Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

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

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

[3]  Inanç Birol,et al.  Hive plots - rational approach to visualizing networks , 2012, Briefings Bioinform..

[4]  Richard S. Sandstrom,et al.  BEDOPS: high-performance genomic feature operations , 2012, Bioinform..

[5]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[6]  R. Mann,et al.  Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins , 2011, Cell.

[7]  Bryan Lajoie,et al.  Enhanced yeast one-hybrid (eY1H) assays for high-throughput gene-centered regulatory network mapping , 2011, Nature Methods.

[8]  Myong-Hee Sung,et al.  Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding. , 2011, Molecular cell.

[9]  Michele Magrane,et al.  UniProt Knowledgebase: a hub of integrated protein data , 2011, Database J. Biol. Databases Curation.

[10]  Trey Ideker,et al.  Cytoscape 2.8: new features for data integration and network visualization , 2010, Bioinform..

[11]  Raymond K. Auerbach,et al.  Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project , 2010, Science.

[12]  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 .

[13]  T. Mikkelsen,et al.  The NIH Roadmap Epigenomics Mapping Consortium , 2010, Nature Biotechnology.

[14]  Juan M. Vaquerizas,et al.  Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. , 2010, Genome research.

[15]  V. Kaartinen,et al.  Signaling via Alk5 controls the ontogeny of lung Clara cells , 2010, Development.

[16]  J. Uhm,et al.  The transcriptional network for mesenchymal transformation of brain tumours , 2010 .

[17]  T. Enver,et al.  Forcing cells to change lineages , 2009, Nature.

[18]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[19]  Daniel E. Newburger,et al.  Diversity and Complexity in DNA Recognition by Transcription Factors , 2009, Science.

[20]  Mikael Bodén,et al.  MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..

[21]  Juan M. Vaquerizas,et al.  A census of human transcription factors: function, expression and evolution , 2009, Nature Reviews Genetics.

[22]  William Stafford Noble,et al.  Global mapping of protein-DNA interactions in vivo by digital genomic footprinting , 2009, Nature Methods.

[23]  Martha L. Bulyk,et al.  UniPROBE: an online database of protein binding microarray data on protein–DNA interactions , 2008, Nucleic Acids Res..

[24]  Daniel E. Newburger,et al.  Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences , 2008, Cell.

[25]  T. Gulick,et al.  Myocyte Enhancer Factor 2A Is Transcriptionally Autoregulated* , 2008, Journal of Biological Chemistry.

[26]  S. Orkin,et al.  An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells , 2008, Cell.

[27]  Ole Winther,et al.  JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update , 2007, Nucleic Acids Res..

[28]  T. Ichisaka,et al.  Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors , 2007, Cell.

[29]  A. Mortazavi,et al.  Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.

[30]  Albertha J. M. Walhout,et al.  Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. , 2006, Genome research.

[31]  S. Yamanaka,et al.  Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors , 2006, Cell.

[32]  G. Swiers,et al.  Genetic regulatory networks programming hematopoietic stem cells and erythroid lineage specification. , 2006, Developmental biology.

[33]  Megan F. Cole,et al.  Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells , 2005, Cell.

[34]  Adam A. Margolin,et al.  Reverse engineering of regulatory networks in human B cells , 2005, Nature Genetics.

[35]  H. Spemann.  Über die Determination der ersten Organanlagen des Amphibienembryo I–VI , 1918, Archiv für Entwicklungsmechanik der Organismen.

[36]  S. Shen-Orr,et al.  Superfamilies of Evolved and Designed Networks , 2004, Science.

[37]  A. Barabasi,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[38]  William Stafford Noble,et al.  Matrix2png: a utility for visualizing matrix data , 2003, Bioinform..

[39]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[40]  Eric H Davidson,et al.  A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. , 2002, Developmental biology.

[41]  L. Hood,et al.  A Genomic Regulatory Network for Development , 2002, Science.

[42]  J. Burch,et al.  Modular regulation of cGATA-5 gene expression in the developing heart and gut. , 2000, Developmental biology.

[43]  S. Weiss,et al.  A role for the POU‐III transcription factor Brn‐4 in the regulation of striatal neuron precursor differentiation , 1999, The EMBO journal.

[44]  Stephen L. Nutt,et al.  Commitment to the B-lymphoid lineage depends on the transcription factor Pax5 , 1999, Nature.

[45]  S. Minucci,et al.  Fusion proteins of the retinoic acid receptor-α recruit histone deacetylase in promyelocytic leukaemia , 1998, Nature.

[46]  Alexander V. Spirov,et al.  Graphical interface to the genetic network database GeNet , 1998, Bioinform..

[47]  E. Olson,et al.  Requirement of the transcription factor GATA4 for heart tube formation and ventral morphogenesis. , 1997, Genes & development.

[48]  D. Lancet,et al.  GeneCards: integrating information about genes, proteins and diseases. , 1997, Trends in genetics : TIG.

[49]  B. Wold,et al.  Skeletal muscle determination and differentiation: story of a core regulatory network and its context. , 1996, Current opinion in cell biology.

[50]  Holger Karas,et al.  TRANSFAC: a database on transcription factors and their DNA binding sites , 1996, Nucleic Acids Res..

[51]  The molecular genetics of retinoic acid receptors: cardiovascular and limb development. , 1996, Biochemical Society symposium.

[52]  S. F. Konieczny,et al.  Myogenin and MEF2 function synergistically to activate the MRF4 promoter during myogenesis , 1995, Molecular and cellular biology.

[53]  Stuart H. Orkin,et al.  Transcription Factors and Hematopoietic Development (*) , 1995, The Journal of Biological Chemistry.

[54]  R. Britten,et al.  Complexity and organization of DNA-protein interactions in the 5′-regulatory region of an endoderm-specific marker gene in the sea urchin embryo , 1994, Mechanisms of Development.

[55]  Myriam Alcalay,et al.  The acute promyelocytic leukemia-specific PML-RARα fusion protein inhibits differentiation and promotes survival of myeloid precursor cells , 1993, Cell.

[56]  R. Pictet,et al.  In vivo footprinting of rat TAT gene: Dynamic interplay between the glucocorticoid receptor and a liver-specific factor , 1991, Cell.

[57]  A. Riggs,et al.  Chromatin differences between active and inactive X chromosomes revealed by genomic footprinting of permeabilized cells using DNase I and ligation-mediated PCR. , 1991, Genes & development.

[58]  Shih-Feng Tsai,et al.  Cloning of cDNA for the major DNA-binding protein of the erythroid lineage through expression in mammalian cells , 1989, Nature.

[59]  Robert Tjian,et al.  Isolation of cDNA encoding transcription factor Sp1 and functional analysis of the DNA binding domain , 1987, Cell.

[60]  S. Brenner,et al.  The structure of the nervous system of the nematode Caenorhabditis elegans. , 1986, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[61]  M. Karin,et al.  Characterization of DNA sequences through which cadmium and glucocorticoid hormones induce human metallothionein-IIA gene , 1984, Nature.

[62]  R. Tjian,et al.  The promoter-specific transcription factor Sp1 binds to upstream sequences in the SV40 early promoter , 1983, Cell.

[63]  Mark Groudine,et al.  Propagation of globin DNAase i-hypersensitive sites in absence of factors required for induction: A possible mechanism for determination , 1982, Cell.

[64]  Carl Wu.  The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I , 1980, Nature.

[65]  J. D. Engel,et al.  Tissue-specific DNA cleavages in the globin chromatin domain introduced by DNAase I , 1980, Cell.

[66]  P Chambon,et al.  DNA methylation: correlation with DNase I sensitivity of chicken ovalbumin and conalbumin chromatin. , 1979, Nucleic acids research.

[67]  Sarah C. R. Elgin,et al.  The chromatin structure of specific genes: I. Evidence for higher order domains of defined DNA sequence , 1979, Cell.

[68]  D. Galas,et al.  DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. , 1978, Nucleic acids research.

[69]  J. H. Ward.  Hierarchical Grouping to Optimize an Objective Function , 1963 .

[70]  C. Waddington,et al.  The strategy of the genes , 1957 .

[71]  C. Waddington.  Organisers and genes. , 1943 .

[72]  C. Waddington.  An Introduction to Modern Genetics , 1939 .

[73]  J. Haldane,et al.  “Introduction to Modern Genetics” , 1939, Nature.