2010 Publications

Lezon TR, Bahar I. (2010). Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology. PLoS Comput Biol. 17;6(6)e:1000816. [JIF=5.215]

Bahar I. (2010). On the functional significance of soft modes predicted by coarse-grained models for membrane proteins. J Gen Physiol. 135:563-73. [JIF=3.970]

Zomot E, Bahar I. (2010). The sodium/galactose symporter crystal structure is a dynamic, not so occluded state. Mol Biosyst. 6: 1040 -1046. [JIF=3.534]

Marcos E, Crehuet R, Bahar I. (2010). On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm. PLoS Comput Biol. 6(4):e1000738. [JIF=5.215]

Bahar I, Lezon TR, Yang LW, Eyal E. (2010). Global Dynamics of Proteins: Bridging Between Structure and Function. Annu Rev Biophys. 39: 23-42. [JIF=13.574] Liu Y, Bahar I. (2010). Toward understanding allosteric signaling mechanisms in the ATPase domain of molecular chaperones. Pac Symp Biocomput. 269-80.
Bahar I, Lezon T, Bakan A, Shrivastava I. (2010). Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem. Rev. 110: 1463-1497. [JIF=40.197] Gierasch, Liu, Bahar I. (2010). Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs. PLoS Comput Biol. 16:6(9). [JIF=5.215]

Dutta, Bahar I. (2010). Metal-binding Sites are designed to achieve optimal mechanical and signaling properties. Structure. 18: 1140-8. [JIF=6.347]

Mustata G, Bahar I, Li M, Zevola N, Bakan A, Zhang L, Epperly M, Greenberger JS, Yu J. (2010). Development of Small-Molecule PUMA Inhibitors for Mitigating Radiation-Induced Cell Death. (2010). Curr Top Med Chem. 11: 281-90. [JIF=1.74]

Bakan A, Bahar I. (2010). Computational generation inhibitor-bound conformers of p38 map kinase and comparison with experiments. Pac Symp Biocomput. 181-92.

Pandit KV, Corcoran D, Yousef H, Yarlagadda M, Tzouvelekis A, Gibson KF, Konishi K, Yousem SA, Singh M, Handley D, Richards T, Selman M, Watkins SC, Pardo A, Ben-Yehudah A, Bouros D, Eickelberg O, Ray P, Benos PV, Kaminski N. (2010). Inhibition and role of let-7d in idiopathic pulmonary fibrosis. Am J Resp Crit Care Med, 182: 220-9. [JIF = 6.330]

Temiz NA, Benos PV, Camacho CJ. (2010). Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains. Nucleic Acids Res., 38: 2134-2144. [JIF=8.026]

Guerrerio AL, Berg JM. (2010). Design of single-stranded nucleic acid binding peptides based on nucleocapsid CCHC-box zinc-binding domains. J Am Chem Soc. 132: 9638-43. [JIF=9.907]

Ghosh D, Berg JM. (2010). A proteome-wide perspective on peroxisome targeting signal 1(PTS1)-Pex5p affinities. J Am Chem Soc. 132: 3973-9. [JIF=9.907]

Jantz D, Berg JM. (2010). Probing the DNA-Binding Affinity and Specificity of Designed Zinc Finger Proteins. Biophys J . 98: 852-60. [JIF=3.653] Berg, JM, Tymoczko JL, Styer L. (2010). Biochemistry. 7th Edition, W.H. Freeman, New York, NY.

Berg JM, Rogers ME, Lyster PM. (2010). Systems Biology and Pharmacology. Clin Pharmacol Ther. 89:339-41. [JIF=6.043]

Berg JM, Rogers ME, Lyster PM. (2010). Systems Biology and Pharmacology. Clin Pharmacol Ther. 88:17-9. [JIF=6.043]

Bueno M, Temiz NA, Camacho CJ. (2010). Novel Modulation Factor Quantifies the Role of Water Molecules in Protein Interactions. Proteins, 78: 15 SI: 3226-3234. [JIF=3.392]

Meireles LM, Dömling AS, Camacho CJ. (2010). ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery. Nucleic Acids Res, 38: Suppl:W407-11. [JIF=8.026]

Temiz AN, Benos PV, Camacho CJ. (2010). Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains. Nucleic Acids Res. 38: 2134-44. [JIF=8.026] Temiz NA, Trapp A, Prokopyev OA, Camacho CJ. (2010). Optimization of minimum set of protein-DNA interactions: a quasi exact solution with minimum over-fitting. Bioinformatics, 26: 319-25. [JIF=5.468] Ramanathan A, Langmead CJ, Agarwal PK, Chennubhotla CS, Agarwal PK. (2010). Discovering conformational sub-states essential to protein function: A multi-scale approach. American Chemical Society. 240: 358-COMP. [JIF=9.907]

Faeder JR, Parson R. (2010). Simulations of ICI-(CO2)(n) Photodissociation: Effects of Structure, Excited State Charge Flow, and Solvent Dynamics. J Phys Chem A, 114: 1347-1356. [JIF=2.946]

Liu J, Faeder JR, Camacho CJ. (2010). Toward a quantitative theory of intrinsically disordered proteins and their function. Proc Natl Acad Sci USA, 106: 19819-23. [JIF=9.681]

Monine MI, Posner RG, Savage PB, Faeder JR, Hlavacek WS. (2010). Modeling multivalent ligand-receptor interactions with steric constraints on configurations of cell-surface receptor aggregates. Biophys J, 98: 48-56. [JIF=4.390] Nag A, Faeder JR, Goldstein B. (2010). Shaping the response: the role of FcRI and Syk expression levels in mast cell signaling. IET Syst Biol. 4: 344. [JIF=1.349]

Ghedin E, Wentworth D, Halpin RA, Lin X, Bera J, DePasse J, Fitch A, Griesemer S, Hine E, Katzel DA, Overton L, Proudfoot K, Sitz J, Szczypinski B, St. George K, Spiro DJ, Holmes EC. (2010). Unseasonal Transmission of H3N2 Influenza A Virus during the Swine-Origin H1N1 Pandemic. J. Virology, 84: 5715-8.

Schriml LM, Arze C, Nadendla S, Ganapathy A, Felix V, Mahurkar A, Phillippy K, Gussman A, Angiuoli S, Ghedin E, White O, Hall N. (2010). GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database. Nucleic Acids Res. 38 Database issue): D754-64. [JIF=8.026]

Liu C, Oliveira A, Chauhan C, Ghedin E, Unnasch TR. Functional analysis of putative operons in Brugia malayi.International Journal of Parasitology. 40:63-71. [JIF=3.393]

Melnikow E, Hailemariam T, Unnasch TR, Ghedin E, Lustigman S. (2010). American Journal of Tropical Medicine and Hygiene. 83: 382-382. [JIF=2.592]

Bennuru S, Meng ZJ, Semnani RT, Ghedin E, Chen K, Lucas D, Ribeiro JM, Veenstra TD, Nutman TB. (2010). American Journal of Tropical Medicine and Hygiene. 83: 246-246. [JIF=2.592]

Giuliano KA, Gough AH, Taylor DL, Vernetti LA, Johnston PA. (2010). Early Safety Assessment Using Cellular Systems Biology Yields Insights into Mechanisms of Action. J Biomol Screen. 15: 783-797. [JIF=2.066]

Giuliano KA, Gough AH, Taylor DL, Vernetti LA, Johnston PA. (2010). Early Safety Assessment Using Cellular Systems Biology Yields Insights into Mechanisms of Action. J Biomol Screen. 15: 783-797. [JIF=2.066]

Kapranov P, Ozsolak F, Kim SW, Foissac S, Lipson D, Hart C, Roels S, Borel C, Antonarakis SE, Monaghan AP, John B, Milos PM. (2010). New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism. Nature. 466: 642-6. [JIF = 36.280]

Kim SW, Li Z, Moore PS, Monaghan AP, Chang Y, Nichols M, John B. (2010). A sensitive non-radioactive northern blot method to detect small RNAs. Nucleic Acids Res, 38: e98. [JIF = 8.026]

Ozsolak F, Kapranov P, Foissac S, Kim SW, Fishilevich E, Monaghan AP, John B, Milos PM. (2010). Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell. 143: 1018-29. [JIF=32.403]

Li ZH, Kim SW, Lin YF, Moore PS, Chang YA, John B. (2010). Ago-associated human usRNAs and other similar small RNAs. Genome Biology. 11: P6, DOI: 10.1186/gb-2010-11-S1-P6. [JIF=9.036]

Maly VI, Maly IV. (2010). Symmetry, stability, and reversibility properties of idealized confined microtubule cytoskeletons. Biophys J. 99: 2931-2840. [JIF=3.653]

Meirovitch H. (2010). Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics. J Mol Recognit, 23: 153-72 [JIF=3.160]

Mihailescu M, Meirovitch H. (2010). Entropy and Free Energy of a Mobile Loop Based on the Crystal Structures of the Free and Bound Proteins. Entropy (Basel). 12: 1946-1974. [JIF=1.183]

General IJ, Meirovitch H. (2010). Absolute free energy and entropy of streptavidin loop. J Am Chem Soc. 239: 63-COMP. [JIF=9.907]

Dudgeon DD, Shinde SN, Shun TY, Lazo JS, Strock CJ, Giuliano KA, Taylor DL, Johnston PA, Johnston PA. (2010). Characterization and optimization of a novel protein-protein interaction biosensor high-content screening assay to identify disruptors of the interactions between p53 and hDM2. Assay Drug Dev Techn. 8: 437-58. [JIF=1.727]

Taylor DL. (2010). A Personal Perspective on High Content Screening (HCS): From the Beginning. J Biomol Screen. 7: 720-725. [JIF=2.049]

Dudgeon DD, Shinde S, Hua Y, Shun TY, Lazo JS, Strock CJ, Giuliano KA, Taylor DL, Johnston PA,
Johnston PA. (2010). Implementation of a 220,000-compound HCS Campaign to Identify disruptors of the interaction between p53 and hDM2 and characterization of the confirmed hits. J Biomol Screen. 15: 766-82. [JIF=2.049]

Giuliano KA, Gough AH, Taylor DL, Vernetti LA, Johnston PA. (2010). Early safety assessment using cellular systems biology yields insights into mechanisms of action. J Biomol Screen. 15: 783-97. [JIF=2.049]

Giuliano KA, Gough AH, Taylor DL, Vernetti LA, Johnston PA. (2010). Early Safety Assessment Using Cellular Systems Biology Yields Insights into Mechanisms of Action. Journal of Biomolecular Screening, 15: 783-797.

Vogt A, Codore H, Day BW, Hukriede NA, Tsang M. (2010). Development of automated imaging and analysis for zebrafish chemical screens. Journal of Visualized Experiments. (40), pii: 1900. [JIF=1.19]

Zhu W, Jimenez M, Jung W-H, Camarco DP, Balachandran R, Vogt A, Day BW, Curran DP. (2010).Streamlined syntheses of (–)-dictyostatin, 25,26-dihydro-16-desmethyldictyostatin, and 6-epi-25,26-dihydro- 16-desmethyldictyostatin. Journal of the American Chemical Society. 132: 9175-9187. [JIF=9.907]

Lazo JS, Reese CE, Vogt A, Vollmer LL, Kitchens CA, Günther E, Graham TH, Hopkins CD, Wipf P. (2010). Deconstructing Resistance Determinants for the Antimitotic Natural Products Disorazole C1 and A1. Journal of Pharmacology and Experimental Therapeutics. 332: 906-911. [JIF=3.828]

Bhatt D, Zhang BW, Zuckerman DM. (2010). Steady-state simulations using weighted ensemble path sampling. J Chem Phys, 133: 014110. [JIF=3.333]

Ding Y, Mamonov AB, Zuckerman DM. (2010). Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo. J Phys Chem B, 114: 5870-7. [JIF=3.696]

Zhang BW, Jasnow D, Zuckerman DM. (2010). The “weighted ensemble” path sampling method is statistically exact for a broad class of stochastic processes and binning procedures. J Chem Phys, 132: 054107. [JIF=3.333] Bhatt D, Zuckerman DM. (2010). Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinase. J Chem Theory Comput. 6: 3527-3539. [JIF=5.215]

Zhang X, Bhatt D, Zuckerman DM. (2010). Automated sampling assessment for molecular simulations using the effective sample size. J Chem Theory Comput. 6: 3048-3057. [JIF=5.215]

Lezon TR, Bahar I. (2010). Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology. PLoS Comput Biol. 17:6e:1000816. [JIF=5.215]

Bahar I, Lezon TR, Yang LW, Eyal E. (2010). Global Dynamics of Proteins: Bridging Between Structure and Function.” Annu Rev Biophys. 39: 23-42. [JIF=13.574]

Bahar I, Lezon TR, Bakan A, Shrivastava I. (2010). Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem. Rev. 110: 1463-1497. [JIF=40.197]

Shrivastava I. (2010). Fluctuation dynamics analysis of gp120 envelope protein reveals a topologically based communication network. Proteins. 78: 2935-49. [JIF=3.392]

Bahar I, Lezon T, Bakan A, Shrivastava I. (2010). Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem Rev. 110, 1463-1497. [JIF=40.197] Chapter for a book: Handbook on Biological Networks. (2010). Ed Vega, Y.M., Cervantes, E. World Scientific Pub. Co., USA.

Cancer Target Discovery and Development Network, Schreiber SL, Shamji AF, Clemons PA, Hon C, Koehler AN, Munoz B, Palmer M, Stern AM, Wagner BK, Powers S, Lowe SW, Guo X, Krasnitz A, Sawey ET, Sordella R, Stein L, Trotman LC, Califano A, Dalla-Favera R, Ferrando A, Iavarone A, Pasqualucci L, Silva J, Stockwell BR, Hahn WC, Chin L, DePinho RA, Boehm JS, Gopal S, Huang A, Root DE, Weir BA, Gerhard DS, Zenklusen JC, Roth MG, White MA, Minna JD, MacMillan JB, Posner BA.  Towards patient-based cancer therapeutics. Nat Biotechnol. 2010 Sep;28(9):904-6.  PMID: 20829823.  PMCID: PMC2939009.