2011 Publications

Jiang J, Shrivastava IH, Watts SD, Bahar I, Amara SG. (2011). Large collective motions regulate the functional properties of glutamate transporter trimmers. Proc Natl Acad Sci USA. 108:15141-6. [JIF=9.681]

Meireles L, Gur M, Bakan A, Bahar I. (2011). Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins. Protein Sci. 2011, doi: 10.1002/pro.711. [JIF=2.798]

Dechancie J, Bahar I, Shrivastava IH. (2011). The mechanisms of substrate release by the aspartate transporter Glt(Ph): insights from simulations. Mol Biosyst. 7: 832-842. [JIF=3.534]

Dechancie J, Bahar I, Shrivastava IH. (2011). Insights into the mechanism of release of substrate in the inward facing glutamate transporter from molecular dynamic simulations. Biophysical Journal. 100: 244-245. [JIF=3.653]

Dechancie J, Bahar I, Shrivastava IH. (2011). Mechanism of substrate release by the aspartate transporter Glt(Ph): insights from simulations. Mol Biosyst. 7: 3376-3376. [JIF=3.534]

Sukumaran M, Rossmann M, Srivastava I, Dutta A, Bahar I, Greger IH. (2011) Dynamics and allosteric potential of the AMPA receptor N-terminal domain. EMBO J. 30: 972-982. [JIF=9.205]

Bakan A, Meireles LM, Bahar I. (2011) ProDy: Protein Dynamics inferred from theory and experiments. Bioinformatics. 27: 2686-7. [JIF=5.468]

Zumot E, Bahar I. (2011) Protonation of glutamate-208 induces the release of agmatine in an outward-facing conformation of arginine/agmatine antiporter. J Biol Chem. 286:19693-701. [JIF=4.773]

Mustata G, Li M, Zevola N, Bakan A, Zhang L, Epperly M, Greenberger JS, Yu J, Bahar I. (2011). Development of Small-Molecule PUMA Inhibitors for Mitigating Radiation-Induced Cell Death. Curr Top Med Chem. 11: 281-90. [JIF=4.174]

Bakan A, Bahar I. (2011). Computational generation inhibitor-bound conformers of p38 map kinase and comparison with experiments. Pac Symp Biocomput. 181-92.

Eyal, E, Anindita, D, Bahar I. (2011). Cooperative dynamics of proteins unraveled by network models. WIREs Computational Molecular Science. May/June:1: 426-439.

Jiang J, Shrivastava IH, Watts SD, Bahar I, Amara SG. (2011). Large collective motions regulate the functional properties of glutamate transporter trimers. PNAS USA. 108:15141-6. [JIF=9.681]

Marcos E, Crehuet R, Bahar I. Changes in dynamics upon oligomerization regulate substrate binding and allostery in amino acid kinase family members. PLoS Comput Biol. 2011 Sep;7(9):e1002201. [JIF=5.215]

Liu L, Gronenborn AM, Bahar I. Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion. Proteins. 2011 Oct 19. doi: 10.1002/prot.23225. [JIF=3.191]

Kadri S, Hinman V, Benos PV. (2011). RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star. PLoS One. 6:e29217. [JIF=4.092]

Zhang Y, Handley D, Kaplan T, Yu H, Bais AS, Richards T, Pandit KV, Zeng Q, Benos PV, Friedman N, Eickelberg O, Kaminski N. (2011). High Throughput determination of TGFb1/SMAD3 targets in A549 lung epithelial cells. PLoS One, 6(5): e20319. [JIF=4.092]

Bais AS, Kaminski N, Benos PV. (2011). Finding subtypes of transcription factor motif pairs with distince regulatory roles. Nucleic Acids Res. 39: e76. [JIF=8.026]

Huang GT, Athanassiou C, Benos PV. (2011). mirConnX: condition-specific mRNA-microRNA network integrator. Nucleic Acids Res. 39: W416-23. [JIF=8.026]

Zhang Y, Handley D, Kaplan T, Yu H, Bais AS, Richards T, Pandit KV, Zeng Q, Benos PV, Friedman N, Eickelberg O, Kaminski N. (2011). High Throughput Determination of TGFβ1/SMAD3 Targets in A549 Lung Epithelial Cells. PLoS One, 6: e20319. [JIF=4.092]

Zinman G, Brower-Sinning R, Emeche CH, Ernst J, Huang GT, Mahony S, Myers AJ, O’Dee DM, Flynn JL, Nau GJ, Ross TM, Salter RD, Benos PV, Bar Joseph Z, Morel PA. (2011). Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque. PLoS One, 6(7): e22401. [JIF=4.092]

Wang R, Ilangovan U, Leal BZ, Robinson AK, Amann BT, Tong CV, Berg JM, Hinck AP, Kim CA. (2011). Identification of nucleic acid binding residues in the FCS domain of the polycomb group protein polyhomeotic. Biochemistry. 50: 4998-5007. [JIF=3.422]

Long, RM, Berg JM. (2011). What to Expect from the Pharmacogenomics Research Network. Clin Pharmacol Ther. 89: 339-41. [JIF=6.043]

Namuswe F, Berg JM (2011). Secondary Interactions Involving Zinc-¬‐Bound Ligands: Roles in Structural Stabilization and Macromolecular Interactions. J Inorg Biochem. 111:146-9. [JIF=3.354]

Koes DR, Camacho CJ. (2011). Pharmer: Efficient and Exact Pharmacophore Search. J Chem Inf Model. 15: 1307-1314. [JIF=4.675]

Camacho CJ. (2011). Novel polarizable empirical code for accurate prediction of protein-DNA interactions. Biophysical Journal. 100: 70. [JIF=3.653]

Camacho CJ, Koes DR, Doemling A. (2011). Enabling design and synthesis of small molecule protein-protein antagonists. Abstracts of Papers of the American Chemical Society. 242: 351-COMP.

Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D. (2011). Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol. 414: 289-302. [JIF=3.981]

Ramanathan A, Savol AJ, Langmead CJ, Agarwal PK, Chennubhotla CS. (2011). Discovering conformational sub-states relevant to protein function. PLoS One. 6(1):e15827. [JIF=4.092]

Savol AJ, Burger VM, Agarwal PK, Ramanathan A, Chennubhotla CS. (2011). QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin. Bioinformatics. 27:152-160.[JIF=5.468]

Burger V, Bahar I, Chennubhotla C. (2011). Hierarchical Elastic Network Modeling of cryo-EM data. Biophysical Journal. 100: 534-534. [JIF=3.653]

Savol A, Ramanathan A, Chennubhotla C. (2011). Generating Global Protein Dynamics with Structure-From-FRET. Biophysical Journal. 100: 476-477. [JIF=3.653]

Ramanathan A, Borreguero JM, Chennubhotla CS. (2011). Protein Flexibility and Energy Flow During Enzyme Catalysis. Biophysical Journal. 100: 194-194. [JIF=3.653]

Ramanathan A, Borreguero JM, Chennubhotla CS. (2011). Conformational fluctuations and long-range effects during enzyme catalysis. American Chemical Society. 241:311-COMP. [JIF=9.907]

Chennubhotla CS, Ramanathan A, Savol AJ, Agarwal PK. (2011). Identifying conformational sub-states directly relevant to protein function. American Chemical Society. 241: 308-COMP. [JIF=9.907]

Gibbons JD, Chennubhotla CS, Madura JD, Bahar I (2011). Investigation or the dopamine active transporter: A study in the motion and communication stochastics of transporter proteins in the neurotransmitter sodium symporter family. American Chemical Society. 241: 214-COMP. [JIF=9.907]

Agarwal PK, Ramanathan A, Chennubhotla CS. (2011). Identifying and characterizing conformational sub-states during enzyme catalysis. American Chemical Society. 242: 33-BIOL. [JIF=9.907]

Kelleher ES, Clark NL, Markow TA. 2011. Diversity Enhancing Selection Acts on a Female Reproductive Protease Family in Four Sub-Species of Drosophila mojavensis. Genetics 187(3):865-76. [JIF=4.087]

Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS. (2011). Guidelines for visualizing and annotating rule-based models. Mol Biosyst. 7: 2779-95. [JIF=3.534]

Sneddon MW, Faeder JR, Emonet T. (2011). Efficient modeling, simulation and coarse-graining of biological complexity wiyh NFsim. Nat Methods. 8: 177-83. [JIF=19.276]

Xu W, Smith AM, Faeder JR, Marai GE. (2010). RuleBender: a visual interface for rule-based modeling. Bioinformatics. 27: 1721-2. [JIF=5.468]

Yi X, Liu J, Faeder JR, Setlow P. (2011). Synergism between different germinant receptors in the germination of Bacillus subtilis spores. Journal of Bacteriology. 193: 4664-71. [JIF=3.825]

Nemenman I, Faeder JR, Hlavacek WS, Jiang Y, Wall ME, Zilman A. Selected papers from the Fourth Annual q-bio Conference on Cellular Information Processing PREFACE. Physical Biology. 8: 5 SI. [JIF=2.595]

Faeder JR. Toward a comprehensive language for biological systems. BMC Biol. 9:68. [JIF=5.750]

Yi X, Liu J, Faeder JR, Setlow P. (2011). Synergism between different germinant receptors in the germination of Bacillus subtilis spores. Journal of Bacteriology. 193:4664-71. [JIF=3.825]

Horton AA, Wang B, Camp L, Price MS, Arshi A, Nagy M, Nadler SA, Faeder JR, Luckhart S. The mitogen-activated protein kinome from Anopheles gambiae: identification, phylogeny and functional characterization of the ERK, JNK and p38 MAP kinases. BMC Genomics. 12: 574. [JIF=4.073]

Kocieniewski P, Faeder JR, Lipniacki T. The interplay of double phosphorylation and scaffolding in MAPK pathways. J Theor Biol. 295: 116-24. [JIF=2.208]

Choi YJ, Ghedin E, Berriman M, McQuillan J, Holroyd N, Mayhew GF, Christensen BM, Michalski ML. (2011). A deep sequencing approach to comparatively analyze the transcriptome of lifecycle stages of the filarial worm, Brugia malayi. PLoS Neglect Trop D. 5:e1409. [JIF=4.716]

Liu C, Kelen PV, Ghedin E, Lustigman S, Unnasch TR. (2011). Analysis of transcriptional regulation of tetracycline responsive genes in Brugia malayi. Mol Biochem Parasitol. 180: 106-11. [JIF=2.551]

Bahl J, Nelson MI, Chan KH, Chen R, Vijaykrishna D, Halpin RA, Stockwell TB, Lin X, Wentworth DE, Ghedin E, Guan Y, Peiris JS, Riley S, Rambaut A, Holmes EC, Smith GJ. (2011). Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans. P Natl Acad Sci USA. 108: 19359-64. [JIF=9.681]

Vlasova AN, Halpin R, Wang S, Ghedin E, Spiro DJ, Saif LJ. (2011). Molecular Characterization of a new alphacoronavirus species associated with mink epizootic catarrhal gastroenteritis. J Gen Virol. 92: 1369-1379. [JIF=3.363]

Holmes EC, Ghedin E, Halpin RA, Stockwell TB, Zhang XQ, Fleming R, Davey R, Benson CA, Mehta S, Taplitz R, Liu YT, Brouwer KC, Wentworth DE, Lin X; INSIGHT FLU002 Study Group, Schooley RT. (2011). Extensive Geographical Mixing of Human H1N1/09 Influenza A Virus in a Single University Community. J Virol 85: 6923-6929. [JIF=5.402]

Ping J, Keleta L, Forbes NE, Dankar S, Stecho W, Tyler S, Zhou Y, Babiuk L, Weingartl H, Halpin RA, Boyne A, Bera J, Hostetler J, Fedorova NB, Proudfoot K, Katzel DA, Stockwell TB, Ghedin E, Spiro DJ, Brown EG. (2011). Genomic and protein structural maps of adaptive evolution of human influenza a virus to increased virulence in the mouse. PLoS One. 6: e21740. [JIF=4.092]

Melnikow E, Xu S, Liu J, Li L, Oksov Y, Ghedin E, Unnasch TR, Lustigman S. (2011). Interaction of a Wolbachia WSP-like protein with a nuclear-encoded protein of Brugia malayi. Int J Parasitol. 41: 1053-61. [JIF=3.393]

Bennuru S, Meng Z, Ribeiro JM, Semnani RT, Ghedin E, Chan K, Lucas DA, Veenstra TD, Nutman TB. (2011). Stage-specific proteomic expression patterns of the human filarial parasite Brugia malayi and its endosymbiont Wolbachia. P Natl Acad Sci USA. 108: 9649-54. [JIF=9.681]

Losada L, Ghedin E, Morris A, Chu HW, Nierman WC. (2011). The Human Lung Microbiome. In : Metagenomics of the Human Body. K.E. Nelson, Editor. Springer

Nelson MI, Tan Y, Ghedin E, Wentworth DE, St George K, Edelman L, Beck ET, Fan J, Lam TT, Kumar S, Spiro DJ, Simonsen L, Viboud C, Holmes EC, Henrickson KJ, Musser JM. (2011). Phylogeography of the spring and fall waves of the H1N1/09 pandemic influenza virus in the United States. J Virol. 85: 828-34. [JIF=5.402]

Stock S, McK Bird D, Ghedin E, Goodrich-Blair H. (2011). Abstracts of NEMASYM: The third nematode-bacteria symbioses research coordination network meeting. Symbiosis. 55: 97-109. [JIF=1.148]

Ghedin E, Upton C. (2011). It’s a small world after all – viral genomics and the global dominance of viruses. Current Opinion in Virology 1(4):280-281.

Melnikow E, Xu S, Liu J, Li L, Oksov Y, Ghedin E, Unnasch TR, Lustigman S. (2011). Interaction of a Wolbachia WSP-like protein with a nuclear-encoded protein of Brugia malayi. International Journal of Parasitology. 41:1053-61. [JIF=3.393]

Dwyer, D.E.; INSIGHT Influenza Study Group. (2011). Surveillance of illness associated with pandemic (H1N1) 2009 virus infection among adults using a global clinical site network approach: the INSIGHT FLU 002 and FLU 003 studies. Vaccine . Jul 22:29 Suppl 2:B56-62. [JIF=3.766]

Nederlof M, Watanabe S, Burnip B, Taylor DL, Critchley-Thorne R (2011) High-throughput profiling of tissue and tissue model microarrays: Combined transmitted light and 3-color fluorescence digital pathology. J Pathol Inform. 2:50. [JIF=6.318]

Zhang X, Bhatt D, Zuckerman DM (2011) Automated sampling assessment for molecular simulations using the effective sample size. J Chem Theory Comput., 6: 3058-3057. [JIF=5.215]

Zuckerman DM (2011) Equilibrium sampling in biomolecular simulations. Annu Rev Biophys. 40: 41-62. [JIF=13.574]

Mamonov AB, Zhang X, Zuckerman DM (2011) Rapid sampling of all-atom peptides using a library-based polymer-growth approach. J Comput Chem. 32: 396-405. [JIF=4.583]

Ding Y, Mamonov AB, Zuckerman DM (2011) Improved Library-Based Monte Carlo, Applied to Multi-level Sampling. Biophysical Journal. 100: 155-155. [JIF=3.653]

Lettieri S, Mamonov AB, Zuckerman DM (2011) Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space. J Comput Chem. 32: 1135-43. [JIF=4.583]

Bhatt D, Zuckerman DM (2011) Beyond Microscopic Reversibility: Are Observable Nonequilibrium Processes Precisely Reversible? Journal of Chemical Theory and Computation. 7: 2520-2527. [JIF=5.215]

Zuckerman DM (2011) Equilibrium Sampling in Biomolecular Simulations. Annu Rev Biophys. 40: 41-62. [JIF=13.574]

Mamonov AB, Zhang X, Zuckerman DM (2011) Rapid sampling of all-atom peptides using a library-based polymer-growth approach. J Comput Chem. 32: 396-405. [JIF=4.583]

Cashman DJ, Mamonov AB, Bhatt D, Zuckerman DM (2011) Thermal Motions of the E. Coli Glucose-Galactose Binding Protein Studied Using Well-Sampled, Semi-Atomistic Simulations. Curr Top Med Chem. 11: 211-20. [JIF=4.174]

Adelman JL, Dale AL, Zwier MC, Bhatt D, Chong LT, Zuckerman DM, Grabe M (2011) Simulations of the alternating access mechanism of the sodium symporter Mhp1. Biophys J. 101: 2399-407. [JIF=3.653]

Wu Z, Sweeney LB, Ayoob JC, Chak K, Andreone BJ, Ohyama T, Kerr R, Luo L, Zlatic M, Kolodkin AL. (2011). A combinatorial semaphorin code instructs the initial steps of sensory circuit assembly in the Drosophila CNS. Neuron, 70: 281-98. [JIF=14.736]

Yiling L, Muller M, Smith D, Dutta B, Komurov K, Iadevaia S, Ruths D, Tseng JT, Yu S, Yu Q, Nakhleh L, Balazsi G, Donnelly J, Schurdak ME, Morgan-Lappe S, Fesik S, Ram PT, Mills GB. (2011). Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling. Oncogene. 30: 4567-77. [JIF=6.373]

Jiang J, Shrivastava IH, Watts SD, Bahar I, Amara SG. (2011). Large collective motions regulate the functional properties of glutamate transporter trimmers. Proc Natl Acad Sci USA. 108: 15141-6. [JIF=9.681]

Dechancie J, Bahar I, Shrivastava IH. (2011). The mechanisms of substrate release by the aspartate transporter Glt(Ph): insights from simulations. Mol Biosyst. 7: 832-842. [JIF=3.534]

Dechancie J, Bahar I, Shrivastava IH. (2011). Insights into the mechanism of release of substrate in the inward facing glutamate transporter from molecular dynamic simulations. Biophysical Journal. 100: 244-245. [JIF=3.653]

Dechancie J, Bahar I, Shrivastava IH. (2011). Mechanism of substrate release by the aspartate transporter Glt(Ph): insights from simulations. Mol Biosyst. 7: 3376-3376. [JIF=3.534]

LaLonde J, Shrivastava I. (2011). Enhanced dynamics of HIV gp120 glycoprotein by small molecule binding. Biochemistry. 50: 4173-83. [JIF=3.422]

Sukumaran M, Rossmann M, Shrivastava I, Dutta A, Bahar I, Greger IH. (2011). Dynamics and allosteric potential of the AMPA receptor N-terminal domain. EMBO J. 30: 972-82. [JIF=8.833]

Mali RS, Ramdas B, Ma P, Shi J, Munugalavadla V, Sims E, Wei L, Vemula S, Nabinger SC, Goodwin CB, Chan RJ, Traina F, Visconte V, Tiu RV, Lewis TA, Stern AM, Wen Q, Crispino JD, Boswell HS, Kapur R.  Rho kinase regulates the survival and transformation of cells bearing oncogenic forms of KIT, FLT3, and BCR-ABL.  Cancer Cell. 2011 Sep 13;20(3):357-69.  PMID: 21907926.  PMCID: PMC3207244.

Raj L, Ide T, Gurkar AU, Foley M, Schenone M, Li X, Tolliday NJ, Golub TR, Carr SA, Shamji AF, Stern AM, Mandinova A, Schreiber SL, Lee SW.  Selective killing of cancer cells by a small molecule targeting the stress response to ROS.  Nature.  2011 Jul 13;475(7355):231-4.  PMID: 21753854.   PMCID: PMC3316487.

Shrivastava I, LaLonde JM (2011) Enhanced dynamics of HIV gp120 glycoprotein by small molecule binding Biochemistry 50(19):4173-83.