Published in J Vis Exp on November 12, 2012
Functional profiling in Streptococcus mutans: construction and examination of a genomic collection of gene deletion mutants. Mol Oral Microbiol (2015) 0.78
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A (2000) 96.90
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol (2006) 40.15
Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science (2001) 24.48
Global mapping of the yeast genetic interaction network. Science (2004) 21.34
An efficient recombination system for chromosome engineering in Escherichia coli. Proc Natl Acad Sci U S A (2000) 17.30
The genetic landscape of a cell. Science (2010) 16.52
Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell (2005) 10.41
Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature (2007) 9.25
Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature (2005) 8.19
Tandem genetic duplications in phage and bacteria. Annu Rev Microbiol (1977) 8.00
Exploring genetic interactions and networks with yeast. Nat Rev Genet (2007) 5.67
Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nat Methods (2009) 4.91
Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions. Nat Genet (2007) 4.59
Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science (2008) 4.36
A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat Methods (2008) 3.79
Phenotypic landscape of a bacterial cell. Cell (2010) 3.50
Combining biological networks to predict genetic interactions. Proc Natl Acad Sci U S A (2004) 3.18
High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods (2008) 3.17
Functional organization of the S. cerevisiae phosphorylation network. Cell (2009) 3.15
The synthetic genetic interaction spectrum of essential genes. Nat Genet (2005) 3.06
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 genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol Cell (2008) 2.96
Regulation of peptidoglycan synthesis by outer-membrane proteins. Cell (2010) 2.86
Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput Biol (2008) 2.46
Sequential Peptide Affinity (SPA) system for the identification of mammalian and bacterial protein complexes. J Proteome Res (2004) 2.16
Genome-scale genetic manipulation methods for exploring bacterial molecular biology. Mol Biosyst (2012) 1.44
Charting the genetic interaction map of a cell. Curr Opin Biotechnol (2010) 1.28
Modeling synthetic lethality. Genome Biol (2008) 1.23
Positional orthology: putting genomic evolutionary relationships into context. Brief Bioinform (2011) 1.07
Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. PLoS Genet (2011) 1.05
Systems-level approaches for identifying and analyzing genetic interaction networks in Escherichia coli and extensions to other prokaryotes. Mol Biosyst (2009) 0.96
Sequential peptide affinity purification system for the systematic isolation and identification of protein complexes from Escherichia coli. Methods Mol Biol (2009) 0.95
Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli. Methods Mol Biol (2011) 0.77
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
Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature (2005) 8.19
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
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
Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae. J Biol Chem (2004) 3.53
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
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
Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics (2005) 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
Sequential Peptide Affinity (SPA) system for the identification of mammalian and bacterial protein complexes. J Proteome Res (2004) 2.16
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
Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109. Mol Cell Biol (2008) 2.05
Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. Nature (2012) 2.05
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
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
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
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
beta-Subunit appendages promote 20S proteasome assembly by overcoming an Ump1-dependent checkpoint. EMBO J (2007) 1.52
The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism. J Biol Chem (2005) 1.52
Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes. Mol Syst Biol (2007) 1.50
Conserved network of proteins essential for bacterial viability. J Bacteriol (2009) 1.48
RPAP1, a novel human RNA polymerase II-associated protein affinity purified with recombinant wild-type and mutated polymerase subunits. Mol Cell Biol (2004) 1.46
The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast. Genome Res (2008) 1.44
Genome-scale genetic manipulation methods for exploring bacterial molecular biology. Mol Biosyst (2012) 1.44
A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency. Mol Cell Proteomics (2010) 1.41
Proteome dynamics during C2C12 myoblast differentiation. Mol Cell Proteomics (2005) 1.36
ER exit sites are physical and functional core autophagosome biogenesis components. Mol Biol Cell (2013) 1.34
A role for SlyD in the Escherichia coli hydrogenase biosynthetic pathway. J Biol Chem (2004) 1.32
Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses. Mol Cell Proteomics (2007) 1.31
Difference detection in LC-MS data for protein biomarker discovery. Bioinformatics (2007) 1.30
Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps. Proteomics (2010) 1.29
An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe. Nat Struct Mol Biol (2009) 1.27
Computational prediction of cancer-gene function. Nat Rev Cancer (2006) 1.25
Two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression. Mol Cell (2009) 1.24
Cardiac-specific overexpression of sarcolipin in phospholamban null mice impairs myocyte function that is restored by phosphorylation. Proc Natl Acad Sci U S A (2006) 1.24
In silico proteome analysis to facilitate proteomics experiments using mass spectrometry. Proteome Sci (2003) 1.24
Perinuclear cohibin complexes maintain replicative life span via roles at distinct silent chromatin domains. Dev Cell (2011) 1.21
Interactions of elongation factor EF-P with the Escherichia coli ribosome. FEBS J (2008) 1.20
JlpA of Campylobacter jejuni interacts with surface-exposed heat shock protein 90alpha and triggers signalling pathways leading to the activation of NF-kappaB and p38 MAP kinase in epithelial cells. Cell Microbiol (2003) 1.19
Structure of a SLC26 anion transporter STAS domain in complex with acyl carrier protein: implications for E. coli YchM in fatty acid metabolism. Structure (2010) 1.19
Defining the budding yeast chromatin-associated interactome. Mol Syst Biol (2010) 1.19
Cardiovascular proteomics: tools to develop novel biomarkers and potential applications. J Am Coll Cardiol (2006) 1.19
Multidimensional protein identification technology (MudPIT): technical overview of a profiling method optimized for the comprehensive proteomic investigation of normal and diseased heart tissue. J Am Soc Mass Spectrom (2005) 1.13
The Arabidopsis BRAHMA chromatin-remodeling ATPase is involved in repression of seed maturation genes in leaves. Plant Physiol (2008) 1.13
Systems-level analyses identify extensive coupling among gene expression machines. Mol Syst Biol (2006) 1.12
Formation of a distinctive complex between the inducible bacterial lysine decarboxylase and a novel AAA+ ATPase. J Biol Chem (2005) 1.10
Recent advances and method development for drug target identification. Trends Pharmacol Sci (2009) 1.09
Human tissue profiling with multidimensional protein identification technology. J Proteome Res (2005) 1.07
Sarcolipin retention in the endoplasmic reticulum depends on its C-terminal RSYQY sequence and its interaction with sarco(endo)plasmic Ca(2+)-ATPases. Proc Natl Acad Sci U S A (2004) 1.06