Carnegie Mellon University

Student Publications

  1. Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I. (2021) ProDy 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python. Bioinformatics [Online ahead of print]. PMID: 33831302
  2. Pei F, Shi Q, Zhang H, Bahar I (2021) Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. J Chem Inf Model [Online ahead of print]. PMID: 33831302
  3. Wang H, Pei F, Vanyukov MM, Bahar I, Wu W, Xing EP. (2021) Coupled mixed model for joint genetic analysis of complex disorders with two independently collected data sets. BMC Bioinformatics 22(1):50. PMID: 33546598
  4. Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T (2021) HiDeF: Identifying Persistent Structures in Multiscale ‘Omics Data. Genome Biol. 22: 21. PMID: 33413539 PMCID: PMC7789082
  5. Wingert B, Krieger JM, Li H, Bahar I (2020) Adaptability and Specificity: How Do Proteins Balance Opposing Needs to Achieve Function? Curr Opin Struct Biol 67:25-32. PMID: 33053463
  6. Cheng MH, Zhang S, Porritt RA, Rivas MN, Paschold L, Willscher E, Binder M, Arditi M*, Bahar I* (2020) Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation. Proc Natl Acad Sci USA 117: 25254-25262 PMID: 32989130 PMCID: PMC7568239 
  7. Zhang Y, Krieger JM, Mikulska-Ruminska K, Kaynak B, Sorzano COS, Carazo JM, Xing J, Bahar I (2020) State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps. Prog Biophys Mol Biol S0079-6107(20)30082-1. PMID: 32866476 

  8. Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T. (2020) Decoding of persistent multiscale structures in complex biological networks. bioRxiv. PMID: 32587977 PMCID: PMC7310637
  9. Shi Q, Pei F, Silverman GA, Pak SC, Perlmutter DH, Liu B*, Bahar I*. (2020) Mechanisms of Action of Autophagy Modulators Dissected by Quantitative Systems Pharmacology Analysis. Int. J. Mol. Sci 21:2855. PMID: 32325894 PMCID: PMC7215584
  10. Li H, Taylor DLBahar I. (2020) QuartataWeb: Integrated Chemical-protein-pathway Mapping for Polypharmacology and ChemogenomicsBioinformatics 36:3935-3937. PMID: 32221612 PMCID: PMC7320630
  11. Cheng MH, Ponzoni L, Sorkina T, Lee JY, Zhang S, Sorkin A, Bahar I. (2019) Trimerization of Dopamine Transporter Triggered by AIM-100 Binding: Molecular Mechanisms and Effect of Mutations. Neuropharmacology 161:107676 PMID: 31228486 PMCID: 6917874 DOI: 10.1016/j.neuropharm.2019.107676
  12. Mikulska-Ruminska K, Shrivastava IH, Krieger JM, Zhang S, Li H, Bayir H, Wenzel SE, VanDemark AP, Kagan VE, Bahar I. (2019) Characterization of differential dynamics, specificity, and allostery of lipoxygenase family members. J Chem Inf Model 59: 2496-2508. PMID: 30762363 PMCID: 6541894
  13. Wang Y, Cobanoglu MC, Li J, Hidvegi T, Hale P, Ewing M, Chu AS, Gong Z, Muzumdar R, Pak SC, Silverman GA, Bahar I, Perlmutter DH (2019) An analog of glibenclamide selectively enhances autophagic degradation of misfolded α1-antitrypsin Z PloS One 14: e0209748. PMID: 30673724 PMCID: 6343872J281. Lee JY, Krieger J, Herguedas B, García-Nafría J, Dutta A, Shaikh SA, Greger IH, Bahar I. (2019) Druggability Simulations and X-ray Crystallography Reveal a Ligand-binding Site in the GluA3 AMPA Receptor N-terminal Domain. Structure 27: 241-252. PMID: 30528594 PMCID: 6365164
  14. Shashank Singh, Yang Yang, Barnabás Póczos, Jian Ma. (2018) Enhancer-Promoter Interaction from Genomic Sequence with Deep Learning. Quantitative Biology, Accepted , Vol to appear, Pgs to appear
  15. Xiangrui Zeng, Miguel Ricardo Leung, Tzviya Zeev-Ben-Mordehai, Min Xu. (2018) A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation. Journal of Structural Biology (202), 150-160
  16. Wingert, Bentley M., Rick Oerlemans, and Carlos J. Camacho. (2018) Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges. Journal of computer-aided molecular design 32.1 (2018): 287-297.
  17. Bondarenko V, Wells MM, Xu Y, Tang P (2018) Solution NMR Studies of Anesthetic Interactions With Ion Channels. Methods in Enzymology, in press
  18. Weiguang Mao, Ryan Hausler, Maria Chikina. (2018) DataRemix: a universal data transformation for optimal inference from gene expression datasets. RECOME Satellite on Genetics (Abstract only)
  19. Natalie Sauerwald and Carl Kingsford.  (2018) Quantifying the similarity of topological domains across normal and cancer human cell types. Proceedings of Intelligent Systems for Molecular Biology (to appear in Bioinformatics)
  20. Chen Q, Wells MM, Arjunan P, Tillman TS, Adell D, Cohen AE, Xu Y, Tang P. (2018) Structures and Functions of ELIC-GABAAR Chimeras. Biophysical Journal, 114(3): 299a. (abstract only)
  21. Marcus Thomas, Russell Schwartz (2018) A method for efficient Bayesian optimization of self-assembly systems from scattering data. BMC Systems Biology
  22. Cong Ma, Mingfu Shao, Carl Kingsford. (2018) SQUID: transcriptomic structural variation detection from RNA-seq. Genome Biology, vol 19, pg 52
  23. Kaya C, Cheng MH, Block ER, Bartol TM, Sejnowski TJ, Sorkin A, Faeder JR, Bahar I. (2018) Heterogeneities in Axonal Structure and Transporter Distribution Lower Dopamine Reuptake Efficiency. eNeuro. 2018 Feb 5;5(1). pii: ENEURO.0298-17.2017. doi: 10.1523/ENEURO.0298-17.2017. eCollection 2018 Jan-Feb.
  24. Ruochi Zhang, Yuchuan Wang, Yang Yang, Yang Zhang, Jian Ma. (2018) Predicting CTCF-mediated chromatin loops using CTCF-MP. Bioinformatics, Accepted ISMB 2018, , Vol: to appear, Pgs: to appear
  25. Raghavendran Partha, Bharesh K Chauhan, Zelia Ferreira, Joseph D Robinson, Kira Lathrop, Ken K Nischal, Maria Chikina, Nathan L Clark. (2017)  Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling. eLife 2017;6:e25884
  26. Cheng MH, Kaya C, Bahar I. (2017) Quantitative Assessment of the Energetics of Dopamine Translocation by Human Dopamine Transporter. J Phys Chem B. 2017 Dec 26. doi: 10.1021/acs.jpcb.7b10340. [Epub ahead of print]
  27. Wells MM, Reinert N, Tang P, Xu Y. (2017) Structure-Based Discovery of Novel Glycinergic Modulators. Biophysical Journal, 112(3): 556a. (abstract only)
  28. Tasan I, Sustackova G, Zhang L, Kim J, Sivaguru M, HamediRad M, Wang Y, Genova J, Ma J, Belmont AS, and Zhao H. (2017) CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci. bioRxiv, doi
  29. Jingyu Zhang, Xiao-Jun Tian, Yi-Jiun Chen, Weikang Wang, Simon Watkins, Jianhua Xing. (2017) Cells Interpret Temporal Information From TGF-β Through A Nested Relay Mechanism. BioRxiv
  30. Wang Y, Wells MM, Dailey W, Eckenhoff R, Tang P, Xu Y. (2017) Multiple Mechanisms of Propofol Inhibition of the Voltage-Gated Sodium Channel NaChBac: A 19F NMR Investigation. Biophysical Journal, 112(3): 18a. (abstract only)
  31. S Sant M Singh, XJ Tian, VS Donnenberg, AM Watson, J Zhang, LP Stabile, SC Watkins, J Xing. (2017) Targeting temporal dynamics of microenvironmental factors halts tumor migration and alleviates effects of dynamic tumor heterogeneity. BioRxiv
  32. Daniel M Spagnolo, Yousef Al-Kofahi, Peihong Zhu, Timothy R Lezon, Albert Gough, Andrew M Stern, Adrian V Lee, Fiona Ginty, Brion Sarachan, D Lansing Taylor, S Chakra Chennubhotla. (2017) Platform for Quantitative Evaluation of Spatial Intratumoral Heterogeneity in Multiplexed Fluorescence Images. Cancer Research, Vol 77, issue 21, Pgs e71-e74
  33. Sabrina Rashid, Darrell N. Kotton, and Ziv Bar-Joseph. (2017) TASIC: Determining branching models from time series single cell data. Bioinformatics, Volume: 33, Issue 16, Pages: 2504-2512
  34. Pellow D, Filippova D, Kingsford C. Improving Bloom Filter Performance on Sequence Data Using k-mer Bloom Filters. Journal of Computational Biology. 2017;24(6):547-557.  
  35. Farrow DC, Brooks LC, Hyun S, Tibshirani RJ, Burke DS, Rosenfeld R. A human judgment approach to epidemiological forecastingAlizon S, ed. PLoS Computational Biology. 2017;13(3):e1005248. 
  36. Ion BF, Wells MM, Xu Y, Tang P. (2017) Ketamine Inhibition of the Pentameric Ligand-Gated Ion Channel GLIC. Biophysical Journal, 113(3): 605-12.
  37. Marcus Thomas, Russell Schwartz (2017) Quantitative computational models of molecular self-assembly in systems biology. Physical Biology, Vol 89, Pg 4123-4133
  38. Chen Q, Wells MM, Tillman TS, Kinde MN, Cohen AE, Xu Y, Tang P (2017) Structural Basis of Alcohol Inhibition of the Pentameric Ligand-Gated Ion Channel ELIC. Structure, 25(1): 180-7.
  39. F. Pei, H. Li, M. J. Henderson, S. A. Titus, A. Jadhav, A. Simeonov, M. Cobanoglu, S. H. Mousavi, T. Shun, L. McDermott, P. Iyer, M. Fioravanti, D. Carlisle, R. M. Friedlander, I. Bahar, D. Lansing Taylor, T. R. Lezon, A. M. Stern, M. E. Schurdak. (2017) Connecting Neuronal Cell Protective Pathways and Drug Combinations in a Huntington’s Disease Model through the Application of Quantitative Systems Pharmacology. Scientific reports, 7, 17803
  40. Q Zhang*, S Gupta*, DL Schipper, GJ Kowalczyk, AE Mancini, JR Faeder, REC Lee.  (2017) NF-κB Dynamics Discriminate between TNF Doses in Single Cells. Cell systems 5 (6), 638-645. e5
  41. J Sunseri, DR Koes, P Roy, D Gau. (2017) Characterization of Profilin Binding Kinetics using Ensemble Molecular Dynamics Simulations. Biophysical Journal 112 (3), 287a (abstract only)
  42. Kleyman, M., Sefer, E., Nicola, T., Espinoza, C., Chhabra, D., Hagood, J.S., Kaminski, N., Ambalavanan, N. and Bar-Joseph, Z., (2017) Selecting the most appropriate time points to profile in high-throughput studies. eLife, 6, p.e18541..
  43. M Ragoza, J Hochuli, E Idrobo, J Sunseri, DR Koes. (2017) Protein–Ligand scoring with Convolutional neural networks. Journal of chemical information and modeling 57 (4), 942-957.
  44. Nicolas A. Pabon, Carlos J. Camacho. (2017) Probing protein flexibility reveals a mechanism for selective promiscuity. eLife 2017: 10.7554/eLife.22889.
  45. R. Ambler, X. Ruan, R.F. Murphy, and C. Wülfing (2017) Systems Imaging of the immune synapse. The Immune Synapse: Methods and Protocols (C. T. Baldari and M. L. Dustin, eds.), Methods in Molecular Biology 1584:409-421.
  46. X. Ruan, C. Wülfing, and R. F. Murphy (2017) Image-based Spatiotemporal Causality Inference for Protein Signaling Networks. Bioinformatics 33:i217-i224
  47. Natalie Sauerwald, She Zhang, Carl Kingsford, Ivet Bahar.  (2017) Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings. Nucleic Acids Research.
  48. Emre Sefer, Michael Kleyman, Ziv Bar-Joseph. (2016) Tradeoffs between Dense and Replicate Sampling Strategies for High-Throughput Time Series Experiments. Cell Systems, Vol 3, Pgs 35-42
  49. Seojin Bang and Wei Wu. (2016) Naïve Bayes ensemble: A new approach to classifying unlabeled multi-class asthma subjects. Bioinformatics and Biomedicine (BIBM), Vol N/A, Pages 460-465
  50. LA Harris, JS Hogg, JJ Tapia, JAP Sekar, S Gupta, I Korsunsky, A Arora, D Barua, RP sheehan, JR Faeder. (2016) BioNetGen 2.2: advances in rule-based modeling. Bioinformatics 32 (21), 3366-3368
  51. A.W. Naik, J.D. Kangas, D. P. Sullivan, and R. F. Murphy (2016) Active Machine Learning-driven Experimentation to Determine Compound Effects on Protein PatternseLife 5:e10047. doi:10.7554/eLife.10047.
  52. K. T. Roybal, T. E. Buck, X. Ruan, B. H. Cho, D. J. Clark, R. Ambler, H. M. Tunbridge, J. Zhang, P. Verkade, C. Wülfing, and R. F. Murphy (2016)  Science Signaling 9:rs3. doi: 10.1126/scisignal.aad4149.
  53. Y. Li, T. D. Majarian, A. W. Naik, G. R. Johnson, and R. F. Murphy (2016) Point process models for localization and interdependence of punctate cellular structures.  Cytometry Part A 89:633-643.  doi: 10.1002/cyto.a.22873.
  54. Sedgewick AJ, Shi I, Donovan RM, Benos PV. Learning mixed graphical models with separate sparsity parameters and stability-based model selection. BMC Bioinformatics. 2016;17(Suppl 5):175.  
  55. R. Ambler, X. Ruan, R.F. Murphy, and C. Wülfing (2016) Systems Imaging of the immune synapse.  Methods Mol. Biol., in press.
  56. Spagnolo DM, Gyanchandani R, Al-Kofahi Y, Stern AM, Lezon TR, Gough A, Meyer DE, Ginty F, Sarachan B, Fine J, Lee AV, Taylor D L, Chennubhotla S C. Pointwise mutual information quantifies intratumor heterogeneity in tissue sections labeled with multiple fluorescent biomarkers. J Pathol Inform 2016;7:47
  57. Zhiguang Huo, Ying Ding, Silvia Liu, Steffi Oesterreich*, George C. Tseng*. (2016) Meta-analytic framework for sparse K-means to identify disease subtypes in multiple transcriptomic studies. Journal of the American Statistical Association. 2015.
  58. Silvia Liu^, Wei-Hsiang Tsai^, Ying Ding^, Rui Chen, Zhou Fang, SungHwan Kim, Tianzhou Ma, Ting-Yu Chang, Jianhua Luo, Hsei-Wei Wang*, I-Fang Chung* and George C. Tseng*. (2016) Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data.  Nucleic Acids Research 44, no. 5 : e47-e47.
  59. Erdem, C., Nagle, A.M., Casa, A.J., Litzenburger, B.C., Wang, Y., Taylor, D.L., Lee, A.V., and Lezon, T.R. (2016). Proteomic Screening and Lasso Regression Reveal Differential Signaling in Insulin and Insulin-like Growth Factor I (IGF1) Pathways. Molecular & Cellular Proteomics 15, 3045-3057. [Published ahead of print on June 30]
  60. Laura Tipton, Elodie Ghedin, and Alison Morris. (2016) The Lung Mycobiome in the Next-generation Sequencing Era.Virulence 2016, 29 Sep 2016
  61. Alison Morris, Joselph N. Paulson, Hisham Talukder, Laura Tipton, Heather Kling, Lijia Cui, Adam Fitch, Mihai Pop, Karen A. Norris and Elodie Ghedin (2016) Longitudinal Analysis of the Lung Microbiota of Cynomolgous Macaques during Long-term SHIV Infection Microbiome 2016 4:38, 8 Jul 2016
  62. Sushma K. Cribbs, Karan Uppal, Shuzhao Li, Dean P. Jones, Laurence Huang, Laura Tipton, Adam Fitch, Ruth M. Greenblatt, Lawrence Kingsley, David M. Guidot, Elodie Ghedin and Alison Morris (2016) Correlation of the lung microbiota with metabolic profiles in bronchoalveolar lavage fluid in HIV infection Microbiome 2016 4:3.
  63. Somayeh Pirhadi, Jocelyn Sunseri, David Ryan Koes . (2016) Open source molecular modeling. Journal of Molecular Graphics and Modelling Volume 69, September 2016, Pages 127–143
  64. J Sunseri, DR Koes (2016 )Pharmit: interactive exploration of chemical space Nucl. Acids Res. doi: 10.1093/nar/gkw287
  65. J Sunseri, M Ragoza, J Collins, (2016) DR Koes A D3R prospective evaluation of machine learning for protein-ligand scoring. Journal of Computer-Aided Molecular Design doi:10.1007/s10822-016-9960-x
  66. Xiao-Jun Tian, Hang Zhang, Jingyu Zhang, Jianhua Xing  (2016)  Reciprocal Regulation Between mRNA and miRNA Enables a Bistable Switch That Directs Cell Fate Decisions FEBS Letters
  67. J Zhang, XJ Tian, J Xing (2016) Signal Transduction Pathways of EMT Induced by TGF-β, SHH, and WNT and Their Crosstalks Journal of clinical medicine 5 (4), 41
  68. Solomon B and Kingsford C. (2016) Fast search of thousands of short-read sequencing experiments. Nature Biotechnology. doi:10.1038/nbt.3442
  69. Donovan RM, Tapia J-J, Sullivan DP, Faeder JR, Murphy RF, Dittrich M, and Zuckerman DM. (2016) Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories. PLoS Comput Biol 12(2): e1004611. doi:10.1371/journal.pcbi.1004611
  70. Ye, Z., Baumgartner, M.P., Wingert, B.M. et al. (2015) Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge.  J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9941-0
  71. Koes DR, Pabon NA, Deng X, Phillips MA, Camacho CJ. (2015) A Teach-Discover-Treat Application of ZincPharmer: An Online Interactive Pharmacophore Modeling and Virtual Screening Tool. PLoS ONE 10(8): e0134697
  72. Shirish Paranjpe, …, Silvia Liu, George C.Tseng, George K. Michalopoulos. (2015) Combined systemic elimination of MET and EGFR signaling completely abolishes liver regeneration and leads to liver decompensation. (accepted by Hepatology on Jun 2016)
  73. Farrow DC, Burke DS, Rosenfeld R. Computational Characterization of Transient Strain-Transcending Immunity against Influenza A. Goldstein E, ed. PLoS ONE. 2015;10(5):e0125047.  
  74. G. R. Johnson, J. Li, A. Shariff, G.K.Rohde, and R.F. Murphy (2015) Automated Learning of Subcellular Pattern Variation among Punctate Proteins and of a Generative Model of their Distributions in Relation to Microtubules.  PLoS Computational Biology 11(12): e1004614
  75. Yan P. Yu^, Silvia Liu^, Zhigang Huo, Amantha Martin, Joel B. Nelson, George C. Tseng and Jian-Hua Luo*. Genomic copy number variations in the genomes of leukocytes predict prostate cancer clinical outcomes. PLoS ONE. 2015 Aug 21; 10(8): e0135982. (PubMed ID: 26295840)
  76. Chen Q, Kinde MN, Arjunan P, Wells MM, Cohen AE, Xu Y, Tang P. (2015) Direct pore binding as a mechanism for isoflurane inhibition of the pentameric ligand-gated ion channel ELIC. Scientific reports. 5:13833.
  77. Malkin AD, Sheehan RP, Mathew S, Federspiel WJ, Redl H, Clermont G. A Neutrophil Phenotype Model for Extracorporeal Treatment of Sepsis. Tan K, ed. PLoS Computational Biology. 2015;11(10):e1004314. 
  78. Mao, W., Kaya, C., Dutta, A., Horovitz, A., & Bahar, I. (2015). Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution. Bioinformatics, 31(12), 1929-1937.
  79. Bahar, I., Cheng, M. H., Lee, J. Y., Kaya, C., & Zhang, S. (2015). Structure-encoded global motions and their role in mediating protein-substrate interactions. Biophysical journal, 109(6), 1101-1109.
  80. Brooks LC, Farrow DC, Hyun S, Tibshirani RJ, Rosenfeld R. Flexible Modeling of Epidemics with an Empirical Bayes Framework. Tanaka MM, ed. PLoS Computational Biology. 2015;11(8):e1004382. 
  81. Hawse WF, Sheehan RP, Miskov-Zivanov N, et al. Differential regulation of PTEN by TCR, Akt and FoxO1 controls CD4+ T cell fate decisions. Journal of immunology (Baltimore, Md : 1950). 2015;194(10):4615-4619. 
  82. Roman, T., Xie, L., & Schwartz, R. (2016). Medoidshift clustering applied to genomic bulk tumor data. BMC Genomics, 17(1), 97.
  83. GR Johnson, TE Buck, DP Sullivan, GK Rohde, RF Murphy. (2015) Joint Modeling of Cell and Nuclear Shape VariationMol. Biol. Cell. Published online 9/9/2015.
  84. Z-H Zuo, Y-P Yu, Y Ding, S Liu, A Michalopoulos, GC Tseng, J-H Luo. (2015) Oncogenic activity of miRNA 650 in prostate cancer is mediated by suppression of CSR1 expression. Accepted, The American Journal of Pathology.
  85. Wells M, Tillman T, Mowrey D, Sun T, Xu Y, Tang P. (2015) Ensemble-based virtual screening for cannabinoid-like potentiators of the human glycine receptor a1 for the treatment of pain. Journal of Medicinal Chemistry. 58(7):2958-66
  86. Mochan-Keef E, Swigon D, Ermentrout GB, Clermont G. (2015) A Three-Tiered Study of Differences in Murine Intrahost Immune Response to Multiple Pneumococcal Strains. PLoS One 10: e0134012.
  87. Price I, Mochan-Keef ED, Swigon D, Ermentrout GB, Lukens S, Toapanta FR, Ross T, Clermont G. (2015) The inflammatory response to influenza A virus (H1N1): An experimental and mathematical study. J Theor Biol. 374: 83–93.
  88. Ramanathan A, Pullum LL, Hobson TC, Quinn, SP et al. Discovering Multi-Scale Co-Occurrence Patterns of Asthma and Influenza with Oak Ridge Bio-Surveillance Toolkit. Frontiers in Public Health. 2015;3:182. doi:10.3389/fpubh.2015.00182. 
  89. Matthew Patrick Baumgartner and Carlos J. Camacho. (2015) On Choosing the Optimal Rigid Receptor for Docking and Scoring in the CSAR 2013/2014 Experiment Journal of Chemical Information and Modeling Just Accepted Manuscript DOI: 10.1021/acs.jcim.5b00338
  90. Quinn SP, Zahid MJ, Durkin JR, Francis RJ, Lo CW, Chennubhotla SC. Automated identification of abnormal respiratory ciliary motion in nasal biopsies. Science translational medicine. 2015;7(299):299ra124. doi:10.1126/scitranslmed.aaa1233
  91. Grover P, Shi H, Baumgartner M, Camacho CJ, Smithgall TE (2015) Fluorescence Polarization Screening Assays for Small Molecule Allosteric Modulators of ABL Kinase Function. PLoS ONE 10(7): e0133590. doi: 10.1371/journal.pone.0133590
  92. J-H Luo, S Liu, Z-H Zuo, R Chen, GC Tseng, YP Yu. (2015) Discovery and classification of fusion transcripts in prostate cancer and normal prostate tissue. Accepted, The American Journal of Pathology
  93. Wise A, Bar-Joseph Z. cDREM: Inferring Dynamic Combinatorial Gene Regulation. Journal of Computational Biology. 2015;22(4):324-333. 
  94. Roman, T., Nayyeri, A., Fasy, B. T., & Schwartz, R. (2015). A simplicial complex-based approach to unmixing tumor progression data. BMC bioinformatics, *16*(1), 254.
  95. Wise A, Bar-Joseph Z. SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data. Bioinformatics. 2015;31(8):1250-1257.  
  96. Raghavendran Partha, Karthik Raman. (2014) Revisiting Robustness and Evolvability: Evolution in Weighted Genotype Spaces. PLoS ONE 9(11): e112792.
  97. Kumar A, Rao A, Bhavani S, Newberg JY, and Murphy RF. (2014) Automated analysis of immunohistochemistry images identifies candidate location biomarkers for cancers. Proc. Natl. Acad. Sci. U.S.A. 111:18249-18254.
  98. Mochan E, Swigon D, Ermentrout GB, Lukens S, Clermont G. A mathematical model of intrahost pneumococcal pneumonia infection dynamics in murine strains. J Theor Biol. Elsevier; 2014;353: 44–54.
  99. YP Yu, Y Ding, Z Chen, S Liu, R Chen, ZG Gulzar, B Yang, KM Cieply, A Luvison, B-G Ren, JD Brooks, D Jarrard, JB Nelson, GK Michalopoulos, GC Tseng, J-H Luo. (2014) Novel Fusion Transcripts Associate with Progressive Prostate Cancer American Journal of Pathology 18:10, pp 2840-2849.
    PMCID: PMC4188871
  100. Moroco JA, Baumgartner MP, Rust HL, Choi HG, Hur W, Gray NS, Camacho CJ, Smithgall TE (2014) A Discovery Strategy for Selective Inhibitors of c-Src in Complex with the Focal Adhesion Kinase SH3/SH2-binding Region Chem Biol Drug Des. [Epub ahead of print]
    PMID: 25376742
  101. Gardner CL, Hritz J, Sun C, Vanlandingham DL, Song TY, Ghedin E, Higgs S, Klimstra WB, Ryman KD (2014) Deliberate attenuation of chikungunya virus by adaptation to heparan sulfate-dependent infectivity: a model for rational arboviral vaccine design PLoS Negl Trop Dis 8(2):e2719.
  102. Mukherjee, S., Zheng, H., Derebe, M., Callenberg, K.M., Partch, C.L., Rollins, D., Propheter, D.C., Rizo, J., Grabe, M., Jiang, Q., Hooper, L.V. (2014). Antibacterial membrane attack by a pore-forming intestinal C-type lectinNature 505: 103-107. doi:10.1038/nature12729.
    PMCID: PMC4160023
  103. D. Filippova, R. Patro, G. Duggal, C. Kingsford (2014) “Identification of alternative topological domains in chromatin”, Algorithms Mol Biol. 9: 14. Published online May 3, 2014. doi: 10.1186.1748-7188-9-14
    PMCID: PMC4019371
  104.  Tan C, Smith RP, Tsai M-C, Schwartz R, You L. Phenotypic Signatures Arising from Unbalanced Bacterial Growth. Przytycka TM, ed. PLoS Computational Biology. 2014;10(8):e1003751.
  105. J. S. Hogg, L. A. Harris, L. J. Stover, N. S. Nair, and J. R. Faeder (2014). “Exact hybrid particle/population simulation of rule-based models of biochemical systems. PLOS Comp. Biol. doi:10.1371/journal.pcbi.1003335.
    PMCID: PMC3974646
  106. Kangas JD, Naik AW, Murphy RF,(2014) “Efficient discovery of responses of proteins to compounds using active learning”, BMC Bioinformatics. 2014 May 16;15:143
    PMCID: PMC4030446
  107. Latorraca, N.R.*, Callenberg, K.M.*, Boyle, J.P., Grabe, M. (2014). Continuum approaches to understanding ion and peptide interactions with the membraneJ Membrane Biol 247 (5): 395-408. * co-first authors
  108. S. A. Chowdhury, S. E. Shackney, K. Heselmeyer-Haddad, T. Ried, A. A. Schäffer, R. Schwartz. (2014) “Algorithms to model single gene, single chromosome, and whole genome copy number changes jointly in tumor phylogenetics.“ PLoS Comput Biol. Jul 31;10(7):e1003740. doi: 10.1371/journal.pcbi.1003740. eCollection 2014. PMCID: PMC4117424
  109. Zhang L and Kim S (2014) “Learning gene networks under SNP perturbations using eQTL datasets”, PLoS Comp. Biol. Feb 27;10(2):e1003420
    PMCID: PMC3937098
  110. G.R. Smith, L. Xie, B. Lee, and R. Schwartz. (2014) “Applying cellular crowding models to simulations of capsid assembly in vitro.” Biophysical Journal, 106(1):310-320.
    PMCID: 3907212
  111. MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues (2013) C Kaya, A Armutlulu, S Ekesan, T Haliloglu Nucleic acids research 41(Web Server issue):W249-55.
    PMID: 23742907
  112. Price I, Ermentrout B, Zamora R, Wang B, Azhar N, Mi Q, Constantine G, Faeder JR, Luckhart S, Vodovotz Y (2013) In vivo, in vitro, and in silico studies suggest a conserved immune module that regulates malaria parasite transmission from mammals to mosquitoes. J Theor Biol pii: S0022-5193(13)00258-0.)
  113. Zinman GE, Naiman S, Kanfi Y, Cohen H, Bar-Joseph Z. (2013) “ExpressionBlast: mining large, unstructured expression databases”, Nat Methods. 2013 Oct;10(10):925-6
  114. S. Quinn, M. Zahid, J. Durkin, R. Francis, C. Lo, and C. Chennubhotla. Dynamic texture analysis for automated clinical diagnosis of abnormal respiratory ciliary motion. 2013 Nature Biotechnology 
  115. Armaghan W Naik, Joshua D Kangas, Christopher J Langmead, Robert F Murphy. Efficient modeling and active learning discovery of biological responses. 2013 PLoS One Vol 8
  116. Duggal, G., Wang, H., Kingsford, C. (2013) “Higher-order chromatin domains link eQTLs with the expression of far-away genes”, Nucleic Acids Research, 42 (1): 87-96.
    PMCID: PMC3874174
  117. Huang GT, Cunningham K, Benos PV, Chennubhotla C (2013) Spectral clustering strategies for heterogeneous disease expression data. Pac Symp Biocomput, 212-223.
    PMID: 23424126
  118. Darya Filippova, Rob PatroGeet Duggal, Carl Kingsford. Multiscale Identification of Topological Domains in Chromatin.  Algorithms in Bioinformatics  Volume 8126, 2013, pp 300-312. 
  119. Luis Pedro Coelho, Joshua D Kangas, Armaghan W Naik, Elvira Osuna-Highley, Estelle Glory-Afshar, Margaret Fuhrman, Ramanuja Simha, Peter B Berget, Jonathan W Jarvik, Robert F Murphy. Determining the subcellular location of new proteins from microscope images using local features 2013 Bioinformatics 29,18
  120. SA Chowdhury, S Shackney, K Heselmeyer-Haddad, T Ried, AA Schiffer and R Schwartz. (2013) Phylogenetic analysis of multiprobe fluroscence in situ hybridization data from tumor cell populations. Bioinformatics, 29(13) i189-i198.
    PMCID: PMC3694640
  121. Duggal G, Patro R, Sefer E, Wang H, Filippova D, Khuller S, Kingsford C. (2013) Resolving spatial inconsistencies in chromosome conformation measurements. Algorithms Mol Biol. 8(1):8.
    PMCID: PMC3655033
  122. Sedgewick AJ, Benz SC, Rabizadeh S, Soon-Shiong P, Vaske CJ. (2013) Learning Subgroup-Specific Regulatory Interactions and Regulator Independence with PARADIGM. Bioinformatics 29: i62-i70.
    (Proceedings Issue for International Conference on Intelligent Systems for Molecular Biology (ISMB 2013))
    PMCID: PMC3694636
  123. Tsai MC, Blelloch G, Schwartz R, Ravi R. (2013) Coalescent-based method for learning parameters of admixture events from large-scale genetic variation data. IEEE/ACM Trans Comput Biol Bioinform. 10(5):1137-49.
    PMCID: PMC4019315
  124. Cobanoglu MC, Liu C, Hu F, Oltvai ZN, Bahar I (2013) Predicting Drug-Target Interactions Using Probabilistic Matrix Factorization J Chem Inf Model 53 (12), pp 3399–3409
    PMCID: PMC3871285
  125. J. J. Tapia and J. R. Faeder (2013). “The Atomizer: Extracting Implicit Molecular Structure from Reaction Network Models.” Proceedings of ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), September 2013.
  126. Zhou, Y., Vazquez, A., Wise, A., Warita, T., Warita, K., Bar-Joseph, Z., & Oltvai, Z. N. (2013) “Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells”, BMC Systems Biology, 7(1), 138.
    PMCID: PMC3924228
  127. Donovan RM, Sedgewick AJ, Faeder JF, and Zuckerman DM. (2013) Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories. J Chem Physics 139(11)
    PMCID: PMC3790806
  128. H. Wang, G. Duggal, R. Patro, M. Girvan, S. Hannenhalli, and C. Kingsford. (2013) “Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin”, ACM BCB 2013.
  129. Rampey RA, Baldridge MT, Farrow DC, Bay SN, Bartel B. Compensatory Mutations in Predicted Metal Transporters Modulate Auxin Conjugate Responsiveness in Arabidopsis. G3: Genes|Genomes|Genetics. 2013;3(1):131-141.  
  130. Chang, K.N., Zhong, S., Weirauch, M.T., Hon, G., Pelizzola, M., Li, H., Huang, S.C., Schmitz, R.J., Urich, M.A., Kuo, D., Nery, J.R., Qiao, H., Yang, A., Jamali, A., Chen, H., Ideker, T. Ren, B., Bar-Joseph, Z., Hughes, T.R., Ecker, J.R. (2013)  “Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis”, eLife 2013;2:e00675.
  131. Taylor DP, Wells JZ, Savol A, C. Chennubhotla C, and Wells A. (2013) Modeling boundary conditions for balanced proliferation in metastatic latency. Clin. Cancer Res., vol. 19, no. 5, pp. 1063.1070, Mar. 2013.
    PMCID: PMC3594128
  132. Ramanathan A, Savol A, Burger V, Chennubhotla CS, Agarwal PK (2013) Protein Conformational Populations and Functionally Relevant Substates Accounts Chem Res 47 (1), 149-156.
  133. Mowrey D, Chen Q, Liang Y, Liang J, Xu Y and Tang P. (2013) Signal transduction pathways in the pentameric ligand-gated ion channelsPLoS ONE 8(5): e64326. doi:10.1371/journal.pone.0064326
    PMCID: PMC3648548
  134. Kang J, Puskar KM, Schwartz RS. LeDuc PR, Modeling Mechanotransduction Signaling through Actin Filament Network Deformation Linked to Biochemical Response. 2013 Biophysical Journal 104, 2.
  135. Mowrey D, Cheng MH, Liu LT, Willenbring D, Wymore T, Xu Y, Tang P. (2013). Asymmetric ligand binding facilitates conformational transitions in pentameric ligand-gated ion channels. J Am Chem Soc. 35(6): 2172-2180.
    PMCID: PMC3582375
  136. Shao H, Travers T, Camacho CJ, Wells A. (2013) The carboxyl tail of alpha-actinin-4 regulates its susceptibility to m-calpain and thus functions in cell migration and spreading. Int J Biochem Cell Biol. 45(6):1051-63.PMCID: PMC3633689
  137. Ziraldo C, Mi Q, An G, Vodovotz Y. (2013) Computational Models of Inflammation and Wound Healing. Advanced Wound Care 2:527-537.
  138. Travers T, Shao H, Wells A, Camacho CJ. (2013) Modeling the assembly of the multiple domains of α-actinin-4 and its role in actin cross-linking. Biophys J. 104(3):705-15.
    PMCID PMC3566466
  139. Koes, DR, Baumgartner, MP, & Camacho, CJ (2013). Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise. J. Chem Info and Modeling 2013 Feb 12.
    PMID: 23379370
  140. Wisastra R, Kok PA, Eleftheriadis N, Baumgartner MP, Camacho CJ, Haisma HJ, Dekker FJ. (2013) “Discovery of a novel activator of 5-lipoxygenase from an anacardic acid derived compound collection. Bioorg Med Chem. 21(24):7763-78 67.
  141. Kanfi Y, Naiman S, Amir G, Peshti V, Zinman G, Nahum L, Bar-Joseph Z, Cohen HY, (2012) The sirtuin SIRT6 regulates lifespan in male mice, Nature. Feb 22;483(7388):218-21
  142. PMID: 22367546
  143. Darya Filippova, Aashish Gadani, Carl Kingsford. Coral: an integrated suite of visualizations for comparing clusterings.  BMC Bioinformatics 2012, 13:276.
  144. D. Filippova, C. Kingsford, M. Fitzgerald, and F. Benadon.  Dynamic exploration of recording sessions between jazz musicians over time. SocialCom, p. 368-76 2012.
  145. The Missing Models: a Data-Driven Approach for Learning How Networks Grow.. R. Patro, G. Duggal, E. Sefer, H. Wang, D. Filippova, and C. Kingsford. KDD 2012.
  146. Graph rigidity reveals well-constrained regions of chromosome conformation embeddings (2012) G. Duggal, C. Kingsford. BMC Bioinformatics: 13:241.
  147. Nieman G, Brown D, Sarkar J, Kubiak B, Ziraldo C, Vieau C, Barclay D, Gatto L, Maier K, Zamora R, Mi Q, Chang S, Vodovotz Y. (2012) Endotoxin-induced acute inflammation in swine: Insights from combined data-driven and mechanistic modeling. Crit. Care Med. 40(4):1052-1063.
    PMCID: PMC3308118
  148. Wise, A., Oltvai, Z., Bar-Joseph, Z. (2012) “Matching experiments across species using expression values and textual information”, ISMB 2012 Proceedings, Bioinformatics 28 (12): i258-i264.
    PMCID: PMC3371837
  149. Dutta A, Shrivastava IH, Sukumaran M, Greger IH, Bahar I (2012) Comparative Dynamics of NMDA- and AMPA-Glutamate Receptor N-Terminal Domains. Structure 20: 1838-49
    PMCID: PMC3496038
  150. Buck TE, Li J, Rohde GK, and Murphy RF. (2012) Towards the virtual cell: Automated approaches to building models of subcellular organization ‘learned’ from microscopy images. Bioessays 34:791-799.
  151. Callenberg, K.M., Latorraca, N.R., Grabe, M. (2012) Membrane bending is critical for the stability of voltage sensor segments in the membrane. J. General Physiology 140 (1): 55. doi: 10.1085/jgp201110766
    PMCID: PMC3382720
  152. Maji S, Bruchez MP. (2012) Inferring Biological Structures from Super-Resolution Single Molecule Images Using Generative Models. PLoS One; 7(5): e36973. Published online 2012 May 22. doi: 10.1371/journal.pone.0036973
    PMCID: PMC3358321
  153. Tapia, J.J., Faeder, J.R., and Munsky, B. (2012) “Adaptive Coarse-Graining for Transient and Quasi-Equilibrium Analyses of Stochastic Gene Regulation.” IEEE 51st Annual Conference on Decision and Control (CDC), pp. 5361-5366.
  154. Song SOK, Hogg J, Peng Z-Y, Parker R, Kellum JA, and Clermont G. (2012) Ensemble Models of Neutrophil Trafficking in Severe Sepsis. PLoS Comput Biol 8(3): e1002422.
    PMCID: PMC3297568
  155. Schulz, M.H.*, Devanny, W.E.*, Gitter, A., Zhong, S., Ernst, J., Bar-Joseph, Z. (2012) “DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data”, BMC Syst Biol. Aug 16;6:104. [Software] *Co-first authors
    PMCID: PMC3464930
  156. Liu Y, Bahar I (2012) Sequence Evolution Correlates with Structural Dynamics. Mol Biol Evol 29: 2253-63. PMCID: PMC3424413
  157. Curtis RE, Xiang J, Parikh A, and Xing EP (2012) Enabling dynamic network analysis through visualization in TVNViewer. BMC Bioinformatics 13:204 doi:10.1186/1471-2105-13-204
  158. Lin, Y., Li, Z., Ozlolak, F., Kim, SW, Arango-Argoty G., Liu TT, Tenenbaum, SA, Bailey, T, Monaghan, AP, Milos, PM, and John, B. (2012) An in-depth map of polyadenylation sites in cancer. Nucleic Acids Research Jun 29. doi: 10.1093/nar/gks637
  159. Saurabh S, Maji S, and Bruchez MP. (2012) Evaluation of sCMOS cameras for detection and localization of single Cy5 molecules. Optics Express 20, 7338-7349.
    PMCID: PMC3500109
  160. Sekar JA , & Faeder JR (2012). Rule-Based Modeling of Signal Transduction: A Primer. In Computational Modeling of Signaling Networks (pp. 139-218). Humana Press.
  161. K. Heselmeyer-Haddad, L. Y. Berroa Garcia, A. Bradley, C. Ortiz-Melendez, W.-J. Lee, R. Christensen, S. A. Prindiville, K. A. Calzone, P. W. Soballe, Y. Hu, S. A. Chowdhury, R. Schwartz, A. A. Schäffer, and T. Ried. (2012) “Single-cell genetic analysis of ductal carcinoma in situ and invasive breast cancer reveals enormous tumor heterogeneity, yet conserved genomic imbalances and gain of MYC during progression.” American Journal of Pathology, 181(11):1807-1822
    PMCID: 3483801.
  162. Bondarenko V, Mowrey D, Tillman T, Cui T, Liu LT, Xu Y, Tang P. (2012) NMR structures of the transmembrane domains of the ∝4β2 nAChR Biochemica et Biophysica Acta 1818(5):1261-8.
  163. M Stolzer, H Lai, M Xu, D Sathaye, B Vernot, D Durand. (2012) Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees. ECCB2012: Bioinformatics 28 (18): i409-i415.
    PMCID: PMC3436813
  164. Burger V and Chennubhotla C. (2012) Nhs: Network-based hierarchical segmentation for Cryo-EM density maps. Biopolymers 97(9):732-41 doi: 10.1002/bip.22041.
    PMCID: PMC3483038
  165. Curtis RE, Yin J, Kinnaird P, Xing EP. (2012) Finding genome-transcriptome-phenome association with structured association mapping and visualization in GenAMap. Pacific Symposium on Biocomputing 17:327-338.
  166. Li J, Shariff A, Wiking M, Lundberg E, Rohde GK, and Murphy RF. (2012) Estimating microtubule distributions from 2D immunofluorescence microscopy images reveals differences among human cultured cell lines. PLoS ONE 7:e0050292.
  167. Pan J, Chen Q, Willenbring D, Mowrey D, Kong XP, Cohen A, Divito CB, Xu Y, Tang P. (2012). Structure of the Pentameric Ligand-Gated Ion Channel GLIC Bound With Anesthetic Ketamine. Structure. 20(9): 1463-1469.
    PMCID: PMC3446250
  168. B. Lee, P. R. LeDuc, and R. Schwartz. (2012) “Three-dimensional stochastic off-lattice model of binding chemistry in crowded environments.” PLoS One, 7(1):e30131
    PMCID: 3260218.
  169. Burger V, Ramanathan A, Savol A, Stanley C, Agarwal P, Chennubhotla C. (2012) Quasi-Anharmonic Analysis Reveals Intermediate States in the Nuclear Co-Activator Receptor Binding Domain Ensemble Pacific Symposium on Biocomputing 17:70-81.
  170. L. Xie, G. Smith, X. Feng, and R. Schwartz. (2012) “Surveying capsid assembly pathways through simulation-based data fitting.” Biophysical Journal, 103:1545-1554
    PMCID: 3471458.
  171. Zamora R, Azhar N, Nammas R, Metukuri MR, Clermont T, Gladstone C, Namas R, Hermus L, Megas C, Constantine G, Billiar TR, Fink MP, Delude R, Vodovotz Y. (2012) Identification of a novel pathway of transforming growth factor-β1 regulation by extracellular NAD+ in mouse macrophages: In vitro and in silico studies. J. Biol. Chem. 287:31003-31014.
    PMCID: PMC3438933
  172. Curtis RE, Goyal A, Xing EP. (2012) Enhancing the usability and performance of structured association mapping algorithms using automation, parallelization, and visualization in the GenAMap Software system. BMC Genetics 13:24 PMCID: PMC3342145
  173. Kim H, Bernard ME, Farkas A, Goff J, Kalash R, Houghton F, Shields D, Franicola D, Dixon T, Zhang X, Epperly M, Wang H, Cobanoglu MC, Greenberger JS. (2012) Ionizing Irradiation Protection and Mitigation of Murine Cells by Carbamazepine is p53 and Autophagy Independent. In Vivo. 2012 May; Vol. 26, No. 3; pages 341-54.
    PMCID: PMC3335174
  174. Cobanoglu MC, Saygin Y, Sezerman U (2011) Classification of GPCRs using family specific motifs IEEE/ACM Trans Comput Biol Bioinform 8: 1495-508. PMID: 20876934.
  175. Cui T, Mowrey D, Bondarenko V, Tillman T, Ma D, Landrum E, Perez-Aguilar JM, He J, Wang W, Saven JG, Eckenhoff RG, Tang P, Xu Y. (2011) NMR structure and dynamics of a designed water-soluble transmembrane domain of nicotinic acetylcholine receptor. Biochemica et Biophysica Acta 1818(3):617-26. doi: 10.1016 PMCID: PMC3273582
  176. Myint K-Z, Ma C, Wang L, and Xie XQ. (2011) The Fragment-Similarity-Based QSAR (FS-QSAR): A Novel 2D-QSAR Method to Predict Biological Activities of Triaryl Bis-sulfone and COX2 analogs. SAR and QSAR in Environmental Research 22, pp. 385-410.
  177. A. Savol, V. Burger, P. Agarwal, A. Ramanathan, and C.S. Chennubhotla (2011) QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin Bioinformatics 27 i52-i60 doi: 10.1093
  178. Boissy R, Ahmed A, Janto B, Earl J, Hall, BG, Hogg JS, Pusch GD, Hiller LN, Powell E, Hayes J, Yu S, Kathju S, Stoodley P, Post JC, Ehrlich GD, Hu FZ. (2011) Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model. BMC Genomics 13; 12:187. PMCID: PMC3094309
  179. G. Zinman, R. Brower-Sinning, C.H. Emeche, J. Ernst, G.T. Huang, S. Mahony, A.J. Myers, D.M. O’Dee, J.L. Flynn, G.J. Nau, T.M. Ross, R.D. Salter, P.V. Benos, Z. Bar-Joseph*, P.A. Morel*. (2011) Large Scale Comparison of Innate Responses to Viral and Bacterial Pathogens in Mouse and Macaque. PLOS ONE 6(7): e22401 * – corresponding authors
  180. Huang GT, Athanassiou C, Benos PV (2011) mirConnX: condition-specific mRNA-microRNA network integrator Nucleic Acids Res. Jul;39(Web Server issue):W416-23. PMCID: PMC3125733
  181. 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 Science 20: 1645-48. PMCID: PMC3218357
  182. J Kang, RL Steward, YT Kim, RS Schwartz, PR LeDuc, KM Puskar. A coarse-Grained Monte Carlo Model of Cytoskeletal Actin Filament Alignment under Cyclic Stretch 2011 Biophysical Journal 100, 3.
  183. Xiong K, Zwier M, Myshakina N, Burger V, Asher A, Chong L. (2011) Direct Observations of Conformational Distributions of Intrinsically Disordered P53 Peptides Using UV Raman and Explicit Solvent Simulations. Journal of Physical Chemistry 115 (34) doi 10.1021/jp112235d
    PMCID: PMC3161171
  184. Kadri S, Hinman VF, Benos PV. (2011) RNA Deep Sequencing Reveals Differential MicroRNA Expression during Development of Sea Urchin and Sea Star. PLoS One. 6(12): e29217. doi: 10.1371/journal.pone.0029217
    PMCID: PMC3247247
  185. Wang L*, Ma C*, Xie X-Q. (2011) Linear and Non-linear Support Vector Machine for the Classification of 5HT1A Ligand Functionality Molecular Informatics 31(1), 85-95.
    * – contributed equally to this manuscript
  186. Curtis RE, Kinnaird P, Xing, EP. (2011) GenAMap: Visualization Strategies for Structured Association Mapping IEEE Symposium on Biological Data Visualization 1:87-95.
  187. Bakan A, Meireles LM, Bahar I. (2011) ProDy: Protein Dynamics Inferred from Theory and Experiments. Bioinformatics. June 1; 27(11): 1575.1577. doi: 10.1093/bioinformatics/btr168
    PMCID: PMC3102222
  188. Chen J-Z, Myint K-Z, and Xie X-Q. (2011) A Novel QSAR Approach for GPCR CB2-Antagonistic Triaryl Bis-Sulfone Analogs: A Combined Molecular Morphological and Pharmacophoric Approach, SAR and QSAR in Environmental Research 22, pp. 525-44.
  189. Curtis RE, Yuen A, Song L, Goyal A, and Xing EP. (2011)TVNVewer: An interactive visualization tool for exploring networks that change over time or space. Bioinformatics 27:13, 1880-1881.
  190. C. Ma, L. Wang, and X.Q. Xie (2011) Ligand Classifier of Adaptively Boosting Ensemble Decision Stumps (LiCABEDS) and Its Application on Modeling Ligand Functionality for 5HT-Subtype GPCR Families Jour of Chem Info and Modeling 51(3) 521-531
    PMCID: PMC3065508
  191. G.E. Zinman*, S. Zhong*, and Z. Bar-Joseph (2011) Biological interaction networks are conserved at the module level BMC Systems Biology 5:134
  192. Willenbring D, Liu LT, Mowrey D, Xu Y, Tang P. (2011) Isoflurane alters the structure and dynamics of GLIC Biophysical Journal 101(8):1905-12. PMCID: PMC3192980.
  193. Myint K-Z, Ma C., Wang L. and Xie XQ. (2011) The Fragment-Similarity-Based QSAR (FS-QSAR): A Novel 2D-QSAR Method to Predict Biological Activities of Triaryl Bis-sulfone and COX2 analogs. SAR and QSAR in Environmental Research 22, pp. 385-410.
  194. C. Ma, J.S. Lazo, X.Q. Xie (2011> Compound Acquisition and Prioritization Algorithm for Constructing Structurally Diverse Compound Libraries ACS Combinatorial Science 13(3) 223-231
  195. 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. PMCID: PMC3049213
  196. P. Huggins, S. Zhong, I. Shiff, R. Beckerman, O. Laptenko, C. Prives, M.H. Schulz, I. Simon, Z. Bar-Joseph (2011) DECOD: Fast and Accurate Discriminative DNA Motif Finding Bioinformatics 27(17):2361-7
  197. Meireles LMC and Mustata G. (2011) Discovery of modulators of protein-proteininteractions: current approaches and limitations. Curr. Top. Med. Chem. 11, 248-257.
  198. Ma C, Wang L, Xie X-Q. (2011) GPU Accelerated Chemical Similarity Calculation for Compound Library Comparison Journal of Chemical Information and Modeling 51(7), 1521-1527.
  199. Kang J, Steward RL, Kim YT, Schwartz RS, LeDuc PR, Puskar KM. (2011) Response of an actin filament network model under cyclic stretching through a coarse grained Monte Carlo approach. Journal of Theoretical Biology 274:1 109-119.
  200. Parikh A, Wu W, Curtis R, Xing EP. (2011) TREEGL: reverse engineering tree-evolving gene networks underlying developing biological lineages Bioinformatics 27:13, i196-i204.
  201. M.-C. Tsai, G. Blelloch, R. Ravi, and R. Schwartz. (2011) “A consensus-tree approach for reconstructing human evolutionary history and identifying population substructure.” IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8(4):918-928.
  202. Chowdhury SA, Nibbe RK, Chance MR, Koyuturk M. (2011) Subnetwork state functions define dysregulated subnetworks in cancer. Journal of Computational Biology. March, 18(3): 263-281.
  203. Eyal E, Dutta A, Bahar I.(2011). Cooperative Dynamics of Proteins Unraveled by Network Models. Wiley Interdisciplinary Reviews: Computational Molecular Science. (Accepted)
  204. A. Ramanathan, J.O. Yoo, C.J. Langmead. (2011) On-the-fly Identification of Conformational Sub-states from Molecular Dynamics Simulations Journal of Chemical Theory and Computation, 7(3) pp. 778-789
  205. Sukumaran, M., Rossman, M., Shrivastava, I., Dutta, A., Bahar, I and Greger, I.H. (2011) Dynamics and allosteric potential of the AMPA receptor N-terminal domain. EMBO J. 30(5):972-82.
  206. Meireles LMC and Mustata G. (2011) Discovery of modulators of protein-proteininteractions: current approaches and limitations. Curr. Top. Med. Chem. 11, 248-257.
  207. Shariff A, Murphy, RF, and Rohde G. (2011) Automated Estimation of Microtubule Model Parameters from 3-D Live Cell Microscopy Images. Proceedings of the 2011 IEEE International Symposium on Biomedical Imaging (ISBI 2011), pp. 1330-1333.
  208. Ramanathan A, Savol AJ, Langmead CJ, Agarwal PK, Chennubhotla CS. (2011) Discovering Conformational Sub-States Relevant to Protein Function. PLoS ONE 6(1): e15827. doi:10.1371/journal.pone.0015827
  209. Wu C, Walsh AS, Rosenfeld R. (2011) Genotype Phenotype Mapping in Rna Viruses – Disjunctive Normal Form Learning. Pacific Symposium on Biocomputing 16:62-73.
  210. Myint K-Z, and Xie X-Q (2010) Recent Advances in Fragment-Based QSAR and Multi-Dimensional QSAR Methods, International Journal of Molecular Sciences 11, pp. 3846-3866.
  211. Kamisetty H, Ramanathan A, Bailey-Kellogg C, Langmead CJ. (2011) Accounting for Conformational Entropy in Predicting Binding Free Energies of Protein-protein Interactions. Proteins: Structure, Function, and Bioinformatics. 79(2) pp. 444-462.
  212. Mi Q, Li NYK, Ziraldo C, Ghuma A, Mikheev M, Squires R, Okonkwo DO, Verdolini-Abbott K, Constantine G, An G, Vodovotz Y. (2010) Translational systems biology of inflammation: Potential applications to personalized medicine. Personalized Medicine. 7 :549-559.
    PMCID: PMC3041597
  213. Callenberg KM, Choudhary OP, de Forest GL, Gohara DW, Baker NA, Grabe M. (2010) APBSmem: A Graphical Interface for Electrostatic Calculations at the Membrane. PLoS ONE 5(9): e12722. doi:10.1371/journal.pone.0012722
    PMCID: PMC2947494
  214. D. Mowrey, E. Haddadian, L. Liu, D. Willenbring, Y. Xu, P. Tang. (2010) Unresponsive Correlated Motion in (alpha)7 nAChR to Halothane Binding Explains Its Functional Insensitivity to Volatile Anesthetics. Journal of Physical Chemistry. 114 (22), pp 7649-7655.
  215. L. P. Coelho, A. Ahmed, A. Arnold, J. Kangas, A.-S. Sheikh, E. Xing, W. Cohen, and R. F. Murphy (2010) Structured Literature Image Finder: Extracting, Information from Text and Images in Biomedical Literature. Lecture Notes in Computer Science 6004:23-32.
  216. Hogg, J. S., Clermont, G., and Parker, R.S. (2010) “Acute Inflammation treatment via Particle Filter State Estimation and Model Predictive Control”. DYCOPS 9. Leuven, Belgium.
  217. Wu C., Walsh AS., Rosenfeld R. (2010) Identification of Viral Protein Genotypic Determinants Using Combinatorial Filtering and Active Learning. BIBE, pp.162-167, 2010 IEEE International Conference on Bioinformatics and Bioengineering.
  218. Hiller NL, Ahmed A, Powell E, Martin DP, Eutsey R, Earl J, Janto B, Boissy RJ, Hogg J, Barbadora K, Sampath R, Lonergan S, Post JC, Hu FZ, Ehrlich GD. (2010) Generation of Genic Diversity among Streptococcus pneumoniae Strains via Horizontal Gene Transfer during a Chronic Polyclonal Pediatric Infection PLoS Pathog. 16;6(9):e1001108. doi: 10.1371/journal.ppat.1001108.
    PMCID: PMC2940740
  219. Dutta A, Bahar I. (2010) Metal-binding sites are designed to achieve optimal mechanical and signaling properties. Structure;18(9):1140-8.
  220. A. Shariff, J. Kangas, L.P. Coelho, S. Quinn and R.F. Murphy (2010) Automated Image Analysis for High Content Screening and Analysis. J. Biomolec. Screening 15:726-734.
  221. A. Ramanathan, P.K. Agarwal, M. Kurnikova, C.J. Langmead. (2010) An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations. Journal of Computational Biology, 17(3), pp. 309-324.
  222. L. P. Coelho, T. Peng, and R. F. Murphy (2010) Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing. Bioinformatics 26:i7-i12
  223. Coelho LP, Glory-Afshar E, Kangas J, Quinn S, Shariff A, and Murphy RF (2010) Principles of Bioimage Informatics: Focus on machine learning of cell patterns. Lecture Notes in Computer Science 6004:.8-18
  224. Klutstein M., Siegfried Z., Gispan A., Farkash-Amar S., Zinman G., Bar-Joseph Z., Simchen G., Simon I. (2010) Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes. BMC Genomics PMID 20716365.
  225. Kuo D., Tan K., Zinman G., Ravasi T., Bar-Joseph Z., Ideker T. (2010) Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol. 11 (7): R77.
  226. A. Ahmed, A. Arnold, L. P. Coelho, J. Kangas, A.-S. Sheikh, E. Xing, W. Cohen, and R. F. Murphy (2010) Structured Literature Image Finder: Parsing Text and Figures in Biomedical Literature. Web Semantics: Science, Services and Agents on the World Wide Web 8:151-154.
  227. Choudhary OP., Ujwal R., Kowallis W., Coalson R., Abramson J., Grabe M. (2010) The electrostatics of VDAC: implications for selectivity and gating. J. Mol. Biol. : 396(3): 580-592.
  228. Von Wald T, Monisova Y, Hacker MR, Yoo SW, Penzias AS, Reindollar RR, Usheva A. Age-related variations in follicular apolipoproteins may influence human oocyte maturation and fertility potentials. Fertility and Sterility. 2010;93(7):2354-2361.
  229.  Shariff A, Murphy RF and Rohde GK (2010) A Generative Model of Microtubule Distributions, and Indirect Estimation of its Parameters from Fluorescence Microscopy Images. Cytometry Part A 77A:457-466 PMC2901542
  230. Liu Y, Gierasch L, Bahar I. (2010) Role of Hsp70 ATPase Domain Intrinsic Dynamics and Sequence Evolution in Enabling its Functional Interactions with NEFs. PLoS Comput Biol 6: e1000931.
  231. Meireles, L.M., A.S. D�mling, and C.J. Camacho, (2010) ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery. Nucleic Acids Res, 38 Suppl: p. W407-11.
  232. Ding Y., Mamonov AB., Zuckerman D. (2010) Efficient equilibrium sampling of all-atom peptides using Library-Based Monte Carlo. The Journal of Physical Chemistry B, 114,5870-5877.
  233. Bakan A, Bahar I. (2009) The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc Natl Acad Sci USA 106(34) 14349-14354 doi:10.1073/pnas.0904214106
  234. Joseph JM, Durand D. (2009) Family Classification Without Domain Chaining. Bioinformatics 25:i45-53.
  235. 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.
  236. Coelho LP, Shariff A, and Murphy RF. (2009) Nuclei Segmentation In Microscope Cell Images: A Hand-Segmented Dataset And Comparison Of Algorithms. Proceedings of the 2009 IEEE International Symposium on Biomedical Imaging (ISBI 2009), pp. 518-521.
  237. 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
  238. Lee B, LeDuc PR, and Schwartz R. (2009) Parameter effects on binding chemistry in crowded media using a two-dimensional stochastic off-lattice model. Physical Review E, 80, 041918.
  239. Harris, L.A., Hogg, J.S., and Faeder, J.R. (2009) Compartmental rule-based modeling of biochemical systems. Proceedings of the 2009 Winter Simulation Conference (WSC) 908-919.
  240. T. E. Buck, A. Rao, L. P. Coelho, M. Fuhrman, J. W. Jarvik, P. B. Berget, and R. F. Murphy (2009) Protein Localization Dependence on Cell Cycle Inferred from Static, Asynchronous Images. Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 1016-1019.
  241. Liu Y. and Bahar I. (2009) Toward understanding allosteric signaling mechanisms in the ATPase domain of molecular chaperones. Pac Symp Biocomput. 2010:269-80.
  242.  Alexandrov BS, Gelev V, Monisova Y, et al. A nonlinear dynamic model of DNA with a sequence-dependent stacking term. Nucleic Acids Research. 2009;37(7):2405-2410.
  243. Joseph JM, Durand D. (2009) Family Classification Without Domain Chaining. Bioinformatics 25:i45-53.
  244. Shariff A, Rohde GK, and Murphy RF (2009) Indirect learning of generative models for microtubule distribution from fluorescence microscope images. Proceedings of the ICML-UAI-COLT 2009 Workshop on Automated Interpretation and Modeling of Cell Images (Cell-Image Learning 2009).
  245. Mamonov AB., Bhatt D., Cashman DJ., Ding Y., Zuckerman D. (2009) General library-based monte carlo technique enables equilibrium sampling of semi-atomistic protein models. The Journal of Physical Chemistry B, 113(31):10891�10904
  246. Zhang L, Xiao Q, Ma C, Xie X-Q, Floreancig PE. (2009) Construction of a Bicyclic �Benzyloxy and �Hydroxy Amide Library through a Multicomponent Cyclization Reaction Journal of Combinatorial Chemistry 11(4), 640-644.
  247. 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.
  248. 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)
  249. 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.
  250. 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
  251. Song N, Joseph JM, Davis GB, Durand D (2008) “Sequence similarity network reveals common ancestry of multidomain proteins; PLoS Comput Biol 4, e1000063. (PDF)
  252. Song N, Joseph JM, Davis GB, Durand D (2008) “Sequence similarity network reveals common ancestry of multidomain proteins; PLoS Comput Biol 4, e1000063.
  253. Liu Y, Eyal E, Bahar I (2008) “Analysis of correlated mutations in HIV-1 protease using spectral  clustering” Bioinformatics 24, 1243-50. (PDF)
  254. 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
  255. 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)
  256. 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.
  257. 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
  258. Lee, J., Li, Z., Brower-Sinning, R., John, B. (2007) Regulatory Circuit of Human MicroRNA Biogenesis. PLoS Computational Biology
  259. Hogg JS, Hu FZ, Janto B, Boissy R, Hayes J, Keefe R, Post JC, Ehrlich GD. (2007) Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains. Genome Biology 8(6):R103 PMCID: PMC2394571
  260. Tsai M-C, Tsui F-C, Wagner MM. An Evaluation of Biosurveillance Grid—Dynamic Algorithm Distribution Across Multiple Computer Nodes. AMIA Annual Symposium Proceedings. 2007:746-750.
  261. 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.