Comparative Genomics of Transcription Factor Binding in Drosophila

[1]  S. Russell,et al.  Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila , 2014, bioRxiv.

[2]  S. Russell,et al.  SoxNeuro orchestrates central nervous system specification and differentiation in Drosophila and is only partially redundant with Dichaete , 2014, Genome Biology.

[3]  D. Odom,et al.  Evolution of transcription factor binding in metazoans — mechanisms and functional implications , 2014, Nature Reviews Genetics.

[4]  Eleni G. Christodoulou,et al.  Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data , 2013, PLoS Comput. Biol..

[5]  Jie Zhang,et al.  Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data , 2013, PLoS Comput. Biol..

[6]  L. Stein,et al.  Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE , 2013, BMC Genomics.

[7]  Tony D. Southall,et al.  Cell-Type-Specific Profiling of Gene Expression and Chromatin Binding without Cell Isolation: Assaying RNA Pol II Occupancy in Neural Stem Cells , 2013, Developmental cell.

[8]  N. Gompel,et al.  Emergence and Diversification of Fly Pigmentation Through Evolution of a Gene Regulatory Module , 2013, Science.

[9]  Michael B. Eisen,et al.  Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression Permalink , 2013 .

[10]  Łukasz M. Boryń,et al.  Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq , 2013, Science.

[11]  James B. Brown,et al.  DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila , 2012, Proceedings of the National Academy of Sciences.

[12]  András Aszódi,et al.  MULTOVL: fast multiple overlaps of genomic regions , 2012, Bioinform..

[13]  D. Stern,et al.  Conserved regulatory architecture underlies parallel genetic changes and convergent phenotypic evolution , 2012, Proceedings of the National Academy of Sciences.

[14]  Sebastian M. Waszak,et al.  Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster , 2012, PLoS genetics.

[15]  K. White,et al.  Adaptive Evolution and the Birth of CTCF Binding Sites in the Drosophila Genome , 2012, PLoS biology.

[16]  V. Corces,et al.  The BEAF-32 insulator coordinates genome organization and function during the evolution of Drosophila species , 2012, Genome research.

[17]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[18]  Shane J. Neph,et al.  An expansive human regulatory lexicon encoded in transcription factor footprints , 2012, Nature.

[19]  Marc D. Perry,et al.  ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia , 2012, Genome research.

[20]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[21]  Rahul Satija,et al.  The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo. , 2012, Genome research.

[22]  Michael D. Wilson,et al.  Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages , 2012, Cell.

[23]  I. Ruvinsky,et al.  Tempo and Mode in Evolution of Transcriptional Regulation , 2012, PLoS genetics.

[24]  J. Zeitlinger,et al.  A computational pipeline for comparative ChIP-seq analyses , 2011, Nature Protocols.

[25]  M. Halfon,et al.  Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules , 2011, BMC Genomics.

[26]  Sergio Contrino,et al.  modMine: flexible access to modENCODE data , 2011, Nucleic Acids Res..

[27]  M. Biggin.  Animal transcription networks as highly connected, quantitative continua. , 2011, Developmental cell.

[28]  Michael B. Eisen,et al.  Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition , 2011, PLoS genetics.

[29]  Manuel Serrano,et al.  Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes , 2011, Nature Structural &Molecular Biology.

[30]  J. Zeitlinger,et al.  High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species , 2011, Nature Genetics.

[31]  J. Stamatoyannopoulos,et al.  The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding , 2011, Genome Biology.

[32]  S. Russell,et al.  Genome-Wide Analysis of the Binding of the Hox Protein Ultrabithorax and the Hox Cofactor Homothorax in Drosophila , 2011, PloS one.

[33]  J. Stamatoyannopoulos,et al.  Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development , 2011, PLoS genetics.

[34]  Uwe Ohler,et al.  Modeling the Evolution of Regulatory Elements by Simultaneous Detection and Alignment with Phylogenetic Pair HMMs , 2010, PLoS Comput. Biol..

[35]  Gos Micklem,et al.  Supporting Online Material Materials and Methods Figs. S1 to S50 Tables S1 to S18 References Identification of Functional Elements and Regulatory Circuits by Drosophila Modencode , 2022 .

[36]  P. Wittkopp,et al.  Nomadic Enhancers: Tissue-Specific cis-Regulatory Elements of yellow Have Divergent Genomic Positions among Drosophila Species , 2010, PLoS genetics.

[37]  Steven M. Gallo,et al.  REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila , 2010, Nucleic Acids Res..

[38]  Mary Goldman,et al.  The UCSC Genome Browser database: update 2011 , 2010, Nucleic Acids Res..

[39]  G. Bourque,et al.  Transposable elements have rewired the core regulatory network of human embryonic stem cells , 2010, Nature Genetics.

[40]  Michael D. Wilson,et al.  Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding , 2010, Science.

[41]  Lior Pachter,et al.  Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species , 2010, PLoS biology.

[42]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[43]  Christopher D. Brown,et al.  A Comprehensive Map of Insulator Elements for the Drosophila Genome , 2010, PLoS genetics.

[44]  Alexander Stark,et al.  Comparative Genomics of Gene Regulation—conservation and Divergence of Cis-regulatory Information This Review Comes from a Themed Issue on Genomes and Evolution Edited Main Text Conflict of Interest , 2022 .

[45]  S. Russell,et al.  ChIPing away at the genome: the new frontier travel guide. , 2009, Molecular bioSystems.

[46]  E. Furlong,et al.  Combinatorial binding predicts spatio-temporal cis-regulatory activity , 2009, Nature.

[47]  James B. Brown,et al.  Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions , 2009, Genome Biology.

[48]  V. Corces,et al.  CTCF: Master Weaver of the Genome , 2009, Cell.

[49]  Saurabh Sinha,et al.  Evolution of Regulatory Sequences in 12 Drosophila Species , 2009, PLoS genetics.

[50]  Michael B. Eisen,et al.  A Careful Look at Binding Site Reorganization in the even-skipped Enhancers of Drosophila and Sepsids , 2008, PLoS genetics.

[51]  Venky N. Iyer,et al.  Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation , 2008, PLoS genetics.

[52]  Manolis Kellis,et al.  Reliable prediction of regulator targets using 12 Drosophila genomes. , 2007, Genome research.

[53]  Obi L. Griffith,et al.  ORegAnno: an open-access community-driven resource for regulatory annotation , 2007, Nucleic Acids Res..

[54]  Colin N. Dewey,et al.  Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures , 2007, Nature.

[55]  Melanie A. Huntley,et al.  Evolution of genes and genomes on the Drosophila phylogeny , 2007, Nature.

[56]  Robert A. H. White,et al.  The Drosophila insulator proteins CTCF and CP190 link enhancer blocking to body patterning , 2007, The EMBO journal.

[57]  Xin He,et al.  MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules , 2007, PLoS Comput. Biol..

[58]  Bas van Steensel,et al.  Detection of in vivo protein–DNA interactions using DamID in mammalian cells , 2007, Nature Protocols.

[59]  G. Wray.  The evolutionary significance of cis-regulatory mutations , 2007, Nature Reviews Genetics.

[60]  David A. Nix,et al.  Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila , 2006, PLoS Comput. Biol..

[61]  Sarah A. Teichmann,et al.  FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster , 2006, Bioinform..

[62]  Michele P Calos,et al.  Construction of transgenic Drosophila by using the site-specific integrase from phage phiC31. , 2004, Genetics.

[63]  William McGinnis,et al.  Evolution of transcription factor function. , 2003, Current opinion in genetics & development.

[64]  Anna G. Nazina,et al.  Homotypic regulatory clusters in Drosophila. , 2003, Genome research.

[65]  Steven Henikoff,et al.  Chromatin profiling using targeted DNA adenine methyltransferase , 2001, Nature Genetics.

[66]  E. Wimmer,et al.  A versatile vector set for animal transgenesis , 2000, Development Genes and Evolution.

[67]  B. van Steensel,et al.  DamID: mapping of in vivo protein-genome interactions using tethered DNA adenine methyltransferase. , 2006, Methods in enzymology.