Stathopoulos, Angelike, Madeleine Van Drenth, Albert Erives, Michele Markstein, and Michael Levine. (2002) 2002. “Whole-Genome Analysis of Dorsal-Ventral Patterning in the Drosophila Embryo.”. Cell 111 (5): 687-701.

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.

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.

Coppey, Mathieu, Alistair N Boettiger, Alexander M Berezhkovskii, and Stanislav Y Shvartsman. (2008) 2008. “Nuclear Trapping Shapes the Terminal Gradient in the Drosophila Embryo.”. Curr Biol 18 (12): 915-9.

Nair, Venugopalan D, Yongchao Ge, Natarajan Balasubramaniyan, Jaeyun Kim, Yuya Okawa, Maria Chikina, Olga Troyanskaya, and Stuart C Sealfon. (2012) 2012. “Involvement of Histone Demethylase LSD1 in Short-Time-Scale Gene Expression Changes During Cell Cycle Progression in Embryonic Stem Cells.”. Mol Cell Biol 32 (23): 4861-76.

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.

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.

Bothma, Jacques P, Hernan G Garcia, Samuel Ng, Michael W Perry, Thomas Gregor, and Michael Levine. 2015. “Enhancer Additivity and Non-Additivity Are Determined by Enhancer Strength in the Drosophila Embryo.”. Elife 4.

Tolwinski, Nicholas S, Marcel Wehrli, Anna Rives, Naz Erdeniz, Stephen DiNardo, and Eric Wieschaus. (2003) 2003. “Wg/Wnt/Signal/Can/Be/Transmitted/through/Arrow/LRP5,6/and/Axin/Independently/of/Zw3/Gsk3beta/Activity.”. Dev Cell 4 (3): 407-18.

Tilghman, S M. (1999) 1999. “The Sins of the Fathers and Mothers: Genomic Imprinting in Mammalian Development.”. Cell 96 (2): 185-93.

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

Stolfi, Alberto, and Michael Levine. (2011) 2011. “Neuronal Subtype Specification in the Spinal Cord of a Protovertebrate.”. Development 138 (5): 995-1004.

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.

Zartman, Jeremiah J, and Stanislav Y Shvartsman. (2007) 2007. “Enhancer Organization: Transistor With a Twist or Something in a Different Vein?”. Curr Biol 17 (24).

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

Navarrete, Ignacio A, and Michael Levine. (2016) 2016. “Nodal and FGF Coordinate Ascidian Neural Tube Morphogenesis.”. Development 143 (24): 4665-75. doi:10.1242/dev.144733.

Shi, Weiyang, Michael Levine, and Brad Davidson. (2005) 2005. “Unraveling Genomic Regulatory Networks in the Simple Chordate, Ciona Intestinalis.”. Genome Res 15 (12): 1668-74.

Hong, Joung-Woo, David A Hendrix, and Michael S Levine. (2008) 2008. “Shadow Enhancers As a Source of Evolutionary Novelty.”. Science 321 (5894): 1314.

Perry, Michael W, Jacques P Bothma, Ryan D Luu, and Michael Levine. (2012) 2012. “Precision of Hunchback Expression in the Drosophila Embryo.”. Curr Biol 22 (23): 2247-52.

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.

Abitua, Philip Barron, Eileen Wagner, Ignacio A Navarrete, and Michael Levine. (2012) 2012. “Identification of a Rudimentary Neural Crest in a Non-Vertebrate Chordate.”. Nature 492 (7427): 104-7.

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.

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.

Rogers, William A, Yogesh Goyal, Kei Yamaya, Stanislav Y Shvartsman, and Michael S Levine. (2017) 2017. “Uncoupling Neurogenic Gene Networks in the Drosophila Embryo.”. Genes Dev 31 (7): 634-38. doi:10.1101/gad.297150.117.

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.

Murphy, Coleen T. (2006) 2006. “The Search for DAF-16 FOXO Transcriptional Targets: Approaches and Discoveries.”. Exp Gerontol 41 (10): 910-21.

Houchmandzadeh, B, E Wieschaus, and S Leibler. (2005) 2005. “Precise Domain Specification in the Developing Drosophila Embryo.”. Phys Rev E Stat Nonlin Soft Matter Phys 72 (6 Pt 1): 061920.

Stolfi, Alberto, Eileen Wagner, Matthew Taliaferro, Seemay Chou, and Michael Levine. (2011) 2011. “Neural Tube Patterning by Ephrin, FGF and Notch Signaling Relays.”. Development 138 (24): 5429-39.

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.

Wieschaus, E. (1996) 1996. “Embryonic Transcription and the Control of Developmental Pathways.”. Genetics 142 (1): 5-10.

Calhoun, Vincent C, and Michael Levine. (2003) 2003. “Coordinate Regulation of an Extended Chromosome Domain.”. Cell 113 (3): 278-80.

Pritykin, Yuri, Tarcisio Brito, Trudi Schüpbach, Mona Singh, and Attilio Pane. (2017) 2017. “Integrative Analysis Unveils New Functions for the Drosophila Cutoff Protein in Noncoding RNA Biogenesis and Gene Regulation.”. RNA 23 (7): 1097-1109. doi:10.1261/rna.058594.116.

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.

Helman, Aharon, Bomyi Lim, María José Andreu, Yoosik Kim, Tatyana Shestkin, Hang Lu, Gerardo Jiménez, Stanislav Y Shvartsman, and Ze’ev Paroush. (2012) 2012. “RTK Signaling Modulates the Dorsal Gradient.”. Development 139 (16): 3032-9.

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.

Perry, Michael W, Alistair N Boettiger, and Michael Levine. (2011) 2011. “Multiple Enhancers Ensure Precision of Gap Gene-Expression Patterns in the Drosophila Embryo.”. Proc Natl Acad Sci U S A 108 (33): 13570-5.

Hong, Joung-Woo, David A Hendrix, Dmitri Papatsenko, and Michael S Levine. (2008) 2008. “How the Dorsal Gradient Works: Insights from Postgenome Technologies.”. Proc Natl Acad Sci U S A 105 (51): 20072-6.

Hilgers, Valérie, Sandra B Lemke, and Michael Levine. (2012) 2012. “ELAV Mediates 3’ UTR Extension in the Drosophila Nervous System.”. Genes Dev 26 (20): 2259-64.

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.

Menon, Rajasree, Edgar A Otto, Austin Kokoruda, Jian Zhou, Zidong Zhang, Euisik Yoon, Yu-Chih Chen, et al. (2018) 2018. “Single-Cell Analysis of Progenitor Cell Dynamics and Lineage Specification in the Human Fetal Kidney.”. Development 145 (16). doi:10.1242/dev.164038.

Grimm, Oliver, Victoria Sanchez Zini, Yoosik Kim, Jordi Casanova, Stanislav Y Shvartsman, and Eric Wieschaus. (2012) 2012. “Torso RTK Controls Capicua Degradation by Changing Its Subcellular Localization.”. Development 139 (21): 3962-8.

Markstein, Michele, Robert Zinzen, Peter Markstein, Ka-Ping Yee, Albert Erives, Angela Stathopoulos, and Michael Levine. (2004) 2004. “A Regulatory Code for Neurogenic Gene Expression in the Drosophila Embryo.”. Development 131 (10): 2387-94.

Tepper, Ronald G, Jasmine M Ashraf, Rachel Kaletsky, Gunnar Kleemann, Coleen T Murphy, and Harmen J Bussemaker. (2013) 2013. “PQM-1 Complements DAF-16 As a Key Transcriptional Regulator of DAF-2-Mediated Development and Longevity.”. Cell 154 (3): 676-90.

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.

Farley, Emma, and Michael Levine. (2012) 2012. “HOT DNAs: A Novel Class of Developmental Enhancers.”. Genes Dev 26 (9): 873-6.

Shvartsman, Stanislav Y, Mathieu Coppey, and Alexander M Berezhkovskii. (2008) 2008. “Dynamics of Maternal Morphogen Gradients in Drosophila.”. Curr Opin Genet Dev 18 (4): 342-7.

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.

Zhou, Jian, Ignacio E Schor, Victoria Yao, Chandra L Theesfeld, Raquel Marco-Ferreres, Alicja Tadych, Eileen E M Furlong, and Olga G Troyanskaya. (2019) 2019. “Accurate Genome-Wide Predictions of Spatio-Temporal Gene Expression During Embryonic Development.”. PLoS Genet 15 (9): e1008382. doi:10.1371/journal.pgen.1008382.

Osterfield, Miriam, XinXin Du, Trudi Schüpbach, Eric Wieschaus, and Stanislav Y Shvartsman. (2013) 2013. “Three-Dimensional Epithelial Morphogenesis in the Developing Drosophila Egg.”. Dev Cell 24 (4): 400-10.

Chopra, Vivek S, Joung-Woo Hong, and Michael Levine. (2009) 2009. “Regulation of Hox Gene Activity by Transcriptional Elongation in Drosophila.”. Curr Biol 19 (8): 688-93.