 48202

Zhao Group

2005
Interlevel optical properties of systems of quantum dots
Published in Proceedings of SPIE (SPIE 2005), 5897(58970M). San Diego, CA, USA. August 1, 2005. [Abstract]
Victor Bondarenko and Yang Zhao
Department of Electrical and Computer Engineering, Wayne State University, Detroit, Michigan 48202, USA
Interlevel Electromagnetic Response of Systems of Spherical Quantum Dots
Published in PHYSICAL REVIEW B 71, 115304 (2005) [Abstract]
Victor Bondarenko1,2, Miroslaw Załużny3, and Yang Zhao1
1. Department of Electrical and Computer Engineering, Wayne State University, Detroit, Michigan 48202, USA
2. Department of Theoretical Physics, Institute of Physics, National Academy of Sciences of Ukraine, Kiev 03650, Ukraine
3. Institute of Physics and Nanotechnology Center, M. Curie-Skłodowska University, 20-031 Lublin, Poland
2006
Interlevel Electromagnetic Response of Quantum Dots of Shapes with Uniaxial Rotation Symmetry
Published in PHYSICAL REVIEW B 73, 035335 (2006) [Abstract]
Victor Bondarenko and Yang Zhao
Wayne State University

Others

Bayesian Variable Selection with Joint Modeling of Categorical and Survival Outcomes: An Application to Individualizing Chemotherapy Treatment in Advanced Colorectal Cancer
Published in Biometrics 2009 Dec; 65(4): 1030-40 [Abstract]
Wei Chen1, Debashis Ghosh2, Trivellore E. Raghunathan3, and Daniel J. Sargent4
1. Biostatistics Core, Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48201, U.S.A.
2. Departments of Statistics and Public Health Sciences, Penn State University, University Park, Pennsylvania 16802, U.S.A.
3. Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, U.S.A.
4. Division of Biostatistics, Mayo Clinic, Rochester, Minnesota 55905, U.S.A.
AAPM Task Group 128: Quality assurance tests for prostate brachytherapy ultrasound systems
Published in Med. Phys. 2008, 35 (12), 5471 [Abstract]
Douglas Pfeiffer1, Steven Sutlief2, Wenzheng Feng3, Heather M. Pierce4 and Jim Kofler5
1. Imaging Department, Boulder Community Foothills Hospital, Boulder, Colorado 80301, USA
2. Radiation Therapy, VA Medical Center, VA Puget Sound Health Care System, Seattle, Washingon 98108, USA
3. Cardiology and Interventional Radiology, William Beaumont Hospital, Royal Oak, Michigan 48073, USA
4. CIRS, Inc., Norfolk, Virginia 23513, USA
4. Heather M. Pierce, CIRS, Inc., Norfolk, Virginia 23513, Radiology, Mayo Clinic, Rochester, Minnesota 55905, USA
Hierarchical Surface Abstraction Using Adaptive Mean Shift
Published in Proceedings of the 21st International Conference on Computer Animation and Social Agents (CASA), 2008 [Abstract]
Chang Liu, Jiaxi Hu, Jing Hua, and Hong Qin
Wayne State University
Stony Brook University
A Scalable Asynchronous Replication-Based Strategy for Fault Tolerant MPI Applications
Published in HiPC’07: the International Conference on High Performance Computing LNCS 4873:257–268, 2007 [Abstract]
J. P. Walters and V. Chaudhary
Department of Computer Science and Engineering, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
Time-Dependent Behaviour of Electron Transport in Methane–Argon mixtures
Published in J. Phys. D: Appl. Phys. 2005, 38 (10), 1577–1587 [Abstract]
Alan A Sebastian and J M Wadehra
Department of Physics and Astronomy, Wayne State University, Detroit, MI 48202, USA
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