Computational methods for transcriptional regulation

Comprehensive Identification of Cell Cycle–regulated Genes of the YeastSaccharomyces cerevisiaeby Microarray Hybridization

1998 • 4,811 citations

Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection

2000 • 3,126 citations

Transcriptional regulatory code of a eukaryotic genome

2004 • 2,174 citations

The Transcriptional Program of Sporulation in Budding Yeast

1998 • 1,876 citations

Sequencing and comparison of yeast species to identify genes and regulatory elements

2003 • 1,785 citations

Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data

2003 • 1,713 citations

Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell

2003 • 1,596 citations

Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae

2004 • 1,532 citations

Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner

2004 • 1,473 citations

Genetic Dissection of Transcriptional Regulation in Budding Yeast

2002 • 1,389 citations

The Evolution of Transcriptional Regulation in Eukaryotes

2003 • 1,207 citations

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

2003 • 1,103 citations

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF

2001 • 1,101 citations

The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster

2003 • 948 citations

Evolutionary changes in cis and trans gene regulation

2004 • 871 citations

Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

2003 • 828 citations

Revealing modular organization in the yeast transcriptional network

2002 • 714 citations

Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection

2000 • 699 citations

Serial Regulation of Transcriptional Regulators in the Yeast Cell Cycle

2001 • 664 citations

Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors

2003 • 639 citations

The Ashbya gossypii Genome as a Tool for Mapping the Ancient Saccharomyces cerevisiae Genome

2004 • 637 citations

Mapping Global Histone Acetylation Patterns to Gene Expression

2004 • 620 citations

Computational discovery of gene modules and regulatory networks

2003 • 615 citations

Predicting Gene Expression from Sequence

2004 • 600 citations

SCPD: a promoter database of the yeast Saccharomyces cerevisiae.

1999 • 445 citations

The core meiotic transcriptome in budding yeasts

2000 • 444 citations

Glocal alignment: finding rearrangements during alignment

2003 • 443 citations

Progress and Prospects in Evolutionary Biology

1997 • 433 citations

Direct Allelic Variation Scanning of the Yeast Genome

1998 • 387 citations

Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo

2001 • 378 citations

Evolution of gene expression in the Drosophila melanogaster subgroup

2003 • 358 citations

Identification and Characterization of Multi-Species Conserved Sequences

2003 • 336 citations

Evolutionary distances for protein-coding sequences: modeling site- specific residue frequencies

1998 • 335 citations

Whole-Genome Analysis of Dorsal-Ventral Patterning in the Drosophila Embryo

2002 • 295 citations

A Gene Expression Map for the Euchromatic Genome of Drosophila melanogaster

2004 • 291 citations

MAVID: Constrained Ancestral Alignment of Multiple Sequences

2004 • 287 citations

Genome-wide discovery of transcriptional modules from DNA sequence and gene expression

2003 • 269 citations

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae

2002 • 265 citations

Dynamical Analysis of Regulatory Interactions in the Gap Gene System of Drosophila melanogaster

2004 • 258 citations

Transcriptional Control in the Segmentation Gene Network of Drosophila

2004 • 254 citations

Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis

2000 • 246 citations

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

2002 • 231 citations

Comparative Genomics

2003 • 229 citations

Program-Specific Distribution of a Transcription Factor Dependent on Partner Transcription Factor and MAPK Signaling

2003 • 228 citations

High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups

1998 • 226 citations

Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.

2004 • 217 citations

A probabilistic method to detect regulatory modules

2003 • 215 citations

PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences

2004 • 195 citations

Deciphering gene expression regulatory networks

2002 • 187 citations

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

2004 • 183 citations

Duplicate genes increase gene expression diversity within and between species

2004 • 180 citations

A regulatory code for neurogenic gene expression in theDrosophilaembryo

2004 • 172 citations

Gene regulatory network controlling embryonic specification in the sea urchin

2004 • 158 citations

Position specific variation in the rate of evolution in transcription factor binding sites.

2003 • 155 citations

Ras and Gpa2 Mediate One Branch of a Redundant Glucose Signaling Pathway in Yeast

2004 • 147 citations

Distinguishing Regulatory DNA From Neutral Sites

2003 • 141 citations

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophilagenome

2002 • 140 citations

Discovery of genes with highly restricted expression patterns in theDrosophilawing disc using DNA oligonucleotide microarrays

2003 • 109 citations

Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery

2004 • 107 citations

Patchy Interspecific Sequence Similarities Efficiently Identify Positive cis-Regulatory Elements in the Sea Urchin

2002 • 104 citations

Conservation of regulatory elements between two species of Drosophila

2003 • 98 citations

Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila

2004 • 90 citations

A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae

2002 • 89 citations

Analysis of the eye developmental pathway in Drosophila using DNA microarrays

2003 • 82 citations

Positive Selection on MMP3 Regulation Has Shaped Heart Disease Risk

2004 • 78 citations

Epigenomic profiling using microarrays

2003 • 73 citations

Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics

2002 • 67 citations

Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches

2004 • 65 citations

Genomic regulatory regions: insights from comparative sequence analysis

2003 • 65 citations

Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura

2004 • 65 citations

Sequence Turnover and Tandem Repeats in cis-Regulatory Modules in Drosophila

2005 • 42 citations

A space-efficient algorithm for aligning large genomic sequences

2000 • 32 citations

Dissecting the transcription networks of a cell using computational genomics

2003 • 29 citations