Published in Proteomics on March 01, 2010
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The quantitative proteome of a human cell line. Mol Syst Biol (2011) 4.57
PaxDb, a database of protein abundance averages across all three domains of life. Mol Cell Proteomics (2012) 2.93
Genetic variation shapes protein networks mainly through non-transcriptional mechanisms. PLoS Biol (2011) 2.08
Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens. Science (2015) 2.06
Cdc48/p97 mediates UV-dependent turnover of RNA Pol II. Mol Cell (2011) 1.91
Protein abundances are more conserved than mRNA abundances across diverse taxa. Proteomics (2010) 1.71
Quantitative functions of Argonaute proteins in mammalian development. Genes Dev (2012) 1.64
Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription. Mol Cell Proteomics (2012) 1.49
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Constraints and plasticity in genome and molecular-phenome evolution. Nat Rev Genet (2010) 1.41
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Stage-specific proteomic expression patterns of the human filarial parasite Brugia malayi and its endosymbiont Wolbachia. Proc Natl Acad Sci U S A (2011) 1.20
Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription. Mol Cell Proteomics (2011) 1.07
Conservation of caspase substrates across metazoans suggests hierarchical importance of signaling pathways over specific targets and cleavage site motifs in apoptosis. Cell Death Differ (2012) 0.97
Scaffold-mediated nucleation of protein signaling complexes: elementary principles. Math Biosci (2011) 0.95
Improving the TFold test for differential shotgun proteomics. Bioinformatics (2012) 0.91
The functional interactome of PYHIN immune regulators reveals IFIX is a sensor of viral DNA. Mol Syst Biol (2015) 0.90
Transcription profiling reveals stage- and function-dependent expression patterns in the filarial nematode Brugia malayi. BMC Genomics (2012) 0.88
Comparative omics-driven genome annotation refinement: application across Yersiniae. PLoS One (2012) 0.86
Proteome sampling by the HLA class I antigen processing pathway. PLoS Comput Biol (2012) 0.85
Comprehensive Analysis of the Naturally Processed Peptide Repertoire: Differences between HLA-A and B in the Immunopeptidome. PLoS One (2015) 0.85
Protein conservation and variation suggest mechanisms of cell type-specific modulation of signaling pathways. PLoS Comput Biol (2014) 0.84
Conserved abundance and topological features in chromatin-remodeling protein interaction networks. EMBO Rep (2014) 0.82
Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring. Mol Cell Proteomics (2016) 0.82
Computational modelling of the regulation of Insulin signalling by oxidative stress. BMC Syst Biol (2013) 0.80
Investment in rapid growth shapes the evolutionary rates of essential proteins. Proc Natl Acad Sci U S A (2011) 0.80
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Comparative metagenomics of microbial communities. Science (2005) 25.88
STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res (2008) 20.62
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res (2010) 18.73
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res (2012) 18.26
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
Toward automatic reconstruction of a highly resolved tree of life. Science (2006) 14.96
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43
Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol (2007) 7.58
The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet (2004) 5.79
Immunity-related genes and gene families in Anopheles gambiae. Science (2002) 5.47
STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res (2007) 4.88
eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res (2007) 4.84
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet (2005) 4.19
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res (2011) 3.94
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eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res (2013) 3.77
Prediction of effective genome size in metagenomic samples. Genome Biol (2007) 3.73
Finding function in novel targets: C. elegans as a model organism. Nat Rev Drug Discov (2006) 3.64
Evidence for widespread degradation of gene control regions in hominid genomes. PLoS Biol (2005) 3.47
Function prediction and protein networks. Curr Opin Cell Biol (2003) 3.46
Deficiency of FANCD2-associated nuclease KIAA1018/FAN1 sensitizes cells to interstrand crosslinking agents. Cell (2010) 3.37
A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol (2007) 3.34
Protein interaction networks from yeast to human. Curr Opin Struct Biol (2004) 3.15
Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci U S A (2009) 3.11
Microtubule-associated protein 1 light chain 3 alpha (LC3)-associated phagocytosis is required for the efficient clearance of dead cells. Proc Natl Acad Sci U S A (2011) 3.11
mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods (2011) 3.10
Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol (2009) 3.09
STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Res (2009) 3.06
Environments shape the nucleotide composition of genomes. EMBO Rep (2005) 2.96
Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Mol Cell Proteomics (2009) 2.96
A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res (2010) 2.85
Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat Biotechnol (2004) 2.83
Functional identification of optimized RNAi triggers using a massively parallel sensor assay. Mol Cell (2011) 2.82
Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog (2010) 2.79
Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote. Science (2013) 2.51
Two pathways converge at CED-10 to mediate actin rearrangement and corpse removal in C. elegans. Nature (2005) 2.49
Chance and necessity in the evolution of minimal metabolic networks. Nature (2006) 2.48
Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects. Genome Res (2006) 2.42
Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci Signal (2010) 2.36
STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Res (2013) 2.32
Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens. Proc Natl Acad Sci U S A (2014) 2.25
HIF-1 antagonizes p53-mediated apoptosis through a secreted neuronal tyrosinase. Nature (2010) 2.23
A pathway for phagosome maturation during engulfment of apoptotic cells. Nat Cell Biol (2008) 2.20
The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea. PLoS Pathog (2010) 2.17
Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Sci Signal (2009) 2.16
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol Syst Biol (2008) 2.12
MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies. BMC Genomics (2010) 2.12
Caenorhabditis elegans HUS-1 is a DNA damage checkpoint protein required for genome stability and EGL-1-mediated apoptosis. Curr Biol (2002) 2.06
STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Res (2011) 2.05
Dock180 and ELMO1 proteins cooperate to promote evolutionarily conserved Rac-dependent cell migration. J Biol Chem (2003) 2.04
Developmental apoptosis in C. elegans: a complex CEDnario. Nat Rev Mol Cell Biol (2006) 1.99
EvolView, an online tool for visualizing, annotating and managing phylogenetic trees. Nucleic Acids Res (2012) 1.90
Phagocytosis of apoptotic cells is regulated by a UNC-73/TRIO-MIG-2/RhoG signaling module and armadillo repeats of CED-12/ELMO. Curr Biol (2004) 1.87
An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species. Plant Physiol (2010) 1.87
Arabidopsis female gametophyte gene expression map reveals similarities between plant and animal gametes. Curr Biol (2010) 1.85
A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans. Nat Methods (2010) 1.82
Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J (2011) 1.75
Protection of C. elegans from anoxia by HYL-2 ceramide synthase. Science (2009) 1.75
X-chromosome-wide profiling of MSL-1 distribution and dosage compensation in Drosophila. Genes Dev (2006) 1.70
An integrated approach to characterize genetic interaction networks in yeast metabolism. Nat Genet (2011) 1.62
Complex genomic rearrangements lead to novel primate gene function. Genome Res (2005) 1.62
Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution. Bioessays (2013) 1.60
OGEE: an online gene essentiality database. Nucleic Acids Res (2011) 1.54
Identification and analysis of evolutionarily cohesive functional modules in protein networks. Genome Res (2006) 1.48
Similar gene expression profiles do not imply similar tissue functions. Trends Genet (2006) 1.46
Plant and animal glycolate oxidases have a common eukaryotic ancestor and convergently duplicated to evolve long-chain 2-hydroxy acid oxidases. Mol Biol Evol (2014) 1.44
A Steric-inhibition model for regulation of nucleotide exchange via the Dock180 family of GEFs. Curr Biol (2005) 1.41
Syndecan regulates cell migration and axon guidance in C. elegans. Development (2005) 1.40
ArrayProspector: a web resource of functional associations inferred from microarray expression data. Nucleic Acids Res (2004) 1.39
PH domain of ELMO functions in trans to regulate Rac activation via Dock180. Nat Struct Mol Biol (2004) 1.36
Assessing systems properties of yeast mitochondria through an interaction map of the organelle. PLoS Genet (2006) 1.31
Caenorhabditis elegans ABL-1 antagonizes p53-mediated germline apoptosis after ionizing irradiation. Nat Genet (2004) 1.29
Aminophospholipid translocase TAT-1 promotes phosphatidylserine exposure during C. elegans apoptosis. Curr Biol (2007) 1.28
RNAi screen of Salmonella invasion shows role of COPI in membrane targeting of cholesterol and Cdc42. Mol Syst Biol (2011) 1.27
Predicting C4 photosynthesis evolution: modular, individually adaptive steps on a Mount Fuji fitness landscape. Cell (2013) 1.24
Mitochondria as a target of environmental toxicants. Toxicol Sci (2013) 1.24
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. Nucleic Acids Res (2004) 1.24
Caenorhabditis elegans N-glycan core beta-galactoside confers sensitivity towards nematotoxic fungal galectin CGL2. PLoS Pathog (2010) 1.23
The Wnt pathway controls cell death engulfment, spindle orientation, and migration through CED-10/Rac. PLoS Biol (2010) 1.20
Younger genes are less likely to be essential than older genes, and duplicates are less likely to be essential than singletons of the same age. Mol Biol Evol (2012) 1.19
URI-1 is required for DNA stability in C. elegans. Development (2006) 1.16
Imprinted chromosomal regions of the human genome have unusually high recombination rates. Genetics (2003) 1.15
C. elegans GLA-3 is a novel component of the MAP kinase MPK-1 signaling pathway required for germ cell survival. Genes Dev (2006) 1.15
Shared components of protein complexes--versatile building blocks or biochemical artefacts? Bioessays (2004) 1.13
Transcriptional coupling of neighboring genes and gene expression noise: evidence that gene orientation and noncoding transcripts are modulators of noise. Genome Biol Evol (2011) 1.12
High confidence prediction of essential genes in Burkholderia cenocepacia. PLoS One (2012) 1.12
Consistency of genome-based methods in measuring Metazoan evolution. FEBS Lett (2005) 1.11
Genome-wide acceleration of protein evolution in flies (Diptera). BMC Evol Biol (2006) 1.10
Gene expression, synteny, and local similarity in human noncoding mutation rates. Mol Biol Evol (2004) 1.09
Limits to robustness and reproducibility in the demarcation of operational taxonomic units. Environ Microbiol (2014) 1.09
Loss of the RhoGAP SRGP-1 promotes the clearance of dead and injured cells in Caenorhabditis elegans. Nat Cell Biol (2010) 1.08
Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens. BMC Genomics (2014) 1.08
Caenorhabditis elegans DNA mismatch repair gene msh-2 is required for microsatellite stability and maintenance of genome integrity. Proc Natl Acad Sci U S A (2002) 1.08
Co-expression of neighbouring genes in Arabidopsis: separating chromatin effects from direct interactions. BMC Genomics (2010) 1.06
Teamed up for transcription. Nature (2002) 1.06
A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens. Bioinformatics (2003) 1.05
Plasticity of the β-trefoil protein fold in the recognition and control of invertebrate predators and parasites by a fungal defence system. PLoS Pathog (2012) 1.05