Searching for regulatory elements in human noncoding sequences.

[1]  Cary Queen,et al.  Improvements to a program for DNA analysis: a procedure to find homologies among many sequences , 1982, Nucleic Acids Res..

[2]  M. Waterman,et al.  Pattern recognition in several sequences: consensus and alignment. , 1984, Bulletin of mathematical biology.

[3]  Wen-Hsiung Li,et al.  Evolution of DNA Sequences , 1985 .

[4]  M. Nei Molecular Evolutionary Genetics , 1987 .

[5]  B. Paterson,et al.  A 40-base-pair sequence in the 3' end of the beta-actin gene regulates beta-actin mRNA transcription during myogenesis. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[6]  M. Goodman,et al.  Embryonic ε and γ globin genes of a prosimian primate (Galago crassicaudatus): Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints , 1988 .

[7]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[8]  B. Moav,et al.  Functional analysis of elements affecting expression of the beta-actin gene of carp. , 1990, Molecular and cellular biology.

[9]  T R Tiersch,et al.  On the evolution of genome size of birds. , 1991, The Journal of heredity.

[10]  L. Hood,et al.  Model genomes: the benefits of analysing homologous human and mouse sequences. , 1992, Trends in biotechnology.

[11]  C Burks,et al.  The density of transcriptional elements in promoter and non-promoter sequences. , 1993, Human molecular genetics.

[12]  Jun S. Liu,et al.  Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. , 1993, Science.

[13]  L. Duret,et al.  Strong conservation of non-coding sequences during vertebrates evolution: potential involvement in post-transcriptional regulation of gene expression. , 1993, Nucleic acids research.

[14]  David Ghosh,et al.  Status of the transcription factors database (TFD) , 1993, Nucleic Acids Res..

[15]  R. Jackson,et al.  Cytoplasmic regulation of mRNA function: The importance of the 3′ untranslated region , 1993, Cell.

[16]  R. Singer,et al.  Sequences responsible for intracellular localization of beta-actin messenger RNA also affect cell phenotype , 1994, The Journal of cell biology.

[17]  M. Gouy,et al.  HOVERGEN: a database of homologous vertebrate genes. , 1994, Nucleic acids research.

[18]  D. S. Prestridge Predicting Pol II promoter sequences using transcription factor binding sites. , 1995, Journal of molecular biology.

[19]  E. Wingender,et al.  A compilation of composite regulatory elements affecting gene transcription in vertebrates. , 1995, Nucleic acids research.

[20]  Hanah Margalit,et al.  Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon , 1995, Comput. Appl. Biosci..

[21]  S. Brenner,et al.  Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Gary D. Stormo,et al.  MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices , 1995, Comput. Appl. Biosci..

[23]  Alexander E. Kel,et al.  Eukaryotic promoter recognition by binding sites for transcription factors , 1995, Comput. Appl. Biosci..

[24]  S Brunak,et al.  Analysis of eukaryotic promoter sequences reveals a systematically occurring CT-signal. , 1995, Nucleic acids research.

[25]  B. Koop,et al.  Human and rodent DNA sequence comparisons: a mosaic model of genomic evolution. , 1995, Trends in genetics : TIG.

[26]  T. Werner,et al.  MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. , 1995, Nucleic acids research.

[27]  A V Ulyanov,et al.  Multi-alphabet consensus algorithm for identification of low specificity protein-DNA interactions. , 1995, Nucleic acids research.

[28]  J. Fickett Quantitative Discrimination of MEF 2 Sites , 1995 .

[29]  Alexander E. Kel,et al.  Computer Tool FUNSITE for Analysis of Eukaryotic Regulatory Genomic Sequences , 1995, ISMB.

[30]  Richard S. Mann,et al.  Segmental expression of Hoxb-1 is controlled by a highly conserved autoregulatory loop dependent upon exd/pbx , 1995, Cell.

[31]  S. Brenner,et al.  Small is beautiful: comparative genomics with the pufferfish (Fugu rubripes). , 1996, Trends in genetics : TIG.

[32]  P. Bucher,et al.  Elf-1 and Stat5 bind to a critical element in a new enhancer of the human interleukin-2 receptor alpha gene , 1996, Molecular and cellular biology.

[33]  M. I. Lomax,et al.  Phylogenetic footprinting of the human cytochrome c oxidase subunit VB promoter. , 1996, Archives of biochemistry and biophysics.

[34]  S. Eddy Hidden Markov models. , 1996, Current opinion in structural biology.

[35]  K Frech,et al.  Common modular structure of lentivirus LTRs. , 1996, Virology.

[36]  M. Goodman,et al.  Evolutionary strategies for the elucidation of cis and trans factors that regulate the developmental switching programs of the beta-like globin genes. , 1996, Molecular phylogenetics and evolution.

[37]  S. Cross,et al.  CpG islands of chicken are concentrated on microchromosomes , 1996, Nature Genetics.

[38]  Analysis and Comparison of the Mouse and Human Immunoglobulin Heavy Chain JH–Cμ–Cδ Locus , 1996 .

[39]  J. Fickett Copyright � 1996, American Society for Microbiology Quantitative Discrimination of MEF2 Sites , 1995 .

[40]  J. Fickett Coordinate positioning of MEF2 and myogenin binding sites. , 1996, Gene.

[41]  Wei Zhu,et al.  Evolutionary Strategies for the Elucidation ofcisandtransFactors That Regulate the Developmental Switching Programs of the β-like Globin Genes , 1996 .

[42]  Grit Herrmann,et al.  Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm , 1996, Comput. Appl. Biosci..

[43]  G. B. Hutchinson,et al.  The prediction of vertebrate promoter regions using differential hexamer frequency analysis , 1996, Comput. Appl. Biosci..

[44]  Dan S. Prestridge,et al.  SIGNAL SCAN 4.0: additional databases and sequence formats , 1996, Comput. Appl. Biosci..

[45]  T. Werner,et al.  GenomeInspector: basic software tools for analysis of spatial correlations between genomic structures within megabase sequences. , 1996, Genomics.

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

[47]  J W Fickett,et al.  Finding genes by computer: the state of the art. , 1996, Trends in genetics : TIG.

[48]  Ying Xu,et al.  Detection of RNA Polymerase II Promoters and Polyadenylation Sites in Human DNA Sequence , 1996, Comput. Chem..

[49]  Pierre Baldi,et al.  Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models , 1996, ISMB.

[50]  P. Bucher,et al.  Elf-1 and Stat5 bind to a critical element in a new enhancer of the human interleukin-2 receptor alpha gene , 1997, Molecular and cellular biology.