Student Publications

 

  1. 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
  2. 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
  3. 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.
  4. Bondarenko V, Wells MM, Xu Y, Tang P (2018) Solution NMR Studies of Anesthetic Interactions With Ion Channels. Methods in Enzymology, in press
  5. 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)
  6. 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)
  7. 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)
  8. Marcus Thomas, Russell Schwartz (2018) A method for efficient Bayesian optimization of self-assembly systems from scattering data. BMC Systems Biology
  9. Cong Ma, Mingfu Shao, Carl Kingsford. (2018) SQUID: transcriptomic structural variation detection from RNA-seq. Genome Biology, vol 19, pg 52
  10. 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.
  11. 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
  12. 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
  13. 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]
  14. Wells MM, Reinert N, Tang P, Xu Y. (2017) Structure-Based Discovery of Novel Glycinergic Modulators. Biophysical Journal, 112(3): 556a. (abstract only)
  15. 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
  16. 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
  17. 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)
  18. 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
  19. 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
  20. 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
  21. 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.  
  22. Farrow DC, Brooks LC, Hyun S, Tibshirani RJ, Burke DS, Rosenfeld R. A human judgment approach to epidemiological forecasting. Alizon S, ed. PLoS Computational Biology. 2017;13(3):e1005248. 
  23. 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.
  24. Marcus Thomas, Russell Schwartz (2017) Quantitative computational models of molecular self-assembly in systems biology. Physical Biology, Vol 89, Pg 4123-4133
  25. 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.
  26. 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
  27. 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
  28. 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)
  29. 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..
  30. 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.
  31. Nicolas A. Pabon, Carlos J. Camacho. (2017) Probing protein flexibility reveals a mechanism for selective promiscuity. eLife 2017: 10.7554/eLife.22889.
  32. 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.
  33. X. Ruan, C. Wülfing, and R. F. Murphy (2017) Image-based Spatiotemporal Causality Inference for Protein Signaling Networks. Bioinformatics 33:i217-i224
  34. 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.
  35. 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
  36. 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
  37. 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
  38. 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 Patterns, eLife 5:e10047. doi:10.7554/eLife.10047.
  39. 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) Computational spatiotemporal analysis identifies WAVE2 and Cofilin as joint regulators of costimulation-mediated T cell actin dynamics.  Science Signaling 9:rs3. doi: 10.1126/scisignal.aad4149.
  40. 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.
  41. 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.  
  42. R. Ambler, X. Ruan, R.F. Murphy, and C. Wülfing (2016) Systems Imaging of the immune synapse.  Methods Mol. Biol., in press.
  43. 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
  44. 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.
  45. 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.
  46. 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]
  47. Laura Tipton, Elodie Ghedin, and Alison Morris. (2016) The Lung Mycobiome in the Next-generation Sequencing Era.Virulence 2016, 29 Sep 2016
  48. 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
  49. 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.
  50. 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
  51. J Sunseri, DR Koes (2016 )Pharmit: interactive exploration of chemical space Nucl. Acids Res. doi: 10.1093/nar/gkw287
  52. 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
  53. 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
  54. 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
  55. Solomon B and Kingsford C. (2016) Fast search of thousands of short-read sequencing experiments. Nature Biotechnology. doi:10.1038/nbt.3442
  56. 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
  57. 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
  58. 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
  59. 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)
  60. 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.  
  61. 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): e1004614http://dx.doi.org/10.1371/journal.pcbi.1004614
  62. 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)
  63. 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.
  64. 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. 
  65. 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.
  66. 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.
  67. 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. 
  68. 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. 
  69. Roman, T., Xie, L., & Schwartz, R. (2016). Medoidshift clustering applied to genomic bulk tumor data. BMC Genomics, 17(1), 97.
  70. 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.
  71. 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.
  72. 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
  73. 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.
  74. 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.
  75. 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. 
  76. 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
  77. 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
  78. 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
  79. 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
  80. Wise A, Bar-Joseph Z. cDREM: Inferring Dynamic Combinatorial Gene Regulation. Journal of Computational Biology. 2015;22(4):324-333. 
  81. 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.
  82. 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.  
  83. Raghavendran Partha, Karthik Raman. (2014) Revisiting Robustness and Evolvability: Evolution in Weighted Genotype Spaces. PLoS ONE 9(11): e112792.
  84. 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.
  85. 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.
  86. 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
  87. 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
  88. 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.
  89. 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
  90. 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
  91.  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.
  92. 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
  93. 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
  94. 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
  95. 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
  96. 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
  97. 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
  98. 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
  99. 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.)
  100. 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
  101. 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 
  102. 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
  103. 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
  104. Huang GT, Cunningham K, Benos PV, Chennubhotla C (2013) Spectral clustering strategies for heterogeneous disease expression data. Pac Symp Biocomput, 212-223.
    PMID: 23424126
  105. Darya Filippova, Rob PatroGeet Duggal, Carl Kingsford. Multiscale Identification of Topological Domains in Chromatin.  Algorithms in Bioinformatics  Volume 8126, 2013, pp 300-312. 
  106. 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
  107. 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
  108. 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
  109. 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
  110. 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
  111. 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
  112. 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.
  113. 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
  114. 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
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  229.  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.
  230. Joseph JM, Durand D. (2009) Family Classification Without Domain Chaining. Bioinformatics 25:i45-53.
  231. 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).
  232. 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
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  234. 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.
  235. 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)
  236. 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.
  237. 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
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  239. Song N, Joseph JM, Davis GB, Durand D (2008) “Sequence similarity network reveals common ancestry of multidomain proteins; PLoS Comput Biol 4, e1000063.
  240. Liu Y, Eyal E, Bahar I (2008) “Analysis of correlated mutations in HIV-1 protease using spectral  clustering” Bioinformatics 24, 1243-50. (PDF)
  241. 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
  242. 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)
  243. 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.
  244. 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
  245. Lee, J., Li, Z., Brower-Sinning, R., John, B. (2007) Regulatory Circuit of Human MicroRNA Biogenesis. PLoS Computational Biology
  246. 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
  247. 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.
  248. 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.