Publications

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

  2. A. Donze, G. Clermont, A. Legay, C.J. Langmead, "Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology". Proc. 13th Annual International Conference on Research in Computational Molecular (RECOMB), 2009 pp. 155-169.

  3. H. Kamisetty and C.J. Langmead "A Bayesian Approach to Protein Model Quality Assessment". 26th International Conference on Machine Learning (ICML), Montreal, Canada, June 14 - 18, 2009 (in press)

  4. A. Ramanathan, J. Borreguero, C.J. Langmead, P. K. Agarwal, "Conserved Protein Flexibility And Pathways Of Energy Flow In Enzyme Catalysis". Biophysical Journal, 2009 96(3) p. 71a.

  5. C.J. Langmead, S.K. Jha, "Symbolic Approaches to Finding Control Strategies in Boolean Networks". Journal of Bioinformatics and Computational Biology, 2009 7(2), pp. 323-338

  6. An, G., Faeder, J. & Vodovotz, Y. (2008) “Translational systems biology: introduction of an engineering approach to the pathophysiology of the burn patient,” J Burn Care Res 29, 277-85.

  7. Bagci, E. Z., Vodovotz, Y., Billiar, T. R., Ermentrout, G. B., & Bahar, I. (2008) “Computational insights on the competing effects of nitric oxide in regulating apoptosis,” PLoS ONE 3, e2249.

  8. H. Kamisetty, E.P. Xing, C.J. Langmead, "Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation". Journal of Computational Biology, 2008 15(7), pp. 755-766

  9. Bagci, E. Z., Vodovotz, Y., Billiar, T. R., Ermentrout, G. B., & Bahar, I. (2006) “Bistability in apoptosis: Roles of Bax, Bcl-2, and mitochondrial permeability transition pores” Biophys J 90, 1546-1559.

  10. Bahar, I., Chennubhotla, C., & Tobi, D. (2007) “Intrinsic dynamics of enzymes in the unbound state and, relation to allosteric regulation” Curr Opin Struct Biol 17, 633-640.

  11. Beg, Q. K., Vazquez, A., Ernst, J., de Menezes, M. A., Bar-Joseph, Z., Barabasi, A. L., & Oltvai, Z. N. (2007) “Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity” Proc Natl Acad Sci USA 104, 12663-12668.

  12. Benos PV, Corcoran DL, Feingold E (2007) “Web-based identification of evolutionary conserved DNA cis-regulatory elements” Methods Mol Biol 395, 425-36.

  13. Blelloch, G. E., Dhamdhere, K., Halperin, E., Ravi, R., Schwartz, R., & Sridhar, S. (2006) “Fixed parameter tractability of binary near-perfect phylogenetic tree reconstruction” Automata, Languages and Programming, Pt 1 4051, 667-678.

  14. H. Kamisetty and C.J. Langmead "Conformational Free Energy of Protein Structures: Computing Upper and Lower bounds". Proc. 3DSIG 2008 Structural Bioinformatics and Computational Biophysics. 2008. pp. 23-24

  15. Bondarenko, V., Xu, Y., & Tang, P. (2007) “Structure of the first transmembrane domain of the neuronal acetylcholine receptor beta(2) subunit” Biophys J 92, 1616-1622.

  16. Bondarenko, V., Yushmanov, V. E., Xu, Y., & Tang, P. (2008) “NMR study of general anesthetic interaction with nAChR beta(2) subunit,” Biophys J 94, 1681-1688.

  17. Chebira, A., Barbotin, Y., Jackson, C., Merryman, T., Srinivasa, G., Murphy, R. F., & Kovacevic, J. (2007) “A multiresolution approach to automated classification of protein subcellular location images” BMC Bioinformatics 8, 210.

  18. Chebira, Amina; Coelho, Luis Pedro; Sandryhaila, Aliaksei; Lin, Stephen; Jenkinson, William G.; MacSleyne, Jeremiah; Hoffman, Christopher; Cuadra, Philipp;  Jackson, Charles; Püschel, Markus; Kovacevic, Jelena (2007) “An Adaptive Multiresolution Approach to Fingerprint Recognition” Proceedings of the International Conference on Image Processing, September 2007.

  19. Cheng MH, Coalson RD, Cascio M, Kurnikova M (2008) “Computational prediction of ion permeation characteristics in the glycine receptor modified by photo-sensitive compounds” J Comput Aided Mol Des, in press.

  20. Chennubhotla, C. & Bahar, I. (2007) “Signal propagation in proteins and relation to equilibrium fluctuations” PLoS Comput Biol 3, 1716-1726.

  21. Chennubhotla, C., Yang, Z., & Bahar, I. (2008) “Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL,” Mol Biosyst 4, 287-292.

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

  23. Ermentrout, G. B., Galan, R. F., & Urban, N. N. (2007) “Relating neural dynamics to neural coding” Phys Rev Lett 99, 248103.

  24. Ernst J, Beg QK, Kay KA, Balázsi G, Oltvai ZN, Bar-Joseph Z (2008) “A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli” PLoS Comput Biol, 4, e1000044.

  25. Eyal, E., Chennubhotla, C., Yang, L. W., & Bahar, I. (2007) “Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models” Bioinformatics 23, I175-I184.

  26. Farkas IJ, Wu C, Chennubhotla C, Bahar I, Oltvai ZN (2006) “Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae” BMC Bioinformatics 7, 478.

  27. Farkas, I. J., Wu, C., Chennubhotla, C., Bahar, I., & Oltvai, Z. N. (2006) “Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae” BMC Bioinformatics 7, 478.

  28. Galan, R. F., Ermentrout, G. B., & Urban, N. N. (2005) “Efficient estimation of phase-resetting curves in real neurons and its significance for neural-network modeling” Phys Rev Lett  94,

  29. Galan, R. F., Ermentrout, G. B., & Urban, N. N. (2006) “Predicting synchronized neural assemblies from experimentally estimated phase-resetting curves” Neurocomput  69, 1112-1115.

  30. Galan, R. F., Ermentrout, G. B., & Urban, N. N. (2006) “Reliability, discriminability and stochastic synchronization of olfactory neurons” Sens Act B 116, 168-173.

  31. Galan, R. F., Ermentrout, G. B., & Urban, N. N. (2007) “Reliability and stochastic synchronization in type I vs. type II neural oscillators” Neurocomputing 70, 2102-2106.

  32. Galan, R. F., Ermentrout, G. B., & Urban, N. N. (2007) “Stochastic dynamics of uncoupled neural oscillators: Fokker-Planck studies with the finite element method” Phys Rev E 76, 056110.

  33. Galan, R. F., Ermentrout, G. B., & Urban, N. N. (2008) “Optimal time scale for spike-time reliability: Theory, simulations, and experiments,” J Neurophysiol 99, 277-283.

  34. Galan, R. F., Fourcaud-Trocme, N., Ermentrout, G. B., & Urban, N. N. (2006) “Correlation-induced synchronization of oscillations in olfactory bulb neurons” J Neurosci 26, 3646-3655.

  35. Ganapathiraju M, Balakrishnan N, Reddy R, Klein-Seetharaman, J (2008) “Transmembrane helix prediction using amino acid property features and latent semantic analysis” BMC Bioinformatics 9 Suppl 1:S4.

  36. Ganapathiraju M, Jursa CJ, Karimi HA, Klein-Seetharaman, J (2007) “TMpro web server and web service: transmembrane helix prediction through amino acid property analysis” Bioinformatics 23, 2795-6.

  37. Genovese, C. R., Roeder, K., & Wasserman, L. (2006) “False discovery control with p-value weighting” Biometrika 93, 509-524.

  38. Howrylak, J., Choi, A.M.K. (2008) “Gene expression profiling in chronic obstructive pulmonary disease” Am J Respir Crit Care Med 177, 364-5.

  39. Isin, B., Rader, A. J., Dhiman, H. K., Klein-Seetharaman, J., & Bahar, I. (2006) “Predisposition of the dark state of rhodopsin to functional changes in structure” Proteins-Structure Function and Bioinformatics 65, 970-983.

  40. Iyer, A. K. V., Tran, K. T., Borysenko, C. W., Cascio, M., Camacho, C. J., Blair, H. C., Bahar, I., & Wells, A. (2007) “Tenascin cytotactin epidermal growth factor-like repeat binds epidermal growth factor receptor with low affinity” J Cell Physiol 211, 748-758.

  41. Kaminski, N. & Bar-Joseph, Z. (2006) “A patient-gene model for temporal expression profiles in clinical studies” Research in Computational Molecular Biology, Proceedings 3909, 69-82.

  42. Kaminski, N. & Bar-Joseph, Z. (2007) “A patient-gene model for temporal expression profiles in clinical studies” J Comput Biol 14, 324-338.

  43. Kou, Z. Z., Cohen, W. W., & Murphy, R. F. (2005) “High-recall protein entity recognition using a dictionary” Bioinformatics 21, I266-I273.

  44. Kovacevic, J. & Murphy, R. F. (2006) “Molecular and cellular bioimaging” IEEE Signal Processing Magazine 23, 19.

  45. 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, 940-947.

  46. Lee J, Li Z, Brower-Sinning R, John B (2007) ”Regulatory circuit of human microRNA biogenesis” PLoS Comput Biol, 3, e67. Epub 2007 Feb 27. PMID: 17447837 [PubMed - indexed for MEDLINE]

  47. Lin, T. , Ray, P. R. , Sandve, G. K., Uguroglu, S., and Xing, E. P. (2008) “BayCis: a Bayesian hierarchical HMM for cis-regulatory module decoding in metazoan genomes” Proceedings of the 12th International Conference on Research in Computational Molecular Biology (RECOMB 2008), Singapore, 2008, in press.

  48. Liu Y, Carbonell J, Weigele P, Gopalakrishnan V (2006) “Protein fold recognition using segmentation conditional random fields (SCRFs)” J Comput Biol 13, 394-406.

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

  50. Lu Y, Rosenfeld R, Bar-Joseph Z (2006) “Identifying cycling genes by combining sequence homology and expression data” Bioinformatics 22, e314-22.

  51. Lu, Y., Mahony, S., Benos, P. V., Rosenfeld, R., Simon, I., Breeden, L. L., & Bar-Joseph, Z. (2007) “Combined analysis reveals a core set of cycling genes” Genome Biol 8, R146.

  52. Ma, D. J., Liu, Z. W., Li, L., Tang, P., & Xu, Y. (2005) “Structure and dynamics of the second and third transmembrane domains of human glycine receptor” Biochemistry 44, 8790-8800.

  53. Ma, D. J., Tang, P., & Xu, Y. (2005) “Modulation of “23” loop between TM2 and TM3 domains of human glycine receptor by volatile anesthetics” Biophys J 88, 188A-189A.

  54. Mahony S, Corcoran DL, Feingold E, Benos PV (2007) “Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome” Genome Biol 8, R84.

  55. Mamonov, A. B., Kurnikova, M. G., & Coalson, R. D. (2006) “Diffusion constant of K+ inside Gramicidin A: A comparative study of four computational methods” Biophys  Chem 124, 268-278.

  56. Mi, Q., Swigon, D., Riviere, B., Cetin, S., Vodovotz, Y., & Hackam, D. J. (2007) “One-dimensional elastic continuum model of enterocyte layer migration” Biophys J 93, 3745-3752.

  57. Munshi R, Coalson RD, Ermentrout GB, Madura JD, Meirovitch H, Stiles JR, Bahar I (2006) “An introduction to simulation and visualization of biological systems at multiple scales: a summer training program for interdisciplinary research” Biotechnol Prog  22, 179-85.

  58. Puskar, K. M., Parisi-Amon, A., Ta’asan, S., Schwartz, R., & Leduc, P. R. (2007) “Modeling molecular interactions to understand spatial crowding effects on heterodimer formations” Phys Rev E 76, 041904.

  59. Puskar, K. M., Parisi-Amon, A., Ta’asan, S., Schwartz, R., & Leduc, P. R. (2007) “Modeling molecular interactions to understand spatial crowding effects on heterodimer formations” Phys Rev E 76, 041904.

  60. Puskar, K., Ta’asan, S., Schwartz, R., & Leduc, P. R. (2006) “Evaluating spatial constraints in cellular assembly processes using a Monte Carlo approach” Cell Biochem Biophys 45, 195-201.

  61. Qi Y, Klein-Seetharaman J, Bar-Joseph Z (2007) “A mixture of feature experts approach for protein-protein interaction prediction” BMC Bioinformatics 8 Suppl 10:S6.

  62. Qi, Y. J., Bar-Joseph, Z., & Klein-Seetharaman, J. (2006) “Evaluation of different biological data and computational classification methods for use in protein interaction prediction” Proteins-Structure Function and Bioinformatics 63, 490-500.

  63. Ray, P.R., Shringarpure, S., Kolar, M. and Xing, E. P. (2008) “CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing” PLoS Comput Biol, in press.

  64. D.C. Whitcomb, V.N. Muddana, C.J. Langmead, J. Lamb, G. I. Papachristou, "Angiopoietin-2, a regulator of vascular permeability in inflammation, is elevated in severe acute pancreatitis and is associated with systemic organ failure". Pancreas, 2008 37(4), pp. 500-501.

  65. Rinaldo, A., Bacanu, S. A., Devlin, B., Sonpar, V., Wasserman, L., & Roeder, K. (2005) “Characterization of multilocus linkage disequilibrium” Genet Epidemiol 28, 193-206.

  66. Roeder, K., Bacanu, S. A., Wasserman, L., & Devlin, B. (2006) “Using linkage genome scans to improve power of association in genome scans” Am J Hum Genet 78, 243-252.

  67. Roeder, K., Devlin, B., & Wasserman, L. (2007) “Improving power in genome-wide association studies: Weights tip the scale” Gen Epidemiol 31, 741-747.

  68. Saladino, A. C., Xu, Y., & Tang, P. (2005) “Homology Modeling and molecular dynamics simulations of transmembrane domain structure of human neuronal nicotinic acetylcholine receptor” Biophys J 88, 1009-1017.

  69. Song N, Joseph JM, Davis GB, Durand D (2008) “Sequence similarity network reveals common ancestry of multidomain proteins” PLoS Comput Biol 4, e1000063.

  70. Sridhar, S., Blelloch, G. E., Ravi, R., & Schwartz, R. (2006) “Optimal imperfect phylogeny reconstruction and haplotyping (IPPH)” Comput Syst Bioinformatics Conf 199-210.

  71. Sridhar, S., Dhamdhere, K., Blelloch, G. E., Halperin, E., Ravi, R., & Schwartz, R. (2007) “Algorithms for efficient near-perfect phylogenetic tree reconstruction in theory and practice” IEEE-ACM Trans Comput Biol Bioinform 4, 561-571.

  72. Sridhar, S., Dhamdhere, K., Blelloch, G. E., Halperin, E., Ravi, R., & Schwartz, R. (2006) “Simple reconstruction of binary near-perfect phylogenetic trees” Computational Science - ICCS 2006, Pt 2, Proceedings 3992, 799-806.

  73. Sridhar, S., Lam, F., Blelloch, G. E., Ravi, R., & Schwartz, R. (2007) “Direct maximum parsimony phylogeny reconstruction from genotype data” BMC Bioinformatics 8, 472.

  74. Szarecka, A., Xu, Y., & Tang, P. (2007) “Dynamics of firefly luciferase inhibition by general anesthetics: Gaussian and anisotropic network analyses” Biophys J 93, 1895-1905.

  75. Szarecka, A., Xu, Y., & Tang, P. (2007) “Dynamics of heteropentameric nicotinic acetylcholine receptor: Implications of the gating mechanism” Proteins-Structure Function and Bioinformatics 68, 948-960.

  76. Tsai, MC, Tsui FC (2007) “An Evaluation of Biosurveillance Grid-Dynamic Algorithm Distribution across Multiple Computer Nodes” American Medical Informatics Association 2007 Annual Symposium, November 12, 2007.

  77. Upperman, J. S., Camerini, V., Lugo, B., Yotov, I., Sullivan, J., Rubin, J., Clermont, G., Zamora, R., Ermentrout, G. B., Ford, H. R., & Vodovotz, Y. (2007) “Mathematical modeling in necrotizing enterocotitis a new took at an ongoing problem” J Pediatr Surg 42, 445-453.

  78. Vazquez A, Beg QK, Demenezes MA, Ernst J, Bar-Joseph Z, Barabási AL, Boros LG, Oltvai ZN (2008) “Impact of the solvent capacity constraint on E. coli metabolism” BMC Syst Biol, 2, 7.

  79. Vodovotz, Y., Chow, C. C., Bartels, J., Lagoa, C., Prince, J. M., Levy, R. M., Kumar, R., Day, J., Rubin, J., Constantine, G., BiIliar, T. R., Fink, M. P., & Clermont, G. (2006) “In silico models of acute inflammation in animals” Shock 26, 235-244.

  80. Vodovotz, Y., Chow, C., Bartels, J., Lagoa, C., Kumar, R., Day, J., Rubin, J., Constantine, G., Billiar, T., Fink, M., & Clermont, G. (2005) “Mathematical simulations of sepsis and trauma” Shock 23, 26-27.

  81. Vodovotz, Y., Clermont, G., Hunt, C. A., Lefering, R., Bartels, J., Seydel, R., Hotchkiss, J., Ta’asan, S., Neugebauer, E., & An, G. (2007) “Evidence-based modeling of critical illness: an initial consensus from the Society for Complexity in Acute Illness” J Crit Care 22, 77-84.

  82. C.J. Langmead and S.K. Jha "Predicting Protein Folding Kinetics via Model Checking: Extended Abstract". Proc. 7th Worskop on Algorithms in Bioinformatics (WABI), 2007, pp. 252-264

  83. Yang, L. W., Eyal, E., Chennubhotla, C., Jungoo, J., Gronenborn, A.M., & Bahar, I. (2007) “Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions” Structure 15, 741-749.

  84. Zhang BW, Jasnow D, Zuckerman DM (2007) “Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin” Proc Natl Acad Sci USA 104, 18043-8.

  85. Zhang BW, Jasnow D, Zuckerman DM (2007) “Transition-event durations in one-dimensional activated processes” J Chem Phys 126, 074504.

  86. K. Arun and C.J. Langmead "Structure based chemical shift prediction using Random Forests nonlinear regression". Proc. of The Forth Asia-Pacific Bioinformatics Conference, (APBC), 2006, pp. 317-326.

  87. C.J. Langmead "A Randomized Algorithm for Learning Mahalanobis Metrics: Application to Classification and Regression of Biological Data". Proc. of The Forth Asia-Pacific Bioinformatics Conference, (APBC). 2006, pp. 217-226.

  88. Wang, Y. L., Hahn, K. M., Murphy, R. F., & Horwitz, A. F. (2006) “Applications to biology - single molecules to single cells” J Cell Biol 174, 903.

  89. Ytreberg FM, Swendsen RH, Zuckerman DM (2006) “Comparison of free energy methods for molecular systems” J Chem Phys 125, 184114.

  90. Wang, Y. L., Hahn, K. M., Murphy, R. F., & Horwitz, A. F. (2006) “From imaging to understanding: Frontiers in Live Cell Imaging, Bethesda, MD, April 19-21, 2006” J Cell Biol 174, 481-484.

  91. Yonkunas, M. J., Xu, Y., & Tang, P. (2005) “Anesthetic interaction with ketosteroid isomerase: Insights from molecular dynamics simulations” Biophys J 89, 2350-2356.

  92. Wu, W., Dave, N., Tseng, G. C., Richards, T., Xing, E. P., & Kaminski, N. (2005) “Comparison of normalization methods for CodeLink Bioarray data” BMC Bioinformatics 6,

  93. A.K. Yan, C.J. Langmead, B.R. Donald, "A Probability-Based Similarity Measure for Saupe Alignment Tensors with Applications to Residual Dipolar Couplings in NMR Structural Biology". The International Journal of Robotics Research, 2005 24(2-3), pp.165-182.

  94. C.J. Langmead, A.K. Yan, L. Wang, R. Lilien and B.R. Donald, "A Polynomial Time Algorithm for Nuclear Vector Replacement for Automated NMR Resonance Assignments". Journal of Computational Biology, 2004 11(2-3), pp. 277-298.
© 2008 Joint Carnegie Mellon - University of Pittsburgh PhD Program in Computational Biology (CPCB)