Bridging structural biology and genomics: assessing protein interaction data with known complexes.

Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data. Bioinformatics (2010) 1.65

Large-scale protein-protein interactions detection by integrating big biosensing data with computational model. Biomed Res Int (2014) 0.85

NERI: network-medicine based integrative approach for disease gene prioritization by relative importance. BMC Bioinformatics (2015) 0.75

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

Global mapping of the yeast genetic interaction network. Science (2004) 21.34

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

Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature (2005) 8.19

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

Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol (2003) 6.79

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

Relating whole-genome expression data with protein-protein interactions. Genome Res (2002) 5.78

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

Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone. Cell (2005) 4.95

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

Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Mol Cell (2007) 4.58

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

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

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

A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol (2010) 2.70

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

Regulation of transcription elongation by phosphorylation. Biochim Biophys Acta (2002) 2.41

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