De Renzis, Stefano, Olivier Elemento, Saeed Tavazoie, and Eric F Wieschaus. (2007) 2007. “Unmasking Activation of the Zygotic Genome Using Chromosomal Deletions in the Drosophila Embryo.”. PLoS Biol 5 (5): e117.

McIsaac, Scott, Benjamin L Oakes, David Botstein, and Marcus B Noyes. 2013. “Rapid Synthesis and Screening of Chemically Activated Transcription Factors With GFP-Based Reporters.”. J Vis Exp, no. 81: e51153.

Rowe, Kevin C, Sonal Singhal, Matthew D Macmanes, Julien Ayroles, Toni Lyn Morelli, Emily M Rubidge, Ke Bi, and Craig C Moritz. (2011) 2011. “Museum Genomics: Low-Cost and High-Accuracy Genetic Data from Historical Specimens.”. Mol Ecol Resour 11 (6): 1082-92.

Garrigan, Daniel, Sarah B Kingan, Anthony J Geneva, Peter Andolfatto, Andrew Clark, Kevin R Thornton, and Daven C Presgraves. (2012) 2012. “Genome Sequencing Reveals Complex Speciation in the Drosophila Simulans Clade.”. Genome Res 22 (8): 1499-511.

Cleary, M A, C D van Raamsdonk, J Levorse, B Zheng, A Bradley, and S M Tilghman. (2001) 2001. “Disruption of an Imprinted Gene Cluster by a Targeted Chromosomal Translocation in Mice.”. Nat Genet 29 (1): 78-82.

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.

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.

Haddrill, Penelope R, Kevin R Thornton, Brian Charlesworth, and Peter Andolfatto. (2005) 2005. “Multilocus Patterns of Nucleotide Variability and the Demographic and Selection History of Drosophila Melanogaster Populations.”. Genome Res 15 (6): 790-9.

Rossi, J M, H Chen, and S M Tilghman. (1994) 1994. “Genetic Map of the Fused Locus on Mouse Chromosome 17.”. Genomics 23 (1): 178-84.

Putnam, Andrea S, Mark Scriber, and Peter Andolfatto. (2007) 2007. “Discordant Divergence Times Among Z-Chromosome Regions Between Two Ecologically Distinct Swallowtail Butterfly Species.”. Evolution 61 (4): 912-27.

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.

Papatsenko, Dmitri, and Michael Levine. (2005) 2005. “Quantitative Analysis of Binding Motifs Mediating Diverse Spatial Readouts of the Dorsal Gradient in the Drosophila Embryo.”. Proc Natl Acad Sci U S A 102 (14): 4966-71.

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.

Sandell, Lisa L, Xiao-Juan Guan, Robert Ingram, and Shirley M Tilghman. (2003) 2003. “Gatm, a Creatine Synthesis Enzyme, Is Imprinted in Mouse Placenta.”. Proc Natl Acad Sci U S A 100 (8): 4622-7.

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.

Lossos, Izidore S, Ash A Alizadeh, Maximilian Diehn, Roger Warnke, Yvonne Thorstenson, Peter J Oefner, Patrick O Brown, David Botstein, and Ronald Levy. (2002) 2002. “Transformation of Follicular Lymphoma to Diffuse Large-Cell Lymphoma: Alternative Patterns With Increased or Decreased Expression of C-Myc and Its Regulated Genes.”. Proc Natl Acad Sci U S A 99 (13): 8886-91.

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.

Riggleman, B, E Wieschaus, and P Schedl. (1989) 1989. “Molecular Analysis of the Armadillo Locus: Uniformly Distributed Transcripts and a Protein With Novel Internal Repeats Are Associated With a Drosophila Segment Polarity Gene.”. Genes Dev 3 (1): 96-113.

Bowman, Aaron B, John M Levorse, Robert S Ingram, and Shirley M Tilghman. (2003) 2003. “Functional Characterization of a Testis-Specific DNA Binding Activity at the H19 Igf2 Imprinting Control Region.”. Mol Cell Biol 23 (22): 8345-51.

Keys, David N, Michael Levine, Richard M Harland, and John B Wallingford. (2002) 2002. “Control of Intercalation Is Cell-Autonomous in the Notochord of Ciona Intestinalis.”. Dev Biol 246 (2): 329-40.

Shakoury-Elizeh, Minoo, John Tiedeman, Jared Rashford, Tracey Ferea, Janos Demeter, Emily Garcia, Ronda Rolfes, Patrick O Brown, David Botstein, and Caroline C Philpott. (2004) 2004. “Transcriptional Remodeling in Response to Iron Deprivation in Saccharomyces Cerevisiae.”. Mol Biol Cell 15 (3): 1233-43.

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.

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.

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.

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.

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.

Hendrix, David, Michael Levine, and Weiyang Shi. 2010. “MiRTRAP, a Computational Method for the Systematic Identification of MiRNAs from High Throughput Sequencing Data.”. Genome Biol 11 (4): R39.

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.

Papatsenko, Dmitri, Andrey Kislyuk, Michael Levine, and Inna Dubchak. (2006) 2006. “Conservation Patterns in Different Functional Sequence Categories of Divergent Drosophila Species.”. Genomics 88 (4): 431-42.

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.

Peifer, M, and E Wieschaus. (1993) 1993. “The Product of the Drosophila Melanogaster Segment Polarity Gene Armadillo Is Highly Conserved in Sequence and Expression in the Housefly Musca Domestica.”. J Mol Evol 36 (3): 224-33.

Mora, Thierry, Aleksandra M Walczak, William Bialek, and Curtis G Callan. (2010) 2010. “Maximum Entropy Models for Antibody Diversity.”. Proc Natl Acad Sci U S A 107 (12): 5405-10.

Metallinos, D L, A J Oppenheimer, E M Rinchik, L B Russell, W Dietrich, and S M Tilghman. (1994) 1994. “Fine Structure Mapping and Deletion Analysis of the Murine Piebald Locus.”. Genetics 136 (1): 217-23.

Cande, Jessica Doran, Yury Goltsev, and Michael S Levine. (2009) 2009. “Conservation of Enhancer Location in Divergent Insects.”. Proc Natl Acad Sci U S A 106 (34): 14414-9.

Ayroles, Julien, Mary Anna Carbone, Eric A Stone, Katherine W Jordan, Richard F Lyman, Michael M Magwire, Stephanie M Rollmann, et al. (2009) 2009. “Systems Genetics of Complex Traits in Drosophila Melanogaster.”. Nat Genet 41 (3): 299-307.

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

Stathopoulos, Angelike, and Michael Levine. (2005) 2005. “Localized Repressors Delineate the Neurogenic Ectoderm in the Early Drosophila Embryo.”. Dev Biol 280 (2): 482-93.

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.

O’Brien, T P, D L Metallinos, H Chen, M K Shin, and S M Tilghman. (1996) 1996. “Complementation Mapping of Skeletal and Central Nervous System Abnormalities in Mice of the Piebald Deletion Complex.”. Genetics 143 (1): 447-61.

, C I Brannan, and S M Tilghman. (1988) 1988. “The Structure and Expression of a Novel Gene Activated in Early Mouse Embryogenesis.”. EMBO J 7 (3): 673-81.

Khan, Zia, Joshua S Bloom, Leonid Kruglyak, and Mona Singh. (2009) 2009. “A Practical Algorithm for Finding Maximal Exact Matches in Large Sequence Datasets Using Sparse Suffix Arrays.”. Bioinformatics 25 (13): 1609-16.

Guan, X J, G Arhin, J Leung, and S M Tilghman. (1996) 1996. “Linkage Between Vitamin D-Binding Protein and Alpha-Fetoprotein in the Mouse.”. Mamm Genome 7 (2): 103-6.

Kurihara, L J, E Semenova, J M Levorse, and S M Tilghman. (2000) 2000. “Expression and Functional Analysis of Uch-L3 During Mouse Development.”. Mol Cell Biol 20 (7): 2498-504.

Cole, Susan E, John M Levorse, Shirley M Tilghman, and Thomas F Vogt. (2002) 2002. “Clock Regulatory Elements Control Cyclic Expression of Lunatic Fringe During Somitogenesis.”. Dev Cell 3 (1): 75-84.

Mukhopadhyay, Ranjan, Eldon Emberly, Chao Tang, and Ned S Wingreen. (2003) 2003. “Statistical Mechanics of RNA Folding: Importance of Alphabet Size.”. Phys Rev E Stat Nonlin Soft Matter Phys 68 (4 Pt 1): 041904.

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.

Tilghman, S M. (1996) 1996. “Lessons Learned, Promises Kept: A biologist’s Eye View of the Genome Project.”. Genome Res 6 (9): 773-80.

Davidson, Brad, and Michael Levine. (2003) 2003. “Evolutionary Origins of the Vertebrate Heart: Specification of the Cardiac Lineage in Ciona Intestinalis.”. Proc Natl Acad Sci U S A 100 (20): 11469-73.

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.