2014 Publications | Computational & Systems Biology

	Lui VW, Peyser ND, Ng PK, Hritz J, Zeng Y, Lu Y, Li H, Wang L, Gilbert BR, General IJ, Bahar I, Ju Z, Wang Z, Pendleton KP, Xiao X, Du Y, Vries JK, Hammerman PS, Garraway LA, Mills GB, Johnson DE, Grandis JR (2014) Frequent mutation of receptor protein tyrosine phosphatases provides a mechanism for STAT3 hyperactivation in head and neck cancer Proc Natl Acad Sci U S A 111(3):1114-1119.
	Vasilakis N, Castro-Llanos F, Widen SG, Aguilar PV, Guzman H, Guevara C, Fernandez R, Auguste AJ, Wood TG, Popov V, Mundal K, Ghedin E, Kochel TJ, Holmes EC, Walker PJ, Tesh RB (2014) Arboretum and Puerto Almendras viruses: two novel rhabdoviruses isolated from mosquitoes in Peru J Gen Virol Apr;95(Pt 4):787-92.
	Findlay GD, Sitnik JL, Wang W, Aquadro CF, Clark NL, Wolfner MF (2014) Evolutionary Rate Covariation Identifies New Members of a Protein Network Required for Drosophila melanogaster Female Post-Mating Responses PLoS Genet 10(1):e1004108 [Epub]
	Joy ME, Vollmer LL, Hulkower K, Stern AM, Peterson CK, Boltz RC, Roy P, Vogt A (2014) A high-content, multiplexed screen in human breast cancer cells identifies profilin-1 inducers with anti-migratory activities PLoS One 9(2):e88350.
	Koes D and Camacho CJ (2014) Indexing Volumetric Shapes with Matching and Packing Knowledge and Information Systems Jan 2014.
	Bale SS, Vernetti L, Senutovitch N , Jindal R, Hegde M, Gough A, McCarty WJ, Bakan A, Bhushan A, Shun TY, Golberg I, DeBiasio R, Usta OB, Yarmush ML, Taylor DL* (co-first authors) (2014) In Vitro Platforms for Evaluating Liver Toxicity Exp Biol Med* 239(9): 1180-91.
	Gardner CL, Hritz J, Sun C, Vanlandingham DL, Song TY, Ghedin E, Higgs S, Klimstra WB, Ryman KD (2014) PLoS Negl Trop Dis 8(2):e2719.
	Jiang J, Bakan A, Kapralov AA, Ishara Silva K, Huang Z, Amoscato AA, Peterson J, Krishna Garapati V, Saxena S, Bayir H, Atkinson J, Bahar I, Kagan VE (2014) Designing Inhibitors of Cytochrome c/Cardiolipin Peroxidase Complexes: Mitochondria-Targeted Imidazole-Substituted Fatty Acids Free Radic Biol Med 71C:221-230.
	Das A, Gur M, Cheng MH, Jo S, Bahar I, Roux B (2014) Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model PLoS Comput Biol Apr;10(4):e1003521.
	Hogg JS, Harris LA, Stover LJ, Nair NS, Faeder JR (2014) Exact hybrid particle/population simulation of rule-based models of biochemical systems PLoS Comput Biol Apr 3; 10(4):e1003544.
	Korotchenko VN, Saydmohammed M, Vollmer LL, Bakan A, Sheetz K, Debiec KT, Greene KA, Agliori CS, Bahar I, Day BW, Vogt A, Tsang M (2014) In Vivo Structure-Activity Relationship Studies Support Allosteric Targeting of a Dual Specificity Phosphatase ChemBioChem 15: 1436-1445.
	Chikina MD, Sealfon SC (2014) Increasing consistency of disease biomarker prediction across dataset. PLoS One 9(4):e91272.
	Edinger RS, Coronnello C, Bodnar AJ, Laframboise WA, Benos PV, Ho J, Johnson JP, Butterworth MB (2014) Aldosterone Regulates MicroRNAs in the Cortical Collecting Duct to Alter Sodium Transport J Am Soc Nephrol 25(11): 2445-57.
	Mahajan A, Barua D, Cutler P, Lidke DS, Espinoza FA, Pehlke C, Grattan R, Kawakami Y, Tung CS, Bradbury AR, Hlavacek WS, Wilson BS (2014) Optimal Aggregation of FcεRI with a Structurally-defined Trivalent Ligand Overrides Negative Regulation Driven by Phosphatases ACS Chem Biol (9)7: 1508-19.
	Poe JA, Vollmer L, Vogt A, Smithgall TE (2014) Development and validation of a high-content bimolecular fluorescence complementation assay for small-molecule inhibitors of HIV-1 Nef dimerization J Biomol Screen 19(4):556-65.
	General IJ, Liu Y, Blackburn ME, Mao W, Gierasch LM, Bahar I (2014) ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones PLoS Comput Biol 10(5):e1003624.
	O'Reilly LP,* Long OS,* Cobanoglu MC,* Benson JA, Luke CJ, Miedel MT, Hale P, Perlmutter DH, Bahar I, Silverman GA, Pak SC (2014) A genome-wide RNAi screen identifies potential drug targets in a C. elegans model of ?1-antitrypsin deficiency Hum Mol Genet 23(19): 5123-32.
	Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I (2014) Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics Bioinformatics 30(18): 2681-83.
	Suárez E, Lettieri S, Zwier MC, Stringer CA, Subramanian SR, Chong LT, Zuckerman DM (2014) Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories J Chem Theory Comput 10(7):2658-2667.
	Bahar I (2014) Coupling between Neurotransmitter Translocation and Protonation State of a Titratable Residue during Na(+)-Coupled Transport. Biophys J. 106: 2547-8
	LaRusch J, Jung J, General I, Lewis MD, Woo Park H, Brand RE, Gelrud A, Anderson MA, Banks PA, Conwell D, Lawrence C, Romagnuolo J, Baillie J, Alkaade S, Cote' G, Gardner TB, Amann ST, Slivka A, Sandhu B, Aloe A, Kienholz ML, Yadav D, Barmada MM, Bahar I, Lee MG, Whitcomb DC, North American Pancreatitis Study Group (2014) Mechanisms of CFTR functional variants that impair regulated bicarbonate permeation and increase risk for pancreatitis but not for cystic fibrosis PLoS Genetics 10:e1004376.
	Gough AH, Chen N, Shun TY, Lezon TR, Boltz RC, Reese CE, Wagner J, Vernetti LA, Grandis JR, Lee AV, Stern AM, Schurdak ME, Taylor DL (2014) Identifying and quantifying heterogeneity in high content analysis: application of heterogeneity indices to drug discovery PLoS One 9(7):e102678.
	Koes DR, Camacho CJ (2014) Shape-based virtual screening with volumetric aligned molecular shapes J Comput Chem 35(25): 1824-34.
	Nemenman I, Faeder JR, Gnanakaran S, Hlavacek WS, Munsky B, Wall ME, Jiang Y (2014) The Seventh q-bio Conference: meeting report and preface Phys Biol 11(4):040301.
	Savol AJ, Chennubhotla CS (2014) Quantifying the Sources of Kinetic Frustration in Folding Simulations of Small Proteins J Chem Theory Comput 10(8):2964-2974.
	Morel PA, Faeder JR, Hawse WF, Miskov-Zivanov N (2014) Modeling the T cell immune response: a fascinating challenge J Pharmacokinet Pharmacodyn 41(5): 401-13.
	Liu B, Bhatt D, Oltvai ZN, Greenberger JS, Bahar I (2014) Significance of p53 dynamics in regulating apoptosis in response to ionizing radiation, and polypharmacological strategies Sci Rep 4:6245.
	Cobanoglu MC, Oltvai ZN, Taylor DL, Bahar I (2014) BalestraWeb: Efficient, online evaluation of drug-target interactions Bioinformatics 31(1): 131-3.
	Wenskovitch JE Jr, Harris LA, Tapia JJ, Faeder JR, Marai GE (2014) MOSBIE: a tool for comparison and analysis of rule-based biochemical models BMC Bioinformatics 15(1):316.
	Badgeley MA, Sealfon SC, Chikina MD (2014) Hybrid Bayesian-rank integration approach improves the predictive power of genomic dataset aggregation Bioinformatics 31(2): 209-15.
	Cheng MH, Bahar I (2014) Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle PLoS Comput Biol 10(10):e1003879.
	Moroco JA, Baumgartner MP, Rust HL, Choi HG, Hur W, Gray NS, Camacho CJ, Smithgall TE (2014) A Discovery Strategy for Selective Inhibitors of c-Src in Complex with the Focal Adhesion Kinase SH3/SH2-binding Region. Chem Biol Drug Des. [Epub ahead of print]
	Zomot E, Gur M, Bahar I (2014) Microseconds Simulations Reveal a New Sodium-Binding Site and the Mechanism of Sodium-Coupled Substrate Uptake by LeuT. J Biol Chem 290(1): 544-55.
	Spiriti J, Zuckerman DM (2014) Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations. J Chem Theory Comput 10(11):5161-5177
	Warita K, Warita T, Beckwitt CH, Schurdak ME, Vazquez A, Wells A, Oltvai ZN(2014) Statin-induced mevalonate pathway inhibition attenuates the growth of mesenchymal-like cancer cells that lack functional E-cadherin mediated cell cohesion. Sci Rep 4:7593.
	Wang Q, Chikina MD, Pincas H, Sealfon SC (2014) Homer1 alternative splicing is regulated by gonadotropin-releasing hormone and modulates gonadotropin gene expression. Mol Cell Biol 34(10):1747-56.