Student Publications

  1. Liu Y. and Bahar I. (2009) Toward understanding allosteric signaling mechanisms in the ATPase domain of molecular chaperones. Pac Symp Biocomput. 2010:269-80.

  2. Li, Z., Kim, S.W., Lin, Y., Moore, P.S., Chang, Y. & John B. (2009) Characterization of viral and human RNAs smaller than canonical microRNAs. Journal of Virology.

  3. Howrylak JA, Dolinay T, Lucht LA, Wang Z, Christiani DC, Sethi JM, Xing EP, Donahoe MP, Choi AM. (2009)"Discovery of the Gene Signature for Acute Lung Injury in Patients with Sepsis." Physiol Genomics (e-pub)

  4. Bahar I, Lezon TR, Bakan A, Shrivastava IH. (2009) Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins Chem Rev In press(0) 0-0

  5. Joseph JM, Durand D. (2009) Family Classification Without Domain Chaining. Bioinformatics 25:i45-53.

  6. Molina G, Voght A, Bakan A, Dai W, de Oliveira PQ, Znosko W, Smithgall TE, Bahar I, Lazo JS, Day BW, Tsang M. (2009) Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages Nat Chem Biol, Jul 5.

  7. Brower-Sinning R, Carter DM, Crevar CJ, Ghedin E, Ross TM, Benos PV.(2009) The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus. Genome Biol. 10(2):R18.

  8. Kadri S, Hinman V, Benos PV. (2009) HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models. BMC Bioinformatics 10 Suppl 1:S35

  9. Howrylak JA, Dolinay T, Lucht LA, Wang Z, Christiani DC, Sethi JM, Xing EP, Donahoe MP, Choi AM. (2009) Discovery of the Gene Signature for Acute Lung Injury in Patients with Sepsis. Physiol Genomics

  10. A. Ramanathan,, P.K. Agarwal, C.J. Langmead (2008) An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations; Proc. 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB) 2009, pp. 138-154

  11. Song N, Joseph JM, Davis GB, Durand D (2008) "Sequence similarity network reveals common ancestry of multidomain proteins; PLoS Comput Biol 4, e1000063. (PDF)

  12. Liu Y, Eyal E, Bahar I (2008) “Analysis of correlated mutations in HIV-1 protease using spectral  clustering” Bioinformatics 24, 1243-50. (PDF)

  13. Bakan A, Lazo JS, Wipf P, Brummond KM, Bahar I. (2008) Toward a Molecular Understanding of the Interaction of Dual Specificity Phosphatases with Substrates: Insights from Structure-Based Modeling and High Throughput Screening; Curr Med Chem 15(25) 2536-2544

  14. Coelho, Luís Pedro; Murphy, Robert F. (2008) “Identifying Subcellular Locations from Images of Unknown Resolution” Proceedings of BioInformatics Research and Development 2008, July 2008. (PDF)

  15. Bakan A, Lazo JS, Wipf P, Brummond KM, Bahar I. (2008) Toward a molecular understanding of the interaction of dual specificity phosphatases with substrates: insights from structure-based modeling and high throughput screening. Curr Med Chem. 15:2536-44. (PDF)

  16. Lee B, Leduc PR, Schwartz R. (2008) "Stochastic off-lattice modeling of molecular self-assembly in crowded environments by Green's function reaction dynamics." Phys Rev E Stat Nonlin Soft Matter Phys. 78:031911.

  17. Lazo JS, Skoko JJ, Werner S, Mitasev B, Bakan A, Koizumi F, Yellow-Duke A, Bahar I, Brummond KM. (2007) Structurally Unique Inhibitors of Human Mitogen-Activated Protein Kinase Phosphatase-1 Identified in a Pyrrole Carboxamide Library; J Pharmacol Exp Ther 322(3) 940-947 doi:10.1124/jpet.107.122242
© 2008 Joint Carnegie Mellon - University of Pittsburgh PhD Program in Computational Biology (CPCB)