Hughes, Kimberly A, Julien Ayroles, Melissa M Reedy, Jenny M Drnevich, Kevin C Rowe, Elizabeth A Ruedi, Carla E Cáceres, and Ken N Paige. (2006) 2006. “Segregating Variation in the Transcriptome: Cis Regulation and Additivity of Effects.”. Genetics 173 (3): 1347-55.

Markowetz, Florian, Dennis Kostka, Olga G Troyanskaya, and Rainer Spang. (2007) 2007. “Nested Effects Models for High-Dimensional Phenotyping Screens.”. Bioinformatics 23 (13).

Lakhina, Vanisha, Rachel Arey, Rachel Kaletsky, Amanda Kauffman, Geneva Stein, William Keyes, Daniel Xu, and Coleen T Murphy. (2015) 2015. “Genome-Wide Functional Analysis of CREB Long-Term Memory-Dependent Transcription Reveals Distinct Basal and Memory Gene Expression Programs.”. Neuron 85 (2): 330-45.

Harbison, Susan T, Mary Anna Carbone, Julien Ayroles, Eric A Stone, Richard F Lyman, and Trudy F C Mackay. (2009) 2009. “Co-Regulated Transcriptional Networks Contribute to Natural Genetic Variation in Drosophila Sleep.”. Nat Genet 41 (3): 371-5.

Kapheim, Karen M, Hailin Pan, Cai Li, Steven L Salzberg, Daniela Puiu, Tanja Magoc, Hugh M Robertson, et al. (2015) 2015. “Social Evolution. Genomic Signatures of Evolutionary Transitions from Solitary to Group Living.”. Science 348 (6239): 1139-43. doi:10.1126/science.aaa4788.

Bejsovec, A, and E Wieschaus. (1993) 1993. “Segment Polarity Gene Interactions Modulate Epidermal Patterning in Drosophila Embryos.”. Development 119 (2): 501-17.

Peifer, M, and E Wieschaus. (1990) 1990. “Mutations in the Drosophila Gene Extradenticle Affect the Way Specific Homeo Domain Proteins Regulate Segmental Identity.”. Genes Dev 4 (7): 1209-23.

Chang, Howard Y, Julie B Sneddon, Ash A Alizadeh, Ruchira Sood, Rob B West, Kelli Montgomery, Jen-Tsan Chi, Matt van de Rijn, David Botstein, and Patrick O Brown. (2004) 2004. “Gene Expression Signature of Fibroblast Serum Response Predicts Human Cancer Progression: Similarities Between Tumors and Wounds.”. PLoS Biol 2 (2): E7.

Bradley, Patrick H, Matthew J Brauer, Joshua D Rabinowitz, and Olga G Troyanskaya. (2009) 2009. “Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces Cerevisiae.”. PLoS Comput Biol 5 (1): e1000270.

Pritykin, Yuri, Tarcisio Brito, Trudi Schüpbach, Mona Singh, and Attilio Pane. (2017) 2017. “Integrative Analysis Unveils New Functions for the Drosophila Cutoff Protein in Noncoding RNA Biogenesis and Gene Regulation.”. RNA 23 (7): 1097-1109. doi:10.1261/rna.058594.116.

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

Nusslein-Volhard, C, and E Wieschaus. (1980) 1980. “Mutations Affecting Segment Number and Polarity in Drosophila.”. Nature 287 (5785): 795-801.

Berezhkovskii, Alexander M, Christine Sample, and Stanislav Y Shvartsman. (2011) 2011. “Formation of Morphogen Gradients: Local Accumulation Time.”. Phys Rev E Stat Nonlin Soft Matter Phys 83 (5 Pt 1): 051906.

Rauskolb, C, and E Wieschaus. (1994) 1994. “Coordinate Regulation of Downstream Genes by Extradenticle and the Homeotic Selector Proteins.”. EMBO J 13 (15): 3561-9.

Guan, Dongyin, Ying Xiong, Patricia C Borck, Cholsoon Jang, Paschalis-Thomas Doulias, Romeo Papazyan, Bin Fang, et al. (2018) 2018. “Diet-Induced Circadian Enhancer Remodeling Synchronizes Opposing Hepatic Lipid Metabolic Processes.”. Cell 174 (4): 831-842.e12. doi:10.1016/j.cell.2018.06.031.

Trinklein, Nathan D, John I Murray, Sara J Hartman, David Botstein, and Richard M Myers. (2004) 2004. “The Role of Heat Shock Transcription Factor 1 in the Genome-Wide Regulation of the Mammalian Heat Shock Response.”. Mol Biol Cell 15 (3): 1254-61.

Trotter, Eleanor W, Camilla M-F Kao, Ludmilla Berenfeld, David Botstein, Gregory A Petsko, and Joseph Gray V. (2002) 2002. “Misfolded Proteins Are Competent to Mediate a Subset of the Responses to Heat Shock in Saccharomyces Cerevisiae.”. J Biol Chem 277 (47): 44817-25.

Godbout, R, R S Ingram, and S M Tilghman. (1988) 1988. “Fine-Structure Mapping of the Three Mouse Alpha-Fetoprotein Gene Enhancers.”. Mol Cell Biol 8 (3): 1169-78.

Slavov, Nikolai, Edoardo M Airoldi, Alexander van Oudenaarden, and David Botstein. (2012) 2012. “A Conserved Cell Growth Cycle Can Account for the Environmental Stress Responses of Divergent Eukaryotes.”. Mol Biol Cell 23 (10): 1986-97.

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.

Spear, B T, and S M Tilghman. (1990) 1990. “Role of Alpha-Fetoprotein Regulatory Elements in Transcriptional Activation in Transient Heterokaryons.”. Mol Cell Biol 10 (10): 5047-54.

He, Bing, Amy A Caudy, Lance Parsons, Adam Rosebrock, Attilio Pane, Sandeep Raj, and Eric Wieschaus. (2012) 2012. “Mapping the Pericentric Heterochromatin by Comparative Genomic Hybridization Analysis and Chromosome Deletions in Drosophila Melanogaster.”. Genome Res 22 (12): 2507-19.

Jeong, Sangyun, Mark Rebeiz, Peter Andolfatto, Thomas Werner, John True, and Sean B Carroll. (2008) 2008. “The Evolution of Gene Regulation Underlies a Morphological Difference Between Two Drosophila Sister Species.”. Cell 132 (5): 783-93.

Godbout, R, and S M Tilghman. (1988) 1988. “Configuration of the Alpha-Fetoprotein Regulatory Domain During Development.”. Genes Dev 2 (8): 949-56.

Benson, Kiara K, Wenxiang Hu, Angela H Weller, Alexis H Bennett, Eric R Chen, Sumeet A Khetarpal, Satoshi Yoshino, et al. (2019) 2019. “Natural Human Genetic Variation Determines Basal and Inducible Expression of , an Obesity-Associated Gene.”. Proc Natl Acad Sci U S A 116 (46): 23232-42. doi:10.1073/pnas.1913199116.

Markstein, Michele, Robert Zinzen, Peter Markstein, Ka-Ping Yee, Albert Erives, Angela Stathopoulos, and Michael Levine. (2004) 2004. “A Regulatory Code for Neurogenic Gene Expression in the Drosophila Embryo.”. Development 131 (10): 2387-94.

Markowetz, Florian, Klaas W Mulder, Edoardo M Airoldi, Ihor R Lemischka, and Olga G Troyanskaya. 2010. “Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells.”. PLoS Comput Biol 6 (12): e1001034.

Semenova, Ekaterina, XiaoFei Wang, Monica M Jablonski, John Levorse, and Shirley M Tilghman. (2003) 2003. “An Engineered 800 Kilobase Deletion of Uchl3 and Lmo7 on Mouse Chromosome 14 Causes Defects in Viability, Postnatal Growth and Degeneration of Muscle and Retina.”. Hum Mol Genet 12 (11): 1301-12.

Oliveira, Riva P, Jess Porter Abate, Kieran Dilks, Jessica Landis, Jasmine M Ashraf, Coleen T Murphy, and Keith Blackwell. (2009) 2009. “Condition-Adapted Stress and Longevity Gene Regulation by Caenorhabditis Elegans SKN-1 Nrf.”. Aging Cell 8 (5): 524-41.

Hsu, Ao-Lin, Coleen T Murphy, and Cynthia Kenyon. (2003) 2003. “Regulation of Aging and Age-Related Disease by DAF-16 and Heat-Shock Factor.”. Science 300 (5622): 1142-5.

Levine, Michael, Claudia Cattoglio, and Robert Tjian. (2014) 2014. “Looping Back to Leap Forward: Transcription Enters a New Era.”. Cell 157 (1): 13-25.

Chi, Jen-Tsan, Howard Y Chang, Guttorm Haraldsen, Frode L Jahnsen, Olga G Troyanskaya, Dustin S Chang, Zhen Wang, et al. (2003) 2003. “Endothelial Cell Diversity Revealed by Global Expression Profiling.”. Proc Natl Acad Sci U S A 100 (19): 10623-8.

McCarroll, Steven A, Coleen T Murphy, Sige Zou, Scott D Pletcher, Chen-Shan Chin, Yuh Nung Jan, Cynthia Kenyon, Cornelia I Bargmann, and Hao Li. (2004) 2004. “Comparing Genomic Expression Patterns across Species Identifies Shared Transcriptional Profile in Aging.”. Nat Genet 36 (2): 197-204.

Vacher, J, S A Camper, R Krumlauf, R S Compton, and S M Tilghman. (1992) 1992. “Raf Regulates the Postnatal Repression of the Mouse Alpha-Fetoprotein Gene at the Posttranscriptional Level.”. Mol Cell Biol 12 (2): 856-64.

Troyanskaya, Olga G. 2007. “Integrated Analysis of Microarray Results.”. Methods Mol Biol 382: 429-37.

Parks, S, and E Wieschaus. (1991) 1991. “The Drosophila Gastrulation Gene Concertina Encodes a G Alpha-Like Protein.”. Cell 64 (2): 447-58.

Jiang, Peng, and Mona Singh. (2014) 2014. “CCAT: Combinatorial Code Analysis Tool for Transcriptional Regulation.”. Nucleic Acids Res 42 (5): 2833-47.

Emerson, J A, J Vacher, L A Cirillo, S M Tilghman, and A L Tyner. (1992) 1992. “The Zonal Expression of Alpha-Fetoprotein Transgenes in the Livers of Adult Mice.”. Dev Dyn 195 (1): 55-66.

Mehta, Pankaj, Sidhartha Goyal, and Ned S Wingreen. 2008. “A Quantitative Comparison of SRNA-Based and Protein-Based Gene Regulation.”. Mol Syst Biol 4: 221.

Tkačik, Gašper, Curtis G Callan, and William Bialek. (2008) 2008. “Information Flow and Optimization in Transcriptional Regulation.”. Proc Natl Acad Sci U S A 105 (34): 12265-70.

Rose, L S, and E Wieschaus. (1992) 1992. “The Drosophila Cellularization Gene Nullo Produces a Blastoderm-Specific Transcript Whose Levels Respond to the Nucleocytoplasmic Ratio.”. Genes Dev 6 (7): 1255-68.

Zartman, Jeremiah J, Nir Yakoby, Christopher A Bristow, Xiaofeng Zhou, Karin Schlichting, Christian Dahmann, and Stanislav Y Shvartsman. (2008) 2008. “Cad74A Is Regulated by BR and Is Required for Robust Dorsal Appendage Formation in Drosophila Oogenesis.”. Dev Biol 322 (2): 289-301.

Sayama, Koichi, Maximilian Diehn, Kentaro Matsuda, Carolina Lunderius, Mindy Tsai, See-Ying Tam, David Botstein, Patrick O Brown, and Stephen J Galli. (2002) 2002. “Transcriptional Response of Human Mast Cells Stimulated via the Fc(epsilon)RI and Identification of Mast Cells As a Source of IL-11.”. BMC Immunol 3: 5.

Troyanskaya, Olga G. (2005) 2005. “Putting Microarrays in a Context: Integrated Analysis of Diverse Biological Data.”. Brief Bioinform 6 (1): 34-43.

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.

Vacher, J, and S M Tilghman. (1990) 1990. “Dominant Negative Regulation of the Mouse Alpha-Fetoprotein Gene in Adult Liver.”. Science 250 (4988): 1732-5.

Smith, Kevin S, Sumit K Chanda, Merel Lingbeek, Douglas T Ross, David Botstein, Maarten van Lohuizen, and Michael L Cleary. (2003) 2003. “Bmi-1 Regulation of INK4A-ARF Is a Downstream Requirement for Transformation of Hematopoietic Progenitors by E2a-Pbx1.”. Mol Cell 12 (2): 393-400.

Fuchs, Alisa, Lily S Cheung, Enrica Charbonnier, Stanislav Y Shvartsman, and George Pyrowolakis. (2012) 2012. “Transcriptional Interpretation of the EGF Receptor Signaling Gradient.”. Proc Natl Acad Sci U S A 109 (5): 1572-7.

Costa, M, E T Wilson, and E Wieschaus. (1994) 1994. “A Putative Cell Signal Encoded by the Folded Gastrulation Gene Coordinates Cell Shape Changes During Drosophila Gastrulation.”. Cell 76 (6): 1075-89.

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.