2012 Publications

Dutta A, Shrivastava I, Sukumaran M, Greger I, Bahar I. (2012). Comparative dynamics of NMDA- and AMPA- glutamate receptor N-terminal domains. Proteins. [Epub ahead of print] [JIF=3.392]

Liu L, Byeon IL, Bahar I, Gronenborn AM. (2012). Domain Swapping Proceeds via Complete Unfolding: A 19F- and 1H- NMR Study of the Cyanovirin-N Protein. J Am Chem Soc. 134:4229-35. [JIF=9.907]

Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S. (2012). The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci. 21:769-85. [JIF=2.798]

Lezon TR, Bahar I. (2012). Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh. Biophys J. 102:1331-40. [JIF=3.653]

Liu Y, Bahar I. (2012). Sequence Evolution Correlates with Structural Dynamics. Mol Biol Evol. 29:2253-63. [JIF=5.550]

Bakan A, Nevins N, Lakdawala AS, Bahar I. (2012). Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules. J Chem Theory Comput. 2012 Jul 10;8(7):2435-2447. [JIF=5.215]

Zomot E, Bahar I. (2012). A conformational switch in a partially unwound helix selectively determines the pathway for substrate release from the carnitine/γ-butyrobetaine antiporter CaiT. J Biol Chem. Jul 29. [Epub ahead of print]. [JIF=4.773]

Barua D, Goldstein B (2012) A mechanistic model of early FcεRI signaling: lipid rafts and the question of protection from dephosphorylation. PLOS ONE; 7: e51669. [JIF=3.730]

Barua D, Hlavacek WS, Lipniacki T (2012) A mechanistic model of early B cell antigen receptor signaling. The Journal of Immunology; 189: 646-658. [JIF=5.520]

Watters RJ, Benos PV, Oesterreich S. (2012). To bind or not to bind – FoxA1 determines estrogen receptor action in breast cancer progression. Breast Cancer Res. 14: 312. [JIF=6.091]

Namuswe F, Berg JM. (2012). Secondary interactions involving zinc-bound ligands: roles in structural stabilization and macromolecular interactions. J Inorg Biochem. 111: 146-9. [JIF=3.354]

Berg JM. (2012). National Centers for Biomedical Computing: from the BISTI report to the future. J Am Med Inform Assoc. 19: 151-2. [JIF=3.609]

Huang Y, Wolf S, Koes D, Popowicz GM, Camacho CJ, Holak TA, Dömling A. (2012) Exhaustive Fluorine Scanning toward Potent p53–Mdm2 Antagonists. ChemMedChem 7: 49-52. [JIF=3.151]

Koes D, Khoury K, Huang Y, Wang W, Bista M, Popowicz GM, Wolf S, Holak TA, Dömling A, Camacho CJ. Enabling large-scale design, synthesis and validation of small molecule protein-protein antagonists. PLoS One. 7:e32839. [JIF=4.092]

Koes DR, Camacho CJ. (2012). Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure. Bioinformatics. 28: 784-91. [JIF=5.468]

Koes DR, Camacho CJ. (2012). PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure. Nucleic Acids Res. 40: W387-92. [JIF=8.026]

Koes DR, Camacho CJ. (2012). ZINCPharmer: pharmacophore search of the ZINC database. Nucleic Acids Res. 40: W409-14. [JIF=8.026]

Koes DR, Camacho CJ. (2012). Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure. Bioinformatics. 28: 1951-1951. [JIF=5.468]

Ramanathan A, Savol AJ, Agarwal PK, Chennubhotla CS (2012) Event detection and sub-state discovery from bio-molecular simulations using higher-order statistics: Application to enzyme adenylate kinase. Proteins. [JIF = 3.392]

Burger VM, Chennubhotla CS. (2012). Nhs: Network-based hierarchical segmentation for cryo-electron microscopy density maps. Biopolymers. 97: SI:732-741. [JIF=2.870]

Burger VM, Ramanathan A, Savol AJ, Stanley CB, Agarwal PK, Chennubhotla CS. (2012). Quasi-anharmonic analysis reveals intermediate States in the nuclear co-activator receptor binding domain ensemble. Pacific Symposium on Biocomputing. 70-81.

Ayoob JC, Chennubhotla C. (2012). First Steps. International Innovation. 30-32.

Clark NL, Alani E, Aquadro CF. (2012) Evolutionary rate covariation reveals shared functionality and coexpression of genes. Genome Res 22(4): 714-720. [JIF=13.608]

Sekar JA, Faeder JR (2012) Rule-based modeling of signal transduction: a primer. Methods Mol Biol 880:139-218.

Smith AM, Xu W, Sun Y, Faeder JR, Marai GE. (2012). RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry. BMC Bioinformatics. 13 Suppl 8:S3. [JIF=2.751]

Kerr PJ, Ghedin E, DePasse JV, Fitch A, Cattadori IM, Hudson PJ, Tscharke DC, Read AF, Holmes EC (2012) Evolutionary history and attenuation of myxoma virus on two continents. PLoS Pathog 8(10):e1002950. Epub 2012 Oct 4. [JIF=9.127]

Dugan VG, Saira K, Ghedin E. (2012). Large-scale sequencing and the natural history of model human RNA viruses. Future Virology. 7: 563-573. [JIF=1.210]

Scott AL, Ghedin E, Nutman TB, McReynolds LA, Poole CB, Slatko BE, Foster JM. (2012). Filarial and Wolbachia Genomics. Parasite Immunol. 34: 121-9. [JIF=2.601]

Lam TT, Ip HS, Ghedin E, Wentworth DE, Halpin RA, Stockwell TB, Spiro DJ, Dusek RJ, Bortner JB, Hoskins J, Bales BD, Yparraguirre DR, Holmes EC. (2012). Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds. Ecol Lett. 15: 24-33. [JIF=17.557]

Gough AH, Giuliano KA, Taylor DL. (2012). Method for Automated Tissue Analysis. Official Gazette of the United States Patent and Trademark Office Patents. Patent: US 08114615.

Li Z, Ender C, Meister G, Moore PS, Chang Y, John B (2012) Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs. Nucleic Acids Res 40(14):6787-99. [JIF=8.026]

Guo Z, Shao LF, Zheng L, Du Q, Li PY, John B, Geller DA (2012) Micra-939 regulates human inducible nitric oxide synthase posttranscriptional gene expression in human hepatocytes. Proceedings of the National Academy of Sciences of the United States of America. 109: 5826-5831. [JIF=9.681]

General IJ, Dragomirova R, Meirovitch H (2012) Absolute free energy of binding of avidin/biotin, revisited. J Phys Chem B 116: 6628-36. [JIF=3.696]

Luo T, Masson K, Jaffe JD, Silkworth W, Ross NT, Scherer CA, Scholl C, Frohling S, Carr SA, Stern AM, Schreiber SL Golub TR. (2012) STK33 kinase inhibitor BRD-8899 has no effect on KRAS- dependent cancer cell viability. Proc Natl Acad Sci USA Feb 21;109(8):2860-2865. [JIF=9.681]

Wen Q, Goldenson B, Silver SJ, Schenone M, Dancik V, Zan Huang, Wang L-Z, Lewis TA, An WF, Xiaoyu L, Bray M-A, Thiollier C, Diebold L, Vokes MS, Moore CB, Bliss-Moreau M, VerPlank L, Tolliday NJ, Mishra R, Vemula S, Shi J, Wei L, Kapur R, Lopez C, Gerby B, Ballerini P, Pflumio F, Gilliland GD, Goldberg L, Birger Y, Izraeli S, Gamis AS, Smith FO, Woods WG, Scherer CA, Bradner J, Goh B-C, Mercher T, Carpenter AE, Gould RJ, Clemons PA, Carr SA, Root DA, Schreiber SL, Stern AM, Crispino JD (2012) Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL. Cell Aug 3;150(3):575-89. [JIF=34.403]

Adams DJ, Dai M, Pellegrino G, Wagner BK, Stern AM, Shamji AF, Schreiber SL (2012) Synthesis and cellular evaluation and action of piperlongumine analogs. Proc Natl Acad Sci USA Sep 18; 109(38):15115-20. [JIF=9.681]

Weiwer M, Spoonamore J, Wei J, Guichard B, Ross N, Masson K, Silkworth W, Dandapani S,
Palmer M, Scherer C, Stern AM, Schreiber S, Munoz B (2012) A potent and selective quinoxalinone-based STK33 inhibitor does not show synthetic lethality in KRAS-dependent cells. ACS Med Chem Lett Dec 13;3(12):1034-38. [JIF=3.355]

Gough AH, Giuliano KA, Taylor DL (2012) Method for Automated Tissue Analysis. Official Gazette of the United States Patent and Trademark Office Patents. Patent: US 08114615.

Sehrawat A, Kim S-H, Vogt A, Singh SV (2012) Suppression of FOXQ1 in benzyl isothiocyanate-mediated inhibition of epithelial-mesenchymal transition in human breast cancer cells Carcinogenesis 2013;34(4):864-873

Li M, Chen X, Ye QZ, Vogt A, Yin XM (2012) A high-throughput FRET-based assay for determination of Atg4 activity. Autophagy. 8: 401-412. [JIF=7.453]

Soares MS, Lessa JA, Mendes IC, Da Silva JG, dos Santos RG, Salum LB, Daghestani H, Andricopulo AD, Day BW, Vogt A, Pequero JL, Rocha WR, Beraldo H (2012) N-4-Phenyl-substitutes 2-acetylpyridine thiosemicarbazones: Cytotoxicity against human tumor cells, structure-activity relationship studies and investigation on the mechanism of action. Bioorganic & Medicinal Chemistry. 20: 3396-3409. [JIF=2.921]

Arora R, Shuda M, Guastafierro A, Feng HC, Toptan T, Tolstov Y, Normolle D, Vollmer LL, Vogt A, Domling A, Bodsky JL, Chang Y, Moore PS. (2012). Survivin is a therapeutic target in merkel cell carcinoma. Science Translational Medicine. 4: 133ra56. [JIF=7.804]

Mamonov A, Lettieri S, Ding Y, Sarver J, Palli R, Cunningham T, Saxena S, Zuckerman DM (2012) Tunable, mixed resolution modeling using library-based Monte Carlo and graphics processing units. Journal of Chemical Theory and Computation. 8: 2921-2929. [JIF=5.215]

Lettieri S, Zuckerman DM (2012) Accelerating molecular Monte Carlo simulations using distance and orientation-dependent energy tables: tuning from atomistic accuracy to smoothed “coarse-grained” models. J Comput Chem. 33: 268-75. [JIF=4.583]

Delubac D, Highley CB, Witzberger-Krajcovic M, Ayoob JC, Furbee EC, Minden JS, Zappe S (2012) Microfluidic system with integrated microinjector for automated Drosophila embryo injection. Lab Chip Nov 21;12(22):4911-9. [JIF=6.260]

Ayoob JC, Chennubhotla C (2012) First Steps. International Innovation. 30-32.

Huang Y, Wolf S, Koes DR, Popowicz GM, Camacho CJ, Holak TA, Dömling A (2012) Exhaustive Fluorine Scanning toward Potent p53–Mdm2 Antagonists. ChemMedChem 7: 49-52. [JIF=3.151]

Koes DR, Camacho CJ (2012) Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure. Bioinformatics. 28: 784-791. [JIF=5.468]

Koes DR, Camacho CJ (2012) PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure. Nucleic Acids Res. 40: W387-92. [JIF=8.026]

Koes DR, Camacho CJ (2012) ZINCPharmer: pharmacophore search of the ZINC database. Nucleic Acids Res. 40: W409-14. [JIF=8.026]

Koes D, Khoury K, Huang Y, Wang W, Bista M, Popowicz GM, Wolf S, Holak TA, Dömling A, Camacho CJ (2012) Enabling large-scale design, synthesis and validation of small molecule protein-protein antagonists. PLoS One. 7:e32839. [JIF=4.092]

Koes DR, Camacho CJ (2012) Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure. Bioinformatics. 28: 1951-1951. [JIF=5.468]

Lezon TR. (2012). The effects of rigid motions on elastic network model force constants. Proteins. 80: 1133-42. [JIF=3.392]

Lezon TR, Bahar I. (2012). Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh. Biophys J. 102:1331-40. [JIF=3.653]

Shrivastava I, Wendel K, LaLonde J. (2012). Spontaneous rearrangement of the β20/β21 strands in simulations of unliganded HIV-1 glycoprotein. Biochemistry. [Epub ahead of print] [JIF=3.422]

Dutta A, Shrivastava I, Sukumaran M, Greger I, Bahar I. (2012). Comparative dynamics of NMDA- and AMPA- glutamate receptor N-terminal domains. Proteins. [Epub ahead of print] [JIF=3.392]

Adams DJ, Dai M, Pellegrino G, Wagner BK, Stern AM, Shamji AF, Schreiber SL. Synthesis and cellular evaluation and action of piperlongumine analogs.  Proc Natl Acad Sci USA.  2012 Sep18;109(38):15115-20.  PMID: 22949699.  PMCID: PMC3458345.

Wen Q, Goldenson B, Silver SJ, Schenone M, Dancik V, Zan Huang, Wang L-Z, Lewis TA, An WF, Xiaoyu L, Bray M-A, Thiollier C, Diebold L, Vokes MS, Moore CB, Bliss-Moreau M, VerPlank L, Tolliday NJ, Mishra R, Vemula S, Shi J, Wei L, Kapur R, Lopez C, Gerby B, Ballerini P, Pflumio F, Gilliland GD, Goldberg L, Birger Y, Izraeli S, Gamis AS, Smith FO, Woods WG, Scherer CA, Bradner J, Goh B-C, Mercher T, Carpenter AE, Gould RJ, Clemons PA, Carr SA, Root DA, Schreiber SL, Stern AM, Crispino JD.  Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL.  Cell.  2012 Aug 3;150(3):575-89.  PMID:22863010.

Luo T, Masson K, Jaffe JD, Silkworth W, Ross NT, Scherer CA, Scholl C, Frohling S, Carr SA, Stern AM, Schreiber SL Golub TR.  STK33 kinase inhibitor BRD-8899 has no effect on KRAS- dependent cancer cell viability.  Proc Natl Acad Sci USA.  2012 Feb 21;109(8):2860-2865.  PMID:        22323609.  PMCID: PMC3286931.

Shrivastava IH, Wendel K, LaLonde JM (2012) Spontaneous rearrangement of the β20/β21 strands in simulations of unliganded HIV-1 glycoprotein, gp120 Biochemistry 51(39):7783-93.