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: Author is Levine, Michael  [Clear All Filters]
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Base Sequence
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.
D. Hendrix, Levine, M., and Shi, W., miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data., Genome Biol, vol. 11, no. 4, p. R39, 2010.
B. Davidson and Levine, M., Evolutionary origins of the vertebrate heart: Specification of the cardiac lineage in Ciona intestinalis., Proc Natl Acad Sci U S A, vol. 100, no. 20, pp. 11469-73, 2003.
D. Papatsenko, Kislyuk, A., Levine, M., and Dubchak, I., Conservation patterns in different functional sequence categories of divergent Drosophila species., Genomics, vol. 88, no. 4, pp. 431-42, 2006.
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.
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.
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.
Animals, Genetically Modified
A. Erives and Levine, M., Coordinate enhancers share common organizational features in the Drosophila genome., Proc Natl Acad Sci U S A, vol. 101, no. 11, pp. 3851-6, 2004.
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.
J. Cowden and Levine, M., The Snail repressor positions Notch signaling in the Drosophila embryo., Development, vol. 129, no. 7, pp. 1785-93, 2002.
B. Haley, Foys, B., and Levine, M., Vectors and parameters that enhance the efficacy of RNAi-mediated gene disruption in transgenic Drosophila., Proc Natl Acad Sci U S A, vol. 107, no. 25, pp. 11435-40, 2010.
D. N. Keys, Levine, M., Harland, R. M., and Wallingford, J. B., Control of intercalation is cell-autonomous in the notochord of Ciona intestinalis., Dev Biol, vol. 246, no. 2, pp. 329-40, 2002.
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.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., Electroporation of transgenic DNAs in the sea squirt Ciona., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5345, 2009.
K. Senger, Armstrong, G. W., Rowell, W. J., Kwan, J. M., Markstein, M., and Levine, M., Immunity regulatory DNAs share common organizational features in Drosophila., Mol Cell, vol. 13, no. 1, pp. 19-32, 2004.
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.
Animals
M. Levine and Tjian, R., Transcription regulation and animal diversity., Nature, vol. 424, no. 6945, pp. 147-51, 2003.
A. Stathopoulos and Levine, M., Whole-genome analysis of Drosophila gastrulation., Curr Opin Genet Dev, vol. 14, no. 5, pp. 477-84, 2004.
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.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., X-gal staining of electroporated sea squirt (Ciona) embryos., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5346, 2009.
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. Lagha, Bothma, J. P., and Levine, M., Mechanisms of transcriptional precision in animal development., Trends Genet, vol. 28, no. 8, pp. 409-16, 2012.
C. Cao, Lemaire, L. A., Wang, W., Yoon, P. H., Choi, Y. A., Parsons, L. R., Matese, J. C., Wang, W., Levine, M., and Chen, K., Comprehensive single-cell transcriptome lineages of a proto-vertebrate., Nature, vol. 571, no. 7765, pp. 349-354, 2019.
B. Haley, Foys, B., and Levine, M., Vectors and parameters that enhance the efficacy of RNAi-mediated gene disruption in transgenic Drosophila., Proc Natl Acad Sci U S A, vol. 107, no. 25, pp. 11435-40, 2010.
Y. Goltsev, Rezende, G. L., Vranizan, K., Lanzaro, G., Valle, D., and Levine, M., Developmental and evolutionary basis for drought tolerance of the Anopheles gambiae embryo., Dev Biol, vol. 330, no. 2, pp. 462-70, 2009.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., The sea squirt Ciona intestinalis., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.emo138, 2009.
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.
K. Senger, Armstrong, G. W., Rowell, W. J., Kwan, J. M., Markstein, M., and Levine, M., Immunity regulatory DNAs share common organizational features in Drosophila., Mol Cell, vol. 13, no. 1, pp. 19-32, 2004.
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.
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.
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.
E. Farley and Levine, M., HOT DNAs: a novel class of developmental enhancers., Genes Dev, vol. 26, no. 9, pp. 873-6, 2012.
D. N. Keys, Levine, M., Harland, R. M., and Wallingford, J. B., Control of intercalation is cell-autonomous in the notochord of Ciona intestinalis., Dev Biol, vol. 246, no. 2, pp. 329-40, 2002.
A. Stathopoulos, Tam, B., Ronshaugen, M., Frasch, M., and Levine, M., pyramus and thisbe: FGF genes that pattern the mesoderm of Drosophila embryos., Genes Dev, vol. 18, no. 6, pp. 687-99, 2004.
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.
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.
A. Stolfi and Levine, M., Neuronal subtype specification in the spinal cord of a protovertebrate., Development, vol. 138, no. 5, pp. 995-1004, 2011.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., Electroporation of transgenic DNAs in the sea squirt Ciona., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5345, 2009.
M. Levine, Cattoglio, C., and Tjian, R., Looping back to leap forward: transcription enters a new era., Cell, vol. 157, no. 1, pp. 13-25, 2014.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., Isolation of sea squirt (Ciona) gametes, fertilization, dechorionation, and development., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5344, 2009.
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.
V. S. Chopra, Hendrix, D. A., Core, L. J., Tsui, C., Lis, J. T., and Levine, M., The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo., Mol Cell, vol. 42, no. 6, pp. 837-44, 2011.
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. 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.
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.
N. Harafuji, Keys, D. N., and Levine, M., Genome-wide identification of tissue-specific enhancers in the Ciona tadpole., Proc Natl Acad Sci U S A, vol. 99, no. 10, pp. 6802-5, 2002.
D. Hendrix, Levine, M., and Shi, W., miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data., Genome Biol, vol. 11, no. 4, p. R39, 2010.
M. Levine, Retrospective. Walter Gehring (1939-2014)., Science, vol. 345, no. 6194, p. 277, 2014.
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.
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.
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.
M. Levine, The contraction of time and space in remote chromosomal interactions., Cell, vol. 158, no. 2, pp. 243-4, 2014.
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.
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.
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.
D. Papatsenko and Levine, M., Computational identification of regulatory DNAs underlying animal development., Nat Methods, vol. 2, no. 7, pp. 529-34, 2005.
B. Davidson and Levine, M., Evolutionary origins of the vertebrate heart: Specification of the cardiac lineage in Ciona intestinalis., Proc Natl Acad Sci U S A, vol. 100, no. 20, pp. 11469-73, 2003.
D. Papatsenko, Kislyuk, A., Levine, M., and Dubchak, I., Conservation patterns in different functional sequence categories of divergent Drosophila species., Genomics, vol. 88, no. 4, pp. 431-42, 2006.
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.
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.
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. 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.
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.
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. 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.
V. C. Calhoun and Levine, M., Coordinate regulation of an extended chromosome domain., Cell, vol. 113, no. 3, pp. 278-80, 2003.
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.
M. Markstein and Levine, M., Decoding cis-regulatory DNAs in the Drosophila genome., Curr Opin Genet Dev, vol. 12, no. 5, pp. 601-6, 2002.
B. Haley, Hendrix, D., Trang, V., and Levine, M., A simplified miRNA-based gene silencing method for Drosophila melanogaster., Dev Biol, vol. 321, no. 2, pp. 482-90, 2008.
M. Levine, Paused RNA polymerase II as a developmental checkpoint., Cell, vol. 145, no. 4, pp. 502-11, 2011.
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.
D. Papatsenko, Levine, M., and Goltsev, Y., Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles., PLoS Biol, vol. 9, no. 1, p. e1000584, 2011.
J. Cowden and Levine, M., The Snail repressor positions Notch signaling in the Drosophila embryo., Development, vol. 129, no. 7, pp. 1785-93, 2002.
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.
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.
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.
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.
B. Davidson, Shi, W., and Levine, M., Uncoupling heart cell specification and migration in the simple chordate Ciona intestinalis., Development, vol. 132, no. 21, pp. 4811-8, 2005.
N. Haupaix, Abitua, P. B., Sirour, C., Yasuo, H., Levine, M., and Hudson, C., Ephrin-mediated restriction of ERK1/2 activity delimits the number of pigment cells in the Ciona CNS., Dev Biol, vol. 394, no. 1, pp. 170-80, 2014.
I. A. Navarrete and Levine, M., Nodal and FGF coordinate ascidian neural tube morphogenesis., Development, vol. 143, no. 24, pp. 4665-4675, 2016.
J. Cowden and Levine, M., Ventral dominance governs sequential patterns of gene expression across the dorsal-ventral axis of the neuroectoderm in the Drosophila embryo., Dev Biol, vol. 262, no. 2, pp. 335-49, 2003.
B. P. Berman, Nibu, Y., Pfeiffer, B. D., Tomancak, P., Celniker, S. E., Levine, M., Rubin, G. M., and Eisen, M. B., 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, vol. 99, no. 2, pp. 757-62, 2002.
V. S. Chopra, Kong, N., and Levine, M., Transcriptional repression via antilooping in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 109, no. 24, pp. 9460-4, 2012.
A. Erives and Levine, M., Coordinate enhancers share common organizational features in the Drosophila genome., Proc Natl Acad Sci U S A, vol. 101, no. 11, pp. 3851-6, 2004.
A. Stathopoulos and Levine, M., Whole-genome expression profiles identify gene batteries in Drosophila., Dev Cell, vol. 3, no. 4, pp. 464-5, 2002.
A. Stathopoulos and Levine, M., Dorsal gradient networks in the Drosophila embryo., Dev Biol, vol. 246, no. 1, pp. 57-67, 2002.
P. Barron Abitua, T Gainous, B., Kaczmarczyk, A. N., Winchell, C. J., Hudson, C., Kamata, K., Nakagawa, M., Tsuda, M., Kusakabe, T. G., and Levine, M., The pre-vertebrate origins of neurogenic placodes., Nature, vol. 524, no. 7566, pp. 462-5, 2015.
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.
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.
A. Stolfi, T Gainous, B., Young, J. J., Mori, A., Levine, M., and Christiaen, L., Early chordate origins of the vertebrate second heart field., Science, vol. 329, no. 5991, pp. 565-8, 2010.
E. Bae, Calhoun, V. C., Levine, M., Lewis, E. B., and Drewell, R. A., Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex., Proc Natl Acad Sci U S A, vol. 99, no. 26, pp. 16847-52, 2002.
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.
M. W. Perry, Boettiger, A. N., Bothma, J. P., and Levine, M., Shadow enhancers foster robustness of Drosophila gastrulation., Curr Biol, vol. 20, no. 17, pp. 1562-7, 2010.
V. S. Chopra, Cande, J., Hong, J. - W., and Levine, M., Stalled Hox promoters as chromosomal boundaries., Genes Dev, vol. 23, no. 13, pp. 1505-9, 2009.
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.
Animal Husbandry
L. Christiaen, Wagner, E., Shi, W., and Levine, M., The sea squirt Ciona intestinalis., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.emo138, 2009.
Alcohol Oxidoreductases
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.
Adaptor Proteins, Signal Transducing
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.

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