Computational Models for Neurogenic Gene Expression in the Drosophila Embryo

[1]  P. V. von Hippel,et al.  Equilibrium and kinetic studies of Escherichia coli lac repressor-inducer interactions. , 1972, Journal of molecular biology.

[2]  G. Rubin,et al.  Genetic transformation of Drosophila with transposable element vectors. , 1982, Science.

[3]  G. K. Ackers,et al.  Quantitative model for gene regulation by lambda phage repressor. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Sean B. Carroll,et al.  The segmentation and homeotic gene network in early Drosophila development , 1987, Cell.

[5]  K. Yamamoto,et al.  Transcription factor interactions: selectors of positive or negative regulation from a single DNA element. , 1990, Science.

[6]  D Kosman,et al.  The dorsal morphogen gradient regulates the mesoderm determinant twist in early Drosophila embryos. , 1991, Genes & development.

[7]  M. Levine,et al.  The dorsal morphogen is a sequence-specific DNA-binding protein that interacts with a long-range repression element in drosophila , 1991, Cell.

[8]  M. Levine,et al.  The dorsal gradient morphogen regulates stripes of rhomboid expression in the presumptive neuroectoderm of the Drosophila embryo. , 1992, Genes & development.

[9]  Michael Levine,et al.  Binding affinities and cooperative interactions with bHLH activators delimit threshold responses to the dorsal gradient morphogen , 1993, Cell.

[10]  M. Levine,et al.  Interactions between dorsal and helix-loop-helix proteins initiate the differentiation of the embryonic mesoderm and neuroectoderm in Drosophila. , 1993, Genes & development.

[11]  P. Grassberger,et al.  On noise reduction methods for chaotic data. , 1993, Chaos.

[12]  M. Levine,et al.  The eve stripe 2 enhancer employs multiple modes of transcriptional synergy. , 1996, Development.

[13]  T. Maniatis,et al.  The mechanism of transcriptional synergy of an in vitro assembled interferon-beta enhanceosome. , 1997, Molecular cell.

[14]  J. Inoue,et al.  Multiple DNA elements for sterol regulatory element-binding protein and NF-Y are responsible for sterol-regulated transcription of the genes for human 3-hydroxy-3-methylglutaryl coenzyme A synthase and squalene synthase. , 1998, Journal of biochemistry.

[15]  A. Arkin,et al.  Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. , 1998, Genetics.

[16]  G. Odell,et al.  The segment polarity network is a robust developmental module , 2000, Nature.

[17]  John Reinitz,et al.  Registration of the expression patterns of Drosophila segmentation genes by two independent methods , 2001, Bioinform..

[18]  M. Baylies,et al.  Dimerization partners determine the activity of the Twist bHLH protein during Drosophila mesoderm development. , 2001, Development.

[19]  F. Netter,et al.  Supplemental References , 2002, We Came Naked and Barefoot.

[20]  M. Levine,et al.  Whole-genome expression profiles identify gene batteries in Drosophila. , 2002, Developmental cell.

[21]  G. Karsenty,et al.  Physical Interaction of the Activator Protein-1 Factors c-Fos and c-Jun with Cbfa1 for Collagenase-3 Promoter Activation* , 2002, The Journal of Biological Chemistry.

[22]  Michael Levine,et al.  Whole-Genome Analysis of Dorsal-Ventral Patterning in the Drosophila Embryo , 2002, Cell.

[23]  Alexander E. Kel,et al.  Composition-sensitive analysis of the human genome for regulatory signals , 2003, Silico Biol..

[24]  Anna G. Nazina,et al.  Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. , 2003, Nucleic acids research.

[25]  David H. Sharp,et al.  Transcriptional Control in Drosophila , 2003, Complexus.

[26]  E. Davidson,et al.  Transcriptional regulatory cascades in development: Initial rates, not steady state, determine network kinetics , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[27]  J. Fak,et al.  Transcriptional Control in the Segmentation Gene Network of Drosophila , 2004, PLoS biology.

[28]  A. Sandelin,et al.  Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. , 2004, Journal of molecular biology.

[29]  Peter W. Markstein,et al.  A regulatory code for neurogenic gene expression in the Drosophila embryo , 2004, Development.

[30]  David H. Sharp,et al.  Dynamical Analysis of Regulatory Interactions in the Gap Gene System of Drosophila melanogaster , 2004, Genetics.

[31]  William McGinnis,et al.  Multiplex Detection of RNA Expression in Drosophila Embryos , 2004, Science.

[32]  R. Laubenbacher,et al.  A computational algebra approach to the reverse engineering of gene regulatory networks. , 2003, Journal of theoretical biology.

[33]  David H. Sharp,et al.  Dynamic control of positional information in the early Drosophila embryo , 2004, Nature.

[34]  L. Mirny,et al.  Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. , 2004, Biophysical journal.

[35]  Michael Levine,et al.  Coordinate enhancers share common organizational features in the Drosophila genome. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[36]  M. Levine,et al.  Immunity regulatory DNAs share common organizational features in Drosophila. , 2004, Molecular cell.

[37]  Casey M. Bergman,et al.  Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster , 2005, Bioinform..

[38]  D. Court,et al.  Switches in bacteriophage lambda development. , 2005, Annual review of genetics.

[39]  M. Caudy,et al.  A DNA Transcription Code for Cell-Specific Gene Activation by Notch Signaling , 2005, Current Biology.

[40]  D. Arnosti,et al.  Functional Interaction between the Drosophila Knirps Short Range Transcriptional Repressor and RPD3 Histone Deacetylase* , 2005, Journal of Biological Chemistry.

[41]  John Reinitz,et al.  Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[42]  Stanislav Y Shvartsman,et al.  Computational analysis of EGFR inhibition by Argos. , 2005, Developmental biology.

[43]  Dmitri Papatsenko,et al.  Computational identification of regulatory DNAs underlying animal development , 2005, Nature Methods.

[44]  E. Davidson,et al.  Gene regulatory networks for development. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[45]  M. Levine,et al.  Genomic regulatory networks and animal development. , 2005, Developmental cell.

[46]  B. Jovanovic,et al.  Quantitative Methods of Analysis of Footprinting Diagrams for the Complexes Formed by a Ligand with a DNA Fragment of Known Sequence , 2005, Annals of the New York Academy of Sciences.

[47]  N. Dostatni,et al.  Bicoid Determines Sharp and Precise Target Gene Expression in the Drosophila Embryo , 2005, Current Biology.

[48]  S. Leibler,et al.  Precise domain specification in the developing Drosophila embryo. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[49]  David N. Arnosti,et al.  cis-Regulatory Logic of Short-Range Transcriptional Repression in Drosophila melanogaster , 2005, Molecular and Cellular Biology.

[50]  Dmitri Papatsenko,et al.  Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Sorin Istrail,et al.  Logic Functions of the Genomic Cis-regulatory Code , 2005, UC.

[52]  John Reinitz,et al.  Removal of background signal from in situ data on the expression of segmentation genes in Drosophila , 2005, Development Genes and Evolution.

[53]  Mark Ptashne,et al.  Regulation of transcription: from lambda to eukaryotes. , 2005, Trends in biochemical sciences.

[54]  A. Dean On a chromosome far, far away: LCRs and gene expression. , 2006, Trends in genetics : TIG.