Ronen, Michal, and David Botstein. (2006) 2006. “Transcriptional Response of Steady-State Yeast Cultures to Transient Perturbations in Carbon Source.”. Proc Natl Acad Sci U S A 103 (2): 389-94.

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.

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.

De Renzis, Stefano, J Yu, R Zinzen, and Eric Wieschaus. (2006) 2006. “Dorsal-Ventral Pattern of Delta Trafficking Is Established by a Snail-Tom-Neuralized Pathway.”. Dev Cell 10 (2): 257-64.

Ewald, Collin Y, Jess N Landis, Jess Porter Abate, Coleen T Murphy, and Keith Blackwell. (2015) 2015. “Dauer-Independent Insulin IGF-1-Signalling Implicates Collagen Remodelling in Longevity.”. Nature 519 (7541): 97-101. doi:10.1038/nature14021.

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.

Goodliffe, Julie M, Eric Wieschaus, and Michael D Cole. (2005) 2005. “Polycomb Mediates Myc Autorepression and Its Transcriptional Control of Many Loci in Drosophila.”. Genes Dev 19 (24): 2941-6.

Lee, Seung-Jae, Coleen T Murphy, and Cynthia Kenyon. (2009) 2009. “Glucose Shortens the Life Span of C. Elegans by Downregulating DAF-16 FOXO Activity and Aquaporin Gene Expression.”. Cell Metab 10 (5): 379-91.

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.

Kobren, Shilpa Nadimpalli, and Mona Singh. (2019) 2019. “Systematic Domain-Based Aggregation of Protein Structures Highlights DNA-, RNA- and Other Ligand-Binding Positions.”. Nucleic Acids Res 47 (2): 582-93. doi:10.1093/nar/gky1224.

Feuerman, M H, R Godbout, R S Ingram, and S M Tilghman. (1989) 1989. “Tissue-Specific Transcription of the Mouse Alpha-Fetoprotein Gene Promoter Is Dependent on HNF-1.”. Mol Cell Biol 9 (10): 4204-12.

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.

Diehn, Maximilian, Ash A Alizadeh, Oliver J Rando, Chih Long Liu, Kryn Stankunas, David Botstein, Gerald R Crabtree, and Patrick O Brown. (2002) 2002. “Genomic Expression Programs and the Integration of the CD28 Costimulatory Signal in T Cell Activation.”. Proc Natl Acad Sci U S A 99 (18): 11796-801.

Bothma, Jacques P, and Michael Levine. (2013) 2013. “Development: Lights, Camera, Action--the Drosophila Embryo Goes Live!”. Curr Biol 23 (21).

Munro, Daniel, Dario Ghersi, and Mona Singh. (2018) 2018. “Two Critical Positions in Zinc Finger Domains Are Heavily Mutated in Three Human Cancer Types.”. PLoS Comput Biol 14 (6): e1006290. doi:10.1371/journal.pcbi.1006290.

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.

Zallen, Jennifer A, and Eric Wieschaus. (2004) 2004. “Patterned Gene Expression Directs Bipolar Planar Polarity in Drosophila.”. Dev Cell 6 (3): 343-55.

Yoshimoto, Hiroyuki, Kirstie Saltsman, Audrey P Gasch, Hong Xia Li, Nobuo Ogawa, David Botstein, Patrick O Brown, and Martha S Cyert. (2002) 2002. “Genome-Wide Analysis of Gene Expression Regulated by the Calcineurin Crz1p Signaling Pathway in Saccharomyces Cerevisiae.”. J Biol Chem 277 (34): 31079-88.

Persikov, Anton, V, Elizabeth F Rowland, Benjamin L Oakes, Mona Singh, and Marcus B Noyes. (2014) 2014. “Deep Sequencing of Large Library Selections Allows Computational Discovery of Diverse Sets of Zinc Fingers That Bind Common Targets.”. Nucleic Acids Res 42 (3): 1497-508.

Wetzel, Joshua L, and Mona Singh. (2020) 2020. “Sharing DNA-Binding Information across Structurally Similar Proteins Enables Accurate Specificity Determination.”. Nucleic Acids Res 48 (2): e9. doi:10.1093/nar/gkz1087.

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.

Armand, P, A C Knapp, A J Hirsch, E F Wieschaus, and M D Cole. (1994) 1994. “A Novel Basic Helix-Loop-Helix Protein Is Expressed in Muscle Attachment Sites of the Drosophila Epidermis.”. Mol Cell Biol 14 (6): 4145-54.

Schaner, Marci E, Douglas T Ross, Giuseppe Ciaravino, Therese Sorlie, Olga Troyanskaya, Maximilian Diehn, Yan C Wang, et al. (2003) 2003. “Gene Expression Patterns in Ovarian Carcinomas.”. Mol Biol Cell 14 (11): 4376-86.

Persikov, Anton, V, and Mona Singh. (2014) 2014. “De Novo Prediction of DNA-Binding Specificities for Cys2His2 Zinc Finger Proteins.”. Nucleic Acids Res 42 (1): 97-108.

Diehn, Maximilian, Gavin Sherlock, Gail Binkley, Heng Jin, John C Matese, Tina Hernandez-Boussard, Christian A Rees, et al. (2003) 2003. “SOURCE: A Unified Genomic Resource of Functional Annotations, Ontologies, and Gene Expression Data.”. Nucleic Acids Res 31 (1): 219-23.

Hilgers, Valérie, Michael W Perry, David Hendrix, Alexander Stark, Michael Levine, and Benjamin Haley. (2011) 2011. “Neural-Specific Elongation of 3’ UTRs During Drosophila Development.”. Proc Natl Acad Sci U S A 108 (38): 15864-9.

Katz, David J, Michael A Beer, John M Levorse, and Shirley M Tilghman. (2005) 2005. “Functional Characterization of a Novel Ku70 80 Pause Site at the H19 Igf2 Imprinting Control Region.”. Mol Cell Biol 25 (10): 3855-63.

Hark, A T, C J Schoenherr, D J Katz, R S Ingram, J M Levorse, and S M Tilghman. (2000) 2000. “CTCF Mediates Methylation-Sensitive Enhancer-Blocking Activity at the H19 Igf2 Locus.”. Nature 405 (6785): 486-9.

Cowden, John, and Michael Levine. (2002) 2002. “The Snail Repressor Positions Notch Signaling in the Drosophila Embryo.”. Development 129 (7): 1785-93.

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.

Zartman, Jeremiah J, Jitendra S Kanodia, Lily S Cheung, and Stanislav Y Shvartsman. (2009) 2009. “Feedback Control of the EGFR Signaling Gradient: Superposition of Domain-Splitting Events in Drosophila Oogenesis.”. Development 136 (17): 2903-11.

Nibu, Yutaka, Kate Senger, and Michael Levine. (2003) 2003. “CtBP-Independent Repression in the Drosophila Embryo.”. Mol Cell Biol 23 (11): 3990-9.

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.

Caspary, T, M A Cleary, C C Baker, X J Guan, and S M Tilghman. (1998) 1998. “Multiple Mechanisms Regulate Imprinting of the Mouse Distal Chromosome 7 Gene Cluster.”. Mol Cell Biol 18 (6): 3466-74.

Rauskolb, C, K M Smith, M Peifer, and E Wieschaus. (1995) 1995. “Extradenticle Determines Segmental Identities Throughout Drosophila Development.”. Development 121 (11): 3663-73.

Goodliffe, Julie M, Michael D Cole, and Eric Wieschaus. 2007. “Coordinated Regulation of Myc Trans-Activation Targets by Polycomb and the Trithorax Group Protein Ash1.”. BMC Mol Biol 8: 40.

Ahmed, Yashi, S Hayashi, A Levine, and E Wieschaus. (1998) 1998. “Regulation of Armadillo by a Drosophila APC Inhibits Neuronal Apoptosis During Retinal Development.”. Cell 93 (7): 1171-82.

Krotov, Dmitry, Julien Dubuis, Thomas Gregor, and William Bialek. (2014) 2014. “Morphogenesis at Criticality.”. Proc Natl Acad Sci U S A 111 (10): 3683-8.

Rauskolb, C, M Peifer, and E Wieschaus. (1993) 1993. “Extradenticle, a Regulator of Homeotic Gene Activity, Is a Homolog of the Homeobox-Containing Human Proto-Oncogene pbx1.”. Cell 74 (6): 1101-12.

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.

Goentoro, Lea A, Nir Yakoby, Joseph Goodhouse, Trudi Schüpbach, and Stanislav Y Shvartsman. (2006) 2006. “Quantitative Analysis of the GAL4 UAS System in Drosophila Oogenesis.”. Genesis 44 (2): 66-74.

Millonig, J H, J A Emerson, J M Levorse, and S M Tilghman. (1995) 1995. “Molecular Analysis of the Distal Enhancer of the Mouse Alpha-Fetoprotein Gene.”. Mol Cell Biol 15 (7): 3848-56.

Persikov, Anton, V, and Mona Singh. (2011) 2011. “An Expanded Binding Model for Cys2His2 Zinc Finger Protein-DNA Interfaces.”. Phys Biol 8 (3): 035010.

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.

Hendrix, David A, Joung-Woo Hong, Julia Zeitlinger, Daniel S Rokhsar, and Michael S Levine. (2008) 2008. “Promoter Elements Associated With RNA Pol II Stalling in the Drosophila Embryo.”. Proc Natl Acad Sci U S A 105 (22): 7762-7.

Coulter, D E, E A Swaykus, M A Beran-Koehn, D Goldberg, E Wieschaus, and P Schedl. (1990) 1990. “Molecular Analysis of Odd-Skipped, a Zinc Finger Encoding Segmentation Gene With a Novel Pair-Rule Expression Pattern.”. EMBO J 9 (11): 3795-804.

Rebeiz, Mark, Margarita Ramos-Womack, Sangyun Jeong, Peter Andolfatto, Thomas Werner, John True, David L Stern, and Sean B Carroll. (2009) 2009. “Evolution of the Tan Locus Contributed to Pigment Loss in Drosophila Santomea: A Response to Matute Et Al.”. Cell 139 (6): 1189-96.

Broedersz, Chase P, Xindan Wang, Yigal Meir, Joseph J Loparo, David Z Rudner, and Ned S Wingreen. (2014) 2014. “Condensation and Localization of the Partitioning Protein ParB on the Bacterial Chromosome.”. Proc Natl Acad Sci U S A 111 (24): 8809-14.

Gregor, Thomas, David W Tank, Eric F Wieschaus, and William Bialek. (2007) 2007. “Probing the Limits to Positional Information.”. Cell 130 (1): 153-64.

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.