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  • Faculty Publications
  • Myers, Chad L, Xing Chen, and Olga G Troyanskaya. 2005. “Visualization-Based Discovery and Analysis of Genomic Aberrations in Microarray Data.”. BMC Bioinformatics 6: 146.
    Reference Link
  • Huttenhower, Curtis, Matt Hibbs, Chad Myers, and Olga G Troyanskaya. (2006) 2006. “A Scalable Method for Integration and Functional Analysis of Multiple Microarray Datasets.”. Bioinformatics 22 (23): 2890-7.
    Reference Link
  • Osborne, Leslie C, Stephanie E Palmer, Stephen G Lisberger, and William Bialek. (2008) 2008. “The Neural Basis for Combinatorial Coding in a Cortical Population Response.”. J Neurosci 28 (50): 13522-31.
    Reference Link
  • Tkačik, Gašper, Curtis G Callan, and William Bialek. (2008) 2008. “Information Capacity of Genetic Regulatory Elements.”. Phys Rev E Stat Nonlin Soft Matter Phys 78 (1 Pt 1): 011910.
    Reference Link
  • Wyart, Matthieu, David Botstein, and Ned S Wingreen. 2010. “Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data.”. PLoS Comput Biol 6 (11): e1000979.
    Reference Link
  • Capra, John A, and Mona Singh. (2008) 2008. “Characterization and Prediction of Residues Determining Protein Functional Specificity.”. Bioinformatics 24 (13): 1473-80.
    Reference Link
  • Lee, Young-suk, Aaron K Wong, Alicja Tadych, Boris M Hartmann, Christopher Y Park, Veronica A DeJesus, Irene Ramos, Elena Zaslavsky, Stuart C Sealfon, and Olga G Troyanskaya. (2018) 2018. “Interpretation of an Individual Functional Genomics Experiment Guided by Massive Public Data.”. Nat Methods 15 (12): 1049-52. doi:10.1038/s41592-018-0218-5.
    Reference Link
  • Hibbs, Matthew A, Nathaniel C Dirksen, Kai Li, and Olga G Troyanskaya. 2005. “Visualization Methods for Statistical Analysis of Microarray Clusters.”. BMC Bioinformatics 6: 115.
    Reference Link
  • Tkačik, Gašper, Thomas Gregor, and William Bialek. 2008. “The Role of Input Noise in Transcriptional Regulation.”. PLoS One 3 (7): e2774.
    Reference Link
  • Banks, Eric, Elena Nabieva, Ryan Peterson, and Mona Singh. 2008. “NetGrep: Fast Network Schema Searches in Interactomes.”. Genome Biol 9 (9): R138.
    Reference Link
  • Huelsenbeck, John P, and Peter Andolfatto. (2007) 2007. “Inference of Population Structure under a Dirichlet Process Model.”. Genetics 175 (4): 1787-802.
    Reference Link
  • Shaevitz, Joshua W, and Daniel A Fletcher. (2007) 2007. “Enhanced Three-Dimensional Deconvolution Microscopy Using a Measured Depth-Varying Point-Spread Function.”. J Opt Soc Am A Opt Image Sci Vis 24 (9): 2622-7.
    Reference Link
  • Qiao, Liang, Robert B Nachbar, Ioannis G Kevrekidis, and Stanislav Y Shvartsman. (2007) 2007. “Bistability and Oscillations in the Huang-Ferrell Model of MAPK Signaling.”. PLoS Comput Biol 3 (9): 1819-26.
    Reference Link
  • Zhou, Jian, Christopher Y Park, Chandra L Theesfeld, Aaron K Wong, Yuan Yuan, Claudia Scheckel, John J Fak, et al. (2019) 2019. “Whole-Genome Deep-Learning Analysis Identifies Contribution of Noncoding Mutations to Autism Risk.”. Nat Genet 51 (6): 973-80. doi:10.1038/s41588-019-0420-0.
    Reference Link
  • McIsaac, Scott, Sanford J Silverman, Lance Parsons, Ping Xu, Ryan Briehof, Megan N McClean, and David Botstein. 2013. “Visualization and Analysis of MRNA Molecules Using Fluorescence in Situ Hybridization in Saccharomyces Cerevisiae.”. J Vis Exp, no. 76: e50382.
    Reference Link
  • Baryshnikova, Anastasia, Michael Costanzo, Yungil Kim, Huiming Ding, Judice Koh, Kiana Toufighi, Ji-Young Youn, et al. (2010) 2010. “Quantitative Analysis of Fitness and Genetic Interactions in Yeast on a Genome Scale.”. Nat Methods 7 (12): 1017-24.
    Reference Link
  • Markowetz, Florian, Dennis Kostka, Olga G Troyanskaya, and Rainer Spang. (2007) 2007. “Nested Effects Models for High-Dimensional Phenotyping Screens.”. Bioinformatics 23 (13).
    Reference Link
  • Wang, Wei, Michael Cherry, Yigal Nochomovitz, Emmitt Jolly, David Botstein, and Hao Li. (2005) 2005. “Inference of Combinatorial Regulation in Yeast Transcriptional Networks: A Case Study of Sporulation.”. Proc Natl Acad Sci U S A 102 (6): 1998-2003.
    Reference Link
  • Chen, Lin S, and John D Storey. (2008) 2008. “Eigen-R2 for Dissecting Variation in High-Dimensional Studies.”. Bioinformatics 24 (19): 2260-2.
    Reference Link
  • DiMaggio, Peter A, Scott R McAllister, Christodoulos A Floudas, Xiao-Jiang Feng, Joshua D Rabinowitz, and Herschel A Rabitz. 2008. “Biclustering via Optimal Re-Ordering of Data Matrices in Systems Biology: Rigorous Methods and Comparative Studies.”. BMC Bioinformatics 9: 458.
    Reference Link
  • Chen, Kathleen M, Evan M Cofer, Jian Zhou, and Olga G Troyanskaya. (2019) 2019. “Selene: A PyTorch-Based Deep Learning Library for Sequence Data.”. Nat Methods 16 (4): 315-18. doi:10.1038/s41592-019-0360-8.
    Reference Link
  • Ochoa, Alejandro, Manuel Llinás, and Mona Singh. 2011. “Using Context to Improve Protein Domain Identification.”. BMC Bioinformatics 12: 90.
    Reference Link
  • Troyanskaya, Olga G. (2005) 2005. “Putting Microarrays in a Context: Integrated Analysis of Diverse Biological Data.”. Brief Bioinform 6 (1): 34-43.
    Reference Link
  • Huttenhower, Curtis, Avi I Flamholz, Jessica N Landis, Sauhard Sahi, Chad L Myers, Kellen L Olszewski, Matthew A Hibbs, Nathan O Siemers, Olga G Troyanskaya, and Hilary A Coller. 2007. “Nearest Neighbor Networks: Clustering Expression Data Based on Gene Neighborhoods.”. BMC Bioinformatics 8: 250.
    Reference Link
  • Huttenhower, Curtis, Matthew A Hibbs, Chad L Myers, Amy A Caudy, David C Hess, and Olga G Troyanskaya. (2009) 2009. “The Impact of Incomplete Knowledge on Evaluation: An Experimental Benchmark for Protein Function Prediction.”. Bioinformatics 25 (18): 2404-10.
    Reference Link
  • Deng, Yi, Philip Coen, Mingzhai Sun, and Joshua W Shaevitz. 2013. “Efficient Multiple Object Tracking Using Mutually Repulsive Active Membranes.”. PLoS One 8 (6): e65769.
    Reference Link
  • Troyanskaya, Olga G, Kara Dolinski, Art B Owen, Russ B Altman, and David Botstein. (2003) 2003. “A Bayesian Framework for Combining Heterogeneous Data Sources for Gene Function Prediction (in Saccharomyces cerevisiae).”. Proc Natl Acad Sci U S A 100 (14): 8348-53.
    Reference Link
  • Zhou, Jian, Ignacio E Schor, Victoria Yao, Chandra L Theesfeld, Raquel Marco-Ferreres, Alicja Tadych, Eileen E M Furlong, and Olga G Troyanskaya. (2019) 2019. “Accurate Genome-Wide Predictions of Spatio-Temporal Gene Expression During Embryonic Development.”. PLoS Genet 15 (9): e1008382. doi:10.1371/journal.pgen.1008382.
    Reference Link
  • Endres, Robert G, Thomas C Schulthess, and Ned S Wingreen. (2004) 2004. “Toward an Atomistic Model for Predicting Transcription-Factor Binding Sites.”. Proteins 57 (2): 262-8.
    Reference Link
  • Guberman, Jonathan M, Allison Fay, Jonathan Dworkin, Ned S Wingreen, and Zemer Gitai. (2008) 2008. “PSICIC: Noise and Asymmetry in Bacterial Division Revealed by Computational Image Analysis at Sub-Pixel Resolution.”. PLoS Comput Biol 4 (11): e1000233.
    Reference Link
  • Segal, Eran, Michael Shapira, Aviv Regev, Dana Pe’er, David Botstein, Daphne Koller, and Nir Friedman. (2003) 2003. “Module Networks: Identifying Regulatory Modules and Their Condition-Specific Regulators from Gene Expression Data.”. Nat Genet 34 (2): 166-76.
    Reference Link
  • Song, Jimin, and Mona Singh. (2009) 2009. “How and When Should Interactome-Derived Clusters Be Used to Predict Functional Modules and Protein Function?”. Bioinformatics 25 (23): 3143-50.
    Reference Link
  • Chikina, Maria D, and Olga G Troyanskaya. (2012) 2012. “An Effective Statistical Evaluation of ChIPseq Dataset Similarity.”. Bioinformatics 28 (5): 607-13.
    Reference Link
  • Huttenhower, Curtis, and Olga G Troyanskaya. 2006. “Bayesian Data Integration: A Functional Perspective.”. Comput Syst Bioinformatics Conf, 341-51.
    Reference Link
  • Wallace, Grant, Otto J Anshus, Peng Bi, Han Chen, Yuqun Chen, Douglas Clark, Perry Cook, et al. (2005) 2005. “Tools and Applications for Large-Scale Display Walls.”. IEEE Comput Graph Appl 25 (4): 24-33.
    Reference Link
  • Khan, Zia, Joshua S Bloom, Benjamin A Garcia, Mona Singh, and Leonid Kruglyak. (2009) 2009. “Protein Quantification across Hundreds of Experimental Conditions.”. Proc Natl Acad Sci U S A 106 (37): 15544-8.
    Reference Link
  • Coppey, Mathieu, Alexander M Berezhkovskii, Yoosik Kim, Alistair N Boettiger, and Stanislav Y Shvartsman. (2007) 2007. “Modeling the Bicoid Gradient: Diffusion and Reversible Nuclear Trapping of a Stable Protein.”. Dev Biol 312 (2): 623-30.
    Reference Link
  • Barutcuoglu, Zafer, Robert E Schapire, and Olga G Troyanskaya. (2006) 2006. “Hierarchical Multi-Label Prediction of Gene Function.”. Bioinformatics 22 (7): 830-6.
    Reference Link
  • Deng, Yi, and Joshua W Shaevitz. (2009) 2009. “Effect of Aberration on Height Calibration in Three-Dimensional Localization-Based Microscopy and Particle Tracking.”. Appl Opt 48 (10): 1886-90.
    Reference Link
  • Huttenhower, C, and O G Troyanskaya. (2008) 2008. “Assessing the Functional Structure of Genomic Data.”. Bioinformatics 24 (13).
    Reference Link
  • Shaevitz, Joshua W. (2008) 2008. “Super-Resolution for a 3D World.”. Nat Methods 5 (6): 471-2.
    Reference Link
  • Heinicke, Sven, Michael S Livstone, Charles Lu, Rose Oughtred, Fan Kang, Samuel Angiuoli V, Owen White, David Botstein, and Kara Dolinski. 2007. “The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists.”. PLoS One 2 (8): e766.
    Reference Link
  • Troyanskaya, O, M Cantor, G Sherlock, P Brown, T Hastie, R Tibshirani, D Botstein, and Russ B Altman. (2001) 2001. “Missing Value Estimation Methods for DNA Microarrays.”. Bioinformatics 17 (6): 520-5.
    Reference Link
  • Goyal, Sidhartha, and Ned S Wingreen. (2007) 2007. “Growth-Induced Instability in Metabolic Networks.”. Phys Rev Lett 98 (13): 138105.
    Reference Link
  • Hansen, Clinton H, Victor Sourjik, and Ned S Wingreen. (2010) 2010. “A Dynamic-Signaling-Team Model for Chemotaxis Receptors in Escherichia Coli.”. Proc Natl Acad Sci U S A 107 (40): 17170-5.
    Reference Link
  • Barutcuoglu, Zafer, Edoardo M Airoldi, Vanessa Dumeaux, Robert E Schapire, and Olga G Troyanskaya. (2009) 2009. “Aneuploidy Prediction and Tumor Classification With Heterogeneous Hidden Conditional Random Fields.”. Bioinformatics 25 (10): 1307-13.
    Reference Link
  • Batsilas, Lazaros, Alexander M Berezhkovskii, and Stanislav Y Shvartsman. (2003) 2003. “Stochastic Model of Autocrine and Paracrine Signals in Cell Culture Assays.”. Biophys J 85 (6): 3659-65.
    Reference Link
  • Capra, John A, Roman A Laskowski, Janet M Thornton, Mona Singh, and Thomas A Funkhouser. (2009) 2009. “Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure.”. PLoS Comput Biol 5 (12): e1000585.
    Reference Link
  • Melamud, Eugene, Livia Vastag, and Joshua D Rabinowitz. (2010) 2010. “Metabolomic Analysis and Visualization Engine for LC-MS Data.”. Anal Chem 82 (23): 9818-26.
    Reference Link
  • Zhou, Jian, and Olga G Troyanskaya. (2014) 2014. “Global Quantitative Modeling of Chromatin Factor Interactions.”. PLoS Comput Biol 10 (3): e1003525.
    Reference Link

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