List of Faculty Publications

Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua

Filters: Keyword is Gene Expression Regulation, Developmental  [Clear All Filters]
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 
Gene Expression Regulation, Developmental
M. Tipping, Kim, Y., Kyriakakis, P., Tong, M., Shvartsman, S. Y., and Veraksa, A., β-arrestin Kurtz inhibits MAPK and Toll signalling in Drosophila development., EMBO J, vol. 29, no. 19, pp. 3222-35, 2010.
M. M. Klosinska, Crutchfield, C. A., Bradley, P. H., Rabinowitz, J. D., and Broach, J. R., Yeast cells can access distinct quiescent states., Genes Dev, vol. 25, no. 4, pp. 336-49, 2011.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., Whole-mount in situ hybridization on sea squirt (Ciona intestinalis) embryos., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5348, 2009.
A. Stathopoulos and Levine, M., Whole-genome analysis of Drosophila gastrulation., Curr Opin Genet Dev, vol. 14, no. 5, pp. 477-84, 2004.
A. Stathopoulos, Van Drenth, M., Erives, A., Markstein, M., and Levine, M., Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo., Cell, vol. 111, no. 5, pp. 687-701, 2002.
N. S. Tolwinski, Wehrli, M., Rives, A., Erdeniz, N., DiNardo, S., and Wieschaus, E., Wg/Wnt signal can be transmitted through arrow/LRP5,6 and Axin independently of Zw3/Gsk3beta activity., Dev Cell, vol. 4, no. 3, pp. 407-18, 2003.
W. Shi, Levine, M., and Davidson, B., Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis., Genome Res, vol. 15, no. 12, pp. 1668-74, 2005.
S. De Renzis, Elemento, O., Tavazoie, S., and Wieschaus, E. F., Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo., PLoS Biol, vol. 5, no. 5, p. e117, 2007.
L. Christiaen, Davidson, B., Kawashima, T., Powell, W., Nolla, H., Vranizan, K., and Levine, M., The transcription/migration interface in heart precursors of Ciona intestinalis., Science, vol. 320, no. 5881, pp. 1349-52, 2008.
O. Grimm, Zini, V. Sanchez, Kim, Y., Casanova, J., Shvartsman, S. Y., and Wieschaus, E., Torso RTK controls Capicua degradation by changing its subcellular localization., Development, vol. 139, no. 21, pp. 3962-8, 2012.
M. Osterfield, Du, X. X., Schüpbach, T., Wieschaus, E., and Shvartsman, S. Y., Three-dimensional epithelial morphogenesis in the developing Drosophila egg., Dev Cell, vol. 24, no. 4, pp. 400-10, 2013.
M. K. Shin, Levorse, J. M., Ingram, R. S., and Tilghman, S. M., The temporal requirement for endothelin receptor-B signalling during neural crest development., Nature, vol. 402, no. 6761, pp. 496-501, 1999.
C. A. Rushlow and Shvartsman, S. Y., Temporal dynamics, spatial range, and transcriptional interpretation of the Dorsal morphogen gradient., Curr Opin Genet Dev, vol. 22, no. 6, pp. 542-6, 2012.
A. Di Gregorio, Harland, R. M., Levine, M., and Casey, E. Silva, Tail morphogenesis in the ascidian, Ciona intestinalis, requires cooperation between notochord and muscle., Dev Biol, vol. 244, no. 2, pp. 385-95, 2002.
R. Lu, Markowetz, F., Unwin, R. D., Leek, J. T., Airoldi, E. M., MacArthur, B. D., Lachmann, A., Rozov, R., Ma'ayan, A., Boyer, L. A., Troyanskaya, O. G., Whetton, A. D., and Lemischka, I. R., Systems-level dynamic analyses of fate change in murine embryonic stem cells., Nature, vol. 462, no. 7271, pp. 358-62, 2009.
A. N. Boettiger and Levine, M., Synchronous and stochastic patterns of gene activation in the Drosophila embryo., Science, vol. 325, no. 5939, pp. 471-3, 2009.
L. Christiaen, Stolfi, A., Davidson, B., and Levine, M., Spatio-temporal intersection of Lhx3 and Tbx6 defines the cardiac field through synergistic activation of Mesp., Dev Biol, vol. 328, no. 2, pp. 552-60, 2009.
F. Biemar, Zinzen, R., Ronshaugen, M., Sementchenko, V., J Manak, R., and Levine, M. S., Spatial regulation of microRNA gene expression in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 102, no. 44, pp. 15907-11, 2005.
J. Lembong, Yakoby, N., and Shvartsman, S. Y., Spatial regulation of BMP signaling by patterned receptor expression., Tissue Eng Part A, vol. 14, no. 9, pp. 1469-77, 2008.
J. Cowden and Levine, M., The Snail repressor positions Notch signaling in the Drosophila embryo., Development, vol. 129, no. 7, pp. 1785-93, 2002.
J. P. Bothma, Magliocco, J., and Levine, M., The snail repressor inhibits release, not elongation, of paused Pol II in the Drosophila embryo., Curr Biol, vol. 21, no. 18, pp. 1571-7, 2011.
S. M. Tilghman, The sins of the fathers and mothers: genomic imprinting in mammalian development., Cell, vol. 96, no. 2, pp. 185-93, 1999.
J. - W. Hong, Hendrix, D. A., and Levine, M. S., Shadow enhancers as a source of evolutionary novelty., Science, vol. 321, no. 5894, p. 1314, 2008.
C. T. Murphy, The search for DAF-16/FOXO transcriptional targets: approaches and discoveries., Exp Gerontol, vol. 41, no. 10, pp. 910-21, 2006.
A. Helman, Lim, B., Andreu, M. José, Kim, Y., Shestkin, T., Lu, H., Jiménez, G., Shvartsman, S. Y., and Paroush, Z. 'ev, RTK signaling modulates the Dorsal gradient., Development, vol. 139, no. 16, pp. 3032-9, 2012.
M. Markstein, Zinzen, R., Markstein, P., Yee, K. - P., Erives, A., Stathopoulos, A., and Levine, M., A regulatory code for neurogenic gene expression in the Drosophila embryo., Development, vol. 131, no. 10, pp. 2387-94, 2004.
V. S. Chopra, Hong, J. - W., and Levine, M., Regulation of Hox gene activity by transcriptional elongation in Drosophila., Curr Biol, vol. 19, no. 8, pp. 688-93, 2009.
Y. Ahmed, Hayashi, S., Levine, A., and Wieschaus, E., Regulation of armadillo by a Drosophila APC inhibits neuronal apoptosis during retinal development., Cell, vol. 93, no. 7, pp. 1171-82, 1998.
C. Hunter and Wieschaus, E., Regulated expression of nullo is required for the formation of distinct apical and basal adherens junctions in the Drosophila blastoderm., J Cell Biol, vol. 150, no. 2, pp. 391-401, 2000.
W. J. Pavan, Mac, S., Cheng, M., and Tilghman, S. M., Quantitative trait loci that modify the severity of spotting in piebald mice., Genome Res, vol. 5, no. 1, pp. 29-41, 1995.
H. G. Garcia, Tikhonov, M., Lin, A., and Gregor, T., Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning., Curr Biol, vol. 23, no. 21, pp. 2140-5, 2013.
L. A. Goentoro, Yakoby, N., Goodhouse, J., Schüpbach, T., and Shvartsman, S. Y., Quantitative analysis of the GAL4/UAS system in Drosophila oogenesis., Genesis, vol. 44, no. 2, pp. 66-74, 2006.
D. Papatsenko and Levine, M., Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 102, no. 14, pp. 4966-71, 2005.
A. H. Morrison, Scheeler, M., Dubuis, J., and Gregor, T., Quantifying the Bicoid morphogen gradient in living fly embryos., Cold Spring Harb Protoc, vol. 2012, no. 4, pp. 398-406, 2012.
A. C. Martin, Kaschube, M., and Wieschaus, E. F., Pulsed contractions of an actin-myosin network drive apical constriction., Nature, vol. 457, no. 7228, pp. 495-9, 2009.
V. C. Calhoun, Stathopoulos, A., and Levine, M., Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex., Proc Natl Acad Sci U S A, vol. 99, no. 14, pp. 9243-7, 2002.
D. A. Hendrix, Hong, J. - W., Zeitlinger, J., Rokhsar, D. S., and Levine, M. S., Promoter elements associated with RNA Pol II stalling in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 105, no. 22, pp. 7762-7, 2008.
T. Schupbach and Wieschaus, E., Probing for gene specificity in epithelial development., Int J Dev Biol, vol. 42, no. 3, pp. 249-55, 1998.
M. W. Perry, Bothma, J. P., Luu, R. D., and Levine, M., Precision of hunchback expression in the Drosophila embryo., Curr Biol, vol. 22, no. 23, pp. 2247-52, 2012.
B. Houchmandzadeh, Wieschaus, E., and Leibler, S., Precise domain specification in the developing Drosophila embryo., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 72, no. 6 Pt 1, p. 061920, 2005.
S. C. Little, Tikhonov, M., and Gregor, T., Precise developmental gene expression arises from globally stochastic transcriptional activity., Cell, vol. 154, no. 4, pp. 789-800, 2013.
R. G. Tepper, Ashraf, J., Kaletsky, R., Kleemann, G., Murphy, C. T., and Bussemaker, H. J., PQM-1 complements DAF-16 as a key transcriptional regulator of DAF-2-mediated development and longevity., Cell, vol. 154, no. 3, pp. 676-90, 2013.
J. O. Dubuis, Tkačik, G., Wieschaus, E. F., Gregor, T., and Bialek, W., Positional information, in bits., Proc Natl Acad Sci U S A, vol. 110, no. 41, pp. 16301-8, 2013.
J. M. Goodliffe, Wieschaus, E., and Cole, M. D., Polycomb mediates Myc autorepression and its transcriptional control of many loci in Drosophila., Genes Dev, vol. 19, no. 24, pp. 2941-6, 2005.
M. Levine, Paused RNA polymerase II as a developmental checkpoint., Cell, vol. 145, no. 4, pp. 502-11, 2011.
M. Lagha, Bothma, J. P., Esposito, E., Ng, S., Stefanik, L., Tsui, C., Johnston, J., Chen, K., Gilmour, D. S., Zeitlinger, J., and Levine, M. S., Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo., Cell, vol. 153, no. 5, pp. 976-87, 2013.
L. S. Cheung, Schüpbach, T., and Shvartsman, S. Y., Pattern formation by receptor tyrosine kinases: analysis of the Gurken gradient in Drosophila oogenesis., Curr Opin Genet Dev, vol. 21, no. 6, pp. 719-25, 2011.
J. S. Kanodia, Liang, H. - L., Kim, Y., Lim, B., Zhan, M., Lu, H., Rushlow, C. A., and Shvartsman, S. Y., Pattern formation by graded and uniform signals in the early Drosophila embryo., Biophys J, vol. 102, no. 3, pp. 427-33, 2012.
J. Lembong, Yakoby, N., and Shvartsman, S. Y., Pattern formation by dynamically interacting network motifs., Proc Natl Acad Sci U S A, vol. 106, no. 9, pp. 3213-8, 2009.
J. J. Zartman, Cheung, L. S., Niepielko, M. G., Bonini, C., Haley, B., Yakoby, N., and Shvartsman, S. Y., Pattern formation by a moving morphogen source., Phys Biol, vol. 8, no. 4, p. 045003, 2011.
D. Papatsenko, Goltsev, Y., and Levine, M., Organization of developmental enhancers in the Drosophila embryo., Nucleic Acids Res, vol. 37, no. 17, pp. 5665-77, 2009.
C. D. van Raamsdonk and Tilghman, S. M., Optimizing the detection of nascent transcripts by RNA fluorescence in situ hybridization., Nucleic Acids Res, vol. 29, no. 8, pp. E42-2, 2001.
M. Coppey, Boettiger, A. N., Berezhkovskii, A. M., and Shvartsman, S. Y., Nuclear trapping shapes the terminal gradient in the Drosophila embryo., Curr Biol, vol. 18, no. 12, pp. 915-9, 2008.
A. Stolfi and Levine, M., Neuronal subtype specification in the spinal cord of a protovertebrate., Development, vol. 138, no. 5, pp. 995-1004, 2011.
V. Hilgers, Perry, M. W., Hendrix, D., Stark, A., Levine, M., and Haley, B., Neural-specific elongation of 3' UTRs during Drosophila development., Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15864-9, 2011.
A. Stolfi, Wagner, E., J Taliaferro, M., Chou, S., and Levine, M., Neural tube patterning by Ephrin, FGF and Notch signaling relays., Development, vol. 138, no. 24, pp. 5429-39, 2011.
M. W. Perry, Boettiger, A. N., and Levine, M., Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 108, no. 33, pp. 13570-5, 2011.
D. Krotov, Dubuis, J. O., Gregor, T., and Bialek, W., Morphogenesis at criticality., Proc Natl Acad Sci U S A, vol. 111, no. 10, pp. 3683-8, 2014.
J. P. Bothma, Levine, M., and Boettiger, A., Morphogen gradients: limits to signaling or limits to measurement?, Curr Biol, vol. 20, no. 5, pp. R232-4, 2010.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., Microinjection of morpholino oligos and RNAs in sea squirt (Ciona) embryos., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5347, 2009.
M. Lagha, Bothma, J. P., and Levine, M., Mechanisms of transcriptional precision in animal development., Trends Genet, vol. 28, no. 8, pp. 409-16, 2012.
S. Y. Shvartsman and Baker, R. E., Mathematical models of morphogen gradients and their effects on gene expression., Wiley Interdiscip Rev Dev Biol, vol. 1, no. 5, pp. 715-30, 2012.
Y. Kim, Coppey, M., Grossman, R., Ajuria, L., Jiménez, G., Paroush, Z. 'ev, and Shvartsman, S. Y., MAPK substrate competition integrates patterning signals in the Drosophila embryo., Curr Biol, vol. 20, no. 5, pp. 446-51, 2010.
V. C. Calhoun and Levine, M., Long-range enhancer-promoter interactions in the Scr-Antp interval of the Drosophila Antennapedia complex., Proc Natl Acad Sci U S A, vol. 100, no. 17, pp. 9878-83, 2003.
A. Stathopoulos and Levine, M., Localized repressors delineate the neurogenic ectoderm in the early Drosophila embryo., Dev Biol, vol. 280, no. 2, pp. 482-93, 2005.
A. Stathopoulos and Levine, M., Linear signaling in the Toll-Dorsal pathway of Drosophila: activated Pelle kinase specifies all threshold outputs of gene expression while the bHLH protein Twist specifies a subset., Development, vol. 129, no. 14, pp. 3411-9, 2002.
B. Lim, Samper, N., Lu, H., Rushlow, C., Jiménez, G., and Shvartsman, S. Y., Kinetics of gene derepression by ERK signaling., Proc Natl Acad Sci U S A, vol. 110, no. 25, pp. 10330-5, 2013.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., Isolation of individual cells and tissues from electroporated sea squirt (Ciona) embryos by fluorescence-activated cell sorting (FACS)., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5349, 2009.
V. D. Nair, Ge, Y., Balasubramaniyan, N., Kim, J., Okawa, Y., Chikina, M., Troyanskaya, O., and Sealfon, S. C., Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells., Mol Cell Biol, vol. 32, no. 23, pp. 4861-76, 2012.
A. Vincent, Blankenship, J. T., and Wieschaus, E., Integration of the head and trunk segmentation systems controls cephalic furrow formation in Drosophila., Development, vol. 124, no. 19, pp. 3747-54, 1997.
P. Barron Abitua, Wagner, E., Navarrete, I. A., and Levine, M., Identification of a rudimentary neural crest in a non-vertebrate chordate., Nature, vol. 492, no. 7427, pp. 104-7, 2012.
P. Morize, Christiansen, A. E., Costa, M., Parks, S., and Wieschaus, E., Hyperactivation of the folded gastrulation pathway induces specific cell shape changes., Development, vol. 125, no. 4, pp. 589-97, 1998.
J. - W. Hong, Hendrix, D. A., Papatsenko, D., and Levine, M. S., How the Dorsal gradient works: insights from postgenome technologies., Proc Natl Acad Sci U S A, vol. 105, no. 51, pp. 20072-6, 2008.
E. Farley and Levine, M., HOT DNAs: a novel class of developmental enhancers., Genes Dev, vol. 26, no. 9, pp. 873-6, 2012.
V. Lakhina, Arey, R. N., Kaletsky, R., Kauffman, A., Stein, G., Keyes, W., Xu, D., and Murphy, C. T., Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs., Neuron, vol. 85, no. 2, pp. 330-45, 2015.
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans., Nature, vol. 424, no. 6946, pp. 277-83, 2003.
M. Levine and Davidson, E. H., Gene regulatory networks for development., Proc Natl Acad Sci U S A, vol. 102, no. 14, pp. 4936-42, 2005.
Y. Kim, Andreu, M. José, Lim, B., Chung, K., Terayama, M., Jiménez, G., Berg, C. A., Lu, H., and Shvartsman, S. Y., Gene regulation by MAPK substrate competition., Dev Cell, vol. 20, no. 6, pp. 880-7, 2011.
L. L. Sandell, Guan, X. - J., Ingram, R., and Tilghman, S. M., Gatm, a creatine synthesis enzyme, is imprinted in mouse placenta., Proc Natl Acad Sci U S A, vol. 100, no. 8, pp. 4622-7, 2003.
W. Shi, Peyrot, S. M., Munro, E., and Levine, M., FGF3 in the floor plate directs notochord convergent extension in the Ciona tadpole., Development, vol. 136, no. 1, pp. 23-8, 2009.
E. Wagner and Levine, M., FGF signaling establishes the anterior border of the Ciona neural tube., Development, vol. 139, no. 13, pp. 2351-9, 2012.
J. J. Zartman, Kanodia, J. S., Yakoby, N., Schafer, X., Watson, C., Schlichting, K., Dahmann, C., and Shvartsman, S. Y., Expression patterns of cadherin genes in Drosophila oogenesis., Gene Expr Patterns, vol. 9, no. 1, pp. 31-6, 2009.
L. J. Kurihara, Semenova, E., Levorse, J. M., and Tilghman, S. M., Expression and functional analysis of Uch-L3 during mouse development., Mol Cell Biol, vol. 20, no. 7, pp. 2498-504, 2000.
J. Doran Cande, Chopra, V. S., and Levine, M., Evolving enhancer-promoter interactions within the tinman complex of the flour beetle, Tribolium castaneum., Development, vol. 136, no. 18, pp. 3153-60, 2009.
B. Houchmandzadeh, Wieschaus, E., and Leibler, S., Establishment of developmental precision and proportions in the early Drosophila embryo., Nature, vol. 415, no. 6873, pp. 798-802, 2002.
J. J. Zartman and Shvartsman, S. Y., Enhancer organization: transistor with a twist or something in a different vein?, Curr Biol, vol. 17, no. 24, pp. R1048-50, 2007.
P. A. Leighton, Saam, J. R., Ingram, R. S., Stewart, C. L., and Tilghman, S. M., An enhancer deletion affects both H19 and Igf2 expression., Genes Dev, vol. 9, no. 17, pp. 2079-89, 1995.
E. Wieschaus, Embryonic transcription and the control of developmental pathways., Genetics, vol. 142, no. 1, pp. 5-10, 1996.
V. Hilgers, Lemke, S. B., and Levine, M., ELAV mediates 3' UTR extension in the Drosophila nervous system., Genes Dev, vol. 26, no. 20, pp. 2259-64, 2012.
S. Y. Shvartsman, Coppey, M., and Berezhkovskii, A. M., Dynamics of maternal morphogen gradients in Drosophila., Curr Opin Genet Dev, vol. 18, no. 4, pp. 342-7, 2008.
J. P. Bothma, Garcia, H. G., Esposito, E., Schlissel, G., Gregor, T., and Levine, M., Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos., Proc Natl Acad Sci U S A, vol. 111, no. 29, pp. 10598-603, 2014.
F. Liu, Morrison, A. H., and Gregor, T., Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network., Proc Natl Acad Sci U S A, vol. 110, no. 17, pp. 6724-9, 2013.
D. Papatsenko and Levine, M. S., Dual regulation by the Hunchback gradient in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 105, no. 8, pp. 2901-6, 2008.
A. Jaźwińska, Kirov, N., Wieschaus, E., Roth, S., and Rushlow, C., The Drosophila gene brinker reveals a novel mechanism of Dpp target gene regulation., Cell, vol. 96, no. 4, pp. 563-73, 1999.
N. Yakoby, Lembong, J., Schüpbach, T., and Shvartsman, S. Y., Drosophila eggshell is patterned by sequential action of feedforward and feedback loops., Development, vol. 135, no. 2, pp. 343-51, 2008.
Y. Ahmed, Nouri, A., and Wieschaus, E., Drosophila Apc1 and Apc2 regulate Wingless transduction throughout development., Development, vol. 129, no. 7, pp. 1751-62, 2002.
C. D. van Raamsdonk and Tilghman, S. M., Dosage requirement and allelic expression of PAX6 during lens placode formation., Development, vol. 127, no. 24, pp. 5439-48, 2000.
J. V. Schmidt, Matteson, P. G., Jones, B. K., Guan, X. J., and Tilghman, S. M., The Dlk1 and Gtl2 genes are linked and reciprocally imprinted., Genes Dev, vol. 14, no. 16, pp. 1997-2002, 2000.
T. Gregor, Bialek, W., van Steveninck, R. R. de Ruyte, Tank, D. W., and Wieschaus, E. F., Diffusion and scaling during early embryonic pattern formation., Proc Natl Acad Sci U S A, vol. 102, no. 51, pp. 18403-7, 2005.
J. Bothma and Levine, M., Development: lights, camera, action--the Drosophila embryo goes live!, Curr Biol, vol. 23, no. 21, pp. R965-7, 2013.
A. Pane, Jiang, P., Zhao, D. Yanling, Singh, M., and Schüpbach, T., The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline., EMBO J, vol. 30, no. 22, pp. 4601-15, 2011.
Y. Nibu, Senger, K., and Levine, M., CtBP-independent repression in the Drosophila embryo., Mol Cell Biol, vol. 23, no. 11, pp. 3990-9, 2003.
J. M. Goodliffe, Cole, M. D., and Wieschaus, E., Coordinated regulation of Myc trans-activation targets by Polycomb and the Trithorax group protein Ash1., BMC Mol Biol, vol. 8, p. 40, 2007.
V. C. Calhoun and Levine, M., Coordinate regulation of an extended chromosome domain., Cell, vol. 113, no. 3, pp. 278-80, 2003.
Y. Kim, Iagovitina, A., Ishihara, K., Fitzgerald, K. M., Deplancke, B., Papatsenko, D., and Shvartsman, S. Y., Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo., Chaos, vol. 23, no. 2, p. 025105, 2013.
J. Cande, Goltsev, Y., and Levine, M. S., Conservation of enhancer location in divergent insects., Proc Natl Acad Sci U S A, vol. 106, no. 34, pp. 14414-9, 2009.
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., A computational statistics approach for estimating the spatial range of morphogen gradients., Development, vol. 138, no. 22, pp. 4867-74, 2011.
F. Biemar, Nix, D. A., Piel, J., Peterson, B., Ronshaugen, M., Sementchenko, V., Bell, I., J Manak, R., and Levine, M. S., Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array., Proc Natl Acad Sci U S A, vol. 103, no. 34, pp. 12763-8, 2006.
M. E. Kavousanakis, Kanodia, J. S., Kim, Y., Kevrekidis, I. G., and Shvartsman, S. Y., A compartmental model for the bicoid gradient., Dev Biol, vol. 345, no. 1, pp. 12-7, 2010.
N. Yakoby, Bristow, C. A., Gong, D., Schafer, X., Lembong, J., Zartman, J. J., Halfon, M. S., Schüpbach, T., and Shvartsman, S. Y., A combinatorial code for pattern formation in Drosophila oogenesis., Dev Cell, vol. 15, no. 5, pp. 725-37, 2008.
S. E. Cole, Levorse, J. M., Tilghman, S. M., and Vogt, T. F., Clock regulatory elements control cyclic expression of Lunatic fringe during somitogenesis., Dev Cell, vol. 3, no. 1, pp. 75-84, 2002.
A. T. Hark and Tilghman, S. M., Chromatin conformation of the H19 epigenetic mark., Hum Mol Genet, vol. 7, no. 12, pp. 1979-85, 1998.
L. Christiaen, Stolfi, A., and Levine, M., BMP signaling coordinates gene expression and cell migration during precardiac mesoderm development., Dev Biol, vol. 340, no. 2, pp. 179-87, 2010.
H. A. Müller and Wieschaus, E., armadillo, bazooka, and stardust are critical for early stages in formation of the zonula adherens and maintenance of the polarized blastoderm epithelium in Drosophila., J Cell Biol, vol. 134, no. 1, pp. 149-63, 1996.
A. Di Gregorio and Levine, M., Analyzing gene regulation in ascidian embryos: new tools for new perspectives., Differentiation, vol. 70, no. 4-5, pp. 132-9, 2002.
E. K. Farley, Olson, K. M., Zhang, W., Brandt, A. J., Rokhsar, D. S., and Levine, M. S., Suboptimization of developmental enhancers., Science, vol. 350, no. 6258, pp. 325-8, 2015.
J. P. Bothma, Garcia, H. G., Ng, S., Perry, M. W., Gregor, T., and Levine, M., Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo., Elife, vol. 4, 2015.
I. A. Navarrete and Levine, M., Nodal and FGF coordinate ascidian neural tube morphogenesis., Development, vol. 143, no. 24, pp. 4665-4675, 2016.
W. A. Rogers, Goyal, Y., Yamaya, K., Shvartsman, S. Y., and Levine, M. S., Uncoupling neurogenic gene networks in the Drosophila embryo., Genes Dev, vol. 31, no. 7, pp. 634-638, 2017.
V. Lakhina, Arey, R. N., Kaletsky, R., Kauffman, A., Stein, G., Keyes, W., Xu, D., and Murphy, C. T., Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs., Neuron, vol. 85, no. 2, pp. 330-45, 2015.
Y. Pritykin, Brito, T., Schüpbach, T., Singh, M., and Pane, A., Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation., RNA, vol. 23, no. 7, pp. 1097-1109, 2017.
R. Menon, Otto, E. A., Kokoruda, A., Zhou, J., Zhang, Z., Yoon, E., Chen, Y. - C., Troyanskaya, O., Spence, J. R., Kretzler, M., and Cebrián, C., Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney., Development, vol. 145, no. 16, 2018.
J. Zhou, Schor, I. E., Yao, V., Theesfeld, C. L., Marco-Ferreres, R., Tadych, A., Furlong, E. E. M., and Troyanskaya, O. G., Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development., PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.