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2013 (5 publications)

• Genome-wide profiles of CtBP link metabolism with genome stability and epithelial reprogramming in breast cancer  Li-Jun Di, Jung S. Byun, Madeline M. Wong, Clay Wakano, Tara Taylor, Sven Bilke, Songjoon Baek, Kent Hunter, Howard Yang, Maxwell Lee, Cecilia Zvosec, Galina Khramtsova, Fan Cheng, Charles M. Perou, C. Ryan Miller, Rachel Raab, Olufunmilayo I. Olopade & Kevin Gardner Nature Communications, doi:10.1038/ncomms2438 (2013)
• Ischemic stroke is associated with the ABO locus: The EuroCLOT study  FMK Williams, AM Carter, PG Hysi et al and EuroCLOT Investigators, the Wellcome Trust Case Control Consortium 2, MORGAM, MetaStroke and the International Stroke Genetics Consortium Annals of Neurology, DOI: 10.1002/ana.23838 (2013)
• Initial Assessment of the Pathogenic Mechanisms of the Recently Identified Alzheimer Risk Loci  P Holton, M Ryten, MA Nalls et al. Annals of Human Genetics, DOI: 10.1111/ahg.12000 (2013)
• Identification of Early Replicating Fragile Sites that Contribute to Genome Instability  JH Barlow, RB Faryabi, E Callen, N Wong, A Malhowski, H Tang Chen, G Gutierrez-Cruz, H-W Sun, P McKinnon, G Wright, R Casellas, DF Robbiani, L Staudt, O Fernandez-Capetillo, A Nussenzweig Cell, doi://10.1016/j.cell.2013.01.006 (2013)
• Genetic variation associated with circulating monocyte count in the eMERGE Network  DR Crosslin, A McDavid, N Weston et al Hum. Mol. Genetics, doi: 10.1093/hmg/ddt010 (2013)

2012 (102 publications)

• RPA Accumulation during Class Switch Recombination Represents 5'-3' DNA-End Resection during the S-G2/M Phase of the Cell Cycle  Arito Yamane, Davide F. Robbiani, Wolfgang Resch, Anne Bothmer, Hirotaka Nakahashi, Thiago Oliveira, Philipp C. Rommel, Eric J. Brown, Andre Nussenzweig, Michel C. Nussenzweig, Rafael Casellas Cell Reports, doi://10.1016/j.celrep.2012.12.006, (2012)
• Molecular structures of trimeric HIV-1 Env in complex with small antibody derivatives  Joel R. Meyerson, Erin E. H. Tran, Oleg Kuybeda, Weizao Chen, Dimiter S. Dimitrov, Andrea Gorlani, Theo Verrips, Jeffrey D. Lifson, and Sriram Subramaniam PNAS, doi:10.1073/pnas.1214810110 (2012)
• Ischaemic stroke is associated with the ABO locus: The euroclot study  FMK WIlliams, AM Carter, PG Hysi et al EuroCLOT Investigators, the Wellcome Trust Case Control Consortium 2 (WTCCC2), MORGAM, MetaStroke and the International Stroke Genetics Consortium Annals of Neurology, DOI: 10.1002/ana.23838 (2012)

• Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. II. Results for hexapeptides with non-polar side chains  O. I. Obolensky, Wells W. Wu, Rong-Fong Shen, Yi-Kuo Yu Rapid Comm. in Mass. Spec., DOI: 10.1002/rcm.6451 (2012)
• Mechanisms for the Insertion of Toxic, Fibril-like β-Amyloid Oligomers into the Membrane  Hyunbum Jang , Laura Connelly , Fernando Teran Arce , Srinivasan Ramachandran , Bruce L. Kagan , Ratnesh Lal , and Ruth Nussinov J. Chem. Theory Compt. , DOI: 10.1021/ct300916f (2012)
• Structural Ensemble of an Intrinsically Disordered Polypeptide  Jeetain Mittal , Tae Hyeon Yoo , George Georgiou , and Thomas Michael Truskett J. Phys. Chem. B, DOI: 10.1021/jp308984e (2012)
• STATs Shape the Active Enhancer Landscape of T Cell Populations  Golnaz Vahedi, Hayato Takahashi, Shingo Nakayamada, Hong-wei Sun, Vittorio Sartorelli, Yuka Kanno, John J. O'Shea Cell, doi://10.1016/j.cell.2012.09.044, (2012)
• Evaluation of Gene Association Methods for Coexpression Network Construction and Biological Knowledge Discovery  Sapna Kumari, Jeff Nie, Huann-Sheng Chen, Hao Ma, Ron Stewart, Xiang Li, Meng-Zhu Lu, William M. Taylor, Hairong Wei PLoS One, doi:10.1371/journal.pone.0050411 (2012)
• Common genetic variation near the Connexin-43 gene is associated with resting heart rate in African Americans: A Genome-wide Association Study of 13,372 participants  R Deo, MA Nalls, CL Avery, JG Smith et al. Heart Rhythm, doi://10.1016/j.hrthm.2012.11.014 (2012)
• Protein Secondary Structure Determination by Constrained Single-Particle Cryo-Electron Tomography  Alberto Bartesaghi, Federico Lecumberry, Guillermo Sapiro, Sriram Subramaniam Structure 20(12):2003-2013 (2012)
• A Systematic Approach for Development of an OPLS-Like Force Field and Its Application to Hydrofluorocarbons  Eugene Paulechka , Kenneth Kroenlein , Andrei Kazakov , and Michael Frenkel J. Phys. Chem. B, DOI: 10.1021/jp309119h (2012)

• The Impact of Ancestry and Common Genetic Variants on QT Interval in African Americans  JG Smith, CL Avery, DS Evans, MA Nalls et al. Circulation: Cardiovascular Genetics, doi: 10.1161/​CIRCGENETICS.112.962787 (2012)
• The effect of spatial smoothing on fMRI decoding of columnar-level organization with linear support vector machine  Masaya Misaki, Wen-Ming Luh, Peter A. Bandettini J. Neuroscience Methods, doi://10.1016/j.jneumeth.2012.11.004 (2012)
• Candidate Gene Association Study of BMI-Related Loci, Weight, and Adiposity in Old Age  Rachel A. Murphy, Michael A. Nalls, Margaux Keller, Melissa Garcia, Stephen B. Kritchevsky, Frances A. Tylavsky, Anne B. Newman, Gregory J. Tranah, Gudny Eiriksdottir, Vilmundur Gudnason and Tamara B. Harris J. Gerontology A, doi: 10.1093/gerona/gls227 (2012)
• Conformational Exploration of Two Peptides and Their Hybrid Polymer Conjugates: Potentialities as Self-Aggregating Materials  Nurit Haspel , Adèle D. Laurent , David Zanuy , Ruth Nussinov , Carlos Aleman , Jordi Puiggali , and Guillermo Revilla-López J. Phys. Chem. B, DOI: 10.1021/jp3043363 (2012)
• Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography  F Schotte, HS Cho, VRI Kaila, H Kamikubo, N Dashdorj, ER Henry, TJ Graber, R Henning, M Wulff, G Hummer, M Kataoka, and PA Anfinrud PNAS, doi: 10.1073/pnas.1210938109 (2012)
• Effects of the BDNF Val66Met Polymorphism on White Matter Microstructure in Healthy Adults  H Tost, T Alam, M Geramita, C Rebsch, B Kolachana, D Dickinson, BA Verchinski, H Lemaitre, AS Barnett, JW Trampush, DR Weinberger and S Marenco Neuropsychopharmacology , doi: 10.1038/npp.2012.214 (2012)
• Sodium and calcium mechanisms of rhythmic bursting in excitatory neural networks of the pre-Bötzinger complex: a computational modelling study  Patrick E. Jasinski, Yaroslav I. Molkov, Natalia A. Shevtsova, Jeffrey C. Smith, Ilya A. Rybak Eur. J. Neuroscience, DOI: 10.1111/ejn.12042 (2012)
• Effects of image contrast on functional MRI image registration  Javier Gonzalez-Castillo, Kristen N. Duthie, Ziad S. Saad, Carlton Chu, Peter A. Bandettini, Wen-Ming Luh NeuroImage, doi://10.1016/j.neuroimage.2012.10.076 (2012)

• Accurate decoding of sub-TR timing differences in stimulations of sub-voxel regions from multi-voxel response patterns  Masaya Misaki, Wen-Ming Luh, Peter A. Bandettini NeuroImage, doi://10.1016/j.neuroimage.2012.10.069, (2012)
• Novel Loci Associated with PR Interval in a Genome-Wide Association Study of Ten African American Cohorts  AM Butler, X Yin, DS Evans, MA Nalls et al. Circulation: Cardiovascular Genetics, doi: 10.1161/​CIRCGENETICS.112.963991 (2012)
• A collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography  Oleg Kuybeda, Gabriel A. Frank, Alberto Bartesaghi, Mario Borgnia, Sriram Subramaniam , Guillermo Sapiro J. Struct. Biol. , doi://10.1016/j.jsb.2012.10.010 (2012)
• Novel inhibitors of a Grb2 SH3C domain interaction identified by a virtual screen  Philip C. Simister, James Luccarelli, Sam Thompson, Daniel H. Appella, Stephan M. Feller , Andrew D. Hamilton Bioorganic & Medicinal Chemistry, doi://10.1016/j.bmc.2012.10.023 (2012)
• Statistical tests for detecting associations with groups of genetic variants: generalization, evaluation, and implementation  John Ferguson, William Wheeler, YiPing Fu, Ludmila Prokunina-Olsson, Hongyu Zhao and Joshua Sampson Eur. J. Hum. Genetics, doi: 10.1038/ejhg.2012.220 (2012)
• Imputation of Exome Sequence Variants into Population- Based Samples and Blood-Cell-Trait-Associated Loci in African Americans: NHLBI GO Exome Sequencing Project  Paul L. Auer, Jill M. Johnsen, Andrew D. Johnson et al. Am. J. Hum. Genetics, doi://10.1016/j.ajhg.2012.08.031 (2012)
• SHAVE: shrinkage estimator measured for multiple visits increases power in GWAS of quantitative traits  Osorio D Meirelles, Jun Ding, Toshiko Tanaka, Serena Sanna, Hsih-Te Yang, Dawood B Dudekula, Francesco Cucca, Luigi Ferrucci, Goncalo Abecasis and David Schlessinger European J. Hum. Genetics, doi: 10.1038/ejhg.2012.215 (2012)
• Membrane Association of the PTEN Tumor Suppressor: Electrostatic Interaction with Phosphatidylserine-Containing Bilayers and Regulatory Role of the C-Terminal Tail  Siddharth S. Shenoy, Hirsh Nanda, c, Mathias Lösche J. Struct. Biol. , doi://10.1016/j.jsb.2012.10.003, (2012)

• Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins  Raghunath Chatterjee, Jianfei Zhao, Ximiao He, Andrey Shlyakhtenko, Ishminder Mann, Joshua J. Waterfall, Paul Meltzer, B. K. Sathyanarayana, Peter C. FitzGerald, Charles Vinson Genes | Genomes | Genetics, doi://10.1534/g3.112.004002 (2012)
• Genetic risk factors for ischaemic stroke and its subtypes (the METASTROKE Collaboration): a meta-analysis of genome-wide association studies  M Traylor, M Farrall, EG Holliday et al & International Stroke Genetics Consortium The Lancet Neurology, doi://10.1016/S1474-4422(12)70234-X, (2012)
• Siblings with Ischemic Stroke Study (SWISS): Results of a Genome-wide Scan for Stroke Loci  JF. Meschia, M Nalls, M Matarin, TG. Brott, RD. Brown, Jr., J Hardy, B Kissela, SS. Rich, A Singleton, D Hernandez, L Ferrucci, K Pearce, M Keller, BB. Worrall, for the Siblings with Ischemic Stroke Study (SWISS) Investigators Stroke, doi: 10.1161/STROKEAHA.111.620484 (2012)
• Effect of Complement CR1 on Brain Amyloid Burden During Aging and Its Modification byAPOEGenotype  M Thambisetty, Y An, M Nalls et al for the Baltimore Longitudinal Study of Aging and the Alzheimer's Disease Neuroimaging Initiative Biological Psychiatry, doi://10.1016/j.biopsych.2012.08.015 (2012)
• CPhos: a program to calculate and visualize evolutionarily conserved functional phosphorylation sites  Boyang Zhao, Trairak Pisitkun, Jason D. Hoffert, Mark A. Knepper, Fahad Saeed Proteomics, DOI: 10.1002/pmic.201200189 (2012)
• Quantitative Phosphoproteomics in Nuclei of Vasopressin-Sensitive Renal Collecting Duct Cells  Steven J. Bolger, Patricia A. Gonzales Hurtado, Jason D. Hoffert, Fahad Saeed, Trairak Pisitkun, and Mark A. Knepper Am J Physiol Cell Physiol, doi:10.1152/ajpcell.00260.2012 (2012)
• Are Myocardial Infarction-Associated Single-Nucleotide Polymorphisms Associated With Ischemic Stroke?  Cheng YC, Anderson CD, Bione S et al Stroke, doi: 10.1161/​STROKEAHA.111.632075 (2012)
• Lin28b Reprograms Adult Bone Marrow Hematopoietic Progenitors to Mediate Fetal-Like Lymphopoiesis  Joan Yuan, Cuong K. Nguyen, Xiuhuai Liu, Chrysi Kanellopoulou, Stefan A. Muljo Science 335 (6073):1195-1200 (2012)

• Mouse model of endemic Burkitt translocations reveals the long-range boundaries of Ig-mediated oncogene deregulation  AL Kovalchuk, C Ansarah-Sobrinho, O Hakim, W Resch, Helena Tolarová, W Dubois, A Yamane, M Takizawa, IKlein, GL Hager, HC Morse III, M Potter, MC Nussenzweig, and R Casellas PNAS, doi: 10.1073/pnas.1200106109 (2012)
• Systems Biology in Physiology: The Vasopressin Signaling Network in Kidney  Mark A. Knepper Am. J. Physiol.: Cell Physiology, doi: 10.​1152/​ajpcell.​00270.​2012 (2012)
• Comparing the Expected Misclassification Cost for Two Classifiers Based on Estimates From the Same Sample  James F. Troendle, Kai F. Yu, Peter H. Westfall, Gene Pennello & Enrique F. Schisterman Statistics in Biopharmaceutical Research, DOI:10.1080/19466315.2012.695263 (2012)
• Theory for cross effect dynamic nuclear polarization under magic-angle spinning in solid state nuclear magnetic resonance: The importance of level crossings  Kent Thurber and Robert Tycko J. Chem. Phys. , doi://10.1063/1.4747449 (2012)
• Prediction of variable translation rate effects on cotranslational protein folding  Edward P. O'Brien, Michele Vendruscolo & Christopher M. Dobson Nature Communications, doi:10.1038/ncomms1850 (2012)
• Using Genome-wide Complex Trait Analysis to quantify 'missing heritability' in Parkinson's disease  MF Keller, M Saad, et al and International Parkinson's Disease Genomics Consortium and the Wellcome Trust Case Control Consortium 2 Human Molecular Genetics, doi: 10.1093/hmg/dds335 (2012)
• Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics  R Schmitz, RM Young et al Nature, doi:10.1038/nature11378 (2012)
• Automated subcortical segmentation using FIRST: Test-retest reliability, interscanner reliability, and comparison to manual segmentation  Allison C. Nugent, David A. Luckenbaugh, Suzanne E. Wood, Wendy Bogers, Carlos A. Zarate Jr., Wayne C Drevets Human Brain Mapping, DOI: 10.1002/hbm.22068 (2012)

• Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone φ, ψ and Side-Chain χ1 and χ2 Dihedral Angles  Robert B. Best, Xiao Zhu, Jihyun Shim, Pedro E. M. Lopes, Jeetain Mittal, Michael Feig, and Alexander D. MacKerell, Jr. J. Chem. Theory Comput., DOI: 10.1021/ct300400x (2012)
• Profibrogenic chemokines and viral evolution predict rapid progression of hepatitis C to cirrhosis  Patrizia Farci, Kurt Wollenberg, Giacomo Diaz, Ronald E. Engle, Maria Eliana Lai, Paul Klenerman, Robert H. Purcell, Oliver G. Pybus, and Harvey J. Alter PNAS, doi: 10.1073/pnas.1210592109 (2012)
• Multiple Testing of Composite Null Hypotheses in Heteroscedastic Models  Wenguang Sun & Alexander C. McLain Journal of the American Statistical Association 107(498):637-687 (2012)
• Use of support vector machines for disease risk prediction in genome-wide association studies: Concerns and opportunities  F Mittag, F Büchel, M Saad, A Jahn, C Schulte, Z Bochdanovits, J Simòn-Sànchez, MA Nalls, M Keller, DG Hernandez, JR Gibbs, S Lesage, A Brice, P Heutink, M Martinez, NW Wood, J Hardy, AB Singleton, A Zell, T Gasser, M Sharma for the International Parkinson's Disease Genomics Consortium (IPDGC) Human Mutation, DOI: 10.1002/humu.22161 (2012)
• Structural Mechanism of Trimeric HIV-1 Envelope Glycoprotein Activation  Erin E. H. Tran, Mario J. Borgnia, Oleg Kuybeda, David M. Schauder, Alberto Bartesaghi, Gabriel A. Frank, Guillermo Sapiro, Jacqueline L. S. Milne, Sriram Subramaniam PLoS Pathogens, doi:10.1371/journal.ppat.1002797 (2012)
• The impact of random-effect misspecification on percentile estimation for longitudinal growth data  Kyeongmi Cheon, Paul S. Albert, Zhiwei Zhang Statistics in Medicine, DOI: 10.1002/sim.5437 (2012)
• Mitochondrial DNA Sequence Variation Associated with Dementia and Cognitive Function in the Elderly  Tranah GJ, Nalls MA, Katzman SM, Yokoyama JS, Lam ET, Zhao Y, Mooney S, Thomas F, Newman AB, Liu Y, Cummings SR, Harris TB, Yaffe K J. Alzheimer's Disease, doi://10.3233/JAD-2012-120466 (2012)
• Weighted logrank tests for interval censored data when assessment times depend on treatment  Michael P. Fay, Joanna H. Shih Statistics in Medicine, DOI: 10.1002/sim.5447 (2012)

• The Peptide-Receptive Transition State of MHC Class I Molecules: Insight from Structure and Molecular Dynamics  Michael G. Mage, Michael A. Dolan, Rui Wang, Lisa F. Boyd, Maria Jamela Revilleza, Howard Robinson, Kannan Natarajan, Nancy B. Myers, Ted H. Hansen and David H. Margulies J. Immunol. , doi: 10.4049/​jimmunol.1200831 (2012)
• The Folliculin-FNIP1 pathway deleted in human Birt-Hogg-Dubé syndrome is required for B cell development  Baba M, Keller JR, Sun HW, Resch W, Kuchen S, Suh HC, Hasumi H, Hasumi Y, Kieffer-Kwon KR, Gonzalez CG, Hughes RM, Klein ME, Oh HF, Bible P, Southon E, Tessarollo L, Schmidt LS, Linehan WM, Casellas R. Blood, DOI 10.1182/blood-2012-02-410407 (2012)
• Identifying Protein Kinase Target Preferences Using Mass Spectrometry  Jacqueline Douglass1, Ruwan Gunaratne1, Davis Bradford, Fahad Saeed, Jason D. Hoffert, Peter J. Steinbach, Mark A. Knepper, and Trairak Pisitkun Cell Physiol., doi: 10.​1152/​ajpcell.​00166.​2012 (2012)
• Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains  Jeffery B. Klauda, Viviana Monje, Taehoon Kim, and Wonpil Im J. Phys. Chem. B, DOI: 10.1021/jp304056p (2012)
• Crystal structure of a plectonemic RNA supercoil  Jason R. Stagno, Buyong Ma, Jess Li, Amanda S. Altieri, R. Andrew Byrd & Xinhua Ji Nature Communications, doi:10.1038/ncomms1903 (2012)
• Trigger factor slows co-translational folding through kinetic trapping while sterically protecting the nascent chain from aberrant cytosolic interactions  Edward P O'Brien, John Christodoulou, Michele Vendruscolo, and Christopher M. Dobson J. Am. Chem. Soc. , DOI: 10.1021/ja302305u (2012)
• Genomic Analysis of Immune Response against Vibrio cholerae Hemolysin in Caenorhabditis elegans  Surasri N. Sahu, Jada Lewis, Isha Patel, Serdar Bozdag, Jeong H. Lee, Joseph E. LeClerc, and Hediye Nese Cinar PLoS One, doi: 10.1371/journal.pone.0038200 (2012)
• Spontaneous High-Gamma Band Activity Reflects Functional Organization of Auditory Cortex in the Awake Macaque  Makoto Fukushima, Richard C. Saunders, David A. Leopold, Mortimer Mishkin, and Bruno B. Averbeck Neuron, DOI 10.1016/j.neuron.2012.04.014 (2012)

• Mitochondrial DNA sequence variation is associated with free-living activity energy expenditure in the elderly  Gregory J. Tranah, Ernest T. Lam, Shana M. Katzman, Michael A. Nalls, Yiqiang Zhao, Daniel S. Evans, Jennifer S. Yokoyama, Ludmila Pawlikowska, Pui-Yan Kwok, Sean Mooney, Stephen Kritchevsky, Bret H. Goodpaster, Anne B. Newman, Tamara B. Harris, Todd M. Manini, Steven R. Cummings, For the Health, Aging and Body Composition Study Biochimica et Biophysica Acta (BBA) - Bioenergetics, doi://10.1016/j.bbabio.2012.05.012 (2012)
• An online tool for calculation of free-energy balance for the renal inner medulla  Ryan L. Vilbig, Abhijit Sarkar, Joseph Zischkau, Mark A. Knepper, and Trairak Pisitkun Am. J. Physiol. , doi: 10.​1152/​ajprenal.​00147.​2012 (2012)
• Methods of adjusted comparison of medians  James F. Troendle, Zhiwei Zhang, Megan E. Mathews, Junchi Guo Biometrical Journal, DOI: 10.1002/bimj.201100220 (2012)
• Characterization of a Dynamic String Method for the Construction of Transition Pathways in Molecular Reactions  Margaret E. Johnson and Gerhard Hummer J. Phys. Chem. B, DOI: 10.1021/jp212611k (2012)
• A Subset-Based Approach Improves Power and Interpretation for the Combined Analysis of Genetic Association Studies of Heterogeneous Traits  Samsiddhi Bhattacharjee, Preetha Rajaraman, Kevin B. Jacobs, William A. Wheeler, Beatrice S. Melin, Patricia Hartge, GliomaScan Consortium, Meredith Yeager, Charles C. Chung, Stephen J. Chanock, Nilanjan Chatterjee Am. J. Human Genetics, doi:/10.1016/j.ajhg.2012.03.015 (2012)
• Seeing is believing: video classification for computed tomographic colonography using multiple-instance learning.  Shijun Wang, Matthew T McKenna, Tan B Nguyen, Joseph E Burns, Nicholas Petrick, Berkman Sahiner, Ronald M Summers IEEE Transactions on Medical Imaging 31 (5):1141 (2012)
• Cross-seeding and Conformational Selection between Three- and Four-repeat Human Tau Proteins  Xiang Yu, Yin Luo, Paul Dinkel, Jie Zheng, Guanghong Wei, Martin Margittai, Ruth Nussinov, Buyong Ma J. Biol. Chem., doi: 10.1074/jbc.M112.340794 (2012)
• An Integrative Segmentation Method for Detecting Germline Copy Number Variations in SNP Arrays  Jianxin Shi, Peng Li Genetic Epidemiology 36(4):373-383, DOI: 10.1002/gepi.21631 (2012)

• Structural and Functional Consequences of Phosphate-Arsenate Substitutions in Selected Nucleotides: DNA, RNA, and ATP  Yu Xu, Buyong Ma, and Ruth Nussinov J. Phys. Chem. B, doi: 10.1021/jp300307u (2012)
• Imino Hydrogen Positions in Nucleic Acids from Density Functional Theory Validated by NMR Residual Dipolar Couplings  Alexander Grishaev, Jinfa Ying, Ad Bax J. Am. Chem. Soc., doi: 10.1021/ja301775j (2012)
• A Two-Platform Design for Next Generation Genome-Wide Association Studies  Joshua N. Sampson, Kevin Jacobs, Zhaoming Wang, Meredith Yeager, Stephen Chanock, Nilanjan Chatterjee Genetic Epidemiology, doi: 10.1002/gepi.21634 (2012)
• Postnatal development-and age-related changes in DNA-methylation patterns in the human genome  Paraskevi Salpea, Valya R. Russanova, Tazuko H. Hirai, Thomae G. Sourlingas, Kalliope E. Sekeri-Pataryas, Roberto Romero, Jonathan Epstein and Bruce H. Howard Nucleic Acids Research, doi: 10.1093/nar/gks312 (2012)
• Restraints on backbone conformations in solid state NMR studies of uniformly labeled proteins from quantitative amide¹⁵N-¹⁵N and carbonyl ¹³C-¹³C dipolar recoupling data  Kan-Nian Hua, Wei Qiang, Guillermo A. Bermejo, Charles D. Schwieters, Robert Tycko J. Magnetic Resonance, doi:10.1016/j.jmr.2012.03.001 (2012)
• The interleukin-6 receptor as a target for prevention of coronary heart disease: a mendelian randomisation analysis  The Interleukin-6 Receptor Mendelian Randomisation Analysis (IL6R MR) Consortium Lancet, doi: 10.1016/S0140-6736(12)60110-X (2012)
• Distinct contributions of human hippocampal theta to spatial cognition and anxiety  Brian R. Cornwell, Nicole Arkin, Cassie Overstreet, Frederick W. Carver, Christian Grillon Hippocampus, doi: 10.1002/hipo.22019 (2012)
• Simple models of human brain functional networks  Petra E. Vèrtes, Aaron F. Alexander-Bloch, Nitin Gogtay, Jay N. Giedd, Judith L. Rapoport, and Edward T. Bullmore PNAS, doi: 10.1073/pnas.1111738109 (2012)

• Quantitative Proteomics Identifies Vasopressin-Responsive Nuclear Proteins in Collecting Duct Cells.  Laura K. Schenk, Steven J. Bolger, Kelli Luginbuhl, Patricia A. Gonzales, Markus M. Rinschen, Ming-Jiun Yu, Jason D. Hoffert, Trairak Pisitkun and Mark A. Knepper J. Am. Soc. Nephrology, doi: 10.1681/ASN.2011070738 (2012)
• Whole-brain, time-locked activation with simple tasks revealed using massive averaging and model-free analysis  Javier Gonzalez-Castillo, Ziad S. Saad, Daniel A. Handwerker, Souheil J. Inati, Noah Brenowitz, and Peter A. Bandettini PNAS, doi: 10.1073/pnas.1121049109 (2012)
• Comprehensive Research Synopsis and Systematic Meta-Analyses in Parkinson's Disease Genetics: The PDGene Database  Lill CM , Roehr JT , McQueen MB , Kavvoura FK , Bagade S , et al. PLoS Genetics, doi:10.1371/journal.pgen.1002548 (2012)
• Cooperative Genome-Wide Analysis Shows Increased Homozygosity in Early Onset Parkinson's Disease  Simòn-Sànchez J , Kilarski LL , Nalls MA , Martinez M , Schulte C , et al. PLoS One, doi:10.1371/journal.pone.0028787 (2012)
• Cross-seeding and conformational selection between three-and four-repeat human Tau proteins  Xiang Yu, Yin Luo, Paul Dinkel, Jie Zheng, Guanghong Wei, Martin Margittai, Ruth Nussinov, and Buyong Ma J. Biol. Chem. , doi: 10.1074/jbc.M112.340794 (2012)
• Marginal analysis of longitudinal count data in long sequences: Methods and applications to a driving study  Zhiwei Zhang, Paul S. Albert, and Bruce Simons-Morton Ann.Appl.Stat. 6(1):27-54 (2012)
• Theory and simulation of ion conduction in the pentameric GLIC channel  Fangqiang Zhu and Gerhard Hummer J. Chem. Theory and Computation, doi: 10.1021/ct2009279 (2012)
• A Meta-Analysis and Genome-Wide Association Study of Platelet Count and Mean Platelet Volume in African Americans  Qayyum R , Snively BM , Ziv E , Nalls MA , Liu Y , et al. PLoS Genetics, doi:10.1371/journal.pgen.1002491 (2012)

• Distinct Regulatory Mechanisms and Functions for p53-Activated and p53-Repressed DNA Damage Response Genes in Embryonic Stem Cells  Mangmang Li, Yunlong He, Wendy Dubois, Xiaolin Wu, Jianxin Shi, Jing Huang Molecular Cell, doi:10.1016/j.molcel.2012.01.020 (2012)
• Modeling fecundity in the presence of a sterile fraction using a semi-parametric transformation model for grouped survival data  Alexander McLain, Rajeshwari Sundaram, Germaine Buck Louis Stat. Meth. in Med. Res. , doi: 10.1177/0962280212438646 (2012)
• Pair diffusion, hydrodynamic interactions, and available volume in dense fluids  Jeetain Mittal, Gerhard Hummer arXiv preprint, arXiv:1202.6039 (2012)
• Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides  O. I. Obolensky, Wells W. Wu, Rong-Fong Shen, Yi-Kuo Yu Rapid Comm. Mass. Spec., doi: 10.1002/rcm.6180 (2012)
• Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA  Pavel P Khil, Fatima Smagulova, Kevin M Brick, R. Daniel Camerini-Otero and Galina V Petukhova Genome Res., doi:10.1101/gr.130583.111 (2012)
• A Bayesian approach to mixture cure models with spatial frailties for population-based cancer relative survival data  Binbing Yu, Ram C. Tiwari Canadian Journal of Statistics, doi: 10.1002/cjs.10135 (2012)
• Using DNAWorks in Designing Oligonucleotides for PCR-Based Gene Synthesis.  David Hoover Methods in Molecular Biology 852(3):215-223 (2012)
• Comparison of Common Homology Modeling Algorithms: Application of User-Defined Alignments.  Michael A. Dolan, James W. Noah and Darrell Hurt Methods in Molecular Biology 857:399-414 (2012)

• The elusive phosphotyrosine: pinning down a rare species. Focus on “Large-scale phosphotyrosine proteomic profiling of rat renal collecting duct epithelium reveals predominance of proteins involved in cell polarity determination  Carolyn M. Ecelbarger Am J Physiol Cell Physiol January  302:C16-C17 (2012)
• Computational separation of conformational heterogeneity using cryo-electron tomography and 3D sub-volume averaging  Gabriel A. Frank, Alberto Bartesaghi, Oleg Kuybeda, Mario J. Borgnia, Tommi A. White, Guillermo Sapiro, Sriram Subramaniam J. Struct. Biol. , doi:/10.1016/j.jsb.2012.01.004 (2012)
• A Joint Mixed Effects Dispersion Model for Menstrual Cycle Length and Time-to-Pregnancy  Alexander C. McLain, Kirsten J. Lum, Rajeshwari Sundaram Biometrics, doi: 10.1111/j.1541-0420.2011.01711.x (2012)
• PDB Ligand Conformational Energies Calculated Quantum-Mechanically  Markus Sitzmann, Iwona Wedlich, Igor V Filippov, Chenzhong Liao, Megan L. Peach, Wolf-Dietrich Ihlenfeldt, Rajeshri G Karki, Yulia V Borodina, Raul E Cachau, and Marc C Nicklaus J. Chem. Inf. Model. , doi: 10.1021/ci200595n (2012)
• Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke  The International Stroke Genetics Consortium (ISGC), the Wellcome Trust Case Control Consortium et al. Nature Genetics, doi:10.1038/ng.1081 (2012)
• DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes  Ofir Hakim, Wolfgang Resch, Arito Yamane, Isaac Klein, Kyong-Rim Kieffer-Kwon, Mila Jankovic, Thiago Oliveira, Anne Bothmer, Ty C. Voss, Camilo Ansarah-Sobrinho, Ewy Mathe, Genqing Liang, Jesse Cobell, Hirotaka Nakahashi, Davide F. Robbiani, Andre Nussenzweig, Gordon L. Hager, Michel C. Nussenzweig & Rafael Casellas Nature, doi:10.1038/nature10909 (2012)
• Bubblegrams Reveal the Inner Body of Bacteriophage φKZ  Weimin Wu, Julie A. Thomas, Naiqian Cheng, Lindsay W. Black, Alasdair C. Steven Science 335 (6065):182 (2012)
• Integrated cross-species transcriptional network analysis of metastatic susceptibility  Ying Hu, Gang Wu, Michael Rusch, Luanne Lukes, Kenneth H. Buetow, Jinghui Zhang, and Kent W. Hunter PNAS, doi: 10.1073/pnas.1117872109 (2012)

• All-D-Enantiomer of β-Amyloid Peptide Forms Ion Channels in Lipid Bilayers  Ricardo Capone, Hyunbum Jang, Samuel A Kotler, Laura S Connelly, Fernando Teran Arce, Srinivasan Ramachandran, Bruce L. Kagan, Ruth Nussinov, and Ratnesh Lal J. Chem. Theory and Computation, doi: 10.1021/ct200885r (2012)
• Probing Structural Features of Alzheimer's β-Amyloid Pores in Bilayers Using Site-Specific Amino Acid Substitutions  Ricardo Capone, Hyunbum Jang, Samuel A Kotler, Bruce L. Kagan, Ruth Nussinov, and Ratnesh Lal J. Phys. Chem. B, doi: 10.1021/bi2017427 (2012)
• Atomic Force Microscopy and MD Simulations Reveal Pore-Like Structures of All-D-Enantiomer of Alzheimer's β-Amyloid Peptide: Relevance to the Ion Channel  Laura S Connelly, Fernando Teran Arce, Hyunbum Jang, Ricardo Capone, Samuel A Kotler, Srinivasan Ramachandran, Bruce L. Kagan, Ruth Nussinov, and Ratnesh Lal J. Phys. Chem. B, doi: 10.1021/jp2108126 (2012)

2011 (103 publications)

• Antimicrobial Protegrin-1 Forms Amyloid-Like Fibrils with Rapid Kinetics Suggesting a Functional Link  Hyunbum Jang, Fernando Teran Arce, Mirela Mustata, Srinivasan Ramachandran, Ricardo Capone, Ruth Nussinov, Ratnesh Lal Biophys J., doi: 10.1016/j.bpj.2011.01.072 (2011)
• Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes.  Klein IA, Resch W, Jankovic M, Oliveira T, Yamane A, Nakahashi H, Di Virgilio M, Bothmer A, Nussenzweig A, Robbiani DF, Casellas R, Nussenzweig MC. Cell 147(1):95-106 (2011)
• Recombination mapping using Boolean logic and high-density SNP genotyping for exome sequence filtering  Thomas C. Markello, Ted Han, Hannah Carlson-Donohoe, Chidi Ahaghotu, Ursula Harper, MaryPat Jones, Settara Chandrasekharappa, Yair Anikster, David R. Adams, NISC Comparative Sequencing Program, William A. Gahl, Cornelius F. Boerkoel Mol. Genetics & Metabolism, doi:10.1016/j.ymgme.2011.12.014 (2011)
• Independent component analysis of resting brain activity reveals transient modulation of local cortical processing by transcranial direct current stimulation.  Venkatakrishnan A, Contreras-Vidal JL, Sandrini M, Cohen LG. Conf Proc IEEE Eng Med Biol Soc. Aug:8102-5 (2011)
• The Anatomical Distance of Functional Connections Predicts Brain Network Topology in Health and Schizophrenia  Aaron F. Alexander-Bloch, Petra E. Vèrtes, Reva Stidd, François Lalonde, Liv Clasen, Judith Rapoport, Jay Giedd, Edward T. Bullmore and Nitin Gogtay Cerebral Cortex, doi:10.1093/cercor/bhr388 (2011)

• Parietofrontal integrity determines neural modulation associated with grasping imagery after stroke  Ethan R. Buch, Amirali Modir Shanechi, Alissa D. Fourkas, Cornelia Weber, Niels Birbaumer and Leonardo G. Cohen Brain, doi:10.1093/brain/awr331 (2011)
• Analysis of Biological Features Associated with Meiotic Recombination Hot and Cold Spots in Saccharomyces cerevisiae  Loren Hansen, Nak-Kyeong Kim, Leonardo Mariño-Ramìrez, David Landsman PLoS One, doi:10.1371/journal.pone.0029711 (2011)
• Tryptic y++ Fragment Ion Distributions Are Guided by Coulombic Repulsion  Karl K. Irikura, John K. Merle and Yamil Simòn-Manso J. Am. Soc. Mass Spec., doi:10.1007/s13361-011-0293-7 (2011)
• Structural models of TREK channels and their gating mechanism  Adina L Milac, Andriy Anishkin, Sarosh N Fatakia, Carson C Chow, Sergei Sukharev, and H Robert Guy Channels, doi: 10.4161/chan.5.1.13905 (2011)
• Condensin dysfunction in human cells induces nonrandom chromosomal breaks in anaphase, with distinct patterns for both unique and repeated genomic regions  Alexander Samoshkin, Stanimir Dulev, Dmitry Loukinov, Jeffrey A. Rosenfeld and Alexander V. Strunnikov Chromosoma Biology of the Nucleus, doi: 10.1007/s00412-011-0353-6 (2011)
• Effects of pH on proteins: Predictions for ensemble and single molecule pulling experiments  Edward P O'Brien , Bernard R. Brooks , and Devarajan Thirumalai JACS, doi: 10.1021/ja206557y (2011)
• Inherited Variation at Chromosome 12p13. 33, Including RAD52, Influences the Risk of Squamous Cell Lung Carcinoma  Jianxin Shi, Nilanjan Chatterjee, Melissa Rotunno, Yufei Wang, Angela C. Pesatori, Dario Consonni, Peng Li, William Wheeler, Peter Broderick, Marc Henrion, Timothy Eisen, Zhaoming Wang, Wei Chen, Qiong Dong, Demetrius Albanes, Michael Thun, Margaret R. Spitz, Pier Alberto Bertazzi, Neil E. Caporaso, Stephen J. Chanock, Christopher I. Amos, Richard S. Houlston and Maria Teresa Landi Cancer Discovery, doi: 10.1158/2159-8290.CD-11-024 (2011)
• Causal Inference on Quantiles with an Obstetric Application  Zhiwei Zhang, Zhen Chen, James F. Troendle, and Jun Zhang Biometrics, doi: 10.1111/j.1541-0420.2011.01712.x (2011)

• Does feature selection improve classification accuracy? Impact of sample size and feature selection on classification using anatomical magnetic resonance images  Carlton Chu, Ai-Ling Hsu, Kun-Hsien Chou, Peter Bandettini, Ching-Po Lin, , and the Alzheimer's Disease Neuroimaging Initiative NeuroImage, doi:10.1016/j.neuroimage.2011.11.066 (2011)
• Structural basis of anthrax edema factor neutralization by a neutralizing antibody  Michelle Makiya, Michael Dolan, Liane Agulto, Robert Purcell, Zhaochun Chen Biochem. Biophys. Res. Comm., doi:10.1016/j.bbrc.2011.11.108 (2011)
• Determination of Molecular Structures of HIV Envelope Glycoproteins using Cryo-Electron Tomography and Automated Sub-tomogram Averaging.  Joel R. Meyerson, Tommi A. White et al J. Visualized Experiments, doi: 10.3791/2770 (2011)
• Gene Expression Databases for Kidney Epithelial Cells  Jennifer C. Huling, Trairak Pisitkun, Jae H. Song, Ming-Jiun Yu, Jason D. Hoffert, and Mark A. Knepper Am. J. Physiol. -- Renal Physiol. , doi: 10.?1152/?ajprenal.?00457.?2011 doi: 10.?1152/?ajprenal.?00457.?2011 (2011)
• Dynamics of the G protein-coupled vasopressin V2 receptor signaling network revealed by quantitative phosphoproteomics  Jason D. Hoffert, Trairak Pisitkun, Fahad Saeed, Jae V. Song, Chung-Lin Chou and Mark A. Knepper Mol. Cell Proteomics, doi: 10.1074/mcp.M111.014613 (2011)
• Standard reactions for comparative rate studies: Experiments on the dehydrochlorination reactions of 2-chloropropane, chlorocyclopentane, and chlorocyclohexane  Iftikhar A. Awan, Donald R. Burgess Jr., Wing Tsang, Jeffrey A. Manion Int. J. Chem. Kinetics, doi: 10.1002/kin.20566 (2011)
• Convergence and error estimation in free energy calculations using the weighted histogram analysis method  Fangqiang Zhu, Gerhard Hummer J. Comp. Chem. , doi: 10.1002/jcc.21989 (2011)
• The discovery of population differences in network community structure: New methods and applications to brain functional networks in schizophrenia  Aaron Alexander-Bloch, Renaud Lambiotte, Ben Roberts, Jay Giedd, Nitin Gogtay, Ed Bullmore NeuroImage, doi:10.1016/j.neuroimage.2011.11.035 (2011)

• A linear mixed model for predicting a binary event from longitudinal data under random effects misspecification  Paul S. Albert Stat. Med., doi: 10.1002/sim.4405 (2011)
• Antimicrobial Properties of Amyloid Peptides  Bruce Kagan , Hyunbum Jang , Ricardo Capone , Fernando Teran Arce , Srinivasan Ramachandran , Ratnesh Lal , and Ruth Nussinov Molecular Pharmaceutics, doi: 10.1021/mp200419b (2011)
• Extensive chromatin remodelling and establishment of transcription factor 'hotspots' during early adipogenesis  Rasmus Siersbæk, Ronni Nielsen, Sam John, Myong-Hee Sung, Songjoon Baek, Anne Loft, Gordon L Hager and Susanne Mandrup Embo. J. , doi:10.1038/emboj.2011.65 (2011)
• Material Properties of Matrix Lipids Determine Conformation and Intermolecular Reactivity of a Diacetylenic Phosphatidylcholine in the Lipid Bilayer  Anu Puri , Hyunbum Jang , Amichai Yavlovich , Athar M Masood , Timothy D. Veenstra , Carlos Luna , Helim Aranda-Espinoza , Ruth Nussinov , and Robert Blumenthal Langmuir, doi: 10.1021/la203453x (2011)
• Genome-Wide Association Analysis of Ischemic Stroke in Young Adults  Yu-Ching Cheng, Jeffrey R. O'Connel et al G3: Genes, Genomes, Genetics, doi: 10.1534/g3.111.001164 (2011)
• Three-Dimensional Structures of Soluble CD4-Bound States of Trimeric Simian Immunodeficiency Virus Envelope Glycoproteins Determined by Using Cryo-Electron Tomography  Tommi A. White, Alberto Bartesaghi, Mario J. Borgnia, M. Jason V. de la Cruz, Rachna Nandwani, James A. Hoxie, Julian W. Bess, Jeffrey D. Lifson, Jacqueline L. S. Milne and Sriram Subramaniam J. Virol., doi: 10.1128/?JVI.05297-11 (2011)
• The Histone Database: an integrated resource for histones and histone fold-containing proteins  Leonardo Mariño-Ramírez, Kevin M. Levine, Mario Morales, Suiyuan Zhang, R. Travis Moreland, Andreas D. Baxevanis and David Landsman J. Biol. Databases and Curation, doi: 10.1093/database/bar048 (2011)
• Water-Exclusion Effects and Liquid-Structure Forces in Implicit Solvation  Sergio A Hassan and Peter J Steinbach J. Phys. Chem. B, doi: 10.1021/jp208184e (2011)

• Impact of surface roughness on diffusion of confined fluids  William P. Krekelberg, Vincent K. Shen, Jeffrey R. Errington, and Thomas M. Truskett J. Chem. Phys. , doi:10.1063/1.3651478 (2011)
• Energetics of direct and water-mediated proton-coupled electron transfer.  Ville R. I. Kaila and Gerhard Hummer JACS, doi: 10.1021/ja2082262 (2011)
• Resting and Active States of the ERK2: HePTP Complex  Dana M. Francis, Bartosz Ròzycki, Antoni Tortajada, Gerhard Hummer, Wolfgang Peti, and Rebecca Page JACS, doi: 10.1021/ja2075136 (2011)
• Dynamic water networks in cytochrome cbb3 oxidase  Vivek Sharma, Mårten Wikströma, Ville R.I. Kaila Biochim. et Biophys. Acta, doi:10.1016/j.bbabio.2011.09.010 (2011)
• Identification, Replication, and Fine-Mapping of Loci Associated with Adult Height in Individuals of African Ancestry  N'Diaye A, Chen GK et al. PLoS Genetics, doi:10.1371/journal.pgen.1002298 (2011)
• Investigation of Anatomical Thalamo-Cortical Connectivity and fMRI Activation in Schizophrenia  Stefano Marenco, Jason L Stein, Antonina A Savostyanova, Fabio Sambataro, Hao-Yang Tan, Aaron L Goldman, Beth A Verchinski, Alan S Barnett, Dwight Dickinson, Josè A Apud, Joseph H Callicott, Andreas Meyer-Lindenberg and Daniel R Weinberger Neuropsychopharmacology, doi: 10.1038/npp.2011.215 (2011)
• NHLBI-AbDesigner: An online tool for design of peptide-directed antibodies  Trairak Pisitkun, Jason D. Hoffert, Fahad Saeed, and Mark A. Knepper Am. J. Cell. Physiol. , doi: 10.1152/ajpcell.00325.201 (2011)
• A coarse-grained model for PEGylated lipids: the effect of PEGylation on size and shape of self-assembled structures  Hwankyu Lee, Richard W. Pastor J. Phys. Chem. B, doi: 10.1021/jp2020148 (2011)

• Oncogenically active MYD88 mutations in human lymphoma  V.N. Ngo, R.M. Young, R. Schmitz et al Nature, doi:10.1038/nature09671 (2011)
• N-Protonated Isomers as Gateways to Peptide Ion Fragmentation  Fredrik Haeffner, John K. Merle and Karl K. Irikura J. Am. Soc. Mass Spec., doi: 10.1007/s13361-011-0241-6 (2011)
• PubChem3D: Biologically relevant 3-D similarity  Sunghwan Kim , Evan E Bolton and Stephen H Bryant J. Cheminform., doi:10.1186/1758-2946-3-26 (2011)
• Genomic Risk Profiling of Ischemic Stroke: Results of an International Genome-Wide Association Meta-Analysis  James F. Meschia, Andrew Singleton, Michael A. Nalls, Stephen S. Rich, Pankaj Sharma, Luigi Ferrucci, Mar Matarin, Dena G. Hernandez, Kerra Pearce, Thomas G. Brott, Robert D. Brown Jr., John Hardy, Bradford B. Worrall PLoS One, doi:10.1371/journal.pone.0023161 (2011)
• 3D structures of sCD4-bound states of trimeric SIV envelope glycoproteins determined using cryo-electron tomography  Tommi A. White, Alberto Bartesaghi, Mario J. Borgnia, M. Jason V. de la Cruz, Rachna Nandwani, James A. Hoxie, Julian W. Bess, Jeffrey D. Lifson, Jacqueline L. S. Milne, and Sriram Subramaniam J. Virol., doi:10.1128/JVI.05297-11 (2011)
• Large-Scale Phosphotyrosine Proteomic Profiling of Rat Renal Collecting Duct Epithelium Reveals Predominance of Proteins Involved in Cell Polarity Determination  Boyang Zhao, Mark A. Knepper, Chung-Lin Chou, and Trairak Pisitkun Cell Physiol. , doi: 10.?1152/ajpcell.00300.2011 (2011)
• Logistic regression analysis of biomarker data subject to pooling and dichotomization  Z. Zhang, A. Liu, R.H., Lyles, B. Mukherjee Statistics in Medicine, doi: 10.1002/sim.4367 (2011)
• Generalized degrees of freedom and adaptive model selection in linear mixed-effects models  Bo Zhang, Xiaotong Shen, Sunni L. Mumford Comp. Stats & Data Anal., doi:10.1016/j.csda.2011.09.001 (2011)

• Flexible cullins in cullin-ring E3 ligases allosterically regulate ubiquitination  Jin Liu and Ruth Nussinov J. Biol. Chem. , doi: 10.1074/jbc.M111.277236 (2011)
• The Core of Ure2p Prion Fibrils Is Formed by the N-Terminal Segment in a Parallel Cross-? Structure: Evidence from Solid-State NMR  Dmitry S. Kryndushkin, Reed B. Wickner, Robert Tycko J. Mol. Biol. , doi://10.1016/j.jmb.2011.03.067 (2011)
• Latent class models for joint analysis of disease prevalence and high-dimensional semicontinuous biomarker data  Bo Zhang, Zhen Chen and Paul S. Albert Biostatistics, doi: 10.1093/biostatistics/kxr024 (2011)
• White Matter Microstructural Correlates of Superior Long-term Skill Gained Implicitly under Randomized Practice  Sunbin Song, Nikhil Sharma, Ethan R. Buch and Leonardo G. Cohen Cerebral Cortex, doi: 10.1093/cercor/bhr247 (2011)
• Genetic Association for Renal Traits among Participants of African Ancestry Reveals New Loci for Renal Function  C-T Liu, MK Garnaas et al. PLoS Genetics, doi:10.1371/journal.pgen.1002264 (2011)
• A Network-Based Approach to Prioritize Results from Genome-Wide Association Studies  N. Akula, A. Baranova, D Seto, J Solka, MA Nalls, A Singleton, L Ferrucci, T Tanaka, S Bandinelli, YS Cho, YJ Kim, J-Y Lee, B-G Han, Bipolar Disorder Genome Study (BiGS) Consortium, The Wellcome Trust Case-Control Consortium, FJ McMahon PLoS One, doi:10.1371/journal.pone.0024220 (2011)
• Conditional Allele Mouse Planner (CAMP): software to facilitate the planning and design of breeding strategies involving mice with conditional alleles  Jason D. Hoffert, Trairak Pisitkun, R. Lance Miller. Transgenic Research, doi: 10.1007/s11248-011-9545-3 (2011)
• Tackling Force-Field Bias in Protein Folding Simulations: Folding of Villin HP35 and Pin WW Domains in Explicit Water  Jeetain MIttal and Robert B. Best Biophys. J. , doi: 10.1016/j.bpj.2010.05.005 (2011)

• Rbx1 Flexible Linker Facilitates Cullin-RING Ligase Function Before Neddylation and After Deneddylation  Jin Liu and Ruth Nussinov Biophys. J. , doi: 10.1016/j.bpj.2010.05.021 (2011)
• Polymorphic Triple β-Sheet Structures Contribute to Amide Hydrogen/Deuterium (H/D) Exchange Protection in the Alzheimer Amyloid β42 Peptide  Buyong Ma and Ruth Nussinov J. Biol. Chem. , doi: 10.1074/jbc.M111.241141 (2011)
• Effect modification by population dietary folate on the association between MTHFR genotype, homocysteine, and stroke risk: a meta-analysis of genetic studies and randomised trials  Holmes MV, Newcombe, P, Hubacek JA et a. The Lancet, doi:10.1016/S0140-6736 (2011)
• Genome-wide Association Study for Serum Urate Concentrations and Gout among African Americans Identifies Genomic Risk Loci and a Novel URAT1 Loss-of-Function Allele  Tin, A, Woordward OM et al. Hum. Mol. Genet., doi: 10.1093/hmg/ddr307 (2011)
• Structural variants of IFNα preferentially promote antiviral functions  Nancy Vàzquez, Hana Schmeisser, Michael A. Dolan, Joseph Bekisz, Kathryn C. Zoon and Sharon M. Wahl Blood, doi:10.1182/blood-2010-12-325027 (2011)
• Enhanced translation by Nucleolin via G-rich elements in coding and non-coding regions of target mRNAs  Kotb Abdelmohsen, Kumiko Tominaga, Eun Kyung Lee, Subramanya Srikantan, Min-Ju Kang, Mihee M. Kim, Roza Selimyan, Jennifer L. Martindale, Xiaoling Yang, France Carrier, Ming Zhan, Kevin G. Becker and Myriam Gorospe Nucleic Acids Research, doi: 10.1093/nar/gkr488 (2011)
• A Two-Stage Meta-Analysis Identifies Several New Loci for Parkinson's Disease  International Parkinson's Disease Genomics Consortium (IPDGC) and Wellcome Trust Case Control Consortium 2 (WTCCC2) PLoS Genetics, doi: 10.1371/journal.pgen.1002142 (2011)
• A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers  Kan-Nian Hu, Wei Qiang and Robert Tycko J. Biomol. NMR, doi: 10.1007/s10858-011-9517-1 (2011)

• Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures  Audray Harris, Mario J. Borgnia, Dan Shi, Alberto Bartesaghi, Haifeng He, Robert Pejchal, Yun (Kenneth) Kang, Rafael Depetris, Andre J. Marozsan, Rogier W. Sanders, Per Johan Klasse, Jacqueline L. S. Milne, Ian A. Wilson, William C. Olson, John P. Moore, and Sriram Subramaniam PNAS, doi: 10.1073/pnas.1101414108 (2011)
• Genome-Wide Association Study of White Blood Cell Count in 16,388 African Americans: the Continental Origins and Genetic Epidemiology Network (COGENT)  Reiner AP, Lettre G, Nalls MA, Ganesh SK, Mathias R, et al. PLoS Genetics, doi:10.1371/journal.pgen.1002108 (2011)
• Multiple Loci Are Associated with White Blood Cell Phenotypes  Nalls MA, Couper DJ, Tanaka T, van Rooij FJA, Chen M-H, et al. PLoS Genetics, doi:10.1371/journal.pgen.1002113 (2011)
• Energetics and dynamics of proton transfer reactions along short water wires  Ville R. I. Kaila and Gerhard Hummer Phys. Chem. Chem. Phys. , doi:10.1039/C1CP21112A (2011)
• A survival analysis approach to modeling human fecundity  Rajeshwari Sundaram, Alexander C. Mclain and Germaine M. Buck Louis Biostatistics, doi: 10.1093/biostatistics/kxr015 doi: 10.1093/biostatistics/kxr015 doi: 10.1093/biostatistics/kxr01 (2011)
• Simulated Self-Assembly of the HIV-1 Capsid: Protein Shape and Native Contacts Are Sufficient for Two-Dimensional Lattice Formation  Bo Chen and Robert Tycko Biophys. J. , doi: 10.1016/j.bpj.2011.05.025 (2011)
• PubChem3D: Similar conformers  Evan Bolton, Sunghwan Kim and Stephen H Bryant J. Cheminform. , doi: 10.1186/1758-2946-3-13. (2011)
• Microscopic events in β-hairpin folding from alternative unfolded ensembles  Robert Best & Jeetain Mittal PNAS, doi: 10.1073/pnas.1016685108 (2011)

• The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-β Enhanceosome Example  Yongping Pan, Ruth Nussinov PLoS Computational Biology, doi:10.1371/journal.pcbi.1002077 (2011)
• Thermodynamics of Boroxine Formation from the Aliphatic Boronic Acid Monomers R-B (OH) 2 (R= H, H3C, H2N, HO, and F): A Computational Investigation  Krishna L. Bhat, George D. Markham, Joseph D. Larkin, and Charles W. Bock J. Phys. Chem. A, doi: 10.1021/jp202409m (2011)
• Agricultural intensification, priming for persistence and the emergence of Nipah virus: a lethal bat-borne zoonosis  Juliet R. C. Pulliam, Jonathan H. Epstein, Jonathan Dushoff, Sohayati A. Rahman, Michel Bunning, Aziz A. Jamaluddin, Alex D. Hyatt, Hume E. Field, Andrew P. Dobson and Peter Daszak, the Henipavirus Ecology Research Group (HERG) Journal of the Royal Society Interface, doi: 10.1098/?rsif.2011.0223 (2011)
• Improved genetic association tests for an ordinal outcome representing the disease progression process  Hong Zhang, Sholom Wacholder, Jing Qin, Allan Hildesheim, Kai Yu Genetic Epidemiology, doi: 10.1002/gepi.20599 (2011)
• Polymorphism of amyloid β peptide in different environments: implications for membrane insertion and pore formation  Fernando Terán Arce, Hyunbum Jang, Srinivasan Ramachandran, Preston B. Landon, Ruth Nussinov and Ratnesh Lal Soft Matter, doi: 10.1039/C1SM05162H (2011)
• The influence of tumor oxygenation on 18F-FDG (Fluorine-18 Deoxyglucose) uptake: A mouse study using positron emission tomography (PET)  Linda W Chan, Sebastien Hapdey, Sean English, Jurgen Seidel, Joann Carson, Anastasia L Sowers, Murali C Krishna, Michael V Green, James B Mitchell and Stephen L Bacharach Radiation Oncology, doi:10.1186/1748-717X-1-3 (2011)
• Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from QM/MM Simulations  Edina Rosta , Marcin Nowotny , Wei Yang , and Gerhard Hummer JACS, doi: 10.1021/ja200173a (2011)
• Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements  Ofir Hakim, Myong-Hee Sung, Ty C. Voss, Erik Splinter, Sam John, Peter J. Sabo, Robert E. Thurman, John A. Stamatoyannopoulos, Wouter de Laat, and Gordon L. Hager Genome Research, doi:10.1101/gr.111153.110 (2011)

• The association between inflammation-related genes and serum androgen levels in men: The prostate, lung, colorectal, and ovarian study  Tamra E. Meyer, Lisa W. Chu, Qizhai Li, Kai Yu, Philip S. Rosenberg, Idan Menashe, Anand P. Chokkalingam, Sabah M. Quraishi, Wen-Yi Huang, Jocelyn M. Weiss, Rudolf Kaaks, Richard B. Hayes, Stephen J. Chanock, Ann W. Hsing The Prostate, doi: 10.1002/pros.21407 (2011)
• Synergistic interactions between repeats in tau protein and Aβ amyloids may be responsible for accelerated aggregation via polymorphic states  Yifat Miller, Buyong Ma, and Ruth Nussinov Biochemistry, doi: 10.1021/bi200400u (2011)
• A joint modeling approach to data with informative cluster size: Robustness to the cluster size model  Zhen Chen, Bo Zhang, Paul S. Albert Statistics in Medicine, doi: 10.1002/sim.4239 (2011)
• On the stability and ranking of predictors from random forest variable importance measures  Kristin K Nicodemus Brief. Bioinfo., doi: 10.1093/bib/bbr016 (2011)
• Thermochemistry of imidazolium-based ionic liquids: experiment and first-principles calculations  Sergey P. Verevkin, Vladimir N. Emel'yanenko, Dzmitry H. Zaitsau, Andreas Heintz, Chris D. Muzny and Michael Frenkel Phys. Chem. Chem. Phys., doi:10.1039/C0CP00747A (2011)
• Intermittent Hypoxia-Induced Sensitization of Central Chemoreceptors Contributes to Sympathetic Nerve Activity during Late Expiration in Rats  Yaroslav I. Molkov, Daniel B Zoccal, Davi J.A. Moraes, Julian F.R. Paton, Benedito H. Machado, and Ilya A Rybak J. Neurophysiol., doi: 10.?1152/jn.00070.2011 (2011)
• Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide  Guillem Revilla-López, Juan Torras, Ruth Nussinov, Carlos Alemán and David Zanuy Physical Chemistry Chemical Physics, doi: 10.1039/C0CP02572K (2011)
• PubChem3D: Diversity of shape  Evan Bolton, Sunghwan Kim, and Stephen Bryant J. Cheminform. , doi: 10.1186/1758-2946-3-9 (2011)

• Conformational Relaxation and Water Penetration Coupled to Ionization of Internal Groups in Proteins  Ana Damjanovic, Bernard R. Brooks, and Bertrand García-Moreno E J. Phys. Chem. , published online 23 Mar (2011)
• Microscopic mechanism of nanocrystal formation from solution by cluster aggregation and coalescence  Sergio A. Hassan J. Chem. Phys. 134:114508 (2011)
• PubChem3D: a new resource for scientists  Evan E Bolton, Jie Chen, Sunghwan Kim, Lianyi Han, Siqian He, Wenyao Shi, Vahan Simonyan, Yan Sun, Paul A Thiessen and Jiyao Wang, et al. J. Cheminform. 3:32 (2011)
• Water Transport through Nanotubes with Varying Interaction Strength between Tube Wall and Water  Matthew Melillo, Fangqiang Zhu, Mark A. Snyder, and Jeetain Mittal J. Phys. Chem. Letters (2011)
• Large-scale Exploration of Gene-Gene Interactions in Prostate Cancer Using a Multistage Genome-wide Association Study  Julia Ciampa, Meredith Yeager, Laufey Amundadottir, Kevin Jacobs, Peter Kraft, Charles Chung, Sholom Wacholder, Kai Yu, William Wheeler, Michael J Thun, W Ryan Divers, Susan Gapstur, Demetrius Albanes, Jarmo Virtamo, Stephanie Weinstein, Edward Giovannucci, Walter C Willet, Geraldine Cancel-Tassin, Olivier Cussenot, Antoine Valeri, David Hunter, Robert Hoover, Gilles Thomas, Stephen Chanock, and Nilanjan Chatterjee Cancer Research, doi: 10.1158/0008-5472.CAN-10-2646 (2011)
• PubChem3D: Conformer generation  Evan E Bolton, Sunghwan Kim, and Stephen H Bryant J. Cheminform., doi: 10.1186/1758-2946-3-4 (2011)
• Molecular-Level Examination of Cu2+ Binding Structure for Amyloid Fibrils of 40-Residue Alzheimer's β by Solid-State NMR Spectroscopy  Sudhakar Parthasarathy, Fei Long, Yifat Miller, Yiling Xiao, Dan McElheny, Kent Thurber, Buyong Ma, Ruth Nussinov, and Yoshitaka Ishii JACS, published online 22 Feb (2011)
• Symmetry-Based Self-Assembled Nanotubes Constructed Using Native Protein Structures: The Key Role of Flexible Linkers  Buch, Idit; Tsai, Chung-Jung; J. Wolfson, Haim; Nussinov, Ruth Protein & Peptide Letters 18(4):362-372 (2011)

• Genome-Wide Association Studies of the PR Interval in African Americans  JG Smith, JW. Magnani, C Palmer, YA Meng, EZ Soliman, SK Musani, KF Kerr, RB Schnabel, SA Lubitz, N Sotoodehnia, S Redline, A Pfeufer, M Müller, DS Evans, MA Nalls, Y Liu, AB Newman, AB Zonderman, MK Evans, R Deo, PT Ellinor, DN Paltoo, C Newton-Cheh, E J Benjamin, R Mehra, A Alonso, SR Heckbert, ER Fox, Candidate-gene Association Resource (CARe) Consortium PLoS Genetics, doi:10.1371/journal.pgen.1001304 (2011)
• Modelling batched Gaussian longitudinal weight data in mice subject to informative dropout  Paul S. Albert, Joanna H Shih Stat. Meth. in Med. Res., doi: 10.1177/0962280210397886 (2011)
• The Unique Alzheimer's β-Amyloid Triangular Fibril Has a Cavity along the Fibril Axis under Physiological Conditions  Yifat Miller, Buyong Ma, and Ruth Nussinov J. Am. Chem. Soc., doi: 10.1021/ja1100273 (2011)
• Novel HIV-1 protease inhibitors (PIs) containing a bicyclic P2 functional moiety, tetrahydropyrano-tetrahydrofuran, that are potent against multi-PI-resistant HIV-1 variants  Kazuhiko Ide, Manabu Aoki, Masayuki Amano, Yasuhiro Koh, Ravikiran S. Yedidi, Debananda Das, Sofiya Leschenko, Bruno Chapsal, Arun K. Ghosh, and Hiroaki Mitsuya Antimicrob. Agents Chemother., doi:10.1128/AAC.01540-10 (2011)
• Binding of a C-end rule peptide to neuropilin-1 receptor: A molecular modeling approach  Nurit Haspel , David Zanuy , Ruth Nussinov , Tambet Teesalu , Erkki Ruoslahti , and Carlos Aleman Biochemistry, doi: 10.1021/bi101662j (2011)
• SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions  Bartosz Ròzycki, Young C. Kim and Gerhard Hummer Structure, doi:10.1016/j.str.2010.10.006 (2011)
• Distinct DNA methylation changes highly correlated with chronological age in the human brain  Dena G Hernandez, Michael A Nalls, J Raphael Gibbs, Sampath Arepalli, Marcel van der Brug, Sean Chong, Matthew Moore, Dan L Longo, Mark Cookson, Bryan J Traynor and Andrew Singleton Human Molecular Genetics, published online 7 Jan (2011)
• An Audit Strategy for Progression-Free Survival  Lori E. Dodd, Edward L. Korn, Boris Freidlin, Robert Gray, Suman Bhattacharya Biometrics, doi: 10.1111/j.1541-0420.2010.01539.x (2011)

• Atomistic modeling of peptides bound to a chemically active surface: conformational implications  David Curcó, Guillem Revilla-López, Carlos Alemán, David Zanuy J. Peptide Science, doi: 10.1002/psc.1321 (2011)
• Genome-wide association study implicates PARD3B-based AIDS restriction  Troyer, J.L., Nelson, G.W., Lautenberger, J.A., Chinn, L., McIntosh, C., Johnson, R.C., Sezgin, E., Kessing, B., Malasky, M., Hendrickson, S.L., Li, G., Pontius, J., Tang, M., An, P., Winkler, C.A., Limou, S., Le Clerc, S., Delaneau, O., Zagury, J.-F., Schuitemaker, H., van Manen, D., Bream, J.H., Gomperts, E.D., Buchbinder, S., Goedert, J.J., Kirk, G.D., O'Brien, S.J. J. Infect. Dis  203(10):1491-502 (2011)

2010 (77 publications)

• Polymorphic C-terminal β-sheet interactions determine the formation of fibril or ADDL-like globulomer for the Alzheimer Aβ42 dodecamer  Buyong Ma and Ruth Nussinov J. Biol. Chem. , doi: 10.1074/jbc.M110.133488 (2010)
• Dependence of Protein Folding Stability and Dynamics on the Density and Composition of Macromolecular Crowders  Jeetain Mittal and Robert B Best BIophys. J.  98(2):315-320 (2010)
• Predicting In Vitro Drug Sensitivity using Random Forests  Gregory Riddick, Hua Song, Susie Ahn, Jennifer Walling, Diego Borges-Rivera, Wei Zhang, and Howard A. Fine Bioinformatics, published online 5 Dec (2010)
• Large-Scale Phosphoproteomic Analysis of Membrane Proteins in Renal Proximal and Distal Tubule  Marina Feric, Boyang Zhao, Jason D. Hoffert, Trairak Pisitkun, and Mark A. Knepper Am. J. Physiology - Cell Physiology, doi: 10.​1152/​ajpcell.​00360.​2010 (2010)
• Microarray Meta-Miner (MMM): An integrated method and a web tool to identify genes with similar expression profile  Nagarajan, V.; Varma, S.; Hurt, D.; Yongjian Guo; Huyen, Y Computer Technology and Development, doi:10.1109/ICCTD.2010.5646068 (2010)
• Atomic-Scale Simulations Confirm that Soluble β-Sheet-Rich Peptide Self-Assemblies Provide Amyloid Mimics Presenting Similar Conformational Properties  Xiang Yu, Jingdai Wang, Jui-Chen Yang, Qiuming Wang, Stephen Z.D. Cheng, Ruth Nussinov, and Jie Zheng Biophys. J.  98(1):27-36 (2010)

• Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks  Margaret E. Johnson and Gerhard Hummer PNAS, doi: 10.1073/pnas.1010954108 (2010)
• Molecular Architectures of Trimeric SIV and HIV-1 Envelope Glycoproteins on Intact Viruses: Strain-Dependent Variation in Quaternary Structure  Tommi A. White, Alberto Bartesaghi, Mario J. Borgnia, Joel R. Meyerson, M. Jason V. de la Cruz, Julian W. Bess, Rachna Nandwani, James A. Hoxie, Jeffrey D. Lifson, Jacqueline L. S. Milne, Sriram Subramaniam PLoS Pathogens, doi:10.1371/journal.ppat.1001249 (2010)
• Nanoscale architecture of integrin-based cell adhesions  Kanchanawong P, Shtengel G, Pasapera AM, Ramko EB, Davidson MW, Hess HF, Waterman CM. Nature 468(7323):580-4 (2010)
• Accounting for multiple comparisons in a genome-wide association study (GWAS)  Randall C Johnson, George W Nelson, Jennifer L Troyer, James A Lautenberger, Bailey D Kessing, Cheryl A Winkler, Stephen J O'Brien BMC Genomics 11:724 (2010)
• Stability tests on known and misfolded structures with discrete and all atom molecular dynamics simulations  Sijung Yun and Robert H Guy J. Mol. Graph. and Modeling, doi:10.1016/j.jmgm.2010.12.002 (2010)
• Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences  Robert B Best, Jeetain Mittal Proteins: Structure, Function, Bioinformatics, doi: 10.1002/prot.22972 (2010)
• The Human Glucocorticoid Receptor as an RNA-Binding Protein: Global Analysis of Glucocorticoid Receptor-Associated Transcripts and Identification of a Target RNA Motif  Ishmael FT, Fang X, Houser KR, Pearce K, Abdelmohsen K, Zhan M, Gorospe M, Stellato C. J. Immunol. , doi:10.4049/jimmunol.1001794 (2010)
• Analysis of progression-free survival data using a discrete time survival model that incorporates measurements with and without diagnostic error  Sally Hunsberger, Paul S Albert, Lori Dodd Clinical Trials, doi: 10.1177/1740774510384887 (2010)

• Microscopic properties of nanopore water from its time-dependent dielectric response  Jürgen Köfinger and Christoph Dellago Phy. Rev. B 82:205416 (2010)
• Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome  Jie Zheng, Pavel P Khil, R Daniel Camerini-Otero and Teresa M Przytycka Genome Biology 11:R103, doi:10.1186/gb-2010-11-10-r103 (2010)
• Analysis of the stabilities of hexameric amyloid-β (1-42) models using discrete molecular dynamics simulations  Sijung Yun, Sajung Yun and H. Robert Guy J. Mol. Graphics and Modelling, doi:10.1016/j.jmgm.2010.11.008 (2010)
• RAId_aPS: MS/MS Analysis with Multiple Scoring Functions and Spectrum-Specific Statistics  Gelio Alves, Aleksey Y. Ogurtsov, and Yi-Kuo Yu PLoS One 5(11):e15438 (2010)
• Approximating probabilities of correlated events  Li QiZhai, Zheng Gang, Liu AiYi, Li ZhaoHai & Yu Kai Science China Mathematics 53(11):2937-2948 (2010)
• Dockomatic-automated ligand creation and docking  Casey W Bullock , Reed B Jacob , Owen M McDougal, Greg Hampikian and Tim Andersen BMC Research Notes, doi:10.1186/1756-0500-3-289 (2010)
• Water in the Polar and Nonpolar Cavities of the Protein Interleukin-1β  Hao Yin, Guogang Feng, G. Marius Clore, Gerhard Hummer, and Jayendran C. Rasaiah J. Phy. Chem. B, doi: 10.1021/jp108731r (2010)
• Assigning statistical significance to proteotypic peptides via database searches  Gelio Alves, Aleksey Ogurtsov, Yi-Kuo Yu J. Proteomics, doi:10.1016/j.jprot.2010.10.005 (2010)

• A Computational Investigation of the Nitrogen-Boron Interaction in o-(N, N-Dialkylaminomethyl) arylboronate Systems  Joseph D. Larkin, John S. Fossey, Tony D. James, Bernard R. Brooks, and Charles W. Bock J. Phys. Chem. A, doi: 10.1021/jp1087674 (2010)
• Multiple imputation for estimating the risk of developing dementia and its impact on survival  Binbing Yu, Jane S. Saczynski, Lenore Launer Biometrical Journal 52(5) :616-627 (2010)
• Pore opening and closing of a pentameric ligand-gated ion channel  Fangqiang Zhu and Gerhard Hummer PNAS, doi: 10.1073/pnas.1009313107 (2010)
• Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse  Robert B Best and Jeetain Mittal J. Phys. Chem. B, doi: 10.1021/jp108618d (2010)
• Nematic Order in Small Systems: Measuring the Elastic and Wall-Anchoring Constants in Vibrofluidized Granular Rods  Jennifer Galanis, Ralph Nossal, Wolfgang Losert, and Daniel Harries Phys. Rev. Let.  105:168001 (2010)
• β-Barrel Topology of Alzheimer's β-Amyloid Ion Channels  Hyunbum Jang, Fernando Teran Arce, Srinivasan Ramachandran, Ricardo Capone, Ratnesh Lal, and Ruth Nussinov J. Mol. Biol. , doi:10.1016/j.jmb.2010.10.025 (2010)
• Quantitative protein and mRNA profiling shows selective post-transcriptional control of protein expression by vasopressin in kidney cells  Sookkasem Khositseth, Trairak Pisitkun, Dane H. Slentz, Guanghui Wang, Jason D. Hoffert, Mark A. Knepper* and Ming-Jiun Yu Molecular & Cellular Proteomics, doi: 10.1074/mcp.M110.004036 (2010)
• An approach for jointly modeling multivariate longitudinal measurements and discrete time-to-event data  Paul S. Albert and Joanna H. Shih Ann. Appl. Stat.  4(3):1517-1532 (2010)
• Electrostatic Interactions and Binding Orientation of HIV-1 Matrix Studied by Neutron Reflectivity  Hirsh Nanda, Siddhartha A.K. Datta, Frank Heinrich, Mathias L�sche, Alan Rein, Susan Krueger, Joseph E. Curtis Biophys. J. , doi: 10.1016/j.bpj.2010.07.062 (2010)
• Biological Validation of Increased Schizophrenia Risk With NRG1, ERBB4, and AKT1 Epistasis via Functional Neuroimaging in Healthy Controls  Kristin K. Nicodemus, Amanda J. Law, Eugenia Radulescu, Augustin Luna, Bhaskar Kolachana, Radhakrishna Vakkalanka, Dan Rujescu, Ina Giegling, Richard E. Straub, Kate McGee, Bert Gold, Michael Dean, Pierandrea Muglia, Joseph H. Callicott, Hao-Yang Tan, Daniel R. Weinberger Arch. Gen. Psych.  67(10):991-1001 (2010)
• Conformational Profile of a Proline-Arginine Hybrid  Guillermo Revilla-López, Ana I. Jiménez, Carlos Cativiela, Ruth Nussinov, Carlos Alemán, and David Zanuy J. Chem. Inf. and Modeling, doi: 10.1021/ci100135f (2010)
• Mapping mouse IL-13 binding regions using structure modeling, molecular docking, and high-density peptide microarray analysis  Satish K Madala, Michael A. Dolan, Deepak Sharma, Thirumalai R. Ramalingam, Mark S. Wilson, Margaret M. Mentink-Kane, Daniel C. Masison, Thomas A. Wynn Proteins: Structure, Function, Bioinformatics, doi: 10.1002/prot.22881 (2010)
• Robust and accurate data enrichment statistics via distribution function of sum of weights.  Stojmirovic A, Yu YK Bioinformatics, doi: 10.1093/bioinformatics/btq511 (2010)
• Using Principal Components of Genetic Variation for Robust and Powerful Detection of Gene-Gene Interactions in Case-Control and Case-Only Studies  Samsiddhi Bhattacharjee, Zhaoming Wang, Julia Ciampa, Peter Kraft, Stephen Chanock, Kai Yu and Nilanjan Chatterjee Am. J. Human Genetics 86(3):331-342 (2010)
• Models of membrane-bound Alzheimer's abeta peptide assemblies  Yinon Shafrir, Stewart Durell, Nelson Arispe, H. Robert Guy Proteins, doi: 10.1002/prot.22853 (2010)
• In Vitro Selection of Highly Darunavir-Resistant and Replication-Competent HIV-1 Variants by Using a Mixture of Clinical HIV-1 Isolates Resistant to Multiple Conventional Protease Inhibitors  Yasuhiro Koh, Masayuki Amano, Tomomi Towata, Matthew Danish, Sofiya Leshchenko-Yashchuk, Debananda Das, Maki Nakayama, Yasushi Tojo, Arun K. Ghosh, and Hiroaki Mitsuya J. Virol. , doi:10.1128/JVI.00967-10 (2010)

• Structural and Dynamic Determinants of Ligand Binding and Regulation of Cyclin-Dependent Kinase 5 by Pathological Activator p25 and Inhibitory Peptide CIP  A. Cardone, S.A. Hassan, R.W. Albers, R.D. Sriram and H.C. Pant J. Mol. Biol., doi:10.1016/j.jmb.2010.06.040 (2010)
• Hollow core of Alzheimer's Aβ42 amyloid observed by cryoEM is relevant at physiological pH  Yifat Miller, Buyong Ma, Chung-Jung Tsai, Ruth Nussinov PNAS, 10.1073/pnas.1004704107 (2010)
• Population dynamics of a pathogen: the conundrum of vivax malaria  Philip G. McQueen Biophys. Revs.  2(3):111-120 (2010)
• Scaling Factors and Uncertainties for ab Initio Anharmonic Vibrational Frequencies  Russell D. Johnson, III, Karl K. Irikura, Raghu N. Kacker and Rdiger Kessel J. Chem. Theory. Comp., doi: 10.1021/ct100244d (2010)
• Molecular Basis for the Structural Stability of an Enclosed β Barrel Loop  Pu Tian and Harris D. Bernstein J. Mol. Biol. , doi:10.1016/j.jmb.2010.07.035 (2010)
• Predictive Correlations Based on Large Experimental Datasets: Critical Constants for Pure Compounds  Andrei Kazakov, Chris D. Muzny, Vladimir Diky, Robert D. Chirico and Michael Frenkel Fluid Phase Equilibria 298(1):131-142 (2010)
• Using Cases to Strengthen Inference on the Association between Single Nucleotide Polymorphisms and a Secondary Phenotype in Genome-Wide Association Studies  Huilin Li, Mitchell H. Gail, Sonja Berndt, and Nilanjan Chatterjee Genet. Epidemiol.  34(5):427-433 (2010)
• Lysine120 Interactions with p53 Response Elements can Allosterically Direct p53 Organization  Yongping Pan and Ruth Nussinov PLoS Comput. Biol. , doi: 10.1371/journal.pcbi.1000878. (2010)

• Structural Convergence Among Diverse, Toxic β-Sheet Ion Channels  Hyunbum Jang, Fernando Teran Arce, Srinivasan Ramachandran, Ricardo Capone, Ratnesh Lal and Ruth Nussinov J. Phys. Chem. B, doi: 10.1021/jp104073k (2010)
• Phosphoproteomic profiling reveals vasopressin-regulated phosphorylation sites in collecting duct  Bansal AD, Hoffert JD, Pisitkun T, Hwang S, Chou CL, Boja ES, Wang G, Knepper MA. J. Am. Soc. Nephrol. 21(2):303-15 (2010)
• De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds  Shen Y, Bryan PN, He Y, Orban J, Baker D, Bax A. Protein Science 19(2):349-56 (2010)
• Balance between α and β Structures in Ab Initio Protein Folding  Robert B. Best and Jeetain Mittal J. Phys. Chem. B , doi: 10.1021/jp102575b (2010)
• Tautomerism and Magnesium Chelation of HIV-1 Integrase Inhibitors: A Theoretical Study  Chenzhong Liao and Marc C. Nicklaus Chem Med Chem, published online 8 Jun (2010)
• FastMEDUSA: A parallelized tool to infer gene regulatory networks  Serdar Bozdag, Aiguo Li, Stefan Wuchty, Howard A. Fine Bioinformatics, doi:10.1093/bioinformatics/btq275 (2010)
• Structural basis of G protein-coupled receptor-G protein interactions  Jianxin Hu, Yan Wang, Xiaohong Zhang, John R Lloyd, Jian Hua Li, Joel Karpiak, Stefano Costanzi, J¨rgen Wess Nature Chem. Biol., doi:10.1038/nchembio.385 (2010)
• Antimicrobial Protegrin-1 Forms Ion Channels: Molecular Dynamic Simulation, Atomic Force Microscopy, and Electrical Conductance Studies  Ricardo Capone, Mirela Mustata, Hyunbum Jang, Fernando Teran Arce, Ruth Nussinov, and Ratnesh Lal Biophys. J., doi: 10.1016/j.bpj.2010.02.024 (2010)

• Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types  Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O'Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor J. Phys. Chem. B, published online 24 May (2010)
• Comparison of multivariate classifiers and response normalizations for pattern-information fMRI  Masaya Misaki, Youn Kima, Peter A. Bandettini and Nikolaus Kriegeskorte Neuroimage, doi:10.1016/j.neuroimage.2010.05.051 (2010)
• Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain  J. Raphael Gibbs, Marcel P. van der Brug, Dena G. Hernandez, Bryan J. Traynor, Michael A. Nalls, Shiao-Lin Lai, Sampath Arepalli, Allissa Dillman, Ian P. Rafferty, Juan Troncoso, Robert Johnson, H. Ronald Zielke, Luigi Ferrucci, Dan L. Longo, Mark R. Cookson, Andrew B. Singleton PLoS Genetics 6(5):e1000952, doi:10.1371/journal.pgen.1000952 (2010)
• Zinc ions promote Alzheimer Aβ aggregation via population shift of polymorphic states  Yifat Miller, Buyong Ma, and Ruth Nussinov PNAS, published online 6 May (2010)
• Emotional Automaticity Is a Matter of Timing  Qian Luo, Tom Holroyd, Catherine Majestic, Xi Cheng, Julia Schechter, and R. James Blair J. Neuroscience 30(17):5825-5829 (2010)
• How Does the Reductase Help To Regulate the Catalytic Cycle of Cytochrome P450 3A4 Using the Conserved Water Channel?  Dan Fishelovitch, Sason Shaik, Haim J. Wolfson and Ruth Nussinov J. Phys. Chem. B 114(17):5964-5970 (2010)
• Improving polyp detection algorithms for CT colonography: Pareto front approach  Adam Huang, Jiang Li, Ronald M. Summers, Nicholas Petrick, Amy K. Hara Pattern Recognition Letters, doi:10.1016/j.patrec.2010.03.013 (2010)
• Solution conformation and dynamics of the HIV-1 integrase core domain  Nicholas C. Fitzkee, James E. Masse, Yang Shen, David R. Davies, and Ad Bax J. Biol. Chem. , doi/10.1074/jbc.M110.113407 (2010)
• Use of Multiple Assays Subject to Detection Limits With Regression Modeling in Assessing the Relationship Between Exposure and Outcome  Albert, Paul S, Harel, Ofer, Perkins, Neil, Browne, Richard Epidemiology, doi: 10.1097/EDE.0b013e3181ce9eed (2010)
• Low-Temperature Dynamic Nuclear Polarization at 9.4 Tesla With a 30 Milliwatt microwave source  Kent R. Thurber, Wai-Ming Yau and Robert Tycko J. Magnetic Resonance :doi:10.1016/j.jmr.20 (2010)
• Neural substrates of graphomotor sequence learning: A combined fMRI and kinematic study  Bruce A. Swett, Jose L. Contreras-Vidal, Rasmus Birn and Allen R. Braun J. Neurophysiol., doi:10.1152/jn.00449.2009 (2010)
• Extensive and Modular Intrinsically Disordered Segments in C. elegans TTN-1 and Implications in Filament Binding, Elasticity and Oblique Striation  Jeffrey G. Forbes, Denise B. Flaherty, Kan Ma, Hiroshi Qadota, Guy M. Benian, and Kuan Wang J. Mol. Biol. , doi:10.1016 (2010)
• A Novel Point Mutation in Helix 10 of the Human Glucocorticoid Receptor Causes Generalized Glucocorticoid Resistance by Disrupting the Structure of the Ligand-Binding Domain  Nancy Nader, Bert E. Bachrach, Darrell E. Hurt, Sonia Gajula, Amy Pittman, Rachel Lescher, and Tomoshige Kino J. Clin. Endocrin. & Metab., published online 24 March (2010)
• Depletion forces drive polymer-like self-assembly in vibrofluidized granular materials  Jennifer Galanis, Ralph Nossal, and Daniel Harries Soft Matter 6:1026-1034 (2010)
• The behaviour of random forest permutation-based variable importance measures under predictor correlation  Kristin Nicodemus, James Malley, Carolin Srobl, Andreas Ziegler BMC Bioinformatics 11:110 (2010)
• Molecular Dynamics Reveal the Essential Role of Linker Motions in the Function of Cullin-RING E3 Ligases  Jin Liu and Ruth Nussinov J. Mol. Biol.  396(5):1508-1523 (2010)

• Quantitative phosphoproteomic analysis reveals vasopressin V2-receptor-dependent signaling pathways in renal collecting duct cells  Markus M. Rinschen, Ming-Jiun Yu, Guanghui Wang, Emily S. Boja, Jason D. Hoffert, Trairak Pisitkun, and Mark A. Knepper PNAS, doi/10.1073/pnas.0910646107 (2010)
• Noncoding RNA Gas5 Is a Growth Arrest-and Starvation-Associated Repressor of the Glucocorticoid Receptor  Tomoshige Kino, Darrell E. Hurt, Takamasa Ichijo, Nancy Nader, and George P. Chrousos Sci. Signal.  3(107):ra8 (2010)
• Functional Significance for an Heterogenous Ribonucleoprotein A18 (hnRNP A18) Signature RNA Motif in the 3'UTR of Ataxia Telengiectasia Mutated and RAD3 Related (ATR) Transcript  Ruiqing Yang, Ming Zhan, Narasimha Rao Nalabothula, Qingyuan Yang, Fred E. Indig and France Carrier J. Biol. Chem., published online 26 Jan (2010)
• Evidence of statistical epistasis between DISC1, CIT and NDEL1 impacting risk for schizophrenia: biological validation with functional neuroimaging  Kristin K. Nicodemus, Joseph H. Callicott, Rachel G. Higier, Augustin Luna, Devon C. Nixon, Barbara K. Lipska, Radhakrishna Vakkalanka, Ina Giegling, Dan Rujescu, David St. Clair, Pierandrea Muglia, Yin Yao Shugart and Daniel R. Weinberger Human Genetics 10.1007:s00439-009-0782-y (2010)
• Meta-analysis of genome-wide association data detects a risk locus for major mood disorders on chromosome 3p21. 1  Francis J McMahon, Nirmala Akula, Thomas G Schulze, Pierandrea Muglia, Federica Tozzi, Sevilla D Detera-Wadleigh, C J M Steele, René Breuer, Jana Strohmaier, Jens R Wendland, Manuel Mattheisen, Thomas W Mühleisen, Wolfgang Maier, Markus M Nöthen, Sven Cichon, Anne Farmer, John B Vincent, Florian Holsboer, Martin Preisig & Marcella Rietschel for the Bipolar Disorder Genome Study (BiGS) Consortium Nature Genetics 42:128-131 (2010)
• Interfacial thermodynamics of confined water near molecularly rough surfaces  Jeetain Mittal and Gerhard Hummer Faraday Discussions: Wetting Dynamics of Hydrophobic and Str (2010)
• Genetic Crossovers Are Predicted Accurately by the Computed Human Recombination Map  Pavel P. Khil and R. Daniel Camerini-Otero PLoS Genetics 6(1):e1000831 (2010)

2009 (63 publications)

• Preferred drifting along the DNA major groove and cooperative anchoring of the p53 core domain: mechanisms and scenarios  Yongpin Pan and Ruth Nussinov J. Mol. Recognit. 23(2):232-40 (2009)
• Computational Investigation of the Oxidative Deboronation of Boroglycine, H2N-CH2-B (OH) 2, Using H2O and H2O2  Larkin JD, Markham GD, Milkevitch M, Brooks BR, Bock CW. J. Phys. Chem. A 113(41):11028-34 (2009)
• Modeling Familial Association of Ages at Onset of Disease in the Presence of Competing Risk  Joanna Shih and Paul S Albert Biometrics, published online 9 Dec (2009)
• Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts  Yang Shen and Ad Bax J. Biomolec. NMR 10.1007:s10858-009-9395-y (2009)
• Homology modeling and molecular dynamics simulations of HgiDII methyltransferase in complex with DNA and S-adenosyl-methionine: Catalytic mechanism and interactions with DNA  Juan A. Castelán-Vega, Alicia Jiménez-Alberto and Rosa M. Ribas-Aparicio J. Molecular Modeling 10.1007:s00894-009-0632-9 (2009)
• Using Compressibility Factor as a Predictor of Confined Hard-Sphere Fluid Dynamics  Jeetain Mittal J. Phys. Chem. B 113(42):13800-13804 (2009)
• Prediction of Potency of Protease Inhibitors Using Free Energy Simulations with Polarizable Quantum Mechanics-Based Ligand Charges and a Hybrid Water Model  Debananda Das, Yasuhiro Koh, Yasushi Tojo, Arun K. Ghosh and Hiroaki Mitsuya J. Chem. Inf. Mod.  49(12):2851-2862 (2009)
• Misfolded Amyloid Ion Channels Present Mobile β-Sheet Subunits in Contrast to Conventional Ion Channels  Hyunbum Jang, Fernando Teran Arce, Ricardo Capone, Srinivasan Ramachandran, Ratnesh Lal, and Ruth Nussinov Biophys. J.  97(11):3029-3037 (2009)
• Effectiveness of Hair Bundle Motility as the Cochlear Amplifier  Bora Sul and Kuni H. Iwasa Biophys. J.  97(10):2653-2663 (2009)

• Symmetry-restrained molecular dynamics simulations improve homology models of potassium channels.  Anishkin A, Milac AL, Guy HR. Proteins 78(4):932-949 (2009)
• NF90 selectively represses the translation of target mRNAs bearing an AU-rich signature motif  Yuki Kuwano, Rudolf Pullmann, Jr., Bernard S. Marasa, Kotb Abdelmohsen, Eun Kyung Lee, Xiaoling Yang, Jennifer L. Martindale, Ming Zhan and Myriam Gorospe Nucleic Acids Research 38(1):225-38 (2009)
• Thermodynamic Perspective on the Dock-Lock Growth Mechanism of Amyloid Fibrils ?  Edward P. O'Brien, Yuko Okamoto, John E. Straub, Bernard R. Brooks and D. Thirumalai J. Phys. Chem. B 113(43):14421-14430 (2009)
• MicroRNA Expression in Squamous Cell Carcinoma and Adenocarcinoma of the Esophagus: Associations with Survival  Ewy A. Mathè, Giang Huong Nguyen, Elise D. Bowman, Yiqiang Zhao, Anuradha Budhu, Aaron J. Schetter, Rosemary Braun, Mark Reimers, Kensuke Kumamoto, Duncan Hughes, Nasser K. Altorki, Alan G. Casson, Chang-Gong Liu, Xin Wei Wang, Nozomu Yanaihara, Nobutoshi Hagiwara, Andrew J. Dannenberg, Masao Miyashita, Carlo M. Croce and Curtis C. Harris Clin. Cancer. Res.  15:6192 (2009)
• K3 Fragment of Amyloidogenic β2-Microglobulin Forms Ion Channels: Implication for Dialysis Related Amyloidosis  Mirela Mustata, Ricardo Capone, Hyunbum Jang, Fernando Teran Arce, Srinivasan Ramachandran, Ratnesh Lal and Ruth Nussinov J. Am. Chem. Soc. 131(41):14938-14945 (2009)
• Modeling Aqueous Solvent Effects through Local Properties of Water  S.A. Hassan and E.L. Mehler , in Modeling Solvent Environments, Ed. M. Feig, Wiley-VCH (2009)
• Evidence for a Partially Structured State of the Amylin Monomer  Sara M. Vaiana, Robert B. Best, Wai-Ming Yau, William A. Eaton, and James Hofrichter Biophys. J.  97(11):2948�2957 (2009)
• The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation  Jin Lui and Ruth Nussinov PLoS Computational Biology 5(10):e1000527 (2009)
• Generalized Rosenfeld scalings for tracer diffusivities in not-so-simple fluids: Mixtures and soft particles  William P. Krekelberg, Mark J. Pond, Gaurav Goel, Vincent K. Shen, Jeffrey R. Errington, Thomas M. Truskett Phys. Rev. E  80:061205 (2009)
• Theoretical Characterization of Substrate Access/Exit Channels in the Human Cytochrome P450 3A4 Enzyme: Involvement of Phenylalanine Residues in the Gating Mechanism  Dan Fishelovitch, Sason Shaik, Haim J. Wolfson, and Ruth Nussinov J. Phys. Chem B 113(39):13018-13025 (2009)
• A simple and efficient algorithm for genome-wide homozygosity analysis in disease  Wei Liu, Jinhui Ding, Jesse Raphael Gibbs, Sue Jane Wang, John Hardy & Andrew Singleton Molecular Systems Biology 5:304 (2009)
• A fast mean-field method for large-scale high-dimensional data and its application in colonic polyp detection at CT colonography  Shijun Wang, Ronald M Summers, Changshui Zhang IEEE International Joint Conference on Neural Networks ijcnn:32511-3258 (2009)
• Polymorphism of Alzheimer's A β< sub> 17-42</sub>(p3) Oligomers: The Importance of the Turn Location and Its Conformation  Yifat Miller, Buyong Ma, and Ruth Nussinov Biophys. J.  97(4):1168-1177 (2009)
• RAId_deNovo: using de novo based spectrum-specific statistics to combine search results from multiple scoring functions and more  Gelio Alves, Aleksey Y. Ogurtsov, Yi-Kuo Yu arXiv.org (2009)
• Quantitative Mitochondrial Phosphoproteomics Using iTRAQ on an LTQ-Orbitrap with High Energy Collision Dissociation  Emily Boja, Darci Phillips, Stephanie A French, Robert A. Harris, and Robert Stephen Balaban J. Proteome Research 8(10):4665-4675 (2009)
• Molecular Dynamics Simulations of PIP< sub> 2</sub> and PIP< sub> 3</sub> in Lipid Bilayers: Determination of Ring Orientation, and the Effects of Surface  Zheng Li, Richard M. Venable, Laura A. Rogers, Diana Murray, and Richard W. Pastor Biophys. J. 97(1):155-163 (2009)

• Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View  Yongpin Pan and Ruth Nussinov PLoS Computational Biology :e1000448. (2009)
• Functional but not structural changes associated with learning: An exploration of longitudinal Voxel-Based Morphometry (VBM)  Thomas AG, Marrett S, Saad ZS, Ruff DA, Martin A, Bandettini PA. Neuroimage 48(1):117-25 (2009)
• Phosphine Polymerization by Nitric Oxide: Experimental Characterization and Theoretical Predictions of Mechanism  Yi-Lei Zhao, Jason W. Flora, William David Thweatt, Stephen L. Garrison, Carlos Gonzalez, K. N. Houk and Manuel Marquez Inorg. Chem.  48(3):1223-1231 (2009)
• Protein Segments with Conformationally Restricted Amino Acids Can Control Supramolecular Organization at the Nanoscale  David Zanuy, Gema Ballano, Ana I. Jimnez, Jordi Casanovas, Nurit Haspel, Carlos Cativiela, David Curc, Ruth Nussinov and Carlos Alemán J. Chem. Info. and Modeling 49(7):1623=9 (2009)
• Kinetic Barriers of H-Atom Transfer Reactions in Alkyl, Allylic, and Oxoallylic Radicals as Calculated by Composite Ab Initio Methods  Carrigan J. Hayes and Donald R. Burgess, Jr. J. Phys. Chem. A 113(11):2473-2482 (2009)
• On the Mechanism of Nitrosoarene-Alkyne Cycloaddition  Andrea Penoni, Giovanni Palmisano, Yi-Lei Zhao, Kendall N. Houk, Jerome Volkman and Kenneth M. Nicholas J. Am. Chem. Soc. 131(2):653-661 (2009)
• Artificial reaction coordinate “tunneling” in free-energy calculations: The catalytic reaction of RNase H  Edina Rosta, H. Lee Woodcock, Bernard R. Brooks, Gerhard Hummer J. Comput. Chem.  30(11):1634-41 (2009)
• Imaging incorporation of circulating docosahexaenoic acid into the human brain using positron emission tomography  John C. Umhau, Weiyin Zhou, Richard E. Carson, Stanley I. Rapoport, Alla Polozova, James Demar, Nahed Hussein, Abesh K. Bhattacharjee, Kaizong Ma, Giuseppe Esposito, Sharon Majchrzak, Peter Herscovitch, William C. Eckelman, Karen A. Kurdziel, and Norman Salem . Jr J. Lipid Res. 50(7):1259-68 (2009)
• Error and efficiency of replica exchange molecular dynamics simulations  Edina Rosta and Gerhard Hummer J. Chem. Phys. 131:165102 (2009)
• Insights Into Crowding Effects on Protein Stability From a Coarse-Grained Model  VK Shen, J Cheung, JR Errington, TM Truskett J. Biomech. Engg. 131(7):0710002 (2009)
• Molecular dynamics study of the structure and interparticle interactions of polyethylene glycol-conjugated PAMAM dendrimers  Hwankyu Lee and Ronald G. Larson J. Phys. Chem. B 113(40):13202-13207 (2009)
• Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides  Robert B Best, Gerhard Hummer J. Phys. Chem B 113(26):9004-9015 (2009)
• Predictor Correlation Impacts Machine Learning Algorithms: Implications for Genomic Studies  Kristin K. Nicodemus and James D. Malley Bioinformatics 25:1884-1889 (2009)
• A Partially Linear Tree-based Regression Model for Multivariate Outcomes  Kai Yu, William Wheeler, Qizhai Li, Andrew W. Bergen, Neil Caporaso, Nilanjan Chatterjee, and Jinbo Chen Biometrics, published online 10 May (2009)
• A finite mixture survival model to characterize risk groups of neuroblastoma  Sally Hunsberger, Paul S. Albert and Wendy B. London Statist. Med. 28:1301-1314 (2009)
• De novo protein structure generation from incomplete chemical shift assignments  Yang Shen, Robert Vernon, David Baker, and Ad Bax J. Biomol. 43(2):63-78 (2009)

• In Silico Molecular Engineering for a Targeted Replacement in a Tumor-Homing Peptide.  Zanuy D, Flores-Ortega A, Jiménez AI, Calaza MI, Cativiela C, Nussinov R, Ruoslahti E, Alemán C. J. Phys. Chem. B 113(22):7879-89 (2009)
• Widespread Reductions of Cortical Thickness in Schizophrenia and Spectrum Disorders and Evidence of Heritability  Aaron L. Goldman, Lukas Pezawas, Venkata S. Mattay, Bruce Fischl, Beth A. Verchinski, Qiang Chen, Daniel R. Weinberger, Andreas Meyer-Lindenberg. Archives of General Psychiatry 66(5):467-477 (2009)
• Available states and available space: static properties that predict self-diffusivity of confined fluids  Gaurav Goel, William P Krekelberg, Mark J Pond, Jeetain Mittal, Vincent K Shen, Jeffrey R Errington and Thomas M Truskett J. Stat. Mech., doi:10.1088/1742-5468/2009/04/P04006 (2009)
• Identification of cis-regulatory elements in gene co-expression networks using A-GLAM.  Mariño-Ramírez L, Tharakaraman K, Bodenreider O, Spouge J, Landsman D. Methods Mol. Biol. 541:1-22 (2009)
• Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations  Edina Rosta, Nicolae-Viorel Buchete and Gerhard Hummer J. Chem. Theory and Computation 5(5):1393-1399 (2009)
• Pathway analysis by adaptive combination of P-values  Kai Yu, Qizhai Li, Andrew W. Bergen, Ruth M. Pfeiffer, Philip S. Rosenberg, Neil Caporaso, Peter Kraft, Nilanjan Chatterjee Genetic Epidemiology 33(8):700-9 (2009)
• Comparison of the Extended Isotropic Periodic Sum and Particle Mesh Ewald Methods for Simulations of Lipid Bilayers and Monolayers  Richard M. Venable, Linda E. Chen and Richard W. Pastor J. Phys. Chem B 113(17):5855-5862 (2009)
• Genetic background comparison using distance-based regression, with applications in population stratification evaluation and adjustment  Qizhai Li, Sholom Wacholder, David J. Hunter, Robert N. Hoover, Stephen Chanock, Gilles Thomas, Kai Yu Genetic Epidemiology 33(5):432-441 (2009)

• Self-guided langevin dynamics study of regulatory interactions in NtrC  Ana Damjanovic, Betrand Garcia-Moreno E., Bernard R. Brooks Proteins: Structure, Function and Bioinformatics 76(4):1007-19 (2009)
• Hybrid Structural Model of the Complete Human ESCRT-0 Complex  Xuefeng Ren, Daniel P. Kloer, Young C. Kim, Rodolfo Ghirlando, Layla F. Saidi, Gerhard Hummer and James H. Hurley Structure 17(3):406-416 (2009)
• Identification of active sites of biomolecules II: Saccharide and transition metal ion in aqueous solution.  Coskuner O, Bergeron DE, Rincon L, Hudgens JW, Gonzalez CA. J. Phys. Chem. A 113(11):2491-9 (2009)
• Intramolecular Disulfide Bonds of the Prolactin Receptor Short Form are Required for its Inhibitory Action on the Function of the Long form of the Receptor  Y-L. Xie, S. A. Hassan, A. M. Qazi, C. H. Tsai-Morris, and M. L. Dufau Mol. Cell. Biol.  29(10):2546-55 (2009)
• Adjacency Method for Finding Connected Subsets of a Graph: An Application of Graph Theory to Spatial Statistics  Jun Luo, Lan Huang, Mark Hachey, Ram Tiwari Comm. in Stat.: Simulation and Computation 38(5):1136-1151 (2009)
• Ionic Hydrogen-Bond Networks and Ion Solvation. 1. An Efficient Monte Carlo/Quantum Mechanical Method for Structural Search and Energy Computations: Ammonium/Water  Yi-Lei Zhao, Michael Meot-Ner (Mautner) and Carlos Gonzalez J. Phys. Chem. A 113(12):2967-74 (2009)
• Theory and simulation of macromolecular crowding effects on protein folding stability and kinetics  Jeetain Mittal and Robert B. Best arXiv.org (2009)
• A Model for Fine Mapping in Family Based Association Studies.  Stefan Boehringer and Ruth M. Pfeiffer Hum. Heredit. 67(4):226-236 (2009)

• Optimizing computer-aided colonic polyp detection for CT colonography by evolving the Pareto front  Jiang Li, Adam Huang, Jack Yao, Jiamin Liu, Robert L. Van Uitert, Nicholas Petrick, Ronald M. Summers Medical Physics 36:201-212 (2009)
• Rigorous treatment of electrostatics for spatially varying dielectrics based on energy minimization  O. I. Obolensky, T. P. Doerr, R. Ray, and Yi-Kuo Yu Bulletin of the American Physical Society 54:P40.00008 (2009)
• Available states and available space: Static properties that predict dynamics of confined fluids  Gaurav Goel, William P. Krekelberg, Mark J. Pond, Jeetain Mittal, Vincent K. Shen, Jeffrey R. Errington, Thomas M. Truskett J. Stat. Mech. :P04006 (2009)
• A coarse-grained model for polyethylene oxide and polyethylene glycol: conformation and hydrodynamics.  Lee H, de Vries AH, Marrink SJ, Pastor RW. J. Phys. Chem. B 113(40):13186-94 (2009)
• Visual Awareness, Emotion, and Gamma Band Synchronization  Qian Luo, Derek Mitchell, Xi Cheng, Krystal Mondillo, Daniel McCaffrey, Tom Holroyd, Frederick Carver, Richard Coppola and James Blair Cerebral Cortex 19(8):1896-1904 (2009)
• Bayesian Inference for Smoking Cessation with a Latent Cure State  Luo S, Crainiceanu, CM, Louis TA, Chatterjee, N Biometrics 65(3):970-8 (2009)

2008 (83 publications)

• Dislocation nucleation during nanoindentation of aluminum  R. J. Wagner, L. Ma, F. Tavazza, and L. E. Levine J. Applied Physics 104:114311 (2008)
• Pathways and populations: stereoelectronic insights into the exocyclic torsion of 5-(hydroxymethyl) tetrahydropyran.  Woodcock HL, Brooks BR, Pastor RW. JACS 130(20):6345-7 (2008)

• Biological Entity Recognition with Conditional Random Fields  Ying He and Mehmet Kayaalp AMIA Annu. Symp. Proc.  2008:293-297 (2008)
• Lipid bilayer curvature and pore formation induced by charged linear polymers and dendrimers: the effect of molecular shape  Hwankyu Lee and Ronald G. Larson J. Phys. Chem. B 112(39):12279-12285 (2008)
• The point mutation A34F causes dimerization of GB1.  JunGoo Jee, In-Ja L. Byeon, John M. Louis, Angela M. Gronenborn Proteins 71(3):1420-31 (2008)
• RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration  Alves G, Ogurtsov AY, Yu YK. BMC Genomics 9:505 (2008)
• Coarse-grained molecular dynamics studies of the concentration and size dependence of fifth-and seventh-generation PAMAM dendrimers on pore formation in DMPC bilayer  Hwankyu Lee and Ronald G. Larson J. Phys. Chem. B 112(26):7778-7784 (2008)
• RNA binding activity of the recessive parkinsonism protein DJ-1 supports involvement in multiple cellular pathways  Marcel P. van der Brug, Jeff Blackinton, Jayanth Chandran, Ling-Yang Hao, Ashish Lal, Krystyna Mazan-Mamczarz, Jennifer Martindale, Chengsong Xie, Rili Ahmad, Kelly J. Thomas, Alexandra Beilina, J. Raphael Gibbs, Jinhui Ding, Amanda J. Myers, Ming Zhan, Huaibin Cai, Nancy M. Bonini, Myriam Gorospe and Mark R. Cookson PNAS 105(29):10244-10249 (2008)
• Influence of the dye presence on the conformational preferences of CREKA, a tumor homing linear pentapeptide.  Zanuy D, Curcó D, Nussinov R, Alemán C Biopolymers 92(2):83-93 (2008)
• Analysis of Smoking Cessation Patterns Using a Stochastic Mixed-Effects Model With a Latent Cured State  Sheng Luo, Ciprian M Crainiceanu, Thomas A Louis, Nilanjan Chatterjee J. Am. Stat. Assoc. 103(483):1002-1013 (2008)

• Inference of non-centrality parameter of a truncated non-central chi-squared distribution  Qizhai Li and Kai Yu J. Stat. Planning and Inference 139(7):2431-2444 (2008)
• Static and dynamic correlations in water at hydrophobic interfaces  Jeetain Mittal and Gerhard Hummer PNAS 105:20130-20135 (2008)
• Thermodynamics and kinetics of protein folding under confinement.  Jeetain Mittal and Robert Best PNAS 105(51):20233-8 (2008)
• Characterization of a protective Escherichia coli-expressed Plasmodium falciparum merozoite surface protein 3 indicates a non-linear, multi-domain  Tsai CW, Duggan PF, Jin AJ, Macdonald NJ, Kotova S, Lebowitz J, Hurt DE, Shimp RL Jr, Lambert L, Miller LH, Long CA, Saul A, Narum DL. Mol. Biochem. Parasitol. 164(1):45-56 (2008)
• Self-assembly of fused homo-oligomers to create nanotubes  Buch I, Tsai CJ, Wolfson HJ, Nussinov R. Methods Mol. Biol.  474:117-31 (2008)
• Identification of a signature motif in target mRNAs of RNA-binding protein AUF1  Krystyna Mazan-Mamczarz, Yuki Kuwano, Ming Zhan, Elizabeth J. White, Jennifer L. Martindale, Ashish Lal and Myriam Gorospe Nucleic Acids Research 37(1):204-14 (2008)
• GRL-02031, a Novel Nonpeptidic Protease Inhibitor (PI) Containing a Stereochemically Defined Fused Cyclopentanyltetrahydrofuran Potent against Multi-PI-Resistant HIV-1 In Vitro   Yasuhiro Koh, Debananda Das, Sofiya Leschenko, Hirotomo Nakata, Hiromi Ogata-Aoki, Masayuki Amano, Maki Nakayama, Arun K. Ghosh, and Hiroaki Mitsuya Antimicrob. Agents Chemother. 53(3):997-1006 (2008)
• A class comparison method with filtering-enhanced variable selection for high-dimensional data sets  Lara Lusa, Edward L. Korn, Lisa M. McShane Stat. Med 28:5834-5849 (2008)

• Models of voltage-dependent conformational changes in NaChBac channels.  Shafrir Y, Durell SR, Guy HR. Biophys. J.  95(8):3663-76 (2008)
• Prediction of evolutionarily conserved interologs in Mus musculus.  Yellaboina S, Dudekula DB, Ko MS. BMC Genomics 9:465 (2008)
• Comparing the Use of Gibbs Ensemble and Grand-Canonical Transition-Matrix Monte Carlo Methods to Determine Phase Equilibria  Andrew S. Paluch, Vincent K. Shen and Jeffrey R. Errington Ind. Eng. Chem. Res. 47(13):4533-4541 (2008)
• Molecular Dynamics Simulations of Perylene and Tetracene Librations: Comparison With Femtosecond Upconversion Data  Tilman Rosales, Jianhua Xu, Xiongwu Wu, Milan Hodoscek, Patrik Callis, Bernard R. Brooks and Jay R. Knutson J. Phys. Chem. A 112(25):5593-5597 (2008)
• Models of Toxic β-Sheet Channels of Protegrin-1 Suggest a Common Subunit Organization Motif Shared with Toxic Alzheimer β-Amyloid Ion Channels.  Jang H, Ma B, Lal R, Nussinov R. Biophys. J.  95(10):4631-42 (2008)
• Computer Simulation of Ion Cluster Speciation in Concentrated Aqueous Solutions at Ambient Conditions  Sergio A. Hassan J. Phys. Chem. B 112:10573-10584 (2008)
• Considerations for Lipid Force Field Development  Jeffery B. Klauda, Richard M. Venable, Alexander D. MacKerell Jr., Richard W. Pastor in Computational Modeling of Membrane Bilayers, in Current Topics in Membranes Vol 60. (2008)
• Developmental and epigenetic regulation of the human TLR3 gene  Analia Porrás, Sarah Kozar, Valya Russanova, Paraskevi Salpea, Tazuko Hirai, Nicholas Sammons, Pooja Mittal, Ji Young Kim, Keiko Ozato, Roberto Romero and Bruce H. Howard Mol. Immunol. 46(1):27-36 (2008)

• Glycosidic linkage conformation of methyl-α-mannopyranoside  Orkid Coskuner, Denis E. Bergeron, Luis Rincon, Jeffrey W. Hudgens, and Carlos A. Gonzalez J. Chem. Phys. 129:045102 (2008)
• Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways.  Lenz G, Wright GW, Emre NC, Kohlhammer H, Dave SS, Davis RE, Carty S, Lam LT, Shaffer AL, Xiao W, Powell J, Rosenwald A, Ott G, Muller-Hermelink HK, Gascoyne RD, Connors JM, Campo E, Jaffe ES, Delabie J, Smeland EB, Rimsza LM, Fisher RI, Weisenburger DD, Chan WC, Staudt LM. PNAS 105(36):13520-5 (2008)
• Ligand Exchange Reactions in the Formation of Diphosphine-Protected Gold Clusters  Denis E. Bergeron, Orkid Coskuner, Jeffrey W. Hudgens, and Carlos A. Gonzalez J. Phys. Chem. C 112(33):12808-12814 (2008)
• Evidence That Proline Focuses Movement of the Floppy Loop of Arylalkylamine N-Acetyltransferase (EC 2.3. 1.87)  Jiri Pavlicek, Steven L. Coon, Surajit Ganguly, Joan L. Weller, Sergio A. Hassan, Dan L. Sackett, and David C. Klein J. Biol. Chem. 283(21):14552-14558 (2008)
• Molecular dynamics studies of polyethylene oxide and polyethylene glycol: Hydrodynamic radius and shape anisotropy  Hwankyu Lee, Richard M. Venable, Alexander D. MacKerell, Jr. and Richard W. Pastor Biophysical Journal 95(4):1590-9 (2008)
• Positron Emission Tomography Imaging Using an Inverse Agonist Radioligand to Assess Cannabinoid CB1 Receptors in Rodents   Terry G, Liow J-S, Chernet E; Zoghbi SS, Phebus L, Felder CC, Tauscher J, Schaus JM, Pike VW, Halldin C, Innis RB. Neuroimage 41(3):690-8 (2008)
• p53-Induced DNA Bending: The Interplay between p53-DNA and p53-p53 Interactions  Yongpin Pan, Ruth Nussinov J. Phys. Chem. B 112(21):6716-24 (2008)
• 11C-Loperamide and its N-desmethyl radiometabolite are avid substrates for brain P-glycoprotein efflux   Zoghbi SS, Liow J-S,Yasuno F, Hong J, Tuan E; Lazarova N, Gladding RL; Pike VW, Innis RB J. Nucl. Med. 49(4):649-56 (2008)
• CHARMM Force Field Parameters for Nitroalkanes and Nitroarenes  Klauda JB, Brooks BR J. Chem. Theory and Computation 4(1):107-115 (2008)
• Binding-induced folding of a natively unstructured transcription factor.   Turjanski, A. G., Gutkind, J.S., Best, R. and Hummer. G. PLoS Computational Biology, e1000060 doi:10.1371 (2008)
• Privileged scaffolds targeting reverse-turn and helix recognition   Che, Ye & Marshall, Garland. Expert Opinion on Therapeutic Targets  12(1):101-114 (2008)
• Genotype, haplotype and copy-number variation in worldwide human populations.   Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung HC, Szpiech ZA, Degnan JH, Wang K, Guerreiro R, Bras JM, Schymick JC, Hernandez DG, Traynor BJ, Simon-Sanchez J, Matarin M, Britton A, van de Leemput J, Rafferty I, Bucan M, Cann HM, Hardy JA, Rosenberg NA, Singleton AB. Nature  451(7181):998-1003 (2008)
• Cluster Without Fluster: The Effect of Correlated Outcomes on Inference in Randomized Clinical Trials   Proschan MA, Follmann, DA. Statistics in Medicine 27(6):795-809 (2008)
• Sigma Stellation: A Design Strategy for Electron Boxes   Irikura, Karl K J. Phys. Chem A 112:983-988 (2008)
• Coordination Studies of Al-EDTA in Aqueous Solution  Orkid Coskuner, Emily A. A. Jarvis J. Phys. Chem.  112(12):2628-2633 (2008)
• Layering and Position-Dependent Diffusive Dynamics of Confined Fluids   Jeetain Mittal, Thomas M. Truskett, Jeffrey R. Errington, and Gerhard Hummer Physical Review Letters 100:145901 (2008)
• Comprehensive Structural Studies of 2', 3'-Difluorinated Nucleosides: Comparison of Theory, Solution, and Solid State  Joseph J. Barchi, Jr., Rajeshri G. Karki, Marc C. Nicklaus, Maqbool A. Siddiqui, Clifford George, Igor A. Mikhailopulo and Victor E. Marquez J. Am. Chem. Soc. 130(28):9048-9057 (2008)
• MAX-rank: a simple and robust genome-wide scan for case-control association studies.  Li Q, Yu K, Li Z, Zheng G. Hum. Genet. 123(6):617-23 (2008)
• Backbone relaxation coupled to the ionization of internal groups in proteins: A self-guided Langevin dynamics study  Ana Damjanovic, Xiongwu Wu, Bertrand Garcia-Moreno and Bernard R Brooks Biophys. J.  95(9):4091-101 (2008)
• Towards an automatic classification of protein structural domains based on structural similarity   Sam V, Tai CH, Garnier J, Gibrat JF, Lee B, Munson PJ. BMC Bioinformatics  9(1):74 (2008)
• Endogenous retrotransposon sequences of the Schistosoma mansoni intermediate snail host, Biomphalaria glabrata.   Knight M, Bridger J, Ittiprasert W, Odoemelam E, Masabanda J, Miller A, Raghavan, N. Mobile Genetic Elements in Metazoan Para, Brindley PJ (ed). Landes Bioscience, in press. (2008)
• On estimating diagnostic accuracy from studies with multiple raters and partial gold standard evaluation  Paul S. Albert and Lori E Dodd J. Am. Stat. Assoc 103(481):61-73 (2008)
• In Situ Gas Phase Diagnostics for Hafnium Oxide Atomic Layer Deposition  J.E. Maslar, W.S. Hurst, D.R. Burgess, W.A. Kimes, N.V. Nguyen, E.F. Moore, J.T. Hodges ECS Transactions 13(2):139-149 (2008)
• Differences in Cysteine Protease Activity in Schistosoma mansoni-Resistant and-Susceptible Biomphalaria glabrata and Characterization of the Hepatopancreas Cathepsin B Full-length cDNA  Jocelyn Myers, Wannaporn Ittiprasert, Nithya Raghavan, Andrè Miller, and Matty Knight J. Parasitol. 94:3:659-668 (2008)

• Molecular architecture of native HIV-1 gp 120 trimers  Jun Liu, Alberto Bartesaghi, Mario J. Borgnia, Guillermo Sapiro & Sriram Subramaniam Nature 455:109-113 (2008)
• Dissecting contact potentials for proteins: relative contributions of individual amino acids.  Buchete NV, Straub JE, Thirumalai D. Proteins  70(1):119-30 (2008)
• Synthesis and evaluation of N-Methyl and S-Methyl 11C-Labeled 6-Methylthio-2-(4'-N,N-dimethylamino)phenylimidazo[1,2-a]pyridines as radioligands for imaging beta-amyloid plaques in Alzheimer's disease.  Cai L, Liow JS, Zoghbi SS, Cuevas J, Baetas C, Hong J, Shetty HU, Seneca NM, Brown AK, Gladding R, Temme SS, Herman MM, Innis RB, Pike VW. J. Med. Chem.  51(1):148-58 (2008)
• Residual multiparticle entropy does not generally change sign near freezing.  Krekelberg WP, Shen VK, Errington JR, Truskett TM. J. Chem. Phys. 128(16):161101 (2008)
• Synthesis and pharmacological effects of the enantiomers of the N-phenethyl analogues of the ortho and para e-and f-oxide-bridged phenylmorphans  Josef Zezula, Lisa Singer, Anna K. Przyby, Akihiro Hashimoto, Christina M. Dersch, Richard B. Rothman, Jeffrey Deschamps, Yong Sok Lee, Arthur E. Jacobson and Kenner C. Rice Org. and Biomol. Chem. 6:2868-2883 (2008)
• A pseudopotential for improving the packing of ellipsoidal protein structures determined by NMR  C.D. Schwieters and G.M. Clore. J. Phys. Chem 112(19):6070-6073 (2008)
• Dynamics of Cholesterol Exchange in the OSBP-Related Protein Family  Canagarajah, B., Hummer, G., Prinz, W. and Hurley, J. H. J. Mol. Biol. 378(3):737-48 (2008)
• Population Substructure and Control Selection in Genome-Wide Association Studies  Kai Yu, Zhaoming Wang, Qizhai Li, Sholom Wacholder, David J. Hunter, Robert N. Hoover, Stephen Chanock, and Gilles Thomas PLoS One 3(7):2551 (2008)
• Testing logistic regression coefficients with clustered data and few positive outcomes   Sally Hunsberger, Ed Korn, and Barry Graubard. Statistics in Medicine 27(8):1305-24 (2008)
• Host Control of Malaria Infections: Constraints on Immune and Erythropoeitic Response Kinetics  McQueen PG, McKenzie FE PLoS Computational Biology 4(8):e1000149 (2008)
• Identification of the transition states in the inversion of 1, 4-benzodiazepines with the Ab Initio Replica Path Method   Yong-Sok Lee, Victor W. Pike, and Milan Hodoscek. J. Phys. Chem A  112:1604-1611 (2008)
• A frailty mixture cure model with application to hospital readmission cata   Yu, B. Biometrical J. 50(3):386-94 (2008)
• Efficient Approximation of P-value of the Maximum of Correlated Tests, with Applications to Genome-Wide Association Studies.   Li Q.Z., Zheng G., Li Z.H. and Yu K. Annals of Human Genetics 72(3):397-406 (2008)
• Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements.   Ma B, Levine AJ. Nucleic Acids Research 35(22):7733-7747 (2008)
• Improved Classifier for Computer-aided Polyp Detection in CT Colonography by Nonlinear Dimensionality Reduction  Shijun Wang, Jianhua Yao and Ronald M. Summers Med. Phys. 35(4):1377-86 (2008)
• β2-microglobulin amyloid fragment organization and morphology and its comparison to Aβ suggests that amyloid aggregation pathways are sequence specific   Zheng J, Jang H, Nussinov R. Biochemistry.  Feb 26;47(8):2497-2509 (2008)

• Morphology of Ion Clusters in Aqueous Electrolytes   SA Hassan. Phys. Rev. E 77:03151 (2008)
• Involvement of the second extracellular loop and transmembrane residues of CCR5 in inhibitor binding and HIV-1 fusion: insights into the mechanism of allosteric inhibition.  Maeda K, Das D, Yin PD, Tsuchiya K, Ogata-Aoki H, Nakata H, Norman RB, Hackney LA, Takaoka Y, Mitsuya H. J. Mol. Biol. 381:956-974 (2008)
• Are Current Molecular Dynamics Force Fields too Helical?  Robert B Best, Nicolae-Viorel Buchete and Gerhard Hummer Biophysical Letters 95(1):L07-9 (2008)
• Concentration and crowding effects on protein stability from a coarse-grained model   J. K. Cheung, V. K. Shen, J. R. Errington, and T. M. Truskett. in Statistical Mechanics of Cellular System, MH Zaman ed, Cambridge University Press. (2008)
• Heritability of brain morphology related to schizophrenia: a large-scale automated magnetic resonance imaging segmentation study.   Goldman AL, Pezawas L, Mattay VS, Fischl B, Verchinski BA, Zoltick B, Weinberger DR, Meyer-Lindenberg A. Biol. Psychiatry  63(5):475-83 (2008)
• Models of the Structure and Gating Mechanisms of the Pore Domain of the NaChBac Ion Channel  Yinon Shafrir, Stewart R Durell and H. Robert Guy Biophys. J. 95(8):3650-62 (2008)
• NIST Computational Chemistry Comparison and Benchmark Database  Some of the calculations in the CCBD were performed by Russell Johnson on the Biowulf cluster. (2008)
• Modeling Longitudinal Biomarker Data from Multiple Assays that Have Different Known Detection Limits  Paul S. Albert Biometrics 64:527-537 (2008)

• Application of 1-Aminocyclohexane Carboxylic Acid to Protein Nanostructure Computer Design.   Rodriguez-Ropero F, Zanuy D, Casanovas J, Nussinov R, Aleman C. J Chem Inf Model. 48(2):333-43 (2008)
• Calcium-dependent inactivation terminates calcium release in skeletal muscle of amphibians   Eduardo Rios, Jingsong Zhou, Gustavo Brum, Bradley S. Launikonis, and Michael D. Stern. J. Gen. Physiol. 131(4):335-48 (2008)
• Classification and 3D averaging with missing wedge correction in biological electron tomography  A. Bartesaghi, P. Sprechmann, J. Liu, G. Randall, G. Sapiro and S. Subramaniam J. Struct. Biol. 162(3):436-450 (2008)
• Detection of co-eluted peptides using database search methods  Gelio Alves, Aleksey Y Ogurtsov, Siwei Kwok, Wells W Wu, Guanghui Wang, Rong-Fong Shen, and Yi-Kuo Yu Biol. Direct. 3:27 (2008)
• Coarse Master Equations for Peptide Folding Dynamics   N.V. Buchete and G. Hummer. J. Phys. Chem. B 112(19):6057-69 (2008)
• Identification of the Active Sites of Biomolecules I  Orkid Coskuner, Denis E. Bergeron, Luis Rincon, Jeffrey W. Hudgens, Carlos A. Gonzalez J. Phys. Chem. A 112(3):2940-2947 (2008)
• New structures help the modeling of toxic amyloidβ ion channels   Jang H, Zheng J, Lal R, Nussinov R. Trends Biochem Sci.  Feb;33(2):91-100 (2008)
• Peptide folding kinetics from replica exchange molecular dynamics  Nicolae-Viorel Buchete and Gerhard Hummer Physical Review E 77:030902 (2008)

• Structure and dynamics of Helix-0 of the N-BAR domain in Lipid Micelles and Bilayers  Christian Löw, Ulrich Weininger, Hwankyu Lee, Kristian Schweimer, Ines Neundorf, Annette G. Beck-Sickinger, Richard W. Pastor and Jochen Balbach Biophys. J.  95(9):4315-23 (2008)

2007 (72 publications)

• Multiple comparisons distortions of parameter estimates   Jeffries, NO. Biostatistics  8(2):500-4 (2007)
• Engineering Metal Complexes of Chiral Pentaazacrowns as Privileged Reverse-turn Scaffolds.   Y Che, Bernard Brooks, Dennis P Riley, Andrea JH Reaka, Garland R Marshall. Chemical Biology & Drug Design  69 (2) : 99-110 (2007)
• RAId_DbS: Peptide identification using database searches with realistic statistics  Alves G, Ogurtsov AY, Yu YK. Biol. Direct.  2:25 (2007)
• Cysteine-cysteine contact preference leads to target-focusing in protein folding   Sardiu ME, Cheung MS, Yu YK. Biophys. J.  93(3):938-51 (2007)
• Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project  The ENCODE Project Consortium Nature 447:799-816 (2007)
• The structure of receptor-associated protein (RAP)   Donghan Lee, Joseph D. Walsh, Molly Migliorini, Ping Yu Tao Cai, Charles D. Schwieters, Susan Krueger, Dudley K. Strickland, and Yun-Xing Wang. Protein Science  16:1628-1640 (2007)
• Accounting for Variability in Sample Size Estimation with Applications to Nonadherence and Estimation of Variance and Effect Size   Fay, MP, Halloran, ME, Follmann, DA. Biometrics  63(2): 465-474 (2007)

• Modeling the Alzheimer A β< sub> 17-42</sub> Fibril Architecture: Tight Intermolecular Sheet-Sheet Association and Intramolecular Hydrated Cavities   Zheng J, Jang H, Ma B, Tsai CJ, Nussinov R. Biophys J.  93(9):3046-57 (2007)
• Ab Initio Modeling of Glycosyl Torsions and Anomeric Effects in a Model Carbohydrate: 2-Ethoxy Tetrahydropyran  H. Lee Woodcock, Damian Moran, Richard W. Pastor, Alexander D. MacKerell, Jr. and Bernard R. Brooks Biophys. J.  93:1-10 (2007)
• Analysis of failure time data with multilevel clustering, with application to the child vitamin a intervention trial in Nepal   Shih JH, Lu SE. Biometrics  63(3):673-80 (2007)
• Liquid-structure forces and electrostatic modulation of biomolecular interactions in solution   SA Hassan. J. Phys. Chem B  111(1):227-41 (2007)
• Natural resonance structures and aromaticity of the nucleobases   Guangyu Sun & Marc Nicklaus. Theoretical Chemistry Accounts: Theory,   117(2): 323-332 (2007)
• Understanding the structural and functional differences between mouse thyrotropin-releasing hormone receptors 1 and 2  Francesca Deflorian, Stanislav Engel, Anny-Odile Colson, Bruce M. Raaka, Marvin C. Gershengorn, Stefano Costanzi Proteins: Structure, Function and Bioinf 71(2):783 - 794 (2007)
• Stability of Tubular Structures Based on β-Helical Proteins: Self-Assembled versus Polymerized Nanoconstructs and Wild-Type versus Mutated Sequences  David Zanuy, Francisco Rodríguez-Ropero, Nurit Haspel, Jie Zheng, Ruth Nussinov, and Carlos Alem´n BIomacromolecules 8(10):3135-3146 (2007)
• N-Nitrosation of amines by NO2 and NO: A theoretical study  Yi-Lei Zhao, Stephen L. Garrison, Carlos Gonzalez, William David Thweatt, and Manuel Marquez J. Phys. Chem. A 111(11):2200-2205 (2007)
• Exploring SCC-DFTB Paths for Mapping QM/MM Reaction Mechanisms  H. Lee Woodcock, Milan Hodošček, and Bernard R. Brooks J. Phys. Chem A 111(26):5720-5728 (2007)
• Comparative Study of the Effect of Tail Corrections on Surface Tension Determined by Molecular Simulation   V. K. Shen, R. D. Mountain, and J. R. Errington. J. Phys. Chem  B 111:6198 (2007)
• A genome-wide genotyping study in patients with ischaemic stroke: initial analysis and data release.   Matarin M, Brown WM, Scholz S, Simon-Sanchez J, Fung HC, Hernandez D, Gibbs JR, De Vrieze FW, Crews C, Britton A, Langefeld CD, Brott TG, Brown RD Jr, Worrall BB, Frankel M, Silliman S, Case LD, Singleton A, Hardy JA, Rich SS, Meschia JF. Lancet Neurol.  6(5):414-20 (2007)
• A physical picture of atomic motions within the Dickerson DNA dodecamer in solution derived from joint ensemble refinement against NMR and large-angle X-ray scattering data.   Schwieters CD, Clore GM. Biochemistry  46(5):1152-66 (2007)
• Sugar binding in lactose permease: anomeric state of a disaccharide influences binding structure.  Klauda JB, Brooks BR. J Mol Biol.  367(5):1523-34 (2007)
• Using Pareto fronts to evaluate polyp detection algorithms for CT colonography  Adam Huang ; Jiang Li ; Ronald M. Summers ; Nicholas Petrick ; Amy K. Hara Medical Imaging: Computer-Aided Diagnosis, doi:10.1117/12.709426 (2007)
• Two-sample Comparison Based on Prediction Error, with Applications to Candidate Gene Association Studies   K. Yu, R. Martin, N. Rothman, T. Zheng, Q. Lan. Annals of Human Genetics  71 (1) :107- 118 (2007)
• Preferred conformation of the glycosidic linkage of methyl-beta-mannose.  Coskuner O. J. Chem. Phys  127(1):015101 (2007)

• Structure and Dynamics of Parallel β-Sheets, Hydrophobic Core, and Loops in Alzheimer's A β Fibrils  Buchete NV, Hummer G. Biophys J.  92(9):3032-9 (2007)
• Molecular dynamics simulation of the P2Y< sub> 14</sub> receptor. Ligand docking and identification of a putative binding site of the distal hexose moiety   Ivanov, A. A.; Fricks, I; Harden, T. K.; Jacobson, K. A. Bioorg. Med. Chem. Lett. 17:761-766 (2007)
• Calculation of the Free Energy and Cooperativity of Protein Folding  Kentsis A, Gindin T, Mezei M, Osman R. PLoS ONE  2:e446 (2007)
• Coarse-grained strategy for modeling protein stability in concentrated solutions. III: directional protein interactions.   J. K. Cheung, V. K. Shen, J. R. Errington, and T. M. Truskett. Biophys J  92:4316 (2007)
• Context-specific amino acid substitution matrices and their use in the detection of protein homologs.   Goonesekere NC, Lee B. Proteins  71(2):910-919 (2007)
• The Origin of Quantal Size Variation: Vesicular Glutamate Concentration Plays a Significant Role   Xin-Sheng Wu, Lei Xue, Raja Mohan, Kenneth Paradiso, Kevin D. Gillis, and Ling-Gang Wu. J. Neurosc.  27(11):3046-3056 (2007)
• Challenges in Projecting Clustering Results Across Gene Expression-Profiling Datasets   Lara Lusa, Lisa M. McShane, James F. Reid, Loris De Cecco, Federico Ambrogi, Elia Biganzoli, Manuela Gariboldi, Marco A. Pierotti. J. National Cancer Institute  99(22): 1715-1723 (2007)
• In Situ Monitoring of Hafnium Oxide Atomic Layer Deposition  J.E. Maslar, W.S. Hurst, D.R. Burgess, Jr., W.A. Kimes, N.V. Nguyen, and E.F. Moore Frontiers of Char. and Metr. for Nanoelectrics (2007)
• The bootstrap variance of the square of a sample mean   Dodd, LE and Korn, EL. The American Statistician. 1(2):127-131 (2007)
• qPrimerDepot: a primer database for quantitative real time PCR  Wenwu Cui, Dennis D. Taub and Kevin Gardner Nucleic Acids Research 35:D805-D809 (2007)
• Probes for Narcotic Receptor Mediated Phenomena. 34. Synthesis and Structure-Activity Relationships of a Potent μ-Agonist δ-Antagonist and an Exceedingly Potent Antinociceptive in the Enantiomeric C9-Substituted 5-(3-Hydroxyphenyl)-N-phenylethylmorphan Series  Anne-C�cile Hiebel, Yong Sok Lee, Edward Bilsky, Denise Giuvelis, Jeffrey R. Deschamps, Damon A. Parrish, Mario D. Aceto, Everette L. May, Louis S. Harris, Andrew Coop, Christina M. Dersch, John S. Partilla, Richard B. Rothman, Kejun Cheng, Arthur E. Jacobson, and Kenner C. Rice J. Med. Chem. 50(16):3765-3776 (2007)
• Effects of Chain Length on the Rates of CC Bond Dissociation in Linear Alkanes and Polyethylene  Knyazev V J. Phys. Chem. A 111(19):3875-83 (2007)
• Molecular modeling of the human P2Y2 receptor and design of a selective agonist, 2'-amino-2'-deoxy-2-thiouridine 5'-triphosphate.   Ivanov AA, Ko H, Cosyn L, Maddileti S, Besada P, Fricks I, Costanzi S, Harden TK, Calenbergh SV, Jacobson KA. J. Med. Chem  50(6):1166-76 (2007)
• Testing β-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: A molecular dynamics study   D. Zanuy, F. Rodriguez-Ropero, R. Nussinov, C. Aleman. J. Struct. Biol.  160(2): 177-189 (2007)
• Nanostructure Design Using Protein Building Blocks Enhanced by Conformationally Constrained Synthetic Residues   Zheng J, Zanuy D, Haspel N, Tsai CJ, Alem C and Nussinov R. Biochemistry  46(5):1205 -1218 (2007)
• Substrate-induced Conformational Changes and Dynamics of UDP- N-Acetylgalactosamine: Polypeptide N-Acetylgalactosaminyltransferase-2  Adina L Milac, Nicolae-Viorel Buchete, Timothy A Fritz, Gerhard Hummer, Lawrence A Tabak J. Mol. Biol.  Oct 19;373(2):439-51 (2007)

• A 2-Year Prospective Study of Human Papillomavirus Persistence among Women with a Cytological Diagnosis of Atypical Squamous Cells of Undetermined Significance or Low-Grade Squamous Intraepithelial Lesion  Plummer M, Schiffman M, Castle PE, Maucort-Boulch D, Wheeler CM; ALTS Group. J Infect Dis.  195(11):1582-9 (2007)
• Nimbus( BgI): An active non-LTR retrotransposon of the Schistosoma mansoni snail host Biomphalaria glabrata   Raghavan N, Tettelin H, Miller A, Hostetler J, Tallon L, Knight M. Int. J. Parasitol.  37(12):1307-18 (2007)
• Competition between Hydrogen Abstraction and Halogen Displacement in the Reaction of Br with CH3I, CH3Br, and CH3Cl   Irikura, Karl K.; Francisco, J. S. J. Phys. Chem 111:6852-6859 (2007)
• Elucidation of a C-Rich Signature Motif in Target mRNAs of RNA-Binding Protein TIAR   Kim HS, Kuwano Y, Zhan M, Pullmann R Jr, Mazan-Mamczarz K, Li H, Kedersha N, Anderson P, Wilce MC, Gorospe M, Wilce JA. Mol. Cell. Biol.  27(19):6806-17 (2007)
• Structural dynamics of the cooperative binding of organic molecules in the human cytochrome P450 3A4   Fishelovitch D, Hazan C, Shaik S, Wolfson HJ, Nussinov R. J Am Chem Soc.  14;129(6):1602-11 (2007)
• Limits on variations in protein backbone dynamics from precise measurements of scalar couplings.   Vogeli B, Ying J, Grishaev A, Bax A. J. Am. Chem. Soc  129(30):9377-85 (2007)
• Identification and regional distribution in rat brain of radiometabolites of the dopamine transporter PET radioligand [11C]PE2I.   Shetty HU, Zoghbi SS, Liow JS, Ichise M, Hong J, Musachio JL, Halldin C, Seidel J, Innis RB, Pike VW. Eur. J. Nucl. Med. Mol. Imaging  34(5):667-78 (2007)
• Effect of a P-glycoprotein inhibitor, Cyclosporin A, on the disposition in rodent brain and blood of the 5-HT1A receptor radioligand, [11C](R)-(-)-RWAY.   Liow JS, Lu S, McCarron JA, Hong J, Musachio JL, Pike VW, Innis RB, Zoghbi SS. Synapse  61(2):96-105 (2007)

• A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences   Joseph C Lee, David Stiles, Jun Lu, and Margaret C Cam. BMC Genomics  8: 284 (2007)
• Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data.   Schymick JC, Scholz SW, Fung HC, Britton A, Arepalli S, Gibbs JR, Lombardo F, Matarin M, Kasperaviciute D, Hernandez DG, Crews C, Bruijn L, Rothstein J, Mora G, Restagno G, Chio A, Singleton A, Hardy J, Traynor BJ. Lancet Neurol.  6(4):322-8 (2007)
• The LeFE algorithm, embracing the complexity of gene expression in the interpretation of microarray data.   Eichler, GS, Reimers, M, Kane, D, Weinstein, JN. Genome Biology  8(9):R185 (2007)
• Imputation Approaches for Estimating Diagnostic Accuracy for Multiple Tests from Partially Verified Designs   Paul S. Albert. Biometrics  63:947-957 (2007)
• An investigation of two multivariate permutation methods for controlling the false discovery proportion   Edward L. Korn , Ming-Chung Li , Lisa M. McShane and Richard Simon. Statistics in Medicine  26:4428-4440 (2007)
• A survey of genetic human cortical gene expression   Myers AJ, Gibbs JR, Webster JA, Rohrer K, Zhao A, Marlowe L, Kaleem M, Leung D, Bryden L, Nath P, Zismann VL, Joshipura K, Huentelman MJ, Hu-Lince D, Coon KD, Craig DW, Pearson JV, Holmans P, Heward CB, Reiman EM, Stephan D, Hardy J. Nature Genetics  39(12):1494-9 (2007)
• Changing the Charge Distribution of β-Helical-Based Nanostructures Can Provide the Conditions for charge transfer.   Haspel N, Zanuy D, Zheng J, Aleman C, Wolfson H, Nussinov R. Biophys J.  93(1):245-53 (2007)
• Similar Binding Sites and Different Partners: Implications to Shared Proteins in Cellular Pathways   Keskin O and Nussinov R. Structure  15:341-354 (2007)
• Random Effects Modeling Approaches for Estimating ROC Curves from Repeated Ordinal Tests without a Gold Standard   Paul Albert. Biometrics  63:593-602 (2007)
• Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect.   Jang H, Ma B, Nussinov R. BMC Struct Biol.  2;7:21 (2007)
• Molecular factors and biochemical pathways induced by febrile temperature in intraerythrocytic Plasmodium falciparum parasites   Miranda S. M. Oakley, Sanjai Kumar, Vivek Anantharaman, Hong Zheng, Babita Mahajan, J. David Haynes, J. Kathleen Moch Rick Fairhurst Thomas F. McCutchan and L. Aravind. Infection and Immunity  75: 2012-2025 (2007)
• Calibrating E-values for MS2 database search methods  Alves G, Ogurtsov AY, Wu WW, Wang G, Shen RF, Yu YK. Biol. Direct.  2:26 (2007)
• Structural basis for p53 binding-induced DNA bending.  Pan Y, Nussinov R. , J Biol Chem.  5;282(1):691-9 (2007)
• Confinement, entropy, and single-particle dynamics of equilibrium hard-sphere mixtures.   Mittal J, Shen VK, Errington JR, Truskett TM. J Chem Phys.  Oct 21;127(15):154513 (2007)
• An Evaluation of Power and Type I Error of Single-Nucleotide Polymorphism Transmission/Disequilibrium-Based Statistical Methods under Different Family Structures, Missing Parental Data, and Population Stratification   Kristin K. Nicodemus Augustin Luna and Yin Yao Shugart. Am. J. Hum. Genet.  80:178-185 (2007)
• Density functional theory study of the clean and hydrated hematite (1[overline 1]02) surfaces  Cynthia S. Lo, Kunaljeet S. Tanwar, Anne M. Chaka, and Thomas P. Trainor Phys. Rev. B 75(7):209901 (2007)
• Density-functional study of magnetism in bare Au nanoclusters: Evidence of permanent size-dependent spin polarization without geometry relaxation  Magyar, R. J.; Mujica, V.; Marquez, M.; Gonzalez, C. Phys. Rev. B 75(14):14421 (2007)
• Neural dynamics for facial threat processing as revealed by gamma band synchronization using MEG   Qian Luo, Tom Holroyd, Matthew Jones, Talma Hendler and James Blair Neuroimage  34:839-847 (2007)
• Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations.  Woodcock HL 3rd, Hodoscek M, Gilbert AT, Gill PM, Schaefer HF 3rd, Brooks BR. J. Comput. Chem 28(9):1485-502 (2007)
• Intrinsic Conformational Characteristics of α, α-Diphenylglycine   Casanovas J, Zanuy D, Nussinov R, Aleman C. J. Org. Chem.  16;72(6):2174-81 (2007)
• Use of constrained synthetic amino acids in β-helix proteins for conformational control.   Zanuy D, Jimenez AI, Cativiela C, Nussinov R, Aleman C. J Phys Chem B.  111(12):3236-42 (2007)
• Models of β-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a Dynamic Process.   Jang H, Zheng J, Nussinov R. Biophys J.  93(6):1938-49 (2007)
• Structures of the CCR5 N Terminus and of a Tyrosine-Sulfated Antibody with HIV-1 gp120 and CD4  Chih-chin Huang, Son N. Lam, Priyamvada Acharya, Min Tang, Shi-Hua Xiang, Syed Shahzad-ul Hussan, Robyn L. Stanfield, James Robinson, Joseph Sodroski, Ian A. Wilson, Richard Wyatt, Carole A. Bewley, Peter D. Kwong Science 317:1930-1934 (2007)
• Protein recognition motifs: Design of peptidomimetics of helix surfaces   Ye Che, Bernard Brooks, Garland R Marshall. Biopolymers  86(4):288 - 297 (2007)
• Water dissociation in the presence of metal ions.  Coskuner O, Jarvis EA, Allison TC. Angew. Chem. Int. Ed  46(41): 7853 (2007)

2006 (55 publications)

• Functionalized Self-Assembled Monolayers on Ultraflat Gold as Platforms for Single Molecule Force Spectroscopy and Imaging  Yadavalli VK, Forbes JG, Wang K. Langmuir 22(16):6969-76 (2006)
• Kinetic Study of the Gas-Phase Reaction of OH with Br2  Mikhail G. Bryukov, Barry Dellinger, and Vadim D. Knyazev J. Phys. Chem. A 110(29):9169-9174 (2006)
• Surface-modulated motion switch: Capture and release of iron-sulfur protein in the cytochrome bc₁ complex  Lothar Esser, Xing Gong, Shaoqing Yang, Linda Yu, Chang-An Yu and Di Xia PNAS 103(35):13045-13050 (2006)
• System size and control parameter effects in reverse perturbation nonequilibrium molecular dynamics.   Mountain RD. J Chem Phys. 124(10):104109 (2006)
• Membrane biophysics   Joshua Zimmerberg. Current Biology  16:R272-R276 (2006)
• De Novo Tubular Nanostructure Design Based on Self-Assembly of β-Helical Protein Motifs  Nurit Haspel, David Zanuy, Carlos Alemàn, Haim Wolfson and Ruth Nussinov Structure 14(7):1137-1148 (2006)
• Structure by design: from single proteins and their building blocks to nanostructures   Tsai C-J, Zheng J, Aleman C, Nussinov R. Trends in Biotechnoloy  24:449-454 (2006)
• Constant surface tension molecular dynamics simulations of lipid bilayers with trehalose   R. M. Venable, A. Skibinsky and R. W. Pastor. Molecular Simulation 32:849-855 (2006)
• Effects of electric fields on proton transport through water chains   S A Hassan, G Hummer and Y S Lee J. Chem. Phys  124:204510 (2006)
• The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements   MAQC Consortium. Nature Biotechnology  24: 1151 - 1161 (2006)
• Global similarity and local divergence in human and mouse gene co-expression networks.   Tsaparas, P., Marino-Ramirez, L., Bodenreider, O., Koonin, E. V. and Jordan, I. K. BMC Evol Biol.  6:70 (2006)
• Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small alpha/beta protein: a unified picture of high probability, fast atomic motions in proteins.   Clore GM, Schwieters CD. J. Mol. Biol.  355(5):879-86 (2006)
• Determination of surface tension in binary mixtures using transition-matrix Monte Carlo   V. K. Shen and J. R. Errington. J. Chem. Phys  124:24721 (2006)
• Genes involved in DNA repair and nitrosamine metabolism and those located on chromosome 14q32 are dysregulated in nasopharyngeal carcinoma.  Dodd LE, Sengupta S, Chen IH, den Boon JA, Cheng YJ, Westra W, Newton MA, Mittl BF, McShane L, Chen CJ, Ahlquist P, Hildesheim A. Cancer Epidemiol Biomarkers Prev. 15(11):2216-25 (2006)
• Predicting domain-domain interactions using a parsimony approach   Katia S Guimaraes, Raja Jothi, Elena Zotenko and Teresa M Przytycka. Genome Biol.  7(11): R104 (2006)
• De novo peptide sequencing using exhaustive enumeration of peptide composition.  Olson MT, Epstein JA, Yergey AL. J. Am. Soc. Mass. Spectrum  17(8):1041-9 (2006)
• PET imaging of brain 5-HT1A receptors in rat in vivo with 18F-FCWAY and improvement by successful inhibition of radioligand defluorination with miconazole.   Tipre DN, Zoghbi SS, Liow JS, Green MV, Seidel J, Ichise M, Innis RB, Pike VW. J. Nucl. Med  47(2):345-53 (2006)
• Chemical shift tensors of protonated base carbons in helical RNA and DNA from NMR relaxation and liquid crystal measurements.   Ying J, Grishaev A, Bryce DL, Bax A. J. Am. Chem. Soc  128(35):11443-54 (2006)
• Using RNA sample titrations to assess microarray platform performance and normalization techniques   Shippy R et al. Nature Biotechnology  24: 1123-1131 (2006)
• Interaction of Protegrin-1 with Lipid Bilayers: Membrane Thinning Effect   Jang H, Ma B, Woolf TB., Nussinov R Biophysical J.  91:2848-2859 (2006)
• The snail ( Biomphalaria glabrata) genome project   Raghavan N. and Knight M. Trends Parasitol.  22(4):148-51 (2006)
• CisView: A Browser and Database of cis-regulatory Modules Predicted in the Mouse Genome   Sharov A, Dudekula D, Ko MSH. DNA Research 13(3):123-34 (2006)
• Augmented designs to assess immune response in vaccine trials.   Follmann, DA. Biometrics  62(4):1161-9 (2006)

• “Similarity Trap” in Protein-Protein Interactions Could Be Carcinogenic: Simulations of p53 Core Domain Complexed with 53BP1 and BRCA1 BRCT Domains   Liu J, Pan Y, Ma B, and Nussinov R. Structure  14(12):1811-21 (2006)
• Engineering Cyclic Tetrapeptides Containing Chimeric Amino Acids as Preferred Reverse-Turn Scaffolds   Ye Che and Garland Marshall. J. Med. Chem.  49 (1):111 -124, (2006)
• Titin as a giant scaffold for integrating stress and Src homology domain 3-mediated signaling pathways   Ma K, Forbes JG, Gutierrez-Cruz G, and Wang K. J. Biol Chem.  281(37):27539-56 (2006)
• Development of small molecules designed to modulate protein-protein interactions   Ye Che, Bernard Brooks, Garland Marshall. J. Computer-Aided Molecular Design  20(2): 109-130 (2006)
• Structural Stability and Dynamics of an Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35   Zheng J, Ma B, Tsai C-J, Nussinov R. Biophysical Journal  91: 824-833 (2006)
• Development of a substrate-based cyclic phosphopeptide inhibitor of protein phosphatase 2Cδ, Wip1  Yamaguchi H, Durell SR, Feng H, Bai Y, Anderson CW, Appella E. Biochemistry 45(44):13193-202 (2006)
• Computational Study of the Fibril Organization of Polyglutamine Repeats Reveals a Common Motif Identified in β-Helices  David Zanuy, Kannan Gunasekaran, Arthur M. Lesk and Ruth Nussinov J. Mol. Biol. 358(1):330-345 (2006)
• Dynamical motions of lipids and a finite size effect in simulations of bilayers.  Klauda JB, Brooks BR, Pastor RW. J Chem Phys.  125(14):144710 (2006)

• The Stability of Monomeric Intermediates Controls Amyloid Formation: A{beta}25-35 and its N27Q Mutant.  Ma B, Nussinov R. Biophys J.  90(10):3365-74 (2006)
• Interpretation of Data and Identification of Information are Sine Qua Non for Modern Digital Information Services   Ying He, and Mehmet Kayaalp. AMIA Annu Symp Proc.  : 946 (2006)
• Rat toxicogenomic study reveals analytical consistency across microarray platforms   Guo, L, Edward K Lobenhofer, Charles Wang, Richard Shippy, Stephen C Harris, Lu Zhang, Nan Mei, Tao Chen, Damir Herman, Federico M Goodsaid, Patrick Hurban, Kenneth L Phillips, Jun Xu, Xutao Deng, Yongming Andrew Sun, Weida Tong, Yvonne P Dragan & Leming Shi Nature Biotechnology.  24: 1162 - 1169 (2006)
• Parallel Computation and Visualization Tools for Codetermination Analysis of Multivariate Gene Expression Relations  Edward B. Suh, Edward R. Dougherty, Seungchan Kim, Michael L. Bittner, Yidong Chen, Daniel E. Russ and Robert L. Martino Computational and Statistical Approaches to Genomics (2006)
• SCIMS: A new algorithm for associating anticancer drug mechanisms with gene ontology categories  Gabriel S. Eichler, Mark Reimers and John N. Weinstein Proc. Amer. Assoc. Cancer Res. 47:1565 (2006)
• Nucleation and cavitation of spherical, cylindrical, and slablike droplets and bubbles in small systems.   L. G. MacDowell, V. K. Shen, and J. R. Errington. J. Chem. Phys  125(3): 34705 (2006)
• Altered HIV-1 Gag protein interactions with cyclophilin A (CypA) on the acquisition of H219Q and H219P substitutions in the CypA binding loop.   Gatanaga H, Das D, Suzuki Y, Yeh DD, Hussain KA, Ghosh AK, Mitsuya H. J Biol Chem.  281(2):1241-50 (2006)
• Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure   Jie Zheng, Buyong Ma and Ruth Nussinov. Phys. Biol.  3: 1478-3975 (2006)
• Impact of Cis-proline analogs on peptide conformation   Ye Che, Garland R. Marshall. Biopolymers  81(5): 392 - 406 (2006)
• Coarse-grained strategy for modeling protein stability in concentrated solutions. II: phase behavior.   V. K. Shen, J. K. Cheung, J. R. Errington, and T. M. Truskett. Biophys J  90:1949 (2006)
• The influence of tumor oxygenation on 18 F-FDG(Fluorine-18 Deoxyglucose) uptake: A mouse study using positron emission tomography(PET)   Linda W Chan, Sebastien Hapdey, Sean English, Jurgen Seidel, Joann Carson, Anastasia L Sowers, Murali C Krishna, Michael V Green, James B Mitchell and Stephen L Bacharach. Radiation Oncology  1:3 (2006)
• A Missense Mutation in the Seven-transmembrane Domain of the Human Ca2+ Receptor Converts a Negative Allosteric Modulator into a Positive Allosteric Modulator   Jianxin Hu, Jiankang Jiang, Stefano Costanzi, Craig Thomas, Wu Yang, Jean H. M. Feyen, Kenneth A. Jacobson, and Allen M. Spiegel. J. Biol. Chem  Vol. 281(3): 21558-21565 (2006)
• The histone database: A comprehensive resource for histones and histone fold-containing proteins   Marino-Ramirez, L., Hsu, B., Baxevanis, A. D. and Landsman, D Proteins  62:838-842 (2006)
• Structural and Molecular Interactions of CCR5 Inhibitors with CCR5.   Maeda K, Das D, Ogata-Aoki H, Nakata H, Miyakawa T, Tojo Y, Norman R, Takaoka Y, Ding J, Arnold GF, Arnold E, Mitsuya H. J Biol Chem.  281(18):12688-98 (2006)
• ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification.   Sam V, Tai CH, Garnier J, Gibrat JF, Lee B, Munson PJ. BMC Bioinformatics  7:206 (2006)
• Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data.   Fung HC, Scholz S, Matarin M, Simon-Sanchez J, Hernandez D, Britton A, Gibbs JR, Langefeld C, Stiegert ML, Schymick J, Okun MS, Mandel RJ, Fernandez HH, Foote KD, Rodriguez RL, Peckham E, De Vrieze FW, Gwinn-Hardy K, Hardy JA, Singleton A. Lancet Neurol. 5:911-916 (2006)

• Multiple independent evolutionary solutions to core histone gene regulation   Marino-Ramirez L, Jordan IK, Landsman D. Genome Biol.  7(12):R122 (2006)
• Comparison of the Human and Worm p53 Structures Suggests a Way for Enhancing Stability  Pan Y, Ma B, Levine AJ, Nussinov R. Biochemistry  45 (12):3925 -3933 (2006)
• PET imaging of the dopamine transporter with 18F-FECNT: a polar radiometabolite confounds brain radioligand measurements.   Zoghbi SS, Shetty HU, Ichise M, Fujita M, Imaizumi M, Liow JS, Shah J, Musachio JL, Pike VW, Innis RB. J. Nucl. Med  47(3):520-7 (2006)
• Appropriateness of some resampling-based inference procedures for assessing performance of prognostic classifiers derived from microarray data.   Lusa L, McShane LM, Radmacher MD, Shih JH, Wright GW, Simon R. Stat Med.  26(5):1102-13 (2006)
• Co-evolutionary Rates of Functionally Related Yeast Genes   Leonardo Marino-Ramirez, Olivier Bodenreider, Natalie Kantz and I. King Jordan Evolutionary Bioinformatics, Donald Forsdyke (ed), Springer (2006)
• Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast.  Balaji S, Babu MM, Iyer LM, Luscombe NM, Aravind L. J. Mol. Biol. 360(1):213-27 (2006)
• Automatic colonic polyp detection using multiobjective evolutionary techniques   Jiang Li, Adam Huang, Jianhua Yao, and Ingmar Bitter, Nicholas Petrick, Ronald M. Summers, Perry J. Pickhardt, J. Richard Choi. In Medical Imaging 2006: Image Processing, Joseph M. Reinhardt, Josien P. W. Pluim (eds) (2006)
• Backbone Conformational Preferences and Pseudorotational Ring Puckering of 1-Aminocyclopentane-1-carboxylic Acid  Aleman C, Zanuy D, Casanovas J, Cativiela C, Nussinov R. J Phys Chem B  110 (42): 21264 -21271 (2006)

2005 (34 publications)

• Score statistics of global sequence alignment from the energy distribution of a modified directed polymer and directed percolation problem   Sardiu ME, Alves G, Yu Y-K. Phys. Rev. E  72: 061917 (2005)
• Agonist-Induced Conformational Changes in Thyrotropin-Releasing Hormone Receptor Type I: Disulfide Cross-Linking and Molecular Modeling Approaches.   Huang W, Osman R, Gershengorn MC. Biochemistry.  44(7):2419-2431 (2005)
• CD4 binding partially locks the bridging sheet in gp120 but leaves the β2/3 strands flexible  Pan Y, Ma B, Nussinov R. J Mol Biol.  350(3):514-27 (2005)
• Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics  Alves G, Yu Y-K. Bioinformatics  21(19):3726-3732 (2005)
• Molecular Dynamics Simulations of Alzheimer's beta-Amyloid Protofilaments  Buchete NV, Tycko R, and Hummer G. Mol. Biol.  353 (4): 804-821 (2005)
• PET imaging of brain with the beta-amyloid probe, [11C]6-OH-BTA-1, in a transgenic mouse model of Alzheimer's disease.   Toyama H, Ye D, Ichise M, Liow JS, Cai L, Jacobowitz D, Musachio JL, Hong J, Crescenzo M, Tipre D, Lu JQ, Zoghbi S, Vines DC, Seidel J, Katada K, Green MV, Pike VW, Cohen RM, Innis RB. Eur. J. Nucl. Med. Mol. Imaging  32(5):593-600 (2005)
• Human P2Y(6) receptor: molecular modeling leads to the rational design of a novel agonist based on a unique conformational preference.  Costanzi S, Joshi BV, Maddileti S, Mamedova L, Gonzalez-Moa MJ, Marquez VE, Harden TK, Jacobson KA. J Med Chem.  48(26):8108-11 (2005)
• In the quest for stable rescuing mutants of p53: computational mutagenesis of flexible loop L1.   Pan Y, Ma B, Venkataraghavan RB, Levine AJ, Nussinov R. Biochemistry 44(5):1423-32 (2005)
• Adjacent Gauche Stabilization in Linear Alkanes: Implications for Polymer Models and Conformational Analysis  Jeffery B. Klauda, Richard W. Pastor, and Bernard R. Brooks J. Phys. Chem.  109(33):15684-15686 (2005)
• An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer  Klauda J, Brooks BR, MacKerell AD, Venable RM, Pastor RW. J. Phys. Chem. B  109 (11): 5300 -5311 (2005)
• Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder.   Tsai HH, Reches M, Tsai CJ, Gunasekaran K, Gazit E, Nussinov R. Proc Natl Acad Sci U S A.  102(23):8174-9 (2005)
• A Molecular Dynamics Study of the Response of Lipid Bilayers and Monolayers to Trehalose   Skibinsky A, Venable RM, Pastor RW. Biophys J  89: 4111-4121 (2005)
• Sequential testing for efficacy in clinical trials with non-transient effects   James F. Troendle, Aiyi Liu, Chengqing Wu, Kai F. Yu. Statistics in Medicine  24(21):3239 - 3250 (2005)
• Amino Acid Side Chain Interactions in the Presence of Salts  Sergio A. Hassan J. Phys. Chem.  109(46):21989-21996 (2005)
• Distinguishing Modes of Eukaryotic Gradient Sensing  R. Skupsky, W. Losert, and R. J. Nossal Biophys. J.  89(4):2806-2823 (2005)
• Accurate Determination of Leucine and Valine Side-chain Conformations using U-[15 N/13 C/2H]/[1H-(methine/methyl)-Leu/Val] Isotope Labeling, NOE Pattern Recognition, and Methine Cγ-Hγ/Cβ-Hβ Residual Dipolar Couplings: Application to the 34-kDa Enzyme IIAChitobiose  Chun Tang, Junji Iwahara and G. Marius Clore J. Biomol. NMR 33(2):1573-5001 (2005)
• Multiple comparisons between two groups on multiple Bernoulli outcomes while accounting for covariates.  JF Troendle Stat. Med. 24(23):3581-91 (2005)
• Polyproline and the “spectroscopic ruler” revisited with single-molecule fluorescence ?   Schuler B, Lipman EA, Steinbach PJ, Kumke M, Eaton WA. Proc Natl Acad Sci U S A.   102(8):2754-9 (2005)
• Measurement of Ribose Carbon Chemical Shift Tensors for A-form RNA by Liquid Crystal NMR Spectroscopy   David L. Bryce, Alexander Grishaev, and Ad Bax. J. Am. Chem. Soc  127 (20):7387 -7396 (2005)
• Molecular Dynamics Simulations of the Influenza Hemagglutinin Fusion Peptide in Micelles and Bilayers: Conformational Analysis of Peptide and Lipids   Lague P, Roux B, Pastor RW. J. Mol. Biol  354: 1129-1141 (2005)
• From quantum chemistry and the classical theory of polar liquids to continuum approximations in molecular mechanics calculations.   SA Hassan, EL Mehler. Int.Quantum Chem.  102(5): 986 - 1001 (2005)
• A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single β-sheet model with a small hydrophobic core.   Haspel N, Zanuy D, Ma B, Wolfson H, Nussinov R. J Mol Biol.  345(5):1213-27 (2005)
• Comparison of the protein-protein interfaces in the p53-DNA crystal structures: towards elucidation of the biological interface.   Ma B, Pan Y, Gunasekaran K, Venkataraghavan RB, Levine AJ, Nussinov R. Proc Natl Acad Sci U S A.  102(11):3988-93 (2005)
• Comprehensive analysis of heterochromatin-and RNAi-mediated epigenetic control of the fission yeast genome  Cam H, Sugiyama T, Chen ES, Chen X, Fitzgerald P, Grewal SI. Nat Genet.  37: 809 - 819 (2005)
• Modelling longitudinal semicontinuous emesis volume data with serial correlation in an acupuncture clinical trial  Paul S. Albert and Joannie Shen Appl. Statist.  54(4):707-720 (2005)
• Ion Transport through Membrane-Spanning Nanopores Studied by Molecular Dynamics Simulations and Continuum Electrostatics Calculations   Christine Peter and Gerhard Hummer. Biophys. J  89:2222-2234 (2005)
• Identification and functional outcome of mRNAs associated with RNA-binding protein TIA-1   Lopez de Silanes I, Galban S, Martindale JL, Yang X, Mazan-Mamczarz K, Indig FE, Falco G, Zhan M, Gorospe M. Mol. Cell. Biol.  25(21):9520-31 (2005)
• Utilization of a Common Pathway for the Synthesis of High Affinity Macrocyclic Grb 2 SH 2 Domain-Binding Peptide Mimetics That Differ in the Configuration at One Ring Junction  Zhen-Dan Shi, Rajeshri G. Karki, Karen M. Worthy, Lakshman K. Bindu, Marc C. Nicklaus, Robert J. Fisher, and Terrence R. Burke Jr. Chem. & Biodiversity 2:447-456 (2005)
• Solution Structure of Enzyme IIAChitobiose from the N, N'-Diacetylchitobiose Branch of the Escherichia coli Phosphotransferase System ?   Chun Tang, David C. Williams, Jr., Rodolfo Ghirlando, and G. Marius Clore. J. Biol. Chem  280, Issue 12:11770-11780 (2005)
• Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: Calculation of structural and dynamic properties.   Li X, Hassan SA, Mehler EL. Proteins.  60(3):464 - 484 (2005)
• Genome-wide assembly and analysis of alternative transcripts in mouse.  Sharov AA, Dudekula DB, Ko MSH. Genome Res.  15:748-754 (2005)
• Computed tomographic virtual colonoscopy computer-aided polyp detection in a screening population.   Summers RM, Yao J, Pickhardt PJ, Franaszek M, Bitter I, Brickman D, Krishna V, Choi JR. Gastroenterology  129(6):1832-44 (2005)
• Titin PEVK segment: charge-driven elasticity of the open and flexible polyampholyte.  Forbes JG, Jin AJ, Ma K, Gutierrez-Cruz G, Tsai WL, Wang K. J Muscle Res Cell Motil. 26(6-8):291-301 (2005)
• Quantification of brain phosphodiesterase 4 in rat with (R)-[11C]Rolipram-PET.   Fujita M, Zoghbi SS, Crescenzo MS, Hong J, Musachio JL, Lu JQ, Liow JS, Seneca N, Tipre DN, Cropley VL, Imaizumi M, Gee AD, Seidel J, Green MV, Pike VW, Innis RB. Neuroimage  26(4):1201-10 (2005)

2004 (47 publications)

• Nucleic acid transport through carbon nanotube membranes   In-Chul Yeh and Gerhard Hummer. PNAS 101(33): 12177-12182 (2004)
• Performance of a genetic algorithm for mass spectrometry proteomics   Jeffries, NO. BMC Bioinformatics  5:180 (2004)
• Combinatorial modeling of protein folding kinetics: free energy profiles and rates   Eric R. Henry and William A. Eaton Chemical Physics 307:163-185 (2004)
• Dynamics of proton transfer in bacteriorhodopsin.   Lee YS, Krauss M. J Am Chem Soc.  126(7):2225-30 (2004)
• Exploring peptide energy landscapes: A test of force fields and implicit solvent models.   Steinbach PJ. Proteins  57(4):665-677 (2004)
• Correcting log ratios for signal saturation in cDNA microarrays.   Dodd LE, Korn EL, McShane LM, Chandramouli GV, Chuang EY. Bioinformatics  20(16):2685-93 (2004)
• An efficient algorithm for generating two-way contingency tables with fixed marginal totals and arbitrary mean proportions, with applications to permutation tests   Craig Borkowf. Comp. Stat. and Data Analysis  44(3): 431-449 (2004)
• Modulating Functional Loop Movements: The Role of Highly Conserved Residues in the Correlated Loop Motions  Kannan Gunasekaran, Ruth Nussinov Chem.Bio.Chem. 5(2):224-230 (2004)
• Side chain interactions determine the amyloid organization: a single layer β-sheet molecular structure of the calcitonin peptide segment 15-19  David Zanuy, Nurit Haspel, Hui-Hsu (Gavin) Tsai, Buyong Ma, Kannan Gunasekaran, Haim J Wolfson and Ruth Nussinov Physical Biology 1(2):89-99 (2004)
• How Much Backbone Motion in Ubiquitin Is Required To Account for Dipolar Coupling Data Measured in Multiple Alignment Media as Assessed by Independent Cross-Validation?  G. Marius Clore and Charles D. Schwieters J. Am. Chem. Soc. 126(9):2923-2938 (2004)
• Structure and Reaction in the Active Site of Mammalian Adenylyl Cyclase  Yong-Sok Lee and Morris Krauss J. Phys. Chem. B 108(14):4508-4515 (2004)
• Large scale validation of a computer aided polyp detection algorithm for CT colonography using cluster computing  I Bitter, JE Brown, D Brickman, RM Summers Medical Imaging 2004 (2004)
• Quantum Chemical Calculations and Mutational Analysis Suggest Heat Shock Protein 90 Catalyzes Trans- Cis Isomerization of Geldanamycin   Lee YS, Marcu MG, Neckers L. Chem Biol. 11(7):991-8 (2004)
• Clustering of DNA sequences in human promoters.   FitzGerald PC, Shlyakhtenko A, Mir AA, Vinson C. Genome Research  14(8):1562-74 (2004)
• Amplitudes of Protein Backbone Dynamics and Correlated Motions in a Small α/β Protein: Correspondence of Dipolar Coupling and Heteronuclear Relaxation Measurements  G. Marius Clore and Charles D. Schwieters Biochemistry 43(33):10678-10691 (2004)
• Semirandom Sampling to Detect Differentiation-Related and Age-Related Epigenome Remodeling   Valya R. Russanova, Tazuko H. Hirai and Bruce H. Howard J. Gerontology  59:1221-1233 (2004)
• Three Roads to Islet Bursting: Emergent Oscillations in Coupled Phantom Bursters   Charles L. Zimliki, David Mears and Arthur Sherman. Biophys. J  87:193-206 (2004)
• β-Hairpin Folding Mechanism of a Nine-Residue Peptide Revealed from Molecular Dynamics Simulations in Explicit Water.   Wu X and Bernard R. Brooks. Biophys J. 86(4):1946-58 (2004)
• Visualization of α-helical features in a density map constructed using 9 molecular images of the 1.8 MDa icosahedral core of pyruvate dehydrogenase  Borgnia MJ, Shi D, Zhang P, Milne JL J. Struct. Biol.  147(2):136-45 (2004)
• A Model of Inverse Agonist Action at Thyrotropin-Releasing Hormone Receptor Type 1: Role of a Conserved Tryptophan in Helix 6.   Lu X, Huang W, Worthington S, Drabik P, Osman R, Gershengorn MC. Mol Pharmacol. 66(5):1192-200 (2004)
• Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function   Goonesekere NC, Lee B. Nucleic Acids Res  32(9):2838-43 (2004)
• Absolute quantification of regional cerebral glucose utilization in mice by 18F-FDG small animal PET scanning and 2-14C-DG autoradiography.   Toyama H, Ichise M, Liow JS, Modell KJ, Vines DC, Esaki T, Cook M, Seidel J, Sokoloff L, Green MV, Innis RB. J. Nucl. Med  45(8):1398-405 (2004)
• Rydberg-London potential for diatomic molecules and unbonded atom pairs  Kevin Cahill, V. Adrian Parsegian J. Chem. Phys.  121:10839 (2004)
• Statistical analysis of over-represented words in human promoter sequences.   Marino-Ramirez L, Spouge JL, Kanga GC, Landsman D. Nucleic Acids Res.  32(3):949-58 (2004)
• Comparative analysis of apicomplexa and genomic diversity in eukaryotes.   Templeton TJ, Iyer LM, Anantharaman V, Enomoto S, Abrahante JE, Subramanian GM, Hoffman SL, Abrahamsen MS, Aravind L. Genome Res.  14(9):1686-95 (2004)
• Peptide sequence and amyloid formation: molecular simulations and experimental study of a human islet amyloid polypeptide fragment and its analogs   Zanuy D, Porat Y, Gazit E, Nussinov R. Structure (Camb).  12(3):439-55 (2004)
• Synthesis and evaluation of two 18F-labeled 6-iodo-2-(4'-N,N-dimethylamino)phenylimidazo[1,2-a]pyridine derivatives as prospective radioligands for beta-amyloid in Alzheimer's disease.  Cai L, Chin FT, Pike VW, Toyama H, Liow JS, Zoghbi SS, Modell K, Briard E, Shetty HU, Sinclair K, Donohue S, Tipre D, Kung MP, Dagostin C, Widdowson DA, Green M, Gao W, Herman MM, Ichise M, Innis RB. J. Med. Chem  47(9):2208-18 (2004)
• Mechanistic insights from a refined three-dimensional model of integrin alphaIIbbeta3.   Filizola M, Hassan SA, Artoni A, Coller BS, Weinstein H. J Biol Chem  279(23):24624-30 (2004)
• In silico protein design by combinatorial assembly of protein building blocks   Hui-Hsu (Gavin) Tsai, Chung-Jung Tsai, Buyong Ma and Ruth Nussinov. Protein Science  13:2753-2765 (2004)
• The stability and dynamics of the human calcitonin amyloid peptide DFNKF.   Tsai HH, Zanuy D, Haspel N, Gunasekaran K, Ma B, Tsai CJ, Nussinov R. Biophys J.  87(1):146-58 (2004)

• Mapping Development-Related and Age-Related Chromatin Remodeling by a High Throughput ChIP-HPLC Approach   Valya R. Russanova, Tazuko H. Hirai, Andrei V. Tchernov and Bruce H. Howard J. Gerontology  59:1234-1243 (2004)
• An Example of Slow Convergence of the Bootstrap in High Dimensions.   Troendle J.F.; Korn E.L.; McShane L.M. The American Statistician  58(1): 25-29 (2004)
• Discriminating the Helical Forms of Peptides by NMR and Molecular Dynamics Simulation   Daron I. Freedberg, Richard M. Venable, Angelo Rossi, Thomas E. Bull, and Richard W. Pastor. J. Am. Chem. Soc 126:10478-10484 (2004)
• Impact of Azaproline on Peptide Conformation   Ye Che and Garland Marshall. J. Org. Chem  69 (26): 9030 -9042 (2004)
• Reversible proton transfer dynamics in bacteriorhodopsin  Lee YS and Krauss M. J. Mol. Stru.  700(3):243-246 (2004)
• Model of full-length HIV-1 integrase complexed with viral DNA as template for anti-HIV drug design.   Karki RG, Tang Y, Burke TR Jr, Nicklaus MC. J Comput Aided Mol Des.  18(12):739-60 (2004)
• Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms   Robert J Clifford, Michael N Edmonson, Cu Nguyen, Kenneth J Buetow. Bioinformatics  20(7):1006-1014 (2004)
• Controlling the number of false discoveries: application to high-dimensional genomic data   Korn EL, Troendle JF, McShane LM, and Simon R. Journal of Statistical Planning and Infe  124(2):379-398 (2004)
• Pressure-Based Long-Range Correction for Lennard-Jones Interactions in Molecular Dynamics Simulations: Application to Alkanes and Interfaces   Patrick Lague, Richard W. Pastor, Bernard R Brooks. J. Phys. Chem. B 108:363-368 (2004)
• Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain.   Pan Y, Ma B, Keskin O, Nussinov R. J Biol Chem  16;279(29):30523-30 (2004)
• Diffusion and Electrophoretic Mobility of Single-Stranded RNA from Molecular Dynamics Simulations   In-Chul Yeh and Gerhard Hummer. Biophys. J  86:681-689 (2004)
• Insights into amyloid structural formation and assembly through computational approaches.   Zanuy D, Gunasekaran K, Ma B, Tsai HH, Tsai CJ, Nussinov R. Amyloid.  11(3):143-61 (2004)
• Identifying multiple changepoints in heterogeneous binary data with an application to molecular genetics.  Albert PS, Hunsberger SA, Hu N, Taylor PR. Biostatistics  5(4):515-529 (2004)
• A cautionary note on the robustness of latent class models for estimating diagnostic error without a gold standard.  Albert PS, Dodd LE. Biometrics  60(2):427-35 (2004)
• Evaluation of anesthesia effects on [18F]FDG uptake in mouse brain and heart using small animal PET.   Toyama H, Ichise M, Liow JS, Vines DC, Seneca NM, Modell KJ, Seidel J, Green MV, Innis RB. Nucl. Med. Biol.  31(2):251-6 (2004)
• Release factors eRF1 and RF2: a universal mechanism controls the large conformational changes.   Ma B, Nussinov R. J Biol Chem.  279(51):53875-85 (2004)

• Intermolecular Potentials of Mean Force of Amino Acid Side Chain Interactions in Aqueous Medium  Hassan SA J. Phys. Chem. B.  108 (50):19501-19509 (2004)

2003 (20 publications)

• Synthesis and Conformational Analysis of a Locked Analogue of Carbovir Built on a Bicyclo [3.1. 0]-hex-2-enyl template.   Choi Y, Sun G, George C, Nicklaus MC, Kelley JA, Marquez VE. Nucleotides Nucleic Acids.  22(12):2077-91 (2003)
• Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL.   Zanuy D, Ma B, Nussinov R. Biophys J.  84(3):1884-94 (2003)
• Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase  H. Lee Woodcock, Milan Hodoŝĉek, Paul Sherwood, Yong S. Lee, Henry F. Schaefer III and Bernard R. Brooks Theoretical Chemistry Accounts 109(3):140-148 (2003)
• Interdependence of Backbone Flexibility, Residue Conservation, and Enzyme Function: A Case Study on β1, 4-Galactosyltransferase-I   Gunasekaran K, Ma B, Ramakrishnan B, Qasba PK, Nussinov R. Biochemistry.  42(13):3674-87 (2003)
• A Random Effects Transition Model For Longitudinal Binary Data With Informative Missingness   Paul S Albert & Dean Follmann. Statistica Neerlandica  57 Issue 1:100-111, (2003)
• Binding and Hydrolysis of Ampicillin in the Active Site of a Zinc Lactamase  M. Krauss, N. Gresh, and J. Antony J. Phys. Chem B 107(5):1215-1229 (2003)
• A super-linear minimization scheme for the nudged elastic band method  Jhih-Wei Chu, Bernhardt L. Trout, Bernard R Brooks J. Chem. Phys. 119:12708-12717 (2003)
• On the kinematics of protein folding   Sean Cahill, Michael Cahill, Kevin Cahill. J. Comp. Chem  Volume 24, Issue 11: Pages 1364-1370 (2003)
• Triggering loops and enzyme function: identification of loops that trigger and modulate movements.   Gunasekaran K, Ma B, Nussinov R. J Mol Biol.  332(1):143-59 (2003)
• The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22-27 and 22-29.  Zanuy D, Nussinov R. J Mol Biol.  329(3):565-84 (2003)
• Docking of Protein-Protein Complexes on the Basis of Highly Ambiguous Intermolecular Distance Restraints Derived from 1HN/15N Chemical Shift Mapping and Backbone 15N/1H Residual Dipolar Couplings Using Conjoined Rigid Body/Torsion Angle Dynamics  G. Marius Clore and Charles D. Schwieters J. Am. Chem. Soc. 125(10):2902-2912 (2003)
• Modeling tumor growth with random onset.  Albert PS, Shih JH. Biometrics  59(4):897-906 (2003)
• Molecular dynamics simulations of the unfolding of β2-microglobulin and its variants   Ma B, Nussinov R. Protein Eng.  16(8):561-75 (2003)
• Application of NMR, molecular simulation, and hydrodynamics to conformational analysis of trisaccharides   Dixon AM, Venable R, Widmalm G, Bull TE, Pastor RW. Biopolymers  69(4):448-60 (2003)
• A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy.   Wu X, Milne JL, Borgnia MJ, Rostapshov AV, Subramaniam S, Brooks BR. J Struct Biol.  141(1):63-76 (2003)

• Transcriptome analysis of mouse stem cells and early embryos.   Sharov AA, Piao Y, Matoba R, Dudekula DB, Qian Y, VanBuren V, Falco G, Martin PR, Stagg CA, Bassey UC, Wang Y, Carter MG, Hamatani T, Aiba K, Akutsu H, Sharova L, Tanaka TS, Kimber WL, Yoshikawa T, Jaradat SA, Pantano S, Nagaraja R, Boheler KR, Taub D, Hodes RJ, Longo DL, Schlessinger D, Keller J, Klotz E, Kelsoe G, Umezawa A, Vescovi AL, Rossant J, Kunath T, Hogan BL, Curci A, D'Urso M, Kelso J, Hide W, Ko MS. PLoS Biol.  1(3):E74 (2003)
• Parallel computation for coefficients of determination in the context of multivariate gene-expression analysis  Edward B Suh, Daniel E Russ, Edward R Dougherty, Seungchan Kim, Michael L Bittner, Yidong Chen, Robert L. Martino in Biocomputing, editor Phillip A Laplante (2003)
• Direct Observation of the Folding and Unfolding of a Hairpin in Explicit Water through Computer Simulation.   Xiongwu Wu, Shaomeng Wang, and Bernard R. Brooks. J. Am. Chem. Soc.  124(19):5282-3 (2003)
• Microarray reveals differences in both tumors and vascular specific gene expression in de novo CD5+ and CD5− diffuse large B-cell lymphomas  Tohru Kobayashi, Motoko Yamaguchi, Seungchan Kim, Jun Morikawa, Shoko Ogawa, Satoshi Ueno, Edward Suh, Edward Dougherty, Ilya Shmulevich, Hiroshi Shiku, and Wei Zhang Cancer Research 63:60 (2003)
• Hydrogen bonding interactions between aldose reductase complexed with NADP(H) and inhibitor tolrestat studied by molecular dynamics simulations and binding assay   Lee YS, Hodoscek M, Kador PF, Sugiyama K. Chem. Biol. Interact  143-144:307-16 (2003)

2002 (12 publications)

• A preliminary transcriptome map of non-small cell lung cancer.   Fujii T, Dracheva T, Player A, Chacko S, Clifford R, Strausberg RL, Buetow K, Azumi N, Travis WD, Jen J. Cancer Res.  62(12):3340-6 (2002)
• Features of the NIH ATLAS Small Animal PET Scanner and Its Use with a Coaxial Small Animal Volume CT Scanner  Seidel J, Vacquero JJ, Pascua J, Desco M, Johnson CA, Green M IEEE International Symposium on Biomedic, Washington, DC, 2002:TP-P1.9 (2002)
• Hydrophobicity Maps of the N-Peptide Coiled Coil of HIV-1 gp41  Xavier Siebert and Gerhard Hummer Biochemistry 41(9):2956-2961 (2002)
• A Latent Autoregressive Model for Longitudinal Binary Data Subject to Informative Missingness  Albert, PS, Follmann, DA, Wang, SA, Suh, EB. Biometrics  58 Issue 3:631-642 (2002)
• Micelle-bound conformation of a hairpin-forming peptide: combined NMR and molecular dynamics study   Dixon AM, Venable RM, Pastor RW, Bull TE. Biopolymers  65(4):284-98 (2002)
• Structure Activity of 3-Aryl-1, 3-diketo-Containing Compounds as HIV-1 Integrase Inhibitors1  Godwin C. G. Pais, Xuechun Zhang, Christophe Marchand, Nouri Neamati, Kiriana Cowansage, Evguenia S. Svarovskaia, Vinay K. Pathak, Yun Tang, Marc Nicklaus, Yves Pommier, and Terrence R. Burke, Jr. J. Med. Chem.  45(15):3184-3194 (2002)
• Parametric and semiparametric approaches to testing for seasonal trend in serial count data.   Hunsberger S, Albert PS, Follmann DA, Suh E. Biostatistics.  3(2):289-98 (2002)
• Fast-growth Thermodynamic Integration: Results for Sodium Ion Hydration  G. Hummer Molecular Simulation 28:81-90 (2002)
• Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent.   Yeh IC, Hummer G. J Am Chem Soc.  124(23):6563-8 (2002)
• Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ_16-22, Aβ_16-35, and Aβ_10-35): Sequence effects  Buyong Ma and Ruth Nussinov PNAS 99(22):14126-14131 (2002)
• Assembly, verification, and initial annotation of the NIA mouse 7.4 K cDNA clone set   VanBuren V, Piao Y, Dudekula DB, Qian Y, Carter MG, Martin PR, Stagg CA, Bassey UC, Aiba K, Hamatani T, Kargul GJ, Luo AG, Kelso J, Hide W, Ko MS. Genome Res.  12(12):1999-2003 (2002)

• Mutant deoxynucleotide carrier is associated with congenital microcephaly.   Rosenberg MJ, Agarwala R, Bouffard G, Davis J, Fiermonte G, Hilliard MS, Koch T, Kalikin LM, Makalowska I, Morton DH, Petty EM, Weber JL, Palmieri F, Kelley RI, Schaffer AA, Biesecker LG. Nat Genet. 32(1):175-9 (2002)

2001 (6 publications)

• Circularly permuted proteins in the protein structure database   Jongsun Jung and Byungkook Lee. Protein Science  10:1881-1886 (2001)
• Simultaneous Determination of Orientational and Order Parameter Distributions from NMR Spectra of Partially Oriented Model Membranes   Edward Sternin, Hartmut Schafer, Ivan V. Polozov and Klaus Gawrisch. J. Mag. Res  149(1): 110-113 (2001)
• Parallel Computing Methods for Analyzing Gene Expression Relationships  Edward B. Suh, Edward R. Dougherty, Seungchan Kim, Daniel E. Russ, and Robert L. Martino Proc. SPIE 4266:213-221 (2001)
• Fast-growth thermodynamic integration: Error and efficiency analysis  G. Hummer J. Chem. Phys. 114(17):7330 (2001)
• PET, CT, and MR Image Registration of the Rat Brain and Skull  Juan Josè Vaquero, Manuel Desco, Javier Pascau, Andrès Santos, E, Injae Lee, Jürgen Seidel, and Michael V. Green IEEE Transactions on Nuclear Science 48(4):1440-1445 (2001)
• Crystal structure of the 14-3-3ζ: serotonin N-acetyltransferase complex: a role for scaffolding in enzyme regulation   Obsil T, Ghirlando R, Klein DC, Ganguly S, Dyda F. Cell.  105(2):257-67 (2001)

2000 (3 publications)

• General nonlinear framework for the analysis of gene interaction via multivariate expression arrays  Kim S, Dougherty ER, Bittner ML, Chen Y, Sivakumar K, Meltzer P, Trent JM. J. Biomed. Opt. 5(4):411-24 (2000)
• Multivariate measurement of gene expression relationships.   Kim S, Dougherty ER, Chen Y, Sivakumar K, Meltzer P, Trent JM, Bittner M. Genomics.  67(2):201-9 (2000)
• Theoretical formalism for kinesin motility I. Bead movement powered by single one-headed kinesins.   Chen Y. Biophys J.  78(1):313-21 (2000)

1999 (1 publications)

• Expression profiling using cDNA microarrays.   Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM. Nat Genet.  21(1 Suppl):10-4 Review. (1999)