Wall, Jeffrey D, Peter Andolfatto, and Molly Przeworski. (2002) 2002. “Testing Models of Selection and Demography in Drosophila Simulans.”. Genetics 162 (1): 203-16.

Rowe, Kevin C, Sonal Singhal, Matthew D Macmanes, Julien Ayroles, Toni Lyn Morelli, Emily M Rubidge, Ke Bi, and Craig C Moritz. (2011) 2011. “Museum Genomics: Low-Cost and High-Accuracy Genetic Data from Historical Specimens.”. Mol Ecol Resour 11 (6): 1082-92.

Levine, Michael, and Eric H Davidson. (2005) 2005. “Gene Regulatory Networks for Development.”. Proc Natl Acad Sci U S A 102 (14): 4936-42.

Gresham, David, Renata Usaite, Susanne Manuela Germann, Michael Lisby, David Botstein, and Birgitte Regenberg. (2010) 2010. “Adaptation to Diverse Nitrogen-Limited Environments by Deletion or Extrachromosomal Element Formation of the GAP1 Locus.”. Proc Natl Acad Sci U S A 107 (43): 18551-6.

Troyanskaya, Olga G, Ora Arbell, Yair Koren, Gad M Landau, and Alexander Bolshoy. (2002) 2002. “Sequence Complexity Profiles of Prokaryotic Genomic Sequences: A Fast Algorithm for Calculating Linguistic Complexity.”. Bioinformatics 18 (5): 679-88.

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.

Ayroles, Julien, Brooke A Laflamme, Eric A Stone, Mariana F Wolfner, and Trudy F C Mackay. (2011) 2011. “Functional Genome Annotation of Drosophila Seminal Fluid Proteins Using Transcriptional Genetic Networks.”. Genet Res (Camb) 93 (6): 387-95.

Zhou, Jian, Chandra L Theesfeld, Kevin Yao, Kathleen M Chen, Aaron K Wong, and Olga G Troyanskaya. (2018) 2018. “Deep Learning Sequence-Based Ab Initio Prediction of Variant Effects on Expression and Disease Risk.”. Nat Genet 50 (8): 1171-79. doi:10.1038/s41588-018-0160-6.

Murphy, Coleen T. (2006) 2006. “The Search for DAF-16 FOXO Transcriptional Targets: Approaches and Discoveries.”. Exp Gerontol 41 (10): 910-21.

Stone, Eric A, and Julien Ayroles. (2009) 2009. “Modulated Modularity Clustering As an Exploratory Tool for Functional Genomic Inference.”. PLoS Genet 5 (5): e1000479.

Banigan, Edward J, Michael A Gelbart, Zemer Gitai, Ned S Wingreen, and Andrea J Liu. (2011) 2011. “Filament Depolymerization Can Explain Chromosome Pulling During Bacterial Mitosis.”. PLoS Comput Biol 7 (9): e1002145.

Wolf, Aaron B, and Joshua Akey. (2018) 2018. “Outstanding Questions in the Study of Archaic Hominin Admixture.”. PLoS Genet 14 (5): e1007349. doi:10.1371/journal.pgen.1007349.

Wingreen, Ned S, Jonathan Miller, and Edward C Cox. (2003) 2003. “Scaling of Mutational Effects in Models for Pleiotropy.”. Genetics 164 (3): 1221-8.

Yuan, Jie, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen, and Joshua D Rabinowitz. 2009. “Metabolomics-Driven Quantitative Analysis of Ammonia Assimilation in E. Coli.”. Mol Syst Biol 5: 302.

Brooks, Dawn J, Jacques R Fresco, Arthur M Lesk, and Mona Singh. (2002) 2002. “Evolution of Amino Acid Frequencies in Proteins over Deep Time: Inferred Order of Introduction of Amino Acids into the Genetic Code.”. Mol Biol Evol 19 (10): 1645-55.

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

Stathopoulos, Angelike, and Michael Levine. (2005) 2005. “Localized Repressors Delineate the Neurogenic Ectoderm in the Early Drosophila Embryo.”. Dev Biol 280 (2): 482-93.

Wieschaus, E. (1996) 1996. “Embryonic Transcription and the Control of Developmental Pathways.”. Genetics 142 (1): 5-10.

Papatsenko, Dmitri, and Michael Levine. (2005) 2005. “Quantitative Analysis of Binding Motifs Mediating Diverse Spatial Readouts of the Dorsal Gradient in the Drosophila Embryo.”. Proc Natl Acad Sci U S A 102 (14): 4966-71.

Botstein, David. (2004) 2004. “Ira Herskowitz: 1946-2003.”. Genetics 166 (2): 653-60.

Simakov, David S A, Lily S Cheung, Len M Pismen, and Stanislav Y Shvartsman. (2012) 2012. “EGFR-Dependent Network Interactions That Pattern Drosophila Eggshell Appendages.”. Development 139 (15): 2814-20.

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, 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.

Putnam, Andrea S, Mark Scriber, and Peter Andolfatto. (2007) 2007. “Discordant Divergence Times Among Z-Chromosome Regions Between Two Ecologically Distinct Swallowtail Butterfly Species.”. Evolution 61 (4): 912-27.

Wilson, Daniel J, Ryan D Hernandez, Peter Andolfatto, and Molly Przeworski. (2011) 2011. “A Population Genetics-Phylogenetics Approach to Inferring Natural Selection in Coding Sequences.”. PLoS Genet 7 (12): e1002395.

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

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.

Tilghman, S M, M S Bartolomei, A L Webber, M E Brunkow, J Saam, P A Leighton, K Pfeifer, and S Zemel. 1993. “Parental Imprinting of the H19 and Igf2 Genes in the Mouse.”. Cold Spring Harb Symp Quant Biol 58: 287-95.

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.

Jim, Kam, Kush Parmar, Mona Singh, and Saeed Tavazoie. (2004) 2004. “A Cross-Genomic Approach for Systematic Mapping of Phenotypic Traits to Genes.”. Genome Res 14 (1): 109-15.

Tilghman, S M. 1991. “Parental Imprinting in the Mouse.”. Harvey Lect 87: 69-84.

Senger, Kate, Grant W Armstrong, William J Rowell, Jennifer M Kwan, Michele Markstein, and Michael Levine. (2004) 2004. “Immunity Regulatory DNAs Share Common Organizational Features in Drosophila.”. Mol Cell 13 (1): 19-32.

Andolfatto, Peter. (2008) 2008. “Controlling Type-I Error of the McDonald-Kreitman Test in Genomewide Scans for Selection on Noncoding DNA.”. Genetics 180 (3): 1767-71.

Simpson, L, and E Wieschaus. (1990) 1990. “Zygotic Activity of the Nullo Locus Is Required to Stabilize the Actin-Myosin Network During Cellularization in Drosophila.”. Development 110 (3): 851-63.

Tkačik, Gašper, Aleksandra M Walczak, and William Bialek. (2012) 2012. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.”. Phys Rev E Stat Nonlin Soft Matter Phys 85 (4 Pt 1): 041903.

Morize, P, A E Christiansen, M Costa, S Parks, and E Wieschaus. (1998) 1998. “Hyperactivation of the Folded Gastrulation Pathway Induces Specific Cell Shape Changes.”. Development 125 (4): 589-97.

Kim, Yoosik, Antonina Iagovitina, Keisuke Ishihara, Kate M Fitzgerald, Bart Deplancke, Dmitri Papatsenko, and Stanislav Y Shvartsman. (2013) 2013. “Context-Dependent Transcriptional Interpretation of Mitogen Activated Protein Kinase Signaling in the Drosophila Embryo.”. Chaos 23 (2): 025105.

Stathopoulos, Angelike, Madeleine Van Drenth, Albert Erives, Michele Markstein, and Michael Levine. (2002) 2002. “Whole-Genome Analysis of Dorsal-Ventral Patterning in the Drosophila Embryo.”. Cell 111 (5): 687-701.

Walczak, Aleksandra M, Gašper Tkačik, and William Bialek. (2010) 2010. “Optimizing Information Flow in Small Genetic Networks. II. Feed-Forward Interactions.”. Phys Rev E Stat Nonlin Soft Matter Phys 81 (4 Pt 1): 041905.

Andolfatto, Peter. (2007) 2007. “Hitchhiking Effects of Recurrent Beneficial Amino Acid Substitutions in the Drosophila Melanogaster Genome.”. Genome Res 17 (12): 1755-62.

Jiang, Peng, Mona Singh, and Hilary A Coller. 2013. “Computational Assessment of the Cooperativity Between RNA Binding Proteins and MicroRNAs in Transcript Decay.”. PLoS Comput Biol 9 (5): e1003075.

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.

Tkačik, Gašper, Aleksandra M Walczak, and William Bialek. (2009) 2009. “Optimizing Information Flow in Small Genetic Networks.”. Phys Rev E Stat Nonlin Soft Matter Phys 80 (3 Pt 1): 031920.

Capra, John A, Katrin Paeschke, Mona Singh, and Virginia A Zakian. 2010. “G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated With Distinct Genomic Features in Saccharomyces Cerevisiae.”. PLoS Comput Biol 6 (7): e1000861.

Thornton, Kevin, and Peter Andolfatto. (2006) 2006. “Approximate Bayesian Inference Reveals Evidence for a Recent, Severe Bottleneck in a Netherlands Population of Drosophila Melanogaster.”. Genetics 172 (3): 1607-19.

Haley, Benjamin, Bryon Foys, and Michael Levine. (2010) 2010. “Vectors and Parameters That Enhance the Efficacy of RNAi-Mediated Gene Disruption in Transgenic Drosophila.”. Proc Natl Acad Sci U S A 107 (25): 11435-40.

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.

Chikina, Maria D, Curtis Huttenhower, Coleen T Murphy, and Olga G Troyanskaya. (2009) 2009. “Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis Elegans.”. PLoS Comput Biol 5 (6): e1000417.

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.

Ober, Ulrike, Julien Ayroles, Eric A Stone, Stephen Richards, Dianhui Zhu, Richard A Gibbs, Christian Stricker, et al. 2012. “Using Whole-Genome Sequence Data to Predict Quantitative Trait Phenotypes in Drosophila Melanogaster.”. PLoS Genet 8 (5): e1002685.