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Abouchar, Laurent, Mariela D Petkova, Cynthia R Steinhardt, and Thomas Gregor. (2014) 2014. “Fly Wing Vein Patterns Have Spatial Reproducibility of a Single Cell.”. J R Soc Interface 11 (97): 20140443.

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Chen, Lin S, and John D Storey. (2008) 2008. “Eigen-R2 for Dissecting Variation in High-Dimensional Studies.”. Bioinformatics 24 (19): 2260-2.

Tkačik, Gašper, Thomas Gregor, and William Bialek. 2008. “The Role of Input Noise in Transcriptional Regulation.”. PLoS One 3 (7): e2774.

Rabinowitz, Joshua D, Jennifer J Hsiao, Kimberly R Gryncel, Evan R Kantrowitz, Xiao-Jiang Feng, Genyuan Li, and Herschel Rabitz. (2008) 2008. “Dissecting Enzyme Regulation by Multiple Allosteric Effectors: Nucleotide Regulation of Aspartate Transcarbamoylase.”. Biochemistry 47 (21): 5881-8.

Lossos, Izidore S, Debra K Czerwinski, Ash A Alizadeh, Mark A Wechser, Rob Tibshirani, David Botstein, and Ronald Levy. (2004) 2004. “Prediction of Survival in Diffuse Large-B-Cell Lymphoma Based on the Expression of Six Genes.”. N Engl J Med 350 (18): 1828-37.

Tkačik, Gašper, and William Bialek. (2009) 2009. “Diffusion, Dimensionality, and Noise in Transcriptional Regulation.”. Phys Rev E Stat Nonlin Soft Matter Phys 79 (5 Pt 1): 051901.

Halligan, Daniel L, Adam Eyre-Walker, Peter Andolfatto, and Peter D Keightley. (2004) 2004. “Patterns of Evolutionary Constraints in Intronic and Intergenic DNA of Drosophila.”. Genome Res 14 (2): 273-9.

Huttenhower, Curtis, and Olga G Troyanskaya. 2006. “Bayesian Data Integration: A Functional Perspective.”. Comput Syst Bioinformatics Conf, 341-51.

Kulkarni, Rahul, V, Kerwyn Casey Huang, Morten Kloster, and Ned S Wingreen. (2004) 2004. “Pattern Formation Within Escherichia Coli: Diffusion, Membrane Attachment, and Self-Interaction of MinD Molecules.”. Phys Rev Lett 93 (22): 228103.

Jensen, Jeffrey D, Kevin R Thornton, and Peter Andolfatto. 2008. “An Approximate Bayesian Estimator Suggests Strong, Recurrent Selective Sweeps in Drosophila.”. PLoS Genet 4 (9): e1000198.

Lee, Young-suk, Arjun Krishnan, Qian Zhu, and Olga G Troyanskaya. (2013) 2013. “Ontology-Aware Classification of Tissue and Cell-Type Signals in Gene Expression Profiles across Platforms and Technologies.”. Bioinformatics 29 (23): 3036-44.

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.

Troyanskaya, Olga G, Mitchell E Garber, Patrick O Brown, David Botstein, and Russ B Altman. (2002) 2002. “Nonparametric Methods for Identifying Differentially Expressed Genes in Microarray Data.”. Bioinformatics 18 (11): 1454-61.

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.

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.

Straile, Dietmar, Reiner Eckmann, Tobias Jüngling, Gregor Thomas, and Herbert Löffler. (2007) 2007. “Influence of Climate Variability on Whitefish (Coregonus Lavaretus) Year-Class Strength in a Deep, Warm Monomictic Lake.”. Oecologia 151 (3): 521-9.

Nabieva, Elena, Kam Jim, Amit Agarwal, Bernard Chazelle, and Mona Singh. (2005) 2005. “Whole-Proteome Prediction of Protein Function via Graph-Theoretic Analysis of Interaction Maps.”. Bioinformatics 21 Suppl 1.

Huelsenbeck, John P, and Peter Andolfatto. (2007) 2007. “Inference of Population Structure under a Dirichlet Process Model.”. Genetics 175 (4): 1787-802.

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.

Emberly, Eldon, and Ned S Wingreen. (2006) 2006. “Hourglass Model for a Protein-Based Circadian Oscillator.”. Phys Rev Lett 96 (3): 038303.

Stephens, Greg J, Thierry Mora, Gašper Tkačik, and William Bialek. (2013) 2013. “Statistical Thermodynamics of Natural Images.”. Phys Rev Lett 110 (1): 018701.

Zhou, Jian, and Olga G Troyanskaya. (2014) 2014. “Global Quantitative Modeling of Chromatin Factor Interactions.”. PLoS Comput Biol 10 (3): e1003525.

Brenner, Naama, Oded Agam, William Bialek, and Rob de Ruyter van Steveninck. (2002) 2002. “Statistical Properties of Spike Trains: Universal and Stimulus-Dependent Aspects.”. Phys Rev E Stat Nonlin Soft Matter Phys 66 (3 Pt 1): 031907.

Guan, Yuanfang, Chad L Myers, Rong Lu, Ihor R Lemischka, Carol J Bult, and Olga G Troyanskaya. 2008. “A Genomewide Functional Network for the Laboratory Mouse.”. PLoS Comput Biol 4 (9): e1000165.

Mukhopadhyay, Ranjan, Eldon Emberly, Chao Tang, and Ned S Wingreen. (2003) 2003. “Statistical Mechanics of RNA Folding: Importance of Alphabet Size.”. Phys Rev E Stat Nonlin Soft Matter Phys 68 (4 Pt 1): 041904.

Park, Christopher Y, Aaron K Wong, Casey S Greene, Jessica Rowland, Yuanfang Guan, Lars A Bongo, Rebecca Burdine, and Olga G Troyanskaya. 2013. “Functional Knowledge Transfer for High-Accuracy Prediction of under-Studied Biological Processes.”. PLoS Comput Biol 9 (3): e1002957.