Conservation and implications of eukaryote transcriptional regulatory regions across multiple species

[1]  J. Andrau,et al.  Genome-wide RNA polymerase II: not genes only! , 2008, Trends in biochemical sciences.

[2]  Paulo P. Amaral,et al.  The Eukaryotic Genome as an RNA Machine , 2008, Science.

[3]  Yvan Saeys,et al.  Generic eukaryotic core promoter prediction using structural features of DNA. , 2008, Genome research.

[4]  W. L. Ruzzo,et al.  Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions. , 2008, Genome research.

[5]  Guo-Cheng Yuan,et al.  Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion , 2007, PLoS Comput. Biol..

[6]  M. Teichmann,et al.  The expanding RNA polymerase III transcriptome. , 2007, Trends in genetics : TIG.

[7]  Stijn van Dongen,et al.  miRBase: tools for microRNA genomics , 2007, Nucleic Acids Res..

[8]  Ronald W. Davis,et al.  A high-resolution atlas of nucleosome occupancy in yeast , 2007, Nature Genetics.

[9]  Michael Q. Zhang.  Computational analyses of eukaryotic promoters , 2007, BMC Bioinformatics.

[10]  M. Gerstein,et al.  Structured RNAs in the ENCODE selected regions of the human genome. , 2007, Genome research.

[11]  T. Gingeras,et al.  Genome-wide transcription and the implications for genomic organization , 2007, Nature Reviews Genetics.

[12]  W. Miller,et al.  Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. , 2007, Genome research.

[13]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

[14]  Shaun Mahony,et al.  Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome , 2007, Genome biology.

[15]  Arcadi Navarro,et al.  Patterns and rates of intron divergence between humans and chimpanzees , 2007, Genome Biology.

[16]  Weixiong Zhang,et al.  Characterization and Identification of MicroRNA Core Promoters in Four Model Species , 2007, PLoS Comput. Biol..

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

[18]  Suresh Cuddapah,et al.  The genomic landscape of histone modifications in human T cells , 2006, Proceedings of the National Academy of Sciences.

[19]  Shane T. Jensen,et al.  MicroRNA promoter element discovery in Arabidopsis. , 2006, RNA.

[20]  W. Wong,et al.  Computational Biology: Toward Deciphering Gene Regulatory Information in Mammalian Genomes , 2006, Biometrics.

[21]  A. Levine,et al.  The P53 pathway: what questions remain to be explored? , 2006, Cell Death and Differentiation.

[22]  D. Lane,et al.  p53/p63/p73 isoforms: an orchestra of isoforms to harmonise cell differentiation and response to stress , 2006, Cell Death and Differentiation.

[23]  G. Sal,et al.  Some p53-binding proteins that can function as arbiters of life and death , 2006, Cell Death and Differentiation.

[24]  Martin S. Taylor,et al.  Genome-wide analysis of mammalian promoter architecture and evolution , 2006, Nature Genetics.

[25]  Z. Weng,et al.  A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome , 2006, Cell.

[26]  O. Borsani,et al.  Endogenous siRNAs Derived from a Pair of Natural cis-Antisense Transcripts Regulate Salt Tolerance in Arabidopsis , 2005, Cell.

[27]  Philipp Bucher,et al.  EPD in its twentieth year: towards complete promoter coverage of selected model organisms , 2005, Nucleic Acids Res..

[28]  R. Myers,et al.  Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. , 2005, Genome research.

[29]  David P Lane,et al.  p53 isoforms can regulate p53 transcriptional activity. , 2005, Genes & development.

[30]  S. Batalov,et al.  Antisense Transcription in the Mammalian Transcriptome , 2005, Science.

[31]  S. Salzberg,et al.  The Transcriptional Landscape of the Mammalian Genome , 2005, Science.

[32]  Megan F. Cole,et al.  Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast , 2005, Cell.

[33]  Leah Barrera,et al.  A high-resolution map of active promoters in the human genome , 2005, Nature.

[34]  Jun Wang,et al.  Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture , 2005, Genome Biology.

[35]  Jun S. Liu,et al.  De novo cis-regulatory module elicitation for eukaryotic genomes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[36]  William Stafford Noble,et al.  Assessing computational tools for the discovery of transcription factor binding sites , 2005, Nature Biotechnology.

[37]  B. Cullen,et al.  Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. , 2004, RNA.

[38]  Reuven Agami,et al.  Inhibition of oncogenic transformation by mammalian Lin‐9, a pRB‐associated protein , 2004, The EMBO journal.

[39]  Sanghyuk Lee,et al.  MicroRNA genes are transcribed by RNA polymerase II , 2004, The EMBO journal.

[40]  Jun S. Liu,et al.  Decoding human regulatory circuits. , 2004, Genome research.

[41]  W. Wong,et al.  CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[42]  S. Harris,et al.  Gene structure and molecular analysis of Arabidopsis thaliana ALWAYS EARLY homologs. , 2004, Gene.

[43]  Xiao-Tu Ma,et al.  Predicting polymerase II core promoters by cooperating transcription factor binding sites in eukaryotic genes. , 2004, Acta biochimica et biophysica Sinica.

[44]  D. Landsman,et al.  Statistical analysis of over-represented words in human promoter sequences. , 2004, Nucleic acids research.

[45]  Ben Lehner,et al.  In search of antisense. , 2004, Trends in biochemical sciences.

[46]  Lu Wang,et al.  Last intron of the chemokine-like factor gene contains a putative promoter for the downstream CKLF super family member 1 gene. , 2004, Biochemical and biophysical research communications.

[47]  Joseph M. Dale,et al.  Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome , 2003, Science.

[48]  R. Tjian,et al.  Transcription regulation and animal diversity , 2003, Nature.

[49]  Saurabh Sinha,et al.  A probabilistic method to detect regulatory modules , 2003, ISMB.

[50]  Jacques van Helden,et al.  Regulatory Sequence Analysis Tools , 2003, Nucleic Acids Res..

[51]  R. Myers,et al.  Identification and functional analysis of human transcriptional promoters. , 2003, Genome research.

[52]  Michael Q. Zhang.  Computational prediction of eukaryotic protein-coding genes , 2002, Nature Reviews Genetics.

[53]  J. Ott,et al.  The p53MH algorithm and its application in detecting p53-responsive genes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[54]  T. Hubbard,et al.  Computational detection and location of transcription start sites in mammalian genomic DNA. , 2002, Genome research.

[55]  Martin C. Frith,et al.  Detection of cis -element clusters in higher eukaryotic DNA , 2001, Bioinform..

[56]  J. Levine,et al.  Surfing the p53 network , 2000, Nature.

[57]  H. Horvitz,et al.  The C. elegans gene lin-9,which acts in an Rb-related pathway, is required for gonadal sheath cell development and encodes a novel protein. , 2000, Gene.

[58]  D. Schübeler,et al.  Stabilized, long-term expression of heterodimeric proteins from tricistronic mRNA. , 2000, Gene.

[59]  J. Fickett,et al.  Identification of regulatory regions which confer muscle-specific gene expression. , 1998, Journal of molecular biology.

[60]  J. Oliver,et al.  Sequence Compositional Complexity of DNA through an Entropic Segmentation Method , 1998 .

[61]  A. Wagner,et al.  A computational genomics approach to the identification of gene networks. , 1997, Nucleic acids research.

[62]  T Lagrange,et al.  The general transcription factors of RNA polymerase II. , 1996, Genes & development.

[63]  B. Barrell,et al.  Life with 6000 Genes , 1996, Science.

[64]  H E Stanley,et al.  Linguistic features of noncoding DNA sequences. , 1994, Physical review letters.

[65]  T. Komari,et al.  Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. , 1994, The Plant journal : for cell and molecular biology.

[66]  M. Bevan,et al.  GUS fusions: beta‐glucuronidase as a sensitive and versatile gene fusion marker in higher plants. , 1987, The EMBO journal.

[67]  Michael Q. Zhang,et al.  High-resolution human core-promoter prediction with CoreBoost_HM. , 2009, Genome research.

[68]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[69]  J. Mattick,et al.  The human genome as an RNA machine , 2007 .

[70]  John M. Walker,et al.  C. elegans , 2006, Methods in Molecular Biology.

[71]  Xiaoqiu Huang,et al.  Over 20% of human transcripts might form sense-antisense pairs. , 2004, Nucleic acids research.

[72]  Michael Ruogu Zhang,et al.  Computational identification of promoters and first exons in the human genome , 2002, Nature Genetics.

[73]  Philipp Bucher,et al.  The Eukaryotic Promoter Database (EPD) , 2000, Nucleic Acids Res..

[74]  Gary D. Stormo,et al.  DNA binding sites: representation and discovery , 2000, Bioinform..

[75]  Terence P. Speed,et al.  Over- and Underrepresentation of Short DNA Words in Herpesvirus Genomes , 1996, J. Comput. Biol..

[76]  Michael Q. Zhang,et al.  Molecular Systems Biology 3; Article number 73; doi:10.1038/msb4100114 Citation: Molecular Systems Biology 3:73 , 2022 .