Applied bioinformatics for the identification of regulatory elements

Initial sequencing and analysis of the human genome

2001 • 23,520 citations

A general method applicable to the search for similarities in the amino acid sequence of two proteins

1970 • 11,049 citations

Database resources of the National Center for Biotechnology Information: update

2003 • 10,877 citations

Initial sequencing and comparative analysis of the mouse genome

2002 • 6,971 citations

Molecular Biology of the Cell

2017 • 5,885 citations

The Genome Sequence of Drosophila melanogaster

2000 • 5,882 citations

The COG database: an updated version includes eukaryotes

2003 • 4,151 citations

Genome Sequence of the Nematode C. elegans : A Platform for Investigating Biology

1998 • 3,683 citations

CpG Islands in vertebrate genomes

1987 • 3,315 citations

Genome sequence of the nematode C-elegans: A platform for investigating biology

1998 • 3,265 citations

Sequence logos: a new way to display consensus sequences

1990 • 3,249 citations

TRANSFAC(R): transcriptional regulation, from patterns to profiles

2003 • 2,010 citations

The UCSC Genome Browser Database

2003 • 1,872 citations

JASPAR: an open-access database for eukaryotic transcription factor binding profiles

2003 • 1,718 citations

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

2002 • 1,612 citations

Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes

2002 • 1,560 citations

A Genomic Regulatory Network for Development

2002 • 1,538 citations

DNA binding sites: representation and discovery

2000 • 1,503 citations

Human–Mouse Alignments with BLASTZ

2002 • 1,254 citations

The Evolution of Transcriptional Regulation in Eukaryotes

2003 • 1,207 citations

Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences

1990 • 1,140 citations

LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA

2003 • 1,103 citations

MATCHTM: a tool for searching transcription factor binding sites in DNA sequences

2003 • 1,093 citations

Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

2003 • 828 citations

Selection of DNA binding sites by regulatory proteins

1987 • 761 citations

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

2003 • 721 citations

Genomic Regulatory Systems: Development and Evolution

2005 • 710 citations

Comparative analyses of multi-species sequences from targeted genomic regions

2003 • 637 citations

Insulators: many functions, many mechanisms

2002 • 635 citations

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome

2002 • 619 citations

The β-globin nuclear compartment in development and erythroid differentiation

2003 • 547 citations

Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome

2003 • 526 citations

AVID: A Global Alignment Program

2002 • 496 citations

Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Conservation and Turnover

2002 • 466 citations

Glocal alignment: finding rearrangements during alignment

2003 • 443 citations

<tt>rVista</tt>for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites

2002 • 442 citations

Structure, function and evolution of CpG island promoters

2003 • 425 citations

Computational identification of promoters and first exons in the human genome

2001 • 411 citations

Identification of regulatory regions which confer muscle-specific gene expression

1998 • 401 citations

Embryonic ε and γ globin genes of a prosimian primate (Galago crassicaudatus)

1988 • 368 citations

A sensitive method for the determination of protein-DNA binding specificities

1990 • 346 citations

Eukaryotic Promoter Recognition

1997 • 341 citations

Additivity in protein-DNA interactions: how good an approximation is it?

2002 • 341 citations

Cluster-Buster: finding dense clusters of motifs in DNA sequences

2003 • 319 citations

Computational Detection and Location of Transcription Start Sites in Mammalian Genomic DNA

2002 • 293 citations

Identification of conserved regulatory elements by comparative genome analysis.

2003 • 272 citations

Cross-Species Sequence Comparisons: A Review of Methods and Available Resources

2003 • 270 citations

Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes.

1995 • 257 citations

Ensembl 2002: accommodating comparative genomics

2003 • 246 citations

Comparative genomics: genome-wide analysis in metazoan eukaryotes

2003 • 236 citations

Quantifying DNA–protein interactions by double-stranded DNA arrays

1999 • 233 citations

Computational detection of genomic cis- regulatory modules applied to body patterning in the early Drosophila embryo

2002 • 231 citations

High-throughput SELEX–SAGE method for quantitative modeling of transcription-factor binding sites

2002 • 210 citations

A Predictive Model for Regulatory Sequences Directing Liver-Specific Transcription

2001 • 209 citations

Toucan: deciphering the cis-regulatory logic of coregulated genes

2003 • 200 citations

TFBS: Computational framework for transcription factor binding site analysis

2002 • 186 citations

Constrained Binding Site Diversity within Families of Transcription Factors Enhances Pattern Discovery Bioinformatics

2004 • 183 citations

DBTSS: DataBase of Transcriptional Start Sites progress report in 2012

2011 • 181 citations

Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome 1 1Edited by M. Gottesman

1997 • 180 citations

Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts

2002 • 175 citations

Homotypic Regulatory Clusters in Drosophila

2003 • 168 citations

Chromatin Insulators and Boundaries: Effects on Transcription and Nuclear Organization

2001 • 162 citations

Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity.

1999 • 155 citations

Evolutionary Conservation of Regulatory Elements in Vertebrate Hox Gene Clusters

2003 • 152 citations

Cross-Referencing Eukaryotic Genomes: TIGR Orthologous Gene Alignments (TOGA)

2002 • 151 citations

Distinguishing Regulatory DNA From Neutral Sites

2003 • 141 citations

Searching for statistically significant regulatory modules

2003 • 139 citations

Computational detection of cis -regulatory modules

2003 • 128 citations

PAINT: A Promoter Analysis and Interaction Network Generation Tool for Gene Regulatory Network Identification

2003 • 126 citations

Promoter prediction in the human genome

2001 • 125 citations

Origins and evolutionary diversification of the nuclear receptor superfamily

2000 • 122 citations

DBTSS, DataBase of Transcriptional Start Sites: progress report 2004

2003 • 122 citations

CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments

2003 • 114 citations

A novel myogenic regulatory circuit controls slow/cardiac troponin C gene transcription in skeletal muscle.

1994 • 113 citations

Quantitative Discrimination of MEF2 Sites

1996 • 112 citations

Identification of transcription factor binding sites in the human genome sequence

2002 • 111 citations

Quantitative prediction of NF-κB DNA– protein interactions

2002 • 104 citations

CONREAL: Conserved Regulatory Elements Anchored Alignment Algorithm for Identification of Transcription Factor Binding Sites by Phylogenetic Footprinting

2003 • 99 citations

The Eukaryotic Promoter Database EPD: the impact of in silico primer extension

2003 • 97 citations

Comparative Genomics of the SOX9 Region in Human and Fugu rubripes: Conservation of Short Regulatory Sequence Elements within Large Intergenic Regions

2001 • 97 citations

Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm

2003 • 85 citations

Coordinate positioning of MEF2 and myogenin binding sites

1996 • 74 citations

Genome Function and Nuclear Architecture: From Gene Expression to Nanoscience

2003 • 74 citations

Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites 1 1Edited by M. Yaniv

2000 • 68 citations

A non-parametric model for transcription factor binding sites

2003 • 66 citations

Consensus Promoter Identification in the Human Genome Utilizing Expressed Gene Markers and Gene Modeling

2002 • 66 citations

Comparative analysis of regulatory patterns in bacterial genomes

2000 • 64 citations

Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis

2001 • 62 citations

Using sequence logos and information analysis of Lrp DNA binding sites to investigate discrepancies between natural selection and SELEX

1999 • 53 citations

Comprehensive Analysis of Orthologous Protein Domains Using the HOPS Database

2003 • 51 citations

Computationally Identifying Novel NF-κB-Regulated Immune Genes in the Human Genome

2003 • 51 citations

Sockeye: A 3D Environment for Comparative Genomics

2004 • 41 citations

PipTools: A Computational Toolkit to Annotate and Analyze Pairwise Comparisons of Genomic Sequences

2002 • 39 citations

Of Chips and ChIPs

2002 • 36 citations

Regulation of the human cardiac/slow-twitch troponin C gene by multiple, cooperative, cell-type-specific, and MyoD-responsive elements.

1993 • 33 citations

AUTOMATIC ANNOTATION OF GENOMIC REGULATORY SEQUENCES BY SEARCHING FOR COMPOSITE CLUSTERS

2001 • 31 citations

OrthoGUI: graphical presentation of Orthostrapper results

2002 • 12 citations

Quantitative approaches to problems of eukaryotic gene expression

2002 • 10 citations