Relating whole-genome expression data with protein-protein interactions.

Coexpression analysis of human genes across many microarray data sets. Genome Res (2004) 9.38

Interactome networks and human disease. Cell (2011) 7.16

Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol (2003) 6.98

A draft map of the human proteome. Nature (2014) 6.58

Network-based prediction of protein function. Mol Syst Biol (2007) 6.13

Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet (2006) 5.82

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet (2008) 5.80

The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63

FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biol (2007) 5.23

Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A (2006) 3.51

A protein complex network of Drosophila melanogaster. Cell (2011) 3.31

L2L: a simple tool for discovering the hidden significance in microarray expression data. Genome Biol (2005) 3.27

Identification of functional modules using network topology and high-throughput data. BMC Syst Biol (2007) 3.00

VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics (2004) 2.88

Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PLoS Comput Biol (2007) 2.84

Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. J Biol (2005) 2.68

The gene balance hypothesis: from classical genetics to modern genomics. Plant Cell (2007) 2.56

Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet (2007) 2.54

Coexpression of neighboring genes in the genome of Arabidopsis thaliana. Genome Res (2004) 2.52

A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinformatics (2007) 2.51

Unequal evolutionary conservation of human protein interactions in interologous networks. Genome Biol (2007) 2.45

Assessing the limits of genomic data integration for predicting protein networks. Genome Res (2005) 2.33

Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes. Chromosome Res (2009) 2.33

Functional modules by relating protein interaction networks and gene expression. Nucleic Acids Res (2003) 2.25

Integrative approaches for finding modular structure in biological networks. Nat Rev Genet (2013) 2.19

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res (2007) 2.17

Predicting co-complexed protein pairs using genomic and proteomic data integration. BMC Bioinformatics (2004) 2.00

Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations. Nucleic Acids Res (2006) 1.93

Expression dynamics of a cellular metabolic network. Mol Syst Biol (2005) 1.85

The organization of the transcriptional network in specific neuronal classes. Mol Syst Biol (2009) 1.74

ExpressYourself: A modular platform for processing and visualizing microarray data. Nucleic Acids Res (2003) 1.68

Cigarette smoking reprograms apical junctional complex molecular architecture in the human airway epithelium in vivo. Cell Mol Life Sci (2010) 1.66

HAPPI: an online database of comprehensive human annotated and predicted protein interactions. BMC Genomics (2009) 1.61

Using protein complexes to predict phenotypic effects of gene mutation. Genome Biol (2007) 1.57

An integrative -omics approach to identify functional sub-networks in human colorectal cancer. PLoS Comput Biol (2010) 1.54

Modeling the evolution of protein domain architectures using maximum parsimony. J Mol Biol (2006) 1.53

Bioinformatics analysis of experimentally determined protein complexes in the yeast Saccharomyces cerevisiae. Genome Res (2003) 1.53

A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. Mol Syst Biol (2008) 1.53

Genome-wide transcriptional plasticity underlies cellular adaptation to novel challenge. Mol Syst Biol (2007) 1.49

Protein synthesis rate is the predominant regulator of protein expression during differentiation. Mol Syst Biol (2013) 1.46

Recent advances in clustering methods for protein interaction networks. BMC Genomics (2010) 1.40

Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit. Mol Syst Biol (2012) 1.38

Bagging statistical network inference from large-scale gene expression data. PLoS One (2012) 1.38

Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data. BMC Bioinformatics (2007) 1.35

Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. BMC Genomics (2009) 1.34

Design principles of molecular networks revealed by global comparisons and composite motifs. Genome Biol (2006) 1.33

Identifying set-wise differential co-expression in gene expression microarray data. BMC Bioinformatics (2009) 1.32

Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms. PLoS Comput Biol (2006) 1.32

Statistical inference and reverse engineering of gene regulatory networks from observational expression data. Front Genet (2012) 1.30

Dosage sensitivity shapes the evolution of copy-number varied regions. PLoS One (2010) 1.30

Host pathogen protein interactions predicted by comparative modeling. Protein Sci (2007) 1.29

Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains. BMC Syst Biol (2010) 1.24

Confirmation of human protein interaction data by human expression data. BMC Bioinformatics (2005) 1.23

A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain. Neuron (2014) 1.23

How biologically relevant are interaction-based modules in protein networks? Genome Biol (2004) 1.22

A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network. BMC Bioinformatics (2010) 1.21

Investigating the predictability of essential genes across distantly related organisms using an integrative approach. Nucleic Acids Res (2010) 1.21

Transcriptional regulation of protein complexes in yeast. Genome Biol (2004) 1.20

A systematic analysis of the skeletal muscle miRNA transcriptome of chicken varieties with divergent skeletal muscle growth identifies novel miRNAs and differentially expressed miRNAs. BMC Genomics (2011) 1.20

Genes encoding subunits of stable complexes are clustered on the yeast chromosomes: an interpretation from a dosage balance perspective. Genetics (2004) 1.19

Characterization and prediction of protein-protein interactions within and between complexes. Proc Natl Acad Sci U S A (2006) 1.19

A comprehensive, quantitative, and genome-wide model of translation. PLoS Comput Biol (2010) 1.17

From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. Bioinformatics (2011) 1.15

The Arabidopsis wall associated kinase-like 10 gene encodes a functional guanylyl cyclase and is co-expressed with pathogen defense related genes. PLoS One (2010) 1.14

Growing functional modules from a seed protein via integration of protein interaction and gene expression data. BMC Bioinformatics (2007) 1.13

Protein complexes are under evolutionary selection to assemble via ordered pathways. Cell (2013) 1.12

Systems-level analyses identify extensive coupling among gene expression machines. Mol Syst Biol (2006) 1.12

Overview of techniques to account for confounding due to population stratification and cryptic relatedness in genomic data association analyses. Heredity (Edinb) (2010) 1.11

Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev (2012) 1.11

Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data. BMC Bioinformatics (2012) 1.10

OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments. BMC Bioinformatics (2006) 1.10

Identifying cooperative transcriptional regulations using protein-protein interactions. Nucleic Acids Res (2005) 1.09

New strategy for the representation and the integration of biomolecular knowledge at a cellular scale. Nucleic Acids Res (2004) 1.09

Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data. Genome Biol (2009) 1.08

Co-expression networks: graph properties and topological comparisons. Bioinformatics (2009) 1.05

Genome-scale analysis of interaction dynamics reveals organization of biological networks. Bioinformatics (2012) 1.05

Assessing and predicting protein interactions by combining manifold embedding with multiple information integration. BMC Bioinformatics (2012) 1.04

KIAA0101 interacts with BRCA1 and regulates centrosome number. Mol Cancer Res (2011) 1.04

Common gene expression strategies revealed by genome-wide analysis in yeast. Genome Biol (2007) 1.04

Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes. Nucleic Acids Res (2006) 1.02

A critical and integrated view of the yeast interactome. Comp Funct Genomics (2004) 1.02

Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis. PLoS Comput Biol (2008) 1.02

Functional genomics identifies neural stem cell sub-type expression profiles and genes regulating neuroblast homeostasis. Dev Biol (2011) 1.02

Proteomic profiling identifies distinct protein patterns in acute myelogenous leukemia CD34+CD38- stem-like cells. PLoS One (2013) 1.01

GEPS: the Gene Expression Pattern Scanner. Nucleic Acids Res (2006) 1.00

Spatiotemporal 16p11.2 protein network implicates cortical late mid-fetal brain development and KCTD13-Cul3-RhoA pathway in psychiatric diseases. Neuron (2015) 0.98

A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles. BMC Bioinformatics (2010) 0.98

An in silico method for detecting overlapping functional modules from composite biological networks. BMC Syst Biol (2008) 0.98

A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands. Genome Res (2006) 0.98

The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks. BMC Syst Biol (2008) 0.97

Biological convergence of cancer signatures. PLoS One (2009) 0.97

Patterns of co-expression for protein complexes by size in Saccharomyces cerevisiae. Nucleic Acids Res (2008) 0.96

InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes. BMC Bioinformatics (2007) 0.95

Preservation of genes involved in sterol metabolism in cholesterol auxotrophs: facts and hypotheses. PLoS One (2008) 0.94

Computational verification of protein-protein interactions by orthologous co-expression. BMC Bioinformatics (2005) 0.94

Physical protein-protein interactions predicted from microarrays. Bioinformatics (2008) 0.94

Relative predicted protein levels of functionally associated proteins are conserved across organisms. Nucleic Acids Res (2005) 0.94

Structural bioinformatics of the interactome. Annu Rev Biophys (2014) 0.93

The prediction of protein-protein interaction networks in rice blast fungus. BMC Genomics (2008) 0.93

Genetic interaction networks: better understand to better predict. Front Genet (2013) 0.92

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52

Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science (1999) 83.27

A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature (2000) 47.15

A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A (2001) 33.71

Functional discovery via a compendium of expression profiles. Cell (2000) 31.39

Dissecting the regulatory circuitry of a eukaryotic genome. Cell (1998) 23.62

A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell (1998) 19.67

Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci U S A (2000) 19.39

Correlation between protein and mRNA abundance in yeast. Mol Cell Biol (1999) 16.95

Analyzing high-density oligonucleotide gene expression array data. J Cell Biochem (2000) 16.73

MIPS: a database for genomes and protein sequences. Nucleic Acids Res (2000) 16.33

Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol (1998) 13.99

Characterization of the yeast transcriptome. Cell (1997) 11.33

Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci U S A (2000) 10.98

Structure and functions of the 20S and 26S proteasomes. Annu Rev Biochem (1996) 10.70

A network of protein-protein interactions in yeast. Nat Biotechnol (2000) 10.31

DIP: the database of interacting proteins. Nucleic Acids Res (2000) 10.06

Large-scale temporal gene expression mapping of central nervous system development. Proc Natl Acad Sci U S A (1998) 9.06

Protein structural topology: Automated analysis and diagrammatic representation. Protein Sci (1999) 8.24

Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase. Cell (1997) 8.23

Protein function in the post-genomic era. Nature (2000) 7.00

A sampling of the yeast proteome. Mol Cell Biol (1999) 5.12

Exploring expression data: identification and analysis of coexpressed genes. Genome Res (1999) 5.09

BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bioinformatics (2000) 4.40

A comparison of selected mRNA and protein abundances in human liver. Electrophoresis (1997) 4.35

Global response of Saccharomyces cerevisiae to an alkylating agent. Proc Natl Acad Sci U S A (1999) 4.27

Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Proc Natl Acad Sci U S A (1999) 4.12

RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodeling. Cell (1996) 4.03

TRAPP, a highly conserved novel complex on the cis-Golgi that mediates vesicle docking and fusion. EMBO J (1998) 3.49

Structural proteomics of an archaeon. Nat Struct Biol (2000) 3.46

The yeast DOA4 gene encodes a deubiquitinating enzyme related to a product of the human tre-2 oncogene. Nature (1993) 3.33

High-throughput yeast two-hybrid assays for large-scale protein interaction mapping. Methods (2001) 3.09

Structural basis for the activation of 20S proteasomes by 11S regulators. Nature (2000) 3.04

Assessment of prediction accuracy of protein function from protein--protein interaction data. Yeast (2001) 2.90

Transcriptional elements involved in the repression of ribosomal protein synthesis. Mol Cell Biol (1999) 2.87

Interaction of the Doa4 deubiquitinating enzyme with the yeast 26S proteasome. Mol Biol Cell (1999) 2.57

Nuclear pore complex number and distribution throughout the Saccharomyces cerevisiae cell cycle by three-dimensional reconstruction from electron micrographs of nuclear envelopes. Mol Biol Cell (1997) 2.53

Integrative analysis of protein interaction data. Proc Int Conf Intell Syst Mol Biol (2000) 2.39

Systematic and large-scale two-hybrid screens. Curr Opin Microbiol (2000) 2.34

Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins. Nucleic Acids Res (2000) 2.17

A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome. J Mol Biol (2000) 2.03

Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions. J Mol Biol (2001) 2.03

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. Bioinformatics (2002) 2.00

Analysis of gene expression microarrays for phenotype classification. Proc Int Conf Intell Syst Mol Biol (2000) 1.82

Regulation of ribosome biosynthesis in Escherichia coli and Saccharomyces cerevisiae: diversity and common principles. J Bacteriol (1999) 1.82

Determination of protein function, evolution and interactions by structural genomics. Curr Opin Struct Biol (2001) 1.75

High-throughput screening for protein-protein interactions using two-hybrid assay. Methods Enzymol (2000) 1.64

Regulation of ribosome synthesis in yeast. Yeast (1997) 1.63

In vivo dynamics of nuclear pore complexes in yeast. J Cell Biol (1997) 1.62

Genomic and proteomic analysis of the myeloid differentiation program. Blood (2001) 1.55

TRAPP stably associates with the Golgi and is required for vesicle docking. EMBO J (2000) 1.50

Genome-wide analysis relating expression level with protein subcellular localization. Trends Genet (2000) 1.50

RNA expression patterns change dramatically in human neutrophils exposed to bacteria. Blood (2001) 1.48

Large-scale functional analysis using peptide or protein arrays. Nat Biotechnol (2000) 1.32

Basic microarray analysis: grouping and feature reduction. Trends Biotechnol (2001) 1.31

Structural proteomics: prospects for high throughput sample preparation. Prog Biophys Mol Biol (2000) 1.28

The current excitement in bioinformatics-analysis of whole-genome expression data: how does it relate to protein structure and function? Curr Opin Struct Biol (2000) 1.26

Quantitative analysis of the protein composition of yeast ribosomes. Eur J Biochem (1978) 1.10

Making the most of microarray data. Nat Genet (2000) 1.03

The 26S proteasome of the fission yeast Schizosaccharomyces pombe. Philos Trans R Soc Lond B Biol Sci (1999) 0.94

New tools and resources for analysing protein structures and their interactions. Acta Crystallogr D Biol Crystallogr (1998) 0.91

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77

The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99

Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29

Landscape of transcription in human cells. Nature (2012) 20.18

GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19

Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85

A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60

Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32

A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07

Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13

Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41

The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24

Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93

Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46

Divergence of transcription factor binding sites across related yeast species. Science (2007) 7.10

Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol (2003) 6.98

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97

The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82

Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14

The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63

Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res (2003) 5.49

Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26

A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80

AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71

New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev (2007) 4.62

Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08

Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A (2003) 3.89

Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res (2006) 3.62

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol (2012) 3.61

Genomic analysis of essentiality within protein networks. Trends Genet (2004) 3.52

Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A (2006) 3.51

Modeling ChIP sequencing in silico with applications. PLoS Comput Biol (2008) 3.48

GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proc Natl Acad Sci U S A (2002) 3.41

Structured digital abstract makes text mining easy. Nature (2007) 3.38

Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol (2008) 3.34

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci U S A (2010) 3.28

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev (2002) 3.27

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res (2005) 3.23

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics (2009) 3.22

The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions. Am J Med Genet A (2012) 3.12

Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature (2012) 3.09

Getting connected: analysis and principles of biological networks. Genes Dev (2007) 3.03

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med (2015) 3.00

Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches. Cell (2007) 2.95

Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction. Curr Opin Microbiol (2004) 2.92

Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A (2010) 2.90

PubNet: a flexible system for visualizing literature derived networks. Genome Biol (2005) 2.89

Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res (2005) 2.89

Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res (2002) 2.89

Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res (2002) 2.88

PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics (2006) 2.85

Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res (2003) 2.85

Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A (2009) 2.83

The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans. Dev Cell (2005) 2.81

Modeling gene expression using chromatin features in various cellular contexts. Genome Biol (2012) 2.76

Genomics. Defining genes in the genomics era. Science (2003) 2.73

Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins (2002) 2.72

MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes Dev (2008) 2.66

DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc Natl Acad Sci U S A (2004) 2.66

Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res (2012) 2.66

Major molecular differences between mammalian sexes are involved in drug metabolism and renal function. Dev Cell (2004) 2.65

Bridging structural biology and genomics: assessing protein interaction data with known complexes. Trends Genet (2002) 2.65

Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium. Methods Enzymol (2005) 2.54

Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet (2004) 2.51

Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biol (2007) 2.48

Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet (2010) 2.46

TOS9 regulates white-opaque switching in Candida albicans. Eukaryot Cell (2006) 2.42

Target hub proteins serve as master regulators of development in yeast. Genes Dev (2006) 2.39

Large-scale analysis of pseudogenes in the human genome. Curr Opin Genet Dev (2004) 2.38

Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet (2003) 2.38

Personal genome sequencing: current approaches and challenges. Genes Dev (2010) 2.38

Conformational changes associated with protein-protein interactions. Curr Opin Struct Biol (2004) 2.37

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet (2005) 2.36

Assessing the limits of genomic data integration for predicting protein networks. Genome Res (2005) 2.33

Integrated pseudogene annotation for human chromosome 22: evidence for transcription. J Mol Biol (2005) 2.32

The protein target list of the Northeast Structural Genomics Consortium. Proteins (2004) 2.31

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Res (2010) 2.30

CREB binds to multiple loci on human chromosome 22. Mol Cell Biol (2004) 2.28

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics (2010) 2.26

Spectral biclustering of microarray data: coclustering genes and conditions. Genome Res (2003) 2.25

The real cost of sequencing: higher than you think! Genome Biol (2011) 2.22

3V: cavity, channel and cleft volume calculator and extractor. Nucleic Acids Res (2010) 2.20

Regulation of gene expression by a metabolic enzyme. Science (2004) 2.15

Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays. Proc Natl Acad Sci U S A (2007) 2.15

Open access: taking full advantage of the content. PLoS Comput Biol (2008) 2.14

Information assessment on predicting protein-protein interactions. BMC Bioinformatics (2004) 2.14

Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. Genome Biol (2010) 2.12

Studying genomes through the aeons: protein families, pseudogenes and proteome evolution. J Mol Biol (2002) 2.07

Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies. Nat Struct Mol Biol (2008) 2.07

A question of size: the eukaryotic proteome and the problems in defining it. Nucleic Acids Res (2002) 2.07

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays. BMC Genomics (2010) 2.03

A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation. Genome Res (2008) 2.01