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. Reference Link
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. Reference Link
Zhou, Jian, and Olga G Troyanskaya. (2014) 2014. “Global Quantitative Modeling of Chromatin Factor Interactions.”. PLoS Comput Biol 10 (3): e1003525. Reference Link
Markstein, Michele, and Michael Levine. (2002) 2002. “Decoding Cis-Regulatory DNAs in the Drosophila Genome.”. Curr Opin Genet Dev 12 (5): 601-6. Reference Link
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. Reference Link
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). Reference Link
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. Reference Link
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. Reference Link
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. Reference Link
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. Reference Link
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. Reference Link
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. Reference Link
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). Reference Link
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. Reference Link
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. Reference Link
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. Reference Link
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. Reference Link
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. Reference Link
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. Reference Link
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. Reference Link
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. Reference Link
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. Reference Link
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. Reference Link
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. Reference Link
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. Reference Link
Vasicek, T J, L Zeng, X J Guan, T Zhang, F Costantini, and S M Tilghman. (1997) 1997. “Two Dominant Mutations in the Mouse Fused Gene Are the Result of Transposon Insertions.”. Genetics 147 (2): 777-86. Reference Link
Di Talia, Stefano, and Eric F Wieschaus. (2012) 2012. “Short-Term Integration of Cdc25 Dynamics Controls Mitotic Entry During Drosophila Gastrulation.”. Dev Cell 22 (4): 763-74. Reference Link
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. Reference Link
Wieschaus, E. (1996) 1996. “Embryonic Transcription and the Control of Developmental Pathways.”. Genetics 142 (1): 5-10. Reference Link
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. Reference Link
Christiaen, Lionel, Brad Davidson, Takeshi Kawashima, Weston Powell, Hector Nolla, Karen Vranizan, and Michael Levine. (2008) 2008. “The Transcription Migration Interface in Heart Precursors of Ciona Intestinalis.”. Science 320 (5881): 1349-52. Reference Link
Murphy, Coleen T. (2006) 2006. “The Search for DAF-16 FOXO Transcriptional Targets: Approaches and Discoveries.”. Exp Gerontol 41 (10): 910-21. Reference Link
Stolfi, Alberto, and Michael Levine. (2011) 2011. “Neuronal Subtype Specification in the Spinal Cord of a Protovertebrate.”. Development 138 (5): 995-1004. Reference Link
Mancini-Dinardo, Debora, Scott J S Steele, John M Levorse, Robert S Ingram, and Shirley M Tilghman. (2006) 2006. “Elongation of the Kcnq1ot1 Transcript Is Required for Genomic Imprinting of Neighboring Genes.”. Genes Dev 20 (10): 1268-82. Reference Link
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. Reference Link
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. Reference Link
Tkačik, Gašper, Thomas Gregor, and William Bialek. 2008. “The Role of Input Noise in Transcriptional Regulation.”. PLoS One 3 (7): e2774. Reference Link
Tu, Kimberly C, Tao Long, Sine L Svenningsen, Ned S Wingreen, and Bonnie L Bassler. (2010) 2010. “Negative Feedback Loops Involving Small Regulatory RNAs Precisely Control the Vibrio Harveyi Quorum-Sensing Response.”. Mol Cell 37 (4): 567-79. Reference Link
Chikina, Maria D, and Olga G Troyanskaya. (2012) 2012. “An Effective Statistical Evaluation of ChIPseq Dataset Similarity.”. Bioinformatics 28 (5): 607-13. Reference Link
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. Reference Link
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. Reference Link
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. Reference Link
Pollack, Jonathan R, Therese Sørlie, Charles M Perou, Christian A Rees, Stefanie S Jeffrey, Per E Lonning, Robert Tibshirani, David Botstein, Anne-Lise Børresen-Dale, and Patrick O Brown. (2002) 2002. “Microarray Analysis Reveals a Major Direct Role of DNA Copy Number Alteration in the Transcriptional Program of Human Breast Tumors.”. Proc Natl Acad Sci U S A 99 (20): 12963-8. Reference Link
Brunkow, M E, and S M Tilghman. (1991) 1991. “Ectopic Expression of the H19 Gene in Mice Causes Prenatal Lethality.”. Genes Dev 5 (6): 1092-101. Reference Link
Godbout, R, and S M Tilghman. (1988) 1988. “Configuration of the Alpha-Fetoprotein Regulatory Domain During Development.”. Genes Dev 2 (8): 949-56. Reference Link
Chopra, Vivek S, Nikki Kong, and Michael Levine. (2012) 2012. “Transcriptional Repression via Antilooping in the Drosophila Embryo.”. Proc Natl Acad Sci U S A 109 (24): 9460-4. Reference Link
Wieschaus, E, and D Sweeton. (1988) 1988. “Requirements for X-Linked Zygotic Gene Activity During Cellularization of Early Drosophila Embryos.”. Development 104 (3): 483-93. Reference Link
Lagha, Mounia, Jacques P Bothma, and Michael Levine. (2012) 2012. “Mechanisms of Transcriptional Precision in Animal Development.”. Trends Genet 28 (8): 409-16. Reference Link
Bothma, Jacques P, Hernan G Garcia, Emilia Esposito, Gavin Schlissel, Thomas Gregor, and Michael Levine. (2014) 2014. “Dynamic Regulation of Eve Stripe 2 Expression Reveals Transcriptional Bursts in Living Drosophila Embryos.”. Proc Natl Acad Sci U S A 111 (29): 10598-603. Reference Link
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. Reference Link