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.

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

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.

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

Levine, Michael, and Robert Tjian. (2003) 2003. “Transcription Regulation and Animal Diversity.”. Nature 424 (6945): 147-51.

Brannan, C I, E C Dees, R S Ingram, and S M Tilghman. (1990) 1990. “The Product of the H19 Gene May Function As an RNA.”. Mol Cell Biol 10 (1): 28-36.

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.

Shapira, Michael, Eran Segal, and David Botstein. (2004) 2004. “Disruption of Yeast Forkhead-Associated Cell Cycle Transcription by Oxidative Stress.”. Mol Biol Cell 15 (12): 5659-69.

Schejter, E D, and E Wieschaus. (1993) 1993. “Bottleneck Acts As a Regulator of the Microfilament Network Governing Cellularization of the Drosophila Embryo.”. Cell 75 (2): 373-85.

Roose, Jeroen P, Maximilian Diehn, Michael G Tomlinson, Joseph Lin, Ash A Alizadeh, David Botstein, Patrick O Brown, and Arthur Weiss. (2003) 2003. “T Cell Receptor-Independent Basal Signaling via Erk and Abl Kinases Suppresses RAG Gene Expression.”. PLoS Biol 1 (2): E53.

Little, Shawn C, Mikhail Tikhonov, and Thomas Gregor. (2013) 2013. “Precise Developmental Gene Expression Arises from Globally Stochastic Transcriptional Activity.”. Cell 154 (4): 789-800.

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.

Leighton, P A, R S Ingram, J Eggenschwiler, A Efstratiadis, and S M Tilghman. (1995) 1995. “Disruption of Imprinting Caused by Deletion of the H19 Gene Region in Mice.”. Nature 375 (6526): 34-9.

Shaevitz, Joshua W, Elio A Abbondanzieri, Robert Landick, and Steven M Block. (2003) 2003. “Backtracking by Single RNA Polymerase Molecules Observed at Near-Base-Pair Resolution.”. Nature 426 (6967): 684-7.

Jumbo-Lucioni, Patricia, Julien Ayroles, Michelle Chambers, Katherine W Jordan, Jeff Leips, Trudy Fc Mackay, and Maria De Luca. 2010. “Systems Genetics Analysis of Body Weight and Energy Metabolism Traits in Drosophila Melanogaster.”. BMC Genomics 11: 297.

Camper, S A, and S M Tilghman. (1989) 1989. “Postnatal Repression of the Alpha-Fetoprotein Gene Is Enhancer Independent.”. Genes Dev 3 (4): 537-46.

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.

Abbondanzieri, Elio A, William J Greenleaf, Joshua W Shaevitz, Robert Landick, and Steven M Block. (2005) 2005. “Direct Observation of Base-Pair Stepping by RNA Polymerase.”. Nature 438 (7067): 460-5.

Teng, Shu-Wen, Jessica N Schaffer, Kimberly C Tu, Pankaj Mehta, Wenyun Lu, N P Ong, Bonnie L Bassler, and Ned S Wingreen. (2011) 2011. “Active Regulation of Receptor Ratios Controls Integration of Quorum-Sensing Signals in Vibrio Harveyi.”. Mol Syst Biol 7: 491.

Wang, Wei, Michael Cherry, David Botstein, and Hao Li. (2002) 2002. “A Systematic Approach to Reconstructing Transcription Networks in Saccharomycescerevisiae.”. Proc Natl Acad Sci U S A 99 (26): 16893-8.

Abbondanzieri, Elio A, Joshua W Shaevitz, and Steven M Block. (2005) 2005. “Picocalorimetry of Transcription by RNA Polymerase.”. Biophys J 89 (6).

Whitfield, Michael L, Gavin Sherlock, Alok J Saldanha, John I Murray, Catherine A Ball, Karen E Alexander, John C Matese, et al. (2002) 2002. “Identification of Genes Periodically Expressed in the Human Cell Cycle and Their Expression in Tumors.”. Mol Biol Cell 13 (6): 1977-2000.

Slavov, Nikolai, and David Botstein. (2013) 2013. “Decoupling Nutrient Signaling from Growth Rate Causes Aerobic Glycolysis and Deregulation of Cell Size and Gene Expression.”. Mol Biol Cell 24 (2): 157-68.

Papazyan, Romeo, Zheng Sun, Yong Hoon Kim, Paul M Titchenell, David A Hill, Wenyun Lu, Manashree Damle, et al. (2016) 2016. “Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP SREBP.”. Cell Metab 24 (6): 863-74. doi:10.1016/j.cmet.2016.10.012.

McIsaac, Scott, Benjamin L Oakes, Xin Wang, Krysta A Dummit, David Botstein, and Marcus B Noyes. (2013) 2013. “Synthetic Gene Expression Perturbation Systems With Rapid, Tunable, Single-Gene Specificity in Yeast.”. Nucleic Acids Res 41 (4): e57.

McIsaac, Scott, Allegra A Petti, Harmen J Bussemaker, and David Botstein. (2012) 2012. “Perturbation-Based Analysis and Modeling of Combinatorial Regulation in the Yeast Sulfur Assimilation Pathway.”. Mol Biol Cell 23 (15): 2993-3007.

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

Markstein, Michele, and Michael Levine. (2002) 2002. “Decoding Cis-Regulatory DNAs in the Drosophila Genome.”. Curr Opin Genet Dev 12 (5): 601-6.

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.

Petti, Allegra A, Christopher A Crutchfield, Joshua D Rabinowitz, and David Botstein. (2011) 2011. “Survival of Starving Yeast Is Correlated With Oxidative Stress Response and Nonrespiratory Mitochondrial Function.”. Proc Natl Acad Sci U S A 108 (45).

Lagha, Mounia, Jacques P Bothma, Emilia Esposito, Samuel Ng, Laura Stefanik, Chiahao Tsui, Jeffrey Johnston, et al. (2013) 2013. “Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo.”. Cell 153 (5): 976-87.

Murphy, Coleen T, Steven A McCarroll, Cornelia I Bargmann, Andrew Fraser, Ravi S Kamath, Julie Ahringer, Hao Li, and Cynthia Kenyon. (2003) 2003. “Genes That Act Downstream of DAF-16 to Influence the Lifespan of Caenorhabditis Elegans.”. Nature 424 (6946): 277-83.

Pane, Attilio, Peng Jiang, Dorothy Yanling Zhao, Mona Singh, and Trudi Schüpbach. (2011) 2011. “The Cutoff Protein Regulates PiRNA Cluster Expression and PiRNA Production in the Drosophila Germline.”. EMBO J 30 (22): 4601-15.

Bailis, Will, Justin A Shyer, Jun Zhao, Juan Carlos Garcia Canaveras, Fatimah J Al Khazal, Rihao Qu, Holly R Steach, et al. (2019) 2019. “Distinct Modes of Mitochondrial Metabolism Uncouple T Cell Differentiation and Function.”. Nature 571 (7765): 403-7. doi:10.1038/s41586-019-1311-3.

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.

Biemar, Frédéric, Robert Zinzen, Matthew Ronshaugen, Victor Sementchenko, Robert Manak, and Michael S Levine. (2005) 2005. “Spatial Regulation of MicroRNA Gene Expression in the Drosophila Embryo.”. Proc Natl Acad Sci U S A 102 (44): 15907-11.

van Raamsdonk, C D, and S M Tilghman. (2001) 2001. “Optimizing the Detection of Nascent Transcripts by RNA Fluorescence in Situ Hybridization.”. Nucleic Acids Res 29 (8).

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.

Lu, Xuemin, Jennifer M Li, Olivier Elemento, Saeed Tavazoie, and Eric F Wieschaus. (2009) 2009. “Coupling of Zygotic Transcription to Mitotic Control at the Drosophila Mid-Blastula Transition.”. Development 136 (12): 2101-10.

Klosinska, Maja M, Christopher A Crutchfield, Patrick H Bradley, Joshua D Rabinowitz, and James R Broach. (2011) 2011. “Yeast Cells Can Access Distinct Quiescent States.”. Genes Dev 25 (4): 336-49.

Riggleman, B, P Schedl, and E Wieschaus. (1990) 1990. “Spatial Expression of the Drosophila Segment Polarity Gene Armadillo Is Posttranscriptionally Regulated by Wingless.”. Cell 63 (3): 549-60.

Tyner, A L, R Godbout, R S Compton, and S M Tilghman. (1990) 1990. “The Ontogeny of Alpha-Fetoprotein Gene Expression in the Mouse Gastrointestinal Tract.”. J Cell Biol 110 (4): 915-27.

Berman, Benjamin P, Yutaka Nibu, Barret D Pfeiffer, Pavel Tomancak, Susan E Celniker, Michael Levine, Gerald M Rubin, and Michael B Eisen. (2002) 2002. “Exploiting Transcription Factor Binding Site Clustering to Identify Cis-Regulatory Modules Involved in Pattern Formation in the Drosophila Genome.”. Proc Natl Acad Sci U S A 99 (2): 757-62.

Brauer, Matthew J, Curtis Huttenhower, Edoardo M Airoldi, Rachel Rosenstein, John C Matese, David Gresham, Viktor M Boer, Olga G Troyanskaya, and David Botstein. (2008) 2008. “Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast.”. Mol Biol Cell 19 (1): 352-67.

Yoo-Warren, H, , R S Ingram, and S M Tilghman. (1988) 1988. “Two Regulatory Domains Flank the Mouse H19 Gene.”. Mol Cell Biol 8 (11): 4707-15.

Bothma, Jacques P, Joe Magliocco, and Michael Levine. (2011) 2011. “The Snail Repressor Inhibits Release, Not Elongation, of Paused Pol II in the Drosophila Embryo.”. Curr Biol 21 (18): 1571-7.

Postner, M A, and E F Wieschaus. (1994) 1994. “The Nullo Protein Is a Component of the Actin-Myosin Network That Mediates Cellularization in Drosophila Melanogaster Embryos.”. J Cell Sci 107 ( Pt 7): 1863-73.

Rizki, Gizem, Terri Naoko Iwata, Ji Li, Christian G Riedel, Colette Lafontaine Picard, Max Jan, Coleen T Murphy, and Siu Sylvia Lee. (2011) 2011. “The Evolutionarily Conserved Longevity Determinants HCF-1 and SIR-2.1 SIRT1 Collaborate to Regulate DAF-16 FOXO.”. PLoS Genet 7 (9): e1002235.

Hickman, Mark J, Allegra A Petti, Olivia Ho-Shing, Sanford J Silverman, Scott McIsaac, Traci A Lee, and David Botstein. (2011) 2011. “Coordinated Regulation of Sulfur and Phospholipid Metabolism Reflects the Importance of Methylation in the Growth of Yeast.”. Mol Biol Cell 22 (21): 4192-204.