If you have published research that has made significant use of the Helix Systems resources, please let us know by sending email to staff@helix.nih.gov

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-KuoYu Bulletin of the American Physical Society 54:P40.00008 (2009)

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, Epub ahead of print Dec 2 (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, doi: 10.1016/j.jspi.2008.11.007 (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 structure. 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., Published online 27 Nov (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)
• 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, published online 1 Dec (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, published online 25 Nov (2008)
• GRL-02031: A Novel Nonpeptidic Protease Inhibitor (PI) Containing A Stereochemically Defined Fused Cyclopentanyltetrahydrofuran (Cp-THF) 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., published online 27 Oct (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)
• Bayesian Inference for Smoking Cessation with a Latent Cure State Luo S, Crainiceanu, CM, Louis TA, Chatterjee, N Biometrics, accepted (2008)

• Models of Toxic {beta}-sheet Channels of Protegrin-1 (PG-1) Suggest a Common Subunit Organization Motif Shared with Toxic Alzheimer {beta}-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, Academic Press (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 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)

• NEIBank: Genomics and bioinformatics resources for vision research Graeme Wistow, Katherine Peterson, James Gao, Patee Buchoff, Cynthia Jaworski, Catherine Bowes-Rickman, Jessica N. Ebright, Michael A. Hauser, and David Hoover Molecular Vision 14:1327-1337 (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 4(4):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)
• 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)
• 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 gp120 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 data 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 J. Med. Phys. 35(4):1377-86 (2008)
• beta(2)-Microglobulin Amyloid Fragment Organization and Morphology and Its Comparison to Abeta 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 amyloid 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

• 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{beta}17-42 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)
• Molecular and functional analyses of a novel class I secretory nuclease from the human pathogen, Leishmania donovani. Joshi MB, Dwyer DM. J. Biol. Chem.  282(13):10079-95 (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)
• 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)
• Spiral structure of Escherichia coli HU{alpha}beta provides foundation for DNA supercoiling Fusheng Guo and Sankar Adhya PNAS 104:4309-4314 (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. g Coskuner O. J. Chem. Phys  127(1):015101 (2007)
• Structure and dynamics of parallel beta-sheets, hydrophobic core, and loops in Alzheimer's A beta fibrils. Buchete NV, Hummer G. Biophys J.  92(9):3032-9 (2007)
• Molecular dynamics simulation of the P2Y14 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)
• 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)
• 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 beta-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)
• Probes for Narcotic Receptor Mediated Phenomena. Hiebel AC, Lee YS, Bilsky E, Giuvelis D, Deschamps JR, Parrish DA, Aceto MD, May EL, Harris LS, Coop A, Dersch CM, Partilla JS, Rothman RB, Cheng K, Jacobson AE, Rice KC. J Med Chem.  50(16):3765-3776 (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 beta-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)
• Optimized clonotypic analysis of T-cell receptor repertoire in immune reconstitution. Packer AN, Muraro PA. Exp. Hematol. 35(3):516-21 (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 alpha,alpha- diphenylglycine. Casanovas J, Zanuy D, Nussinov R, Aleman C. J. Org. Chem.  16;72(6):2174-81 (2007)
• Identification and Biochemical Characterization of Unique Secretory Nucleases of the Human Enteric Pathogen, Entamoeba histolytica Glen C. McGugan, Jr., Manju B. Joshi, and Dennis M. Dwyer J. Biol. Chem.  282(43):31789-31802 (2007)
• Use of constrained synthetic amino acids in beta-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

• 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 SH3-mediated signaling pathways: The clustering of novel overlap ligand motifs in the elastic PEVK segment. 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)
• 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)
• 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 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  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

• 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)
• Progress in refining virtual colonoscopy for colorectal cancer screening. Bond JH. Gastroenterology  129(6):1832-44 (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 beta2/3 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)
• Mutations in PIP5K3 are associated with François-Neetens mouchetée fleck corneal dystrophy. Li S, Tiab L, Jiao X, Munier FL, Zografos L, Frueh BE, Sergeev Y, Smith J, Rubin B, Meallet MA, Forster RK, Hejtmancik JF, Schorderet DF. Am. J. Hum. Genet.  77(1):54-63 (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)
• 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)

• 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)
• Molecular architecture of a eukaryotic DNA transposase. Hickman AB, Perez ZN, Zhou L, Musingarimi P, Ghirlando R, Hinshaw JE, Craig NL, Dyda F. Nat Struct Mol Biol.  12: 715 - 721 (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)
• Variable tick protein in two genomic groups of the relapsing fever spirochete Borrelia hermsii in western North America. Porcella SF, Raffel SJ, Anderson DE Jr, Gilk SD, Bono JL, Schrumpf ME, Schwan TG. Infect. Immun.  73(10):6647-58 (2005)
• Distinguishing Modes of Eukaryotic Gradient Sensing R. Skupsky, W. Losert, and R. J. Nossal Biophys. J.  89(4):2806-2823 (2005)
• Bacterial 16S ribosomal DNA in house dust mite cultures. Valerio CR, Murray P, Arlian LG, Slater JE. J. Allergy Clin. Immunol.  116(6):1296-300 (2005)
• Multiple comparisons between two groups on multiple Bernoulli outcomes while accounting for covariates. JF Troendle Stat. Med. 24(23):3581-91 (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 beta-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)
• SspA is required for acid resistance in stationary phase by downregulation of H-NS in Escherichia coli. Hansen AM, Qiu Y, Yeh N, Blattner FR, Durfee T, Jin DJ. Mol. Microbiol. 56(3):719-34 (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)

• 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)
• The genome of bacteriophage K1F, a T7-like phage that has acquired the ability to replicate on K1 strains of Escherichia coli. Scholl D, Merril C. J. Bacteriol. 187(24):8499-503 (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)
• Utilization of a common pathway for the synthesis of high affinity macrocyclic Grb2 SH2 domain-binding peptide mimetics that differ in the configuration at one ring junction Shi ZD, Karki RG, Worthy KM, Bindu LK, Nicklaus MC, Fisher RJ, Burke TR. Chem. & Biodivers 2:447-456 (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)
• Expression of estrogen receptor alpha exon-deleted mRNA variants in the human and non-human primate frontal cortex W.R. Perlman, M. Matsumoto, S. Beltaifa, T.M. Hyde, R.C. Saunders, M.J. Webster, D.R. Rubinow, J.E. Kleinman and C.S. Weickert Neuroscience 134(1):81-95 (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

• 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)
• A Spontaneous Translational Fusion of Bacillus cereus PlcR and PapR Activates Transcription of PlcR-Dependent Genes in Bacillus anthracis via Binding with a Specific Palindromic Sequence Andrei P. Pomerantsev, Olga M. Pomerantseva, and Stephen H. Leppla Infection & Immunity 72(10):5814-5823 (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)
• IL-15 and IL-2 reciprocally regulate expression of the chemokine receptor CX3CR1 through selective NFAT1- and NFAT2-dependent mechanisms Jana Barlic, David H. McDermott, Maya N. Merrell, Jacqueline Gonzales, Laura E. Via, and Philip M. Murphy J. Biol. Chem.  279(47):48520-48534 (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 (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)
• DBParser: web-based software for shotgun proteomic data analyses. Yang X, Dondeti V, Dezube R, Maynard DM, Geer LY, Epstein J, Chen X, Markey SP, Kowalak JA. J. Proteome Res.  3(5):1002-8 (2004)

• Clustering of DNA sequences in human promoters. FitzGerald PC, Shlyakhtenko A, Mir AA, Vinson C. Genome Res.  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)
• Interleukin (IL)-15 and IL-2 reciprocally regulate expression of the chemokine receptor CX3CR1 through selective NFAT1- and NFAT2-dependent mechanisms. Barlic J, McDermott DH, Merrell MN, Gonzales J, Via LE, Murphy PM. J. Biol. Chem.  279(47):48520-34 (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)
• A chlamydial type III translocated protein is tyrosine-phosphorylated at the site of entry and associated with recruitment of actin D. R. Clifton, K. A. Fields, S. S. Grieshaber, C. A. Dooley, E. R. Fischer, D. J. Mead, R. A. Carabeo, and T. Hackstadt Proc. Natl. Acad. Sci. 101(27):10166-10171 (2004)
• Beta-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 alpha-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)
• Simian cytomegalovirus encodes five rapidly evolving chemokine receptor homologues. Sahagun-Ruiz A, Sierra-Honigmann AM, Krause P, Murphy PM. Virus Genes 28(1):71-83 (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)
• Identification and functional characterization of novel scorpion venom peptides with no disulfide bridge from Buthus martensii Karsch. Zeng XC, Wang SX, Zhu Y, Zhu SY, Li WX. Peptides 25(2):143-50 (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)

• Evolutionary and functional relationships within the DJ1 superfamily. Bandyopadhyay S, Cookson MR. BMC Evol Biol. 4(1):6 (2004)
• Functionalization of tumor necrosis factor-alpha using phage display technique and PEGylation improves its antitumor therapeutic window. Shibata H, Yoshioka Y, Ikemizu S, Kobayashi K, Yamamoto Y, Mukai Y, Okamoto T, Taniai M, Kawamura M, Abe Y, Nakagawa S, Hayakawa T, Nagata S, Yamagata Y, Mayumi T, Kamada H, Tsutsumi Y. Clin. Cancer Res. 10(24):8293-300 (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)
• LdARF1 in Trafficking and Structural Maintenance of the trans-Golgi Cisternal Network in the Protozoan Pathogen Leishmania donovani Johanna M. Porter-Kelley, Noel J. Gerald, Juan C. Engel, Elodie Ghedin and Dennis M. Dwyer Traffic 5(11):868-883 (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)
• MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli. Chen S, Zhang A, Blyn LB, Storz G. J. Bacteriol.  186(20):6689-97 (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

• Genomic analysis of bacteriophages SP6 and K1-5, an estranged subgroup of the T7 supergroup. D. Scholl, J. Kieleczawa, P. Kemp, J. Rush, C. C. Richardson, C. Merril. Adhya5 and I. J. Molineux J. Mol. Biol. 335(5):1151-1171 (2003)
• 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)
• A peptide with three hyaluronan binding motifs inhibits tumor growth and induces apoptosis. Xu XM, Chen Y, Chen J, Yang S, Gao F, Underhill CB, Creswell K, Zhang L. Cancer Res.  63(18):5685-90 (2003)
• Characterization of a new gammaTuRC subunit with WD repeats. Gunawardane RN, Martin OC, Zheng Y. Mol. Biol. Cell 14(3):1017-26 (2003)
• Interdependence of backbone flexibility, residue conservation, and enzyme function: a case study on beta1,4-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)
• 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)
• Changes in mumps virus gene sequence associated with variability in neurovirulent phenotype. Rubin SA, Amexis G, Pletnikov M, Li Z, Vanderzanden J, Mauldin J, Sauder C, Malik T, Chumakov K, Carbone KM. J. Virol.  77(21):11616-24 (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)
• Characterization of a New gamma TuRC Subunit with WD Repeats Ruwanthi N. Gunawardane, Ona C. Martin, and Yixian Zheng Mol. Biol. Cell 14(3):1017-1026 (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)
• Modeling tumor growth with random onset. Albert PS, Shih JH. Biometrics  59(4):897-906 (2003)

• Molecular dynamics simulations of the unfolding of beta(2)-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)
• Lathosterolosis: an inborn error of human and murine cholesterol synthesis due to lathosterol 5-desaturase deficiency. Krakowiak PA, Wassif CA, Kratz L, Cozma D, Kovárová M, Harris G, Grinberg A, Yang Y, Hunter AG, Tsokos M, Kelley RI, Porter FD. Hum. Mol. Genet. 12(13):1631-41 (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)
• The influenza A virus PB1-F2 protein targets the inner mitochondrial membrane via a predicted basic amphipathic helix that disrupts mitochondrial function. Gibbs JS, Malide D, Hornung F, Bennink JR, Yewdell JW. J. Virol.  77(13):7214-24 (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)
• 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)
• Cyclin E expression during development in Caenorhabditis elegans. Brodigan TM, Liu J, Park M, Kipreos ET, Krause M. Dev. Biol. 254(1):102-115 (2003)

2002

• 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)
• The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Zhang A, Wassarman KM, Ortega J, Steven AC, Storz G. Mol. Cell 9(1):11-22 (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)
• Isolation and sequencing of a putative promoter region of the murine G protein beta 1 subunit (GNB1) gene. Kitanaka J, Kitanaka N, Takemura M, Wang XB, Hembree CM, Goodman NL, Uhl GR. DNA Seq. 13(1):39-45 (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)
• Ssdp proteins interact with the LIM-domain-binding protein Ldb1 to regulate development. Chen L, Segal D, Hukriede NA, Podtelejnikov AV, Bayarsaihan D, Kennison JA, Ogryzko VV, Dawid IB, Westphal H. Proc. Natl. Acad. Sci 99(22):14320-5 (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)
• Ixolaris, a novel recombinant tissue factor pathway inhibitor (TFPI) from the salivary gland of the tick, Ixodes scapularis: identification of factor X and factor Xa as scaffolds for the inhibition of factor VIIa/tissue factor complex. Francischetti IM, Valenzuela JG, Andersen JF, Mather TN, Ribeiro JM. Blood 99(10):3602-12 (2002)
• Assembly, verification, and initial annotation of the NIA mouse 7.4K 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)
• The neurogenetics of mucolipidosis type IV G. Altarescu, MD, M. Sun, MD, PhD, D. F. Moore, MD, PhD, DIC, J. A. Smith, MD, E. A. Wiggs, PhD, B. I. Solomon, MS, N. J. Patronas, MD, K. P. Frei, MD, S. Gupta, MD, C. R. Kaneski, MS, O. W. Quarrell, MD, S. A. Slaugenhaupt, PhD, E. Goldin, PhD and R. Schiffmann, MD Neurology 59:306-313 (2002)

2001

• Identification of fifteen novel mutations and genotype-phenotype relationship in Fabry disease. Altarescu GM, Goldfarb LG, Park KY, Kaneski C, Jeffries N, Litvak S, Nagle JW, Schiffmann R. Clin. Genet. 60(1):46-51 (2001)
• Circularly permuted proteins in the protein structure database Jongsun Jung and Byungkook Lee. Protein Science  10:1881-1886 (2001)
• Limited heterogeneity of T cell receptor BV usage in aplastic anemia. Zeng W, Maciejewski JP, Chen G, Young NS. J. Clin. Invest. 108(5):765-73 (2001)
• Molecular Dynamics Simulations of Octyl Glucoside Micelles: Dynamic Properties Stephen Bogusz, Richard M. Venable, and Richard W. Pastor J. Phys. Chem. 105(35):8312-8321 (2001)
• ERGL, a novel gene related to ERGIC-53 that is highly expressed in normal and neoplastic prostate and several other tissues. Yerushalmi N, Keppler-Hafkemeyer A, Vasmatzis G, Liu XF, Olsson P, Bera TK, Duray P, Lee B, Pastan I. Gene 265(1-2):55-60 (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)
• Lowering the isoelectric point of the Fv portion of recombinant immunotoxins leads to decreased nonspecific animal toxicity without affecting antitumor activity. Onda M, Nagata S, Tsutsumi Y, Vincent JJ, Wang Q, Kreitman RJ, Lee B, Pastan I. Cancer Res. 61(13):5070-7 (2001)
• Cloning, mRNA distribution, and functional expression of an avian counterpart of the chemokine receptor/HIV coreceptor CXCR4. Liang TS, Hartt JK, Lu S, Martins-Green M, Gao JL, Murphy PM. J. Leukoc. Biol.  69(2):297-305 (2001)
• Fast-growth thermodynamic integration: Error and efficiency analysis G. Hummer J. Chem. Phys. 114(17):7330 (2001)
• Genomic Organization of the Murine G Protein (3 Subunit Genes and Related Processed Pseudogenes XB Wang, N Kitanaka, CM Hembree, GR Uhl DNA Sequence 12:345-354 (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 14-3-3zeta: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)
• A novel myeloid-restricted zebrafish CCAAT/enhancer-binding protein with a potent transcriptional activation domain. Lyons SE, Shue BC, Oates AC, Zon LI, Liu PP. Blood 97(9):2611-7 (2001)

2000

• Structure and Promoter Analysis of the Human unc-33-like Phosphoprotein Gene Tatsuya Matsuo, Jimmy K. Stauffer, Robert L. Walker , Paul Meltzer , and Carol J. Thiele J. Biol. Chem.  275(22):16560-16568 (2000)
• Multiple quantum solid-state NMR indicates a parallel, not antiparallel, organization of beta-sheets in Alzheimer's beta-amyloid fibrils. Antzutkin ON, Balbach JJ, Leapman RD, Rizzo NW, Reed J, Tycko R. Proc Natl Acad Sci U S A.  97(24):13045-50 (2000)

• Characterization and Sequencing of Prototypic Human T-Lymphotropic Virus Type 1 (HTLV-1) from an HTLV-1/2 Seroindeterminate Patient Allen Waziri, Samantha S. Soldan, Michael D. Graf, Jim Nagle, and Steven Jacobson J. Virol. 74(5):2178-2185 (2000)
• Amyloid fibril formation by A beta 16-22, a seven-residue fragment of the Alzheimer's beta-amyloid peptide, and structural characterization by solid state NMR. Balbach JJ, Ishii Y, Antzutkin ON, Leapman RD, Rizzo NW, Dyda F, Reed J, Tycko R. Biochemistry  39(45):13748-59 (2000)
• Oligodendrocytes in aging mice lacking myelin-associated glycoprotein are dystrophic but not apoptotic. Weiss MD, Hammer J, Quarles RH. J. Neurosci. Res.  62(6):772-80 (2000)
• Genomic imbalance in rat mammary gland carcinomas induced by 2-Amino-1-methyl-6-phenylimidazo(4,5-b)pyridine Minshu Yu, Doug-Young Ryu, Elizabeth G. Snyderwine Molecular Carcinogenesis 27(2):76-83 (2000)
• Molecular Dynamics Simulations of Octyl Glucoside Micelles: Structural Properties Stephen Bogusz, Richard M. Venable, and Richard W. Pastor J. Phys. Chem. 104(23):5462-5470 (2000)
• 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)
• XAGE-1, a new gene that is frequently expressed in Ewing's sarcoma. Liu XF, Helman LJ, Yeung C, Bera TK, Lee B, Pastan I. Cancer Res. 60(17):4752-5 (2000)

• Bioactive motifs of agouti signal protein. Virador VM, Santis C, Furumura M, Kalbacher H, Hearing VJ. Exp. Cell Res. 259(1):54-63 (2000)
• Mutation analysis and description of sixteen RSH/Smith-Lemli-Opitz syndrome patients: Polymerase chain reaction-based assays to simplify genotyping Patrycja A. Krakowiak, Ngozi A. Nwokoro, Christopher A. Wassif, Kevin P. Battaile, Magorzata J.M. Nowaczyk, William E. Connor, Cheryl Maslen, Robert D. Steiner, Forbes D. Porter Am. J. Med. Genetics 94(3):214-227 (2000)
• Rhesus and pig-tailed macaque parvoviruses: identification of two new members of the erythrovirus genus in monkeys. Green SW, Malkovska I, O'Sullivan MG, Brown KE. Virology 269(1):105-12 (2000)
• A stage-specific preparation to study the Ca2+-triggered fusion steps of exocytosis: Rationale and perspectives Joshua Zimmerberg, Paul S. Blank, Irina Kolosova, Myoung-Soon Cho, Masahiro Tahara, and Jens R. Coorssen Biochimie 82(4):303-314 (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

• The zebrafish genome contains two distinct selenocysteine tRNA[Ser]sec genes. Xu XM, Zhou X, Carlson BA, Kim LK, Huh TL, Lee BJ, Hatfield DL FEBS Lett. 454(1-2):16-20 (1999)
• Characterization of a multicopy family of genes encoding a surface-expressed serine endoprotease in rat Pneumocystis carinii. Russian DA, Andrawis-Sorial V, Goheen MP, Edman JC, Vogel P, Turner RE, Klivington DL, Angus CW, Kovacs JA. Proc. Assoc. Am. Physicians 111(4):347-56 (1999)
• Asymmetry and direction reversal in fluctuation-induced biased Brownian motion. Chen YD, Yan B, Miura R. Phys Rev E Stat Phys Plasmas Fluids Rela  60(4 Pt A):3771-5 (1999)

• Novel Genes in the PAGE and GAGE Family of Tumor Antigens Found by Homology Walking in the dbEST Database Ulrich Brinkmann, George Vasmatzis, Byungkook Lee and Ira Pastan Cancer Res. 59:1445-1448 (1999)
• Reduction of the nonspecific animal toxicity of anti-Tac(Fv)-PE38 by mutations in the framework regions of the Fv which lower the isoelectric point. Onda M, Kreitman RJ, Vasmatzis G, Lee B, Pastan I. J. Immunol. 163(11):6072-7 (1999)
• Expression profiling using cDNA microarrays. Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM. Nat Genet.  21(1 Suppl):10-4 Review. (1999)
• Genomic organization and mapping of the human and mouse neuronal beta2-nicotinic acetylcholine receptor genes. Lueders KK, Elliott RW, Marenholz I, Mischke D, DuPree M, Hamer D. Mamm. Genome 10(9):900-5 (1999)
• GalR mutants defective in repressosome formation. Geanacopoulos M, Vasmatzis G, Lewis DE, Roy S, Lee B, Adhya S. Genes Dev.  13(10):1251-62 (1999)
• Analysis of selenocysteine (Sec) tRNA([Ser]Sec) genes in Chinese hamsters. Xu XM, Carlson BA, Kim LK, Lee BJ, Hatfield DL, Diamond AM. Gene 239(1):49-53 (1999)

1998

• Information technology applications in biomedical research Martino, R.L. Kempner, K.M. Johnson, C.A. Information Technology Applications in B ITAB98:28-34 (1998)
• Parallel computing strategies for determining viral capsidstructure by cryoelectron microscopy Lanczycki, C.J. Johnson, C.A. Trus, B.L. Conway, J.F. Steven, A.C. Martino, R.L. Computational Science & Engineering, IEE 5(2):76-91 (1998)