A regulatory code for neurogenic gene expression in the Drosophila embryo

Markstein, Michele, Zinzen, Robert, Markstein, Peter, Yee, Ka-Ping, Erives, Albert, Stathopoulos, Angela, Levine, Michael·2004·Development

Cited by (164)

Items 101–164 of 164

  1. Microfluidics for High-Throughput Quantitative Studies of Early Development
    Thomas J. Levario, Bomyi Lim, Stanislav Y. Shvartsman, Hang Lu · 2016 · Annual Review of Biomedical Engineering
  2. Identification of Ind transcription activation and repression domains required for dorsoventral patterning of the CNS
    Tonia L. Von Ohlen, Cade Moses · 2009 · Mechanisms of Development
  3. BMP-dependent gene repression cascade in Drosophila eggshell patterning
    Enrica Charbonnier, Alisa Fuchs, Lily S. Cheung, Mrinal Chayengia, Ville Veikkolainen, Janine Seyfferth, Stanislav Y. Shvartsman, George Pyrowolakis · 2015 · Developmental Biology
  4. Enhancer diversity and the control of a simple pattern of Drosophila CNS midline cell expression
    Joseph C. Pearson, Stephen T. Crews · 2014 · Developmental Biology
  5. Ancestral and conserved cis-regulatory architectures in developmental control genes
    Mark Rebeiz, Brian Castro, Feng Liu, Feng Yue, James W. Posakony · 2011 · Developmental Biology
  6. Divergent MLS1 Promoters Lie on a Fitness Plateau for Gene Expression
    Andrew C. Bergen, Gerilyn M. Olsen, Justin C. Fay · 2016 · Molecular Biology and Evolution
  7. Identification of an upstream regulatory element reveals a novel requirement for Ind activity in maintaining ind expression
    Tonia L. Von Ohlen, Canda Harvey, Manasa Panda · 2006 · Mechanisms of Development
  8. The Nature, Extent, and Consequences of Genetic Variation in the opa Repeats of Notch in Drosophila
    Clinton Rice, D. Beekman, Li-Ping Liu, Albert J. Erives · 2015 · G3: Genes, Genomes, Genetics
  9. Deciphering deuterostome phylogeny: molecular, morphological, and palaeontological perspectives
    Andrew Benjamin Smith, Billie J. Swalla · 2009 · Oxford University Press eBooks
  10. The evolution of nervous system centralization
    Detlev Arendt, Alexandru Stefan Denes, Gáspár Jékely, Kristin Tessmar‐Raible · 2009 · Oxford University Press eBooks
  11. The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records
    Kevin J. Peterson, James Anthony Cotton, James G. Gehlîng, Davide Pisani · 2009 · Oxford University Press eBooks
  12. Involvement of co-repressors Groucho and CtBP in the regulation of single-minded in Drosophila
    Anja C. Nagel, Irmgard Wech, Daniela Schwinkendorf, Anette Preiss · 2007 · Hereditas
  13. Invertebrate Problematica: kinds, causes, and solutions
    Ronald A. Jenner, Dallen J. Timothy, D. Timothy J. Littlewood · 2009 · Oxford University Press eBooks
  14. Computational Methods for Locating and Analyzing Conserved Gene Regulatory DNA Elements
    Kimmo Palin · 2007 · Työväentutkimus Vuosikirja
  15. Zelda potentiates transcription factor binding to zygotic enhancers by increasing local chromatin accessibility during early Drosophila melanogaster embryogenesis
    Xiaoyong Li, Michael B. Eisen · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  16. Genetic regulation and function of epidermal growth factor receptor signalling in patterning of the embryonicDrosophilabrain
    David Jussen, Janina von Hilchen, Rolf Urbach · 2016 · Open Biology
  17. Integration of Orthogonal Signaling by the Notch and Dpp Pathways in Drosophila
    Elizabeth Stroebele, Albert J. Erives · 2016 · Genetics
  18. Twine: display and analysis of cis-regulatory modules
    Joseph C. Pearson, Stephen T. Crews · 2013 · Bioinformatics
  19. Conserved and novel enhancers in the Aedes aegypti single-minded locus recapitulate embryonic ventral midline gene expression
    Isabella Schember, William R Reid, Geyenna Sterling-Lentsch, Marc S. Halfon · 2024 · PLoS Genetics
  20. Making evolutionary predictions about the structure of development and morphology: beyond the neo-Darwinian and constraints paradigms
    Isaac Salazar‐Ciudad · 2008 · Cambridge University Press eBooks
  21. Ind represses msh expression in the intermediate column of the Drosophila neuroectoderm, through direct interaction with upstream regulatory DNA
    Tonia L. Von Ohlen, Cade Moses, Will Poulson · 2009 · Developmental Dynamics
  22. Animal Evolution
    2009
  23. The earliest fossil record of the animals and its significance
    Graham E. Budd · 2009 · Oxford University Press eBooks
  24. Enhancer architecture and chromatin accessibility constrain phenotypic space during development
    Rafael Galupa, Gilberto Álvarez-Canales, Noa Ottilie Borst, Timothy Fuqua, Lautaro Gándara, Natalia Misunou, Kerstin Richter, Mariana R. P. Alves, Esther Karumbi, Melinda Liu Perkins et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  25. Mesodermal repression of single-minded in Drosophila embryo is mediated by a cluster of Snail-binding sites proximal to the early promoter
    Kye Won Park, Joung‐Woo Hong · 2012 · BMB Reports
  26. Fitting structure to function in gene regulatory networks
    Ellen V. Rothenberg · 2017 · History & Philosophy of the Life Sciences
  27. The evolution of developmental gene networks: lessons from comparative studies on holometabolous insects
    Andrew Peel · 2009 · Oxford University Press eBooks
  28. Discovery and information-theoretic characterization of transcription factor binding sites that act cooperatively
    Jacob Clifford, Christoph Adami · 2015 · Physical Biology
  29. c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression
    Katerina J. Kechris, Hao Li · 2008 · BMC Bioinformatics
  30. The origins and evolution of the Ecdysozoa
    Maximilian J. Telford, Sarah J. Bourlat, Andrew D. Economou, Daniel Papillon, Omar Rota‐Stabelli · 2009 · Oxford University Press eBooks
  31. Origins of metazoan body plans: the larval revolution
    Rudolf A. Raff · 2009 · Oxford University Press eBooks
  32. Reassembling animal evolution: a four-dimensional puzzle
    Maximilian J. Telford, Dallen J. Timothy, D. Timothy J. Littlewood · 2009 · Oxford University Press eBooks
  33. Conserved developmental processes and the evolution of novel traits: wounds, embryos, veins, and butterfly eyespots
    Patrícia Beldade, Suzanne V. Saenko · 2009 · Oxford University Press eBooks
  34. Sequence Analyses to Study the Evolutionary History and Cis-Regulatory Elements of Hedgehog Genes
    Ferenc Müller, Anne‐Gaëlle Borycki · 2007 · Methods in molecular biology
  35. Spatial-scERA: a method for reconstructing spatial single-cell enhancer activity in multicellular organisms
    Baptiste Alberti, Séverine Vincent, Isabelle Stévant, Damien Lajoignie, Hélène Tarayre, Juliette Mendes, Sergio Sarnataro, Paul Villoutreix, Yad Ghavi-Helm · 2025 · Nucleic Acids Research
  36. Target gene responses differ when transcription factor levels are acutely decreased by nuclear export versus degradation
    James M. McGehee, Angelike Stathopoulos · 2024 · Development
  37. Identification and characterization of conserved regulatory elements by comparative genomics
    Krish Jon Mathavan · 2008 · National University of Singapore
  38. Genomic dimensions of Su(H)-targeted regulatory belts in Drosophila
    Elizabeth Stroebele, Timothy Fuqua, Melvyn Warren, Danielle K. Herrig, Christian Noblett, Xin Yuan, Albert J. Erives · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
  39. Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction
    Jeffrey L. Boore, Susan I. Fuerstenberg · 2009 · Oxford University Press eBooks
  40. The Sheep and the Goats: Distinguishing transcriptional enhancers in a complex chromatin landscape
    Anne Sonnenschein, Ian M. Dworkin, David N. Arnosti · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  41. The animal in the genome: comparative genomics and evolution
    Richard R. Copley · 2009 · Oxford University Press eBooks
  42. Zur Entwicklung des Nervensystems: Wandernde Zellen, Zielfindung und Selbstorganisation bei der Synapsenbildung
    Werner A. Müller, Monika Hassel · 2003 · Springer-Lehrbuch
  43. Discrimination in partnership: compartment-specific interactions of Hox proteins
    K. G. Guruharsha, Krishnaswamy VijayRaghavan · 2004 · Journal of Genetics
  44. Identification of downstream targets of Alk signaling in Drosophila melanogaster
    Gaurav K. Varshney · 2008 · KTH Publication Database DiVA (KTH Royal Institute of Technology)
  45. Dorsal-Ventral Patterning and Gene Regulation in the Early Embryo of Drosophila melanogaster
    Mayra García · 2012
  46. Thinking about evolution by taking development on board
    Alessandro Minelli · 2008 · Cambridge University Press eBooks
  47. Analysis of Cooperative Transcription Factor Binding at the Sequence Level
    Jacob Clifford · 2015 · Michigan State University Libraries
  48. Computational Methods for Inferring Transcription Factor Binding Sites
    Vyacheslav Morozov · 2012 · uO Research (University of Ottawa)
  49. Chromatin Topology and Transcription in Myogenesis
    Katherine I. Fisher-Aylor · 2016 · CaltechTHESIS (California Institute of Technology)
  50. Unbiased genome-scale identification of cis -regulatory modules in the human genome by GRAMc
    Catherine L. Guay, Jongmin Nam · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  51. Shadow Enhancers Provide Precision and Robustness for the Patterning of the Precellular Drosophila Embryo
    Michael Perry · 2011 · eScholarship (California Digital Library)
  52. 2. Mise en place du plan d’organisation de la drosophile
    Lewis Wolpert, C. Tickle, Alfonso Martinez Arias, P. Lawrence, A. Lumsden, Elizabeth Robertson, Jim C. Smith · 2017 · Biologie du développement
  53. Zur Entwicklung des Nervensystems: wandernde Zellen, Zielfindung und Selbstorganisation bei der Synapsenbildung
    2006 · Springer eBooks
  54. Molecular genetic insights into deuterostome evolution from the direct-developing hemichordateSaccoglossus kowalevskii
    Christopher J. Lowe · 2009 · Oxford University Press eBooks
  55. REFERENCES
    2006 · Elsevier eBooks
  56. Foreword
    2009 · Oxford University Press eBooks
  57. Copyright Page
    2009 · Oxford University Press eBooks
  58. Contributors
    2009 · Oxford University Press eBooks
  59. Introduction
    2009 · Oxford University Press eBooks
  60. Transcriptional Regulatory Activity as the Default State for DNA in Animal Development
    Rafael Galupa, Gilberto Álvarez-Canales, Noa Ottilie Borst, Timothy Fuqua, Lautaro Gándara, Natalia Misunou, Kerstin Richter, Mariana R. P. Alves, Esther Karumbi, Melinda Liu Perkins et al. · 2022 · SSRN Electronic Journal
  61. Inferring chromatin architecture at a single locus through probabilistic in situ DNA localization
    Minh Tam Le, James M. McGehee, Leslie Dunipace, David Rumph, Angelike Stathopoulos · 2026 · Nature Communications
  62. Identification à l'échelle génomique des éléments cis-régulateurs actifs au cours du développement des ascidies
    Mathieu Gineste · 2013
  63. An asymmetric Ising model for spatial gene regulation
    Mélody Merle · 2019
  64. GENOMIC APPROACHES TO IDENTIFYING TRANSCRIPTIONAL TARGETS OF AP-1, CREB AND JNK SIGNALING IN THE NERVOUS SYSTEM OF DROSOPHILA MELANOGASTER
    Paul D. Etter · 2005 · UA Campus Repository (The University of Arizona)