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.

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.

Reeves, Gregory T, Rachel Kalifa, Daryl E Klein, Mark A Lemmon, and Stanislav Y Shvartsman. (2005) 2005. “Computational Analysis of EGFR Inhibition by Argos.”. Dev Biol 284 (2): 523-35.

Schupbach, T, and E Wieschaus. 1998. “Probing for Gene Specificity in Epithelial Development.”. Int J Dev Biol 42 (3): 249-55.

Ghersi, Dario, and Mona Singh. (2014) 2014. “Interaction-Based Discovery of Functionally Important Genes in Cancers.”. Nucleic Acids Res 42 (3): e18.

Houchmandzadeh, Bahram, Eric Wieschaus, and Stanislas Leibler. (2002) 2002. “Establishment of Developmental Precision and Proportions in the Early Drosophila Embryo.”. Nature 415 (6873): 798-802.

Osada, Robert, Elena Zaslavsky, and Mona Singh. (2004) 2004. “Comparative Analysis of Methods for Representing and Searching for Transcription Factor Binding Sites.”. Bioinformatics 20 (18): 3516-25.

Fong, Jessica H, Amy E Keating, and Mona Singh. 2004. “Predicting Specificity in BZIP Coiled-Coil Protein Interactions.”. Genome Biol 5 (2): R11.

Vincent, A, J T Blankenship, and E Wieschaus. (1997) 1997. “Integration of the Head and Trunk Segmentation Systems Controls Cephalic Furrow Formation in Drosophila.”. Development 124 (19): 3747-54.

Leighton, P A, J R Saam, R S Ingram, C L Stewart, and S M Tilghman. (1995) 1995. “An Enhancer Deletion Affects Both H19 and Igf2 Expression.”. Genes Dev 9 (17): 2079-89.

Petti, Allegra A, Scott McIsaac, Olivia Ho-Shing, Harmen J Bussemaker, and David Botstein. (2012) 2012. “Combinatorial Control of Diverse Metabolic and Physiological Functions by Transcriptional Regulators of the Yeast Sulfur Assimilation Pathway.”. Mol Biol Cell 23 (15): 3008-24.

Endres, Robert G, and Ned S Wingreen. (2006) 2006. “Weight Matrices for Protein-DNA Binding Sites from a Single Co-Crystal Structure.”. Phys Rev E Stat Nonlin Soft Matter Phys 73 (6 Pt 1): 061921.

Persikov, Anton, V, Robert Osada, and Mona Singh. (2009) 2009. “Predicting DNA Recognition by Cys2His2 Zinc Finger Proteins.”. Bioinformatics 25 (1): 22-9.

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.

Papatsenko, Dmitri, and Michael S Levine. (2008) 2008. “Dual Regulation by the Hunchback Gradient in the Drosophila Embryo.”. Proc Natl Acad Sci U S A 105 (8): 2901-6.

Dubuis, Julien, Reba Samanta, and Thomas Gregor. 2013. “Accurate Measurements of Dynamics and Reproducibility in Small Genetic Networks.”. Mol Syst Biol 9: 639.