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Levine Lab

Center for Integrative Genomics, University of California at Berkeley



 

2014

Wagner E, Stolfi A, Gi Choi Y, Levine M. (2014) Islet is a key determinant of ascidian palp morphogenesis. Development. 141(15):3084-92.
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Haupaix N, Abitua PB, Sirour C, Yasuo H, Levine M, Hudson C. (2014) Ephrin-mediated restriction of ERK1/2 activity delimits the number of pigment cells in the Ciona CNS. Dev Biol. [Epub ahead of print].
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Levine M. (2014) The contraction of time and space in remote chromosomal interactions. Cell. 158(2):243-4.
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Levine M. (2014) Retrospective. Walter Gehring (1939-2014). Science. 345(6194):277.
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Bothma JP, Garcia HG, Esposito E, Schlissel G, Gregor T, Levine M. (2014) Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos. PNAS. 111(29):10598-603.
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Levine M, Cattoglio C, Tjian R. (2014) Looping back to leap forward: transcription enters a new era.Cell. 157(1):13-25.
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2013

Bothma J, Levine M. (2013) Development: lights, camera, action--the Drosophila embryo goes live! Curr Biol. 23(21):R965-7.
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Levine M. (2013) Computing away the magic? eLife. 2:e01135.
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Lagha M*, Bothma JP*, Esposito E, Ng S, Stefanik L, Tsui C, Johnston J, Chen K, Gilmour DS, Zeitlinger J, Levine MS. (2013) Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo. Cell. 153(5):976-87. (*)These authors contributed equally to this work
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Hong JW, Won Park K, Levine MS. (2013) Temporal regulation of single-minded target genes in the ventral midline of the Drosophila central nervous system. Dev Biol. 3(1):8-15.
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Boettiger AN, Levine M. (2013) Rapid transcription fosters coordinate snail expression in the Drosophila embryo. Cell Rep. 3(1):8-15.
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2012

Abitua PB, Wagner E, Navarrete IA, Levine M. (2012) Identification of a rudimentary neural crest in a non-vertebrate chordate. Nature. 492(7427):104-7.
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Perry MW, Bothma JP, Luu RD, Levine M. (2012) Precision of hunchback expression in the Drosophila embryo. Curr Biol. 22(23):2247-52.
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Hilgers V, Lemke SB, Levine M. (2012) ELAV mediates 3' UTR extension in the Drosophila nervous system. Genes Dev. 26(20):2259-64.
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Chopra VS, Kong N, Levine M. (2012)Transcriptional repression via antilooping in the Drosophila embryo. Proc Natl Acad Sci U S A 109(24):9460-4.
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Wagner E, Levine M. (2012) FGF signaling establishes the anterior border of the Ciona neural tube. Development.139(13):2351-9.
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Farley E, Levine M. (2012) HOT DNAs: a novel class of developmental enhancers. Genes Dev. 26(9):873-6.
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Lagha M, Bothma JP, Levine M. (2012) Mechanisms of transcriptional precision in animal development. Trends Genet. Apr 16. [Epub ahead of print]
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2011

Kratsios P, Stolfi A, Levine M, Hobert O. (2011) Coordinated regulation of cholinergic motor neuron traits through a conserved terminal selector gene. Nat Neurosci. 15(2):205-14.
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Stolfi A, Wagner E, Taliaferro JM, Chou S, Levine M. (2011) Neural tube patterning by Ephrin, FGF and Notch signaling relays. Development. 138(24):5429-39.
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Bothma JP, Magliocco J, Levine M. (2011) The snail repressor inhibits release, not elongation, of paused Pol II in the Drosophila embryo. Curr Biol. 21(18):1571-7.
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Hilgers V, Perry MW, Hendrix D, Stark A, Levine M, Haley B. (2011) Neural-specific elongation of 3' UTRs during Drosophila development. Proc Natl Acad Sci U S A. 108(38):15864-9.
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Perry MW, Boettiger AN, Levine M. (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.
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Chopra VS, Hendrix DA, Core LJ, Tsui C, Lis JT, Levine M. (2011) The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo. Mol Cell. 42(6):837-44.
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Levine M.  (2011) Paused RNA polymerase II as a developmental checkpoint. Cell. 13;145(4):502-11.
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Stolfi A, Levine M. (2011) Neuronal subtype specification in the spinal cord of a protovertebrate. Development. 138(5):995-1004.
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Papatsenko D, Levine M, Goltsev Y.  (2011)Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles.PLoS Biol. 9(1):e1000584
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2010

Levine M.  (2010) Transcriptional enhancers in animal development and evolution.  Curr Biol. 20(17):R754-63.
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Papatsenko I, Levine M, Papatsenko D. (2010)
Temporal waves of coherent gene expression during Drosophila embryogenesis.  Bioinformatics. 2010 Sep 6.
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Perry MW, Boettiger AN, Bothma JP, Levine M. (2010) Shadow enhancers foster robustness of Drosophila gastrulation. Curr Biol. 20(17):1562-7.
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Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L. (2010)  Early chordate origins of the vertebrate second heart field.  Science.  329(5991):565-8.
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Haley B, Foys B, Levine M.  (2010) Vectors and parameters that enhance the efficacy of RNAi-mediated gene disruption in transgenic Drosophila.  PNAS. 107(25):11435-40
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Hendrix D, Levine M, Shi W.(2010)  miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data.  Genome Biol. 11:R39

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2009

Christiaen L, Wagner E, Shi W, and Levine M. (2009)  The sea squirt Ciona intestinalis.  CSH Protoc. 2009. 

CSH Protocols


Christiaen L, Stolfi A, and Levine M. (2009) BMP signaling coordinates gene expression and cell migration during precardiac mesoderm development. Dev Biol. 340(2):179-87.

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Perry MW, Cande JD, Boettiger AN, Levine M. (2009).  Evolution of Insect Dorsoventral Patterning Mechanisms. Cold Spring Harb Symp Quant Biol. Oct 20.

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Cande JD, Chopra VS, Levine M. (2009).  Evolving enhancer-promoter interactions within the tinman complex of the flour beetle, Tribolium castaneum.  Development. 136(18):3153

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Cande J, Goltsev Y, Levine MS. (2009) Conservation of enhancer location in divergent insects. PNAS. 106(34):14414-9. 

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Papatsenko D, Goltsev Y, Levine M. (2009)  Organization of developmental enhancers in the Drosophila embryo.  Nucleic Acids Res. 37(17):5665-77.

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Chopra VS, Levine M. (2009) Combinatorial patterning mechanisms in the Drosophila embryo.  Brief. Funct. Genomic Proteomic. 8(4):243-249. 

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Boettiger AN, Levine M.  (2009) Synchronous and stochastic patterns of gene activation in the Drosophila embryo.  Science. 325:471-3.
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Christiaen L, Stolfi A, Davidson B, Levine M. (2009) Spatio-temporal intersection of Lhx3 and Tbx6 defines the cardiac field through synergistic activation of Mesp. Dev Biol. 328(2):552-60.

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Chopra VS, Cande J, Hong JW, Levine M. (2009) Stalled Hox promoters as chromosomal boundaries.  Genes and Dev. 23(13):1505-9.

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Chopra VS, Hong JW, Levine M.  (2009) Regulation of Hox Gene Activity by Transcriptional Elongation in Drosophila. Curr. Biol.  19(8):688-93

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Goltsev Y, Rezende GL, Vranizan K, Lanzaro G, Valle D, Levine M. (2009) Developmental and evolutionary basis for drought tolerance of the Anopheles gambiae embryo.  Dev Biol. 330(2):462-70

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Shi W, Hendrix D, Levine M, and Haley B.  (2009)  A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate.  Nature Struct Mol Biol. 16:183-9.

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Imai KS, Stolfi A, Levine M, Satou Y.  (2009)  Gene regulatory networks underlying the compartmentalization of the Ciona central nervous system. Development 136(2):285-93

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Shi W, Peyrot SM, Munro E, Levine M. (2009) FGF3 in the floor plate directs notochord convergent extension in the Ciona tadpole. Development 136(1):23-8

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2008

Hong JW, Hendrix DA, Levine MS.  (2008) Shadow enhancers as a source of evolutionary novelty.  Science. 321:1314.

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Hong JW, Hendrix DA, Paptsendo D, Levine MS. (2008) How the Dorsal gradient works: insights from postgenome technologies.  PNAS 105:20072-6.

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Haley B, Hendrix D, Trang V, Levine M. (2008) A simplified miRNA-based gene silencing method for Drosophila melanogaster. Dev Biol.  321:482-90.

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Davidson EH, Levine MS.  (2008) Properties of developmental gene regulatory networks.  PNAS.  105:20063-6. 

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Reed DE, Huang XM, Wohlschlegel JA, Levine MS, Senger K. (2008)  DEAF-1 regulates immunity gene expression in Drosophila.  PNAS;105(24):8351-6.

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Hendrix DA, Hong JW, Zeitlinger J, Rokhsar DS, Levine MS. (2008) Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. PNAS 105(22):7762-7.

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Christiaen L, Davidson B, Kawashima T, Powell W, Nolla H, Vranizan K, Levine M.  (2008)  The transcription/migration interface in heart precursors of Ciona intestinalisScience;320(5881):1349-52.

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Shippy TD, Ronshaugen M, Cande J, He J, Beeman RW, Levine M, Brown SJ, Denell RE. (2008) Analysis of the Tribolium homeotic complex: insights into mechanisms constraining insect Hox clusters.  Dev Genes Evol. 218(3-4):127-39.

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Papatsenko D, Levine MS. (2008) Dual regulation by the Hunchback gradient in the Drosophila embryo. PNAS 105(8):2901-6.

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Levine, M. A systems view of Drosophila segmentation.  (2008) Genome Biol. 9:207

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Shi W, Levine M. (2008)  Ephrin signaling establishes asymmetric cell fates in an endomesoderm lineage of the Ciona embryo.  Development 135(5):931-40

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2007

Zeitlinger J, Stark A, Kellis M, Hong JW, Nechaev S, Adelman K, Levine M, Young RA. (2007)

RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

Nat Genet;39(12):1512-6.

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Zeitlinger J, Zinzen RP, Stark A, Kellis M, Zhang H, Young RA, Levine M (2007) Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes and Development 21, 385-390.

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Papatsenko D, Levine M.  (2007)  A rationale for the enhanceosome and other evolutionarily constrained enhancers.  Curr. Biol.  17:R955-7.

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Goltsev Y, Fuse N, Frasch M, Zinzen RP, Lanzaro G, Levine M. (2007)  Evolution of the dorsal-ventral patterning network in the mosquito, Anopheles gambiae.  Development.  134:2415-24. 

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Beh J, Shi W, Levine M, Davidson B, Christiaen L.  (2007)  FoxF is essential for FGF-induced migration of heart progenitor cells in the ascidian Ciona intestinalis. Development 134(18):3297-305

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2006

Zinzen R, Cande JD, Papatsenko D, Levine M (2006) Evolution of the ventral midline in insect embryos  Developmental Cell 11, 895-902. 


Imai KS, Levine M, Satoh N, Satou Y (2006) Regulatory blueprint for a chordate embryo  Science 312(5777):1183-7.


Davidson B, Shi W, Beh J, Christiaen L, Levine M (2006) FGF signaling delineates the cardiac progenitor field in the simple chordate, Ciona intestinalisGenes and Development 20(19):2728-38.


Zinzen RP, Senger K, Levine M, Papatsenko D (2006) Computational models for neurogenic gene expression in the Drosophila embryo  Current Biology 16(13):1358-65.


Senger K, Harris K, Levine M (2006) GATA factors participate in tissue-specific immune responses in Drosophila larvae  PNAS 103(43):15957-62.


Biemar F, Nix DA, Piel J, Peterson B, Ronshaugen M, Sementchenko V, Bell I, Manak JR, Levine MS (2006) Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array  PNAS 103(34):12763-8.


Papatsenko D, Kislyuk A, Levine M, Dubchak I. (2006) Conservation patterns in different functional sequence categories of divergent Drosophila species. Genomics. 88(4):431-42


2005

Biemar F, Zinzen R, Ronshaugen M, Sementchenko V, Manak JR, Levine MS (2005) Spatial regulation of microRNA gene expression in the Drosophila embryo  PNAS 102(44): 15907-11.


Ronshaugen M, Biemar F, Piel J, Levine M, Lai EC (2005) The Drosophila microRNA iab-4 causes a dominant homeotic transformation of halteres to wings  Genes and Development 19, 2947-2952.


Shi W, Levine M, Davidson B. (2005) Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis.  Genome Res.;15(12):1668-74.


Satoh N, Levine M. (2005)  Surfing with the tunicates into the post-genome era.  Genes Dev. 19(20):2407-11. Review.


Davidson B, Shi W, Levine M.  (2005) Uncoupling heart cell specification and migration in the simple chordate Ciona intestinalis.   Development 132(21):4811-8..


Keys DN, Lee BI, Di Gregorio A, Harafuji N, Detter JC, Wang M, Kahsai O, Ahn S, Zhang C, Doyle SA, Satoh N, Satou Y, Saiga H, Christian AT, Rokhsar DS, Hawkins TL, Levine M, Richardson PM.  (2005)  A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis. Proc Natl Acad Sci 102(3):679-83.


Stathopoulos A, Levine M.  (2005) Genomic regulatory networks and animal development.

Dev Cell. 9(4):449-62. Review.


Stathopoulos A, Levine M. (2005)  Localized repressors delineate the neurogenic ectoderm in the early Drosophila embryo. Dev Biol. ;280(2):482-93.


Papatsenko D, Levine M.  (2005) Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo. Proc Natl Acad Sci 102(14):4966-71.


Levine M, Davidson EH.  (2005) Gene regulatory networks for development. Proc Natl Acad Sci 102(14):4936-42.


Publications