Published in Nature on February 03, 2005
Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science (2010) 11.37
High-quality binary protein interaction map of the yeast interactome network. Science (2008) 10.65
Hfq and its constellation of RNA. Nat Rev Microbiol (2011) 4.94
Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res (2006) 4.25
A census of human soluble protein complexes. Cell (2012) 3.90
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics (2005) 3.75
Differential network biology. Mol Syst Biol (2012) 3.74
A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci U S A (2008) 3.57
How complete are current yeast and human protein-interaction networks? Genome Biol (2006) 3.50
Phenotypic landscape of a bacterial cell. Cell (2010) 3.50
ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet (2012) 3.23
SSB as an organizer/mobilizer of genome maintenance complexes. Crit Rev Biochem Mol Biol (2008) 3.19
High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods (2008) 3.17
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol (2009) 3.03
Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PLoS Comput Biol (2007) 2.84
A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol (2010) 2.70
Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. Nucleic Acids Res (2006) 2.67
Post-reductionist protein science, or putting Humpty Dumpty back together again. Nat Chem Biol (2009) 2.52
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Database (Oxford) (2010) 2.47
The bacterial actin-like cytoskeleton. Microbiol Mol Biol Rev (2006) 2.18
Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput Biol (2009) 2.14
A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol (2007) 2.13
Protein analysis by shotgun/bottom-up proteomics. Chem Rev (2013) 2.13
The ribosome challenge to the RNA world. J Mol Evol (2015) 2.10
The binary protein-protein interaction landscape of Escherichia coli. Nat Biotechnol (2014) 2.10
Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nat Rev Mol Cell Biol (2009) 2.09
Inferring protein domain interactions from databases of interacting proteins. Genome Biol (2005) 1.97
Actin homolog MreB and RNA polymerase interact and are both required for chromosome segregation in Escherichia coli. Genes Dev (2006) 1.93
The life-cycle of operons. PLoS Genet (2006) 1.91
Panorama of ancient metazoan macromolecular complexes. Nature (2015) 1.89
Fe-S cluster assembly pathways in bacteria. Microbiol Mol Biol Rev (2008) 1.88
Loss-of-function mutations in HINT1 cause axonal neuropathy with neuromyotonia. Nat Genet (2012) 1.85
Building Fe-S proteins: bacterial strategies. Nat Rev Microbiol (2010) 1.83
Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages. Proc Natl Acad Sci U S A (2008) 1.78
Unraveling protein networks with power graph analysis. PLoS Comput Biol (2008) 1.77
The yeast iron regulatory proteins Grx3/4 and Fra2 form heterodimeric complexes containing a [2Fe-2S] cluster with cysteinyl and histidyl ligation. Biochemistry (2009) 1.75
High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proc Natl Acad Sci U S A (2008) 1.72
A pooling-deconvolution strategy for biological network elucidation. Nat Methods (2006) 1.68
Operon formation is driven by co-regulation and not by horizontal gene transfer. Genome Res (2005) 1.64
Bacterial small RNA-based negative regulation: Hfq and its accomplices. J Biol Chem (2013) 1.63
Mapping the Sinorhizobium meliloti 1021 solute-binding protein-dependent transportome. Proc Natl Acad Sci U S A (2006) 1.61
Septum enlightenment: assembly of bacterial division proteins. J Bacteriol (2006) 1.61
A network of multi-tasking proteins at the DNA replication fork preserves genome stability. PLoS Genet (2005) 1.61
Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J Mol Biol (2006) 1.60
PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Res (2012) 1.59
An in vitro microfluidic approach to generating protein-interaction networks. Nat Methods (2008) 1.59
The binary protein interactome of Treponema pallidum--the syphilis spirochete. PLoS One (2008) 1.59
A two-component phosphotransfer network involving ArcB, ArcA, and RssB coordinates synthesis and proteolysis of sigmaS (RpoS) in E. coli. Genes Dev (2005) 1.55
Resolution of converging replication forks by RecQ and topoisomerase III. Mol Cell (2008) 1.55
Bacterial topoisomerase I as a target for discovery of antibacterial compounds. Nucleic Acids Res (2008) 1.55
DOMINE: a database of protein domain interactions. Nucleic Acids Res (2007) 1.54
The extinction dynamics of bacterial pseudogenes. PLoS Genet (2010) 1.53
An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics (2006) 1.52
Conserved network of proteins essential for bacterial viability. J Bacteriol (2009) 1.48
The universally conserved prokaryotic GTPases. Microbiol Mol Biol Rev (2011) 1.47
Transcriptional regulation by competing transcription factor modules. PLoS Comput Biol (2006) 1.47
Predicting domain-domain interactions using a parsimony approach. Genome Biol (2006) 1.47
Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics (2007) 1.47
Stable evolutionary signal in a yeast protein interaction network. BMC Evol Biol (2006) 1.45
Rapid changes in gene expression dynamics in response to superoxide reveal SoxRS-dependent and independent transcriptional networks. PLoS One (2007) 1.43
Anticipating chromosomal replication fork arrest: SSB targets repair DNA helicases to active forks. EMBO J (2007) 1.42
A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency. Mol Cell Proteomics (2010) 1.41
CsrA inhibits translation initiation of Escherichia coli hfq by binding to a single site overlapping the Shine-Dalgarno sequence. J Bacteriol (2007) 1.41
DNA reshaping by MukB. Right-handed knotting, left-handed supercoiling. J Biol Chem (2005) 1.40
What we can learn about Escherichia coli through application of Gene Ontology. Trends Microbiol (2009) 1.40
Antibacterial drug discovery in the resistance era. Nature (2016) 1.40
Persistence drives gene clustering in bacterial genomes. BMC Genomics (2008) 1.37
RecJ exonuclease: substrates, products and interaction with SSB. Nucleic Acids Res (2006) 1.35
The RNA binding protein Hfq interacts specifically with tRNAs. RNA (2008) 1.35
Identification of novel Escherichia coli ribosome-associated proteins using isobaric tags and multidimensional protein identification techniques. J Bacteriol (2007) 1.34
Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PLoS Genet (2011) 1.33
Operons. Cell Mol Life Sci (2009) 1.33
Promiscuous substrate recognition in folding and assembly activities of the trigger factor chaperone. Cell (2009) 1.32
Deconstructing ribosome construction. Trends Biochem Sci (2009) 1.31
Probabilistic prediction and ranking of human protein-protein interactions. BMC Bioinformatics (2007) 1.31
Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS. Nat Methods (2013) 1.30
Refining protein subcellular localization. PLoS Comput Biol (2005) 1.28
Acid stress response in Escherichia coli: mechanism of regulation of gadA transcription by RcsB and GadE. Nucleic Acids Res (2010) 1.27
Purification and characterization of HIV-human protein complexes. Methods (2010) 1.26
Cooperative and critical roles for both G domains in the GTPase activity and cellular function of ribosome-associated Escherichia coli EngA. J Bacteriol (2006) 1.26
False positive reduction in protein-protein interaction predictions using gene ontology annotations. BMC Bioinformatics (2007) 1.25
Bacterial translation elongation factor EF-Tu interacts and colocalizes with actin-like MreB protein. Proc Natl Acad Sci U S A (2010) 1.25
The conservation and evolutionary modularity of metabolism. Genome Biol (2009) 1.24
The C-terminal domain of the bacterial SSB protein acts as a DNA maintenance hub at active chromosome replication forks. PLoS Genet (2010) 1.24
The role of UbiX in Escherichia coli coenzyme Q biosynthesis. Arch Biochem Biophys (2007) 1.24
NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes. J Bacteriol (2007) 1.23
The Escherichia coli proteome: past, present, and future prospects. Microbiol Mol Biol Rev (2006) 1.23
Expression profiles reveal parallel evolution of epistatic interactions involving the CRP regulon in Escherichia coli. PLoS Genet (2008) 1.23
Inferring genome-wide functional linkages in E. coli by combining improved genome context methods: comparison with high-throughput experimental data. Genome Res (2007) 1.23
Matching cross-linked peptide spectra: only as good as the worse identification. Mol Cell Proteomics (2013) 1.23
Thematic review series: Glycerolipids. Acyltransferases in bacterial glycerophospholipid synthesis. J Lipid Res (2008) 1.22
The Modular Organization of Protein Interactions in Escherichia coli. PLoS Comput Biol (2009) 1.20
Concurrent growth rate and transcript analyses reveal essential gene stringency in Escherichia coli. PLoS One (2009) 1.20
The SOSS1 single-stranded DNA binding complex promotes DNA end resection in concert with Exo1. EMBO J (2012) 1.19
A network perspective on the evolution of metabolism by gene duplication. Genome Biol (2007) 1.19
Roles for the transcription elongation factor NusA in both DNA repair and damage tolerance pathways in Escherichia coli. Proc Natl Acad Sci U S A (2010) 1.18
Interaction between cell division proteins FtsE and FtsZ. J Bacteriol (2007) 1.18
A comprehensive resource of interacting protein regions for refining human transcription factor networks. PLoS One (2010) 1.17
Monothiol CGFS glutaredoxins and BolA-like proteins: [2Fe-2S] binding partners in iron homeostasis. Biochemistry (2012) 1.16
Tandem affinity purification of functional TAP-tagged proteins from human cells. Nat Protoc (2007) 1.15
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
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science (2010) 11.37
Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature (2007) 9.25
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell (2005) 7.21
Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol (2003) 6.79
Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One (2010) 6.61
Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell (2006) 5.72
A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol Cell (2003) 5.57
Draft genome of the filarial nematode parasite Brugia malayi. Science (2007) 5.28
RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol Cell Biol (2002) 5.04
Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone. Cell (2005) 4.95
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
A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery. Nature (2005) 4.33
High-definition macromolecular composition of yeast RNA-processing complexes. Mol Cell (2004) 4.18
A census of human soluble protein complexes. Cell (2012) 3.90
Activation of antibacterial autophagy by NADPH oxidases. Proc Natl Acad Sci U S A (2009) 3.87
Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae. J Biol Chem (2004) 3.53
IL-4 dependent alternatively-activated macrophages have a distinctive in vivo gene expression phenotype. BMC Immunol (2002) 3.44
A Rich1/Amot complex regulates the Cdc42 GTPase and apical-polarity proteins in epithelial cells. Cell (2006) 3.38
A panoramic view of yeast noncoding RNA processing. Cell (2003) 3.11
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol (2009) 3.03
eSGA: E. coli synthetic genetic array analysis. Nat Methods (2008) 3.01
A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol (2010) 2.92
Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4. Proc Natl Acad Sci U S A (2004) 2.80
Characterization of the proteins released from activated platelets leads to localization of novel platelet proteins in human atherosclerotic lesions. Blood (2003) 2.73
A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator. Cell (2006) 2.71
Amino acid starvation induced by invasive bacterial pathogens triggers an innate host defense program. Cell Host Microbe (2012) 2.70
A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol (2010) 2.70
Bridging structural biology and genomics: assessing protein interaction data with known complexes. Trends Genet (2002) 2.65
Nanoparticle size and surface chemistry determine serum protein adsorption and macrophage uptake. J Am Chem Soc (2012) 2.55
Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomics. Nat Protoc (2006) 2.52
Regulation of transcription elongation by phosphorylation. Biochim Biophys Acta (2002) 2.41
Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics (2004) 2.25
Xrcc4 physically links DNA end processing by polynucleotide kinase to DNA ligation by DNA ligase IV. EMBO J (2004) 2.24
Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics (2005) 2.24
Bundle-branch block with short P-R interval in healthy young people prone to paroxysmal tachycardia. 1930. Ann Noninvasive Electrocardiol (2006) 2.24
Protein corona fingerprinting predicts the cellular interaction of gold and silver nanoparticles. ACS Nano (2014) 2.17
Proteasome involvement in the repair of DNA double-strand breaks. Mol Cell (2004) 2.17
An epidemiologic survey of pediatric sepsis in regional hospitals in China. Pediatr Crit Care Med (2014) 2.16
Sequential Peptide Affinity (SPA) system for the identification of mammalian and bacterial protein complexes. J Proteome Res (2004) 2.16
Listeria monocytogenes evades killing by autophagy during colonization of host cells. Autophagy (2007) 2.13
Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3'-ends. J Biol Chem (2003) 2.10
Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. Nature (2012) 2.05
Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109. Mol Cell Biol (2008) 2.05
WW domains provide a platform for the assembly of multiprotein networks. Mol Cell Biol (2005) 1.97
ALIS are stress-induced protein storage compartments for substrates of the proteasome and autophagy. Autophagy (2006) 1.97
Identifying functional modules in the physical interactome of Saccharomyces cerevisiae. Proteomics (2007) 1.96
Impaired tRNA nuclear export links DNA damage and cell-cycle checkpoint. Cell (2007) 1.94
PRISM, a generic large scale proteomic investigation strategy for mammals. Mol Cell Proteomics (2003) 1.91
Listeriolysin O allows Listeria monocytogenes replication in macrophage vacuoles. Nature (2008) 1.89
The ctf13-30/CTF13 genomic haploinsufficiency modifier screen identifies the yeast chromatin remodeling complex RSC, which is required for the establishment of sister chromatid cohesion. Mol Cell Biol (2004) 1.87
Integrating gene and protein expression data: pattern analysis and profile mining. Methods (2005) 1.83
H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex. Mol Cell Biol (2005) 1.82
Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast. Mol Syst Biol (2007) 1.79
Protein profiling with Epstein-Barr nuclear antigen-1 reveals an interaction with the herpesvirus-associated ubiquitin-specific protease HAUSP/USP7. J Biol Chem (2003) 1.78
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell. Mol Syst Biol (2009) 1.75
Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain. Nat Chem Biol (2013) 1.72
PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. BMC Bioinformatics (2006) 1.71
New approaches to drug safety: a pharmacovigilance tool kit. Nat Rev Drug Discov (2009) 1.71
The VPS33B-binding protein VPS16B is required in megakaryocyte and platelet α-granule biogenesis. Blood (2012) 1.67
Toll-like receptor 2 plays a critical role in the progression of atherosclerosis that is independent of dietary lipids. Atherosclerosis (2007) 1.67
Slx4 regulates DNA damage checkpoint-dependent phosphorylation of the BRCT domain protein Rtt107/Esc4. Mol Biol Cell (2005) 1.66
Role for PSF in mediating transcriptional activator-dependent stimulation of pre-mRNA processing in vivo. Mol Cell Biol (2005) 1.64
Palmitoylation by the DHHC protein Pfa4 regulates the ER exit of Chs3. J Cell Biol (2006) 1.53