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]
“Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.”, PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
, “Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney.”, Development, vol. 145, no. 16, 2018.
, “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.
, “Uncoupling neurogenic gene networks in the Drosophila embryo.”, Genes Dev, vol. 31, no. 7, pp. 634-638, 2017.
, “Nodal and FGF coordinate ascidian neural tube morphogenesis.”, Development, vol. 143, no. 24, pp. 4665-4675, 2016.
, “Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo.”, Elife, vol. 4, 2015.
, “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.
, “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.
, “Suboptimization of developmental enhancers.”, Science, vol. 350, no. 6258, pp. 325-8, 2015.
, “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.
, “Morphogenesis at criticality.”, Proc Natl Acad Sci U S A, vol. 111, no. 10, pp. 3683-8, 2014.
, “Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo.”, Chaos, vol. 23, no. 2, p. 025105, 2013.
, “Development: lights, camera, action--the Drosophila embryo goes live!”, Curr Biol, vol. 23, no. 21, pp. R965-7, 2013.
, “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.
, “Kinetics of gene derepression by ERK signaling.”, Proc Natl Acad Sci U S A, vol. 110, no. 25, pp. 10330-5, 2013.
, “Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo.”, Cell, vol. 153, no. 5, pp. 976-87, 2013.
, “Positional information, in bits.”, Proc Natl Acad Sci U S A, vol. 110, no. 41, pp. 16301-8, 2013.
, “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.
, “Precise developmental gene expression arises from globally stochastic transcriptional activity.”, Cell, vol. 154, no. 4, pp. 789-800, 2013.
, “Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning.”, Curr Biol, vol. 23, no. 21, pp. 2140-5, 2013.
, “Three-dimensional epithelial morphogenesis in the developing Drosophila egg.”, Dev Cell, vol. 24, no. 4, pp. 400-10, 2013.
, “ELAV mediates 3' UTR extension in the Drosophila nervous system.”, Genes Dev, vol. 26, no. 20, pp. 2259-64, 2012.
, “FGF signaling establishes the anterior border of the Ciona neural tube.”, Development, vol. 139, no. 13, pp. 2351-9, 2012.
, “HOT DNAs: a novel class of developmental enhancers.”, Genes Dev, vol. 26, no. 9, pp. 873-6, 2012.
, “Identification of a rudimentary neural crest in a non-vertebrate chordate.”, Nature, vol. 492, no. 7427, pp. 104-7, 2012.
, “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.
, “Mathematical models of morphogen gradients and their effects on gene expression.”, Wiley Interdiscip Rev Dev Biol, vol. 1, no. 5, pp. 715-30, 2012.
, “Mechanisms of transcriptional precision in animal development.”, Trends Genet, vol. 28, no. 8, pp. 409-16, 2012.
, “Pattern formation by graded and uniform signals in the early Drosophila embryo.”, Biophys J, vol. 102, no. 3, pp. 427-33, 2012.
, “Precision of hunchback expression in the Drosophila embryo.”, Curr Biol, vol. 22, no. 23, pp. 2247-52, 2012.
, “Quantifying the Bicoid morphogen gradient in living fly embryos.”, Cold Spring Harb Protoc, vol. 2012, no. 4, pp. 398-406, 2012.
, “RTK signaling modulates the Dorsal gradient.”, Development, vol. 139, no. 16, pp. 3032-9, 2012.
, “Temporal dynamics, spatial range, and transcriptional interpretation of the Dorsal morphogen gradient.”, Curr Opin Genet Dev, vol. 22, no. 6, pp. 542-6, 2012.
, “Torso RTK controls Capicua degradation by changing its subcellular localization.”, Development, vol. 139, no. 21, pp. 3962-8, 2012.
, “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
, “The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline.”, EMBO J, vol. 30, no. 22, pp. 4601-15, 2011.
, “Gene regulation by MAPK substrate competition.”, Dev Cell, vol. 20, no. 6, pp. 880-7, 2011.
, “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.
, “Neural tube patterning by Ephrin, FGF and Notch signaling relays.”, Development, vol. 138, no. 24, pp. 5429-39, 2011.
, “Neural-specific elongation of 3' UTRs during Drosophila development.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15864-9, 2011.
, “Neuronal subtype specification in the spinal cord of a protovertebrate.”, Development, vol. 138, no. 5, pp. 995-1004, 2011.
, “Pattern formation by a moving morphogen source.”, Phys Biol, vol. 8, no. 4, p. 045003, 2011.
, “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.
, “Paused RNA polymerase II as a developmental checkpoint.”, Cell, vol. 145, no. 4, pp. 502-11, 2011.
, “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.
, “Yeast cells can access distinct quiescent states.”, Genes Dev, vol. 25, no. 4, pp. 336-49, 2011.
, “BMP signaling coordinates gene expression and cell migration during precardiac mesoderm development.”, Dev Biol, vol. 340, no. 2, pp. 179-87, 2010.
, “A compartmental model for the bicoid gradient.”, Dev Biol, vol. 345, no. 1, pp. 12-7, 2010.
, “MAPK substrate competition integrates patterning signals in the Drosophila embryo.”, Curr Biol, vol. 20, no. 5, pp. 446-51, 2010.
, “Morphogen gradients: limits to signaling or limits to measurement?”, Curr Biol, vol. 20, no. 5, pp. R232-4, 2010.
, “β-arrestin Kurtz inhibits MAPK and Toll signalling in Drosophila development.”, EMBO J, vol. 29, no. 19, pp. 3222-35, 2010.
, “Conservation of enhancer location in divergent insects.”, Proc Natl Acad Sci U S A, vol. 106, no. 34, pp. 14414-9, 2009.
, “Evolving enhancer-promoter interactions within the tinman complex of the flour beetle, Tribolium castaneum.”, Development, vol. 136, no. 18, pp. 3153-60, 2009.
, “Expression patterns of cadherin genes in Drosophila oogenesis.”, Gene Expr Patterns, vol. 9, no. 1, pp. 31-6, 2009.
, “FGF3 in the floor plate directs notochord convergent extension in the Ciona tadpole.”, Development, vol. 136, no. 1, pp. 23-8, 2009.
, “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.
, “Microinjection of morpholino oligos and RNAs in sea squirt (Ciona) embryos.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5347, 2009.
, “Organization of developmental enhancers in the Drosophila embryo.”, Nucleic Acids Res, vol. 37, no. 17, pp. 5665-77, 2009.
, “Pattern formation by dynamically interacting network motifs.”, Proc Natl Acad Sci U S A, vol. 106, no. 9, pp. 3213-8, 2009.
, “Pulsed contractions of an actin-myosin network drive apical constriction.”, Nature, vol. 457, no. 7228, pp. 495-9, 2009.
, “Regulation of Hox gene activity by transcriptional elongation in Drosophila.”, Curr Biol, vol. 19, no. 8, pp. 688-93, 2009.
, “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.
, “Synchronous and stochastic patterns of gene activation in the Drosophila embryo.”, Science, vol. 325, no. 5939, pp. 471-3, 2009.
, “Systems-level dynamic analyses of fate change in murine embryonic stem cells.”, Nature, vol. 462, no. 7271, pp. 358-62, 2009.
, “Whole-mount in situ hybridization on sea squirt (Ciona intestinalis) embryos.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5348, 2009.
, “A combinatorial code for pattern formation in Drosophila oogenesis.”, Dev Cell, vol. 15, no. 5, pp. 725-37, 2008.
, “Drosophila eggshell is patterned by sequential action of feedforward and feedback loops.”, Development, vol. 135, no. 2, pp. 343-51, 2008.
, “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.
, “Dynamics of maternal morphogen gradients in Drosophila.”, Curr Opin Genet Dev, vol. 18, no. 4, pp. 342-7, 2008.
, “How the Dorsal gradient works: insights from postgenome technologies.”, Proc Natl Acad Sci U S A, vol. 105, no. 51, pp. 20072-6, 2008.
, “Nuclear trapping shapes the terminal gradient in the Drosophila embryo.”, Curr Biol, vol. 18, no. 12, pp. 915-9, 2008.
, “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.
, “Shadow enhancers as a source of evolutionary novelty.”, Science, vol. 321, no. 5894, p. 1314, 2008.
, “Spatial regulation of BMP signaling by patterned receptor expression.”, Tissue Eng Part A, vol. 14, no. 9, pp. 1469-77, 2008.
, “The transcription/migration interface in heart precursors of Ciona intestinalis.”, Science, vol. 320, no. 5881, pp. 1349-52, 2008.
, “Coordinated regulation of Myc trans-activation targets by Polycomb and the Trithorax group protein Ash1.”, BMC Mol Biol, vol. 8, p. 40, 2007.
, “Enhancer organization: transistor with a twist or something in a different vein?”, Curr Biol, vol. 17, no. 24, pp. R1048-50, 2007.
, “Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo.”, PLoS Biol, vol. 5, no. 5, p. e117, 2007.
, “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.
, “Quantitative analysis of the GAL4/UAS system in Drosophila oogenesis.”, Genesis, vol. 44, no. 2, pp. 66-74, 2006.
, “The search for DAF-16/FOXO transcriptional targets: approaches and discoveries.”, Exp Gerontol, vol. 41, no. 10, pp. 910-21, 2006.
, “Diffusion and scaling during early embryonic pattern formation.”, Proc Natl Acad Sci U S A, vol. 102, no. 51, pp. 18403-7, 2005.
, “Gene regulatory networks for development.”, Proc Natl Acad Sci U S A, vol. 102, no. 14, pp. 4936-42, 2005.
, “Localized repressors delineate the neurogenic ectoderm in the early Drosophila embryo.”, Dev Biol, vol. 280, no. 2, pp. 482-93, 2005.
, “Polycomb mediates Myc autorepression and its transcriptional control of many loci in Drosophila.”, Genes Dev, vol. 19, no. 24, pp. 2941-6, 2005.
, “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.
, “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.
, “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.
, “Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis.”, Genome Res, vol. 15, no. 12, pp. 1668-74, 2005.
, “A regulatory code for neurogenic gene expression in the Drosophila embryo.”, Development, vol. 131, no. 10, pp. 2387-94, 2004.
, “Whole-genome analysis of Drosophila gastrulation.”, Curr Opin Genet Dev, vol. 14, no. 5, pp. 477-84, 2004.
, “Coordinate regulation of an extended chromosome domain.”, Cell, vol. 113, no. 3, pp. 278-80, 2003.
, “CtBP-independent repression in the Drosophila embryo.”, Mol Cell Biol, vol. 23, no. 11, pp. 3990-9, 2003.
, “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.
, “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
, “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.
, “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.
, “Analyzing gene regulation in ascidian embryos: new tools for new perspectives.”, Differentiation, vol. 70, no. 4-5, pp. 132-9, 2002.
, “Clock regulatory elements control cyclic expression of Lunatic fringe during somitogenesis.”, Dev Cell, vol. 3, no. 1, pp. 75-84, 2002.
, “Drosophila Apc1 and Apc2 regulate Wingless transduction throughout development.”, Development, vol. 129, no. 7, pp. 1751-62, 2002.
, “Establishment of developmental precision and proportions in the early Drosophila embryo.”, Nature, vol. 415, no. 6873, pp. 798-802, 2002.
, “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.
, “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.
, “The Snail repressor positions Notch signaling in the Drosophila embryo.”, Development, vol. 129, no. 7, pp. 1785-93, 2002.
, “Tail morphogenesis in the ascidian, Ciona intestinalis, requires cooperation between notochord and muscle.”, Dev Biol, vol. 244, no. 2, pp. 385-95, 2002.
, “Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo.”, Cell, vol. 111, no. 5, pp. 687-701, 2002.
, “Optimizing the detection of nascent transcripts by RNA fluorescence in situ hybridization.”, Nucleic Acids Res, vol. 29, no. 8, pp. E42-2, 2001.
, “The Dlk1 and Gtl2 genes are linked and reciprocally imprinted.”, Genes Dev, vol. 14, no. 16, pp. 1997-2002, 2000.
, “Dosage requirement and allelic expression of PAX6 during lens placode formation.”, Development, vol. 127, no. 24, pp. 5439-48, 2000.
, “Expression and functional analysis of Uch-L3 during mouse development.”, Mol Cell Biol, vol. 20, no. 7, pp. 2498-504, 2000.
, “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.
, “The Drosophila gene brinker reveals a novel mechanism of Dpp target gene regulation.”, Cell, vol. 96, no. 4, pp. 563-73, 1999.
, “The sins of the fathers and mothers: genomic imprinting in mammalian development.”, Cell, vol. 96, no. 2, pp. 185-93, 1999.
, “The temporal requirement for endothelin receptor-B signalling during neural crest development.”, Nature, vol. 402, no. 6761, pp. 496-501, 1999.
, “Chromatin conformation of the H19 epigenetic mark.”, Hum Mol Genet, vol. 7, no. 12, pp. 1979-85, 1998.
, “Hyperactivation of the folded gastrulation pathway induces specific cell shape changes.”, Development, vol. 125, no. 4, pp. 589-97, 1998.
, “Probing for gene specificity in epithelial development.”, Int J Dev Biol, vol. 42, no. 3, pp. 249-55, 1998.
, “Regulation of armadillo by a Drosophila APC inhibits neuronal apoptosis during retinal development.”, Cell, vol. 93, no. 7, pp. 1171-82, 1998.
, “Integration of the head and trunk segmentation systems controls cephalic furrow formation in Drosophila.”, Development, vol. 124, no. 19, pp. 3747-54, 1997.
, “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.
, “Embryonic transcription and the control of developmental pathways.”, Genetics, vol. 142, no. 1, pp. 5-10, 1996.
, “An enhancer deletion affects both H19 and Igf2 expression.”, Genes Dev, vol. 9, no. 17, pp. 2079-89, 1995.
, “Quantitative trait loci that modify the severity of spotting in piebald mice.”, Genome Res, vol. 5, no. 1, pp. 29-41, 1995.
,