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).

Parks, S, and E Wieschaus. (1991) 1991. “The Drosophila Gastrulation Gene Concertina Encodes a G Alpha-Like Protein.”. Cell 64 (2): 447-58.

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.

Rose, L S, and E Wieschaus. (1992) 1992. “The Drosophila Cellularization Gene Nullo Produces a Blastoderm-Specific Transcript Whose Levels Respond to the Nucleocytoplasmic Ratio.”. Genes Dev 6 (7): 1255-68.

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.

Zhen, Ying, and Peter Andolfatto. 2012. “Methods to Detect Selection on Noncoding DNA.”. Methods Mol Biol 856: 141-59.

Tilghman, S M. (1993) 1993. “DNA Methylation: A Phoenix Rises.”. Proc Natl Acad Sci U S A 90 (19): 8761-2.

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.

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.

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.

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.

Calhoun, Vincent C, and Michael Levine. (2003) 2003. “Long-Range Enhancer-Promoter Interactions in the Scr-Antp Interval of the Drosophila Antennapedia Complex.”. Proc Natl Acad Sci U S A 100 (17): 9878-83.

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.

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.

Pelham, Robert J, Linda Rodgers, Ira Hall, Robert Lucito, Ken C Q Nguyen, Nicholas Navin, James Hicks, et al. (2006) 2006. “Identification of Alterations in DNA Copy Number in Host Stromal Cells During Tumor Progression.”. Proc Natl Acad Sci U S A 103 (52): 19848-53.

Tkačik, Gašper, and William Bialek. (2009) 2009. “Diffusion, Dimensionality, and Noise in Transcriptional Regulation.”. Phys Rev E Stat Nonlin Soft Matter Phys 79 (5 Pt 1): 051901.

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

Rossi, J M, D T Burke, J C Leung, D S Koos, H Chen, and S M Tilghman. (1992) 1992. “Genomic Analysis Using a Yeast Artificial Chromosome Library With Mouse DNA Inserts.”. Proc Natl Acad Sci U S A 89 (6): 2456-60.

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.

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.

Markstein, Michele, Peter Markstein, Vicky Markstein, and Michael S Levine. (2002) 2002. “Genome-Wide Analysis of Clustered Dorsal Binding Sites Identifies Putative Target Genes in the Drosophila Embryo.”. Proc Natl Acad Sci U S A 99 (2): 763-8.

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.

, 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.

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.

Slavov, Nikolai, and David Botstein. (2011) 2011. “Coupling Among Growth Rate Response, Metabolic Cycle, and Cell Division Cycle in Yeast.”. Mol Biol Cell 22 (12): 1997-2009.

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.

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.

Papatsenko, Dmitri, and Michael Levine. (2005) 2005. “Computational Identification of Regulatory DNAs Underlying Animal Development.”. Nat Methods 2 (7): 529-34.

Calhoun, Vincent C, Angelike Stathopoulos, and Michael Levine. (2002) 2002. “Promoter-Proximal Tethering Elements Regulate Enhancer-Promoter Specificity in the Drosophila Antennapedia Complex.”. Proc Natl Acad Sci U S A 99 (14): 9243-7.

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.

Hark, A T, and S M Tilghman. (1998) 1998. “Chromatin Conformation of the H19 Epigenetic Mark.”. Hum Mol Genet 7 (12): 1979-85.

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.

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.

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.

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

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.

Pfeifer, K, and S M Tilghman. (1994) 1994. “Allele-Specific Gene Expression in Mammals: The Curious Case of the Imprinted RNAs.”. Genes Dev 8 (16): 1867-74.

Haddrill, Penelope R, Doris Bachtrog, and Peter Andolfatto. (2008) 2008. “Positive and Negative Selection on Noncoding DNA in Drosophila Simulans.”. Mol Biol Evol 25 (9): 1825-34.

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

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.

Haddrill, Penelope R, Brian Charlesworth, Daniel L Halligan, and Peter Andolfatto. 2005. “Patterns of Intron Sequence Evolution in Drosophila Are Dependent Upon Length and GC Content.”. Genome Biol 6 (8): R67.

Bartolomei, M S, A L Webber, M E Brunkow, and S M Tilghman. (1993) 1993. “Epigenetic Mechanisms Underlying the Imprinting of the Mouse H19 Gene.”. Genes Dev 7 (9): 1663-73.

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.

Tilghman, S M, M S Bartolomei, A L Webber, M E Brunkow, J Saam, P A Leighton, K Pfeifer, and S Zemel. 1993. “Parental Imprinting of the H19 and Igf2 Genes in the Mouse.”. Cold Spring Harb Symp Quant Biol 58: 287-95.

Christiaen, Lionel, Eileen Wagner, Weiyang Shi, and Michael Levine. (2009) 2009. “Electroporation of Transgenic DNAs in the Sea Squirt Ciona.”. Cold Spring Harb Protoc 2009 (12): pdb.prot5345.