Published in Genome Biol on April 14, 2011
Exploring the yeast acetylome using functional genomics. Cell (2012) 1.05
The calcineurin signaling network evolves via conserved kinase-phosphatase modules that transcend substrate identity. Mol Cell (2014) 1.04
Combining genetic perturbations and proteomics to examine kinase-phosphatase networks in Drosophila embryos. Dev Cell (2014) 0.94
Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs. Genome Res (2012) 0.93
Pathway connectivity and signaling coordination in the yeast stress-activated signaling network. Mol Syst Biol (2014) 0.90
Pyrosequencing-based transcriptome analysis of the asian rice gall midge reveals differential response during compatible and incompatible interaction. Int J Mol Sci (2012) 0.80
Allele-specific behavior of molecular networks: understanding small-molecule drug response in yeast. PLoS One (2013) 0.79
Dissection of Cdk1-cyclin complexes in vivo. Proc Natl Acad Sci U S A (2013) 0.79
Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. Methods Cell Biol (2012) 0.79
Evolutionary and Biochemical Aspects of Chemical Stress Resistance in Saccharomyces cerevisiae. Front Genet (2012) 0.79
The Hsp70 homolog Ssb and the 14-3-3 protein Bmh1 jointly regulate transcription of glucose repressed genes in Saccharomyces cerevisiae. Nucleic Acids Res (2016) 0.77
Top-down network analysis to drive bottom-up modeling of physiological processes. J Comput Biol (2013) 0.77
Machine Learning of Global Phosphoproteomic Profiles Enables Discrimination of Direct versus Indirect Kinase Substrates. Mol Cell Proteomics (2017) 0.75
Functional Analysis of Kinases and Transcription Factors in Saccharomyces cerevisiae Using an Integrated Overexpression Library. G3 (Bethesda) (2017) 0.75
Delineating functional principles of the bow tie structure of a kinase-phosphatase network in the budding yeast. BMC Syst Biol (2017) 0.75
A prior-based integrative framework for functional transcriptional regulatory network inference. Nucleic Acids Res (2016) 0.75
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76
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Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature (2002) 45.19
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
The protein kinase complement of the human genome. Science (2002) 35.36
Global analysis of protein localization in budding yeast. Nature (2003) 33.22
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41
Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77
The genetic landscape of a cell. Science (2010) 16.52
The BioGRID Interaction Database: 2008 update. Nucleic Acids Res (2007) 11.83
High-quality binary protein interaction map of the yeast interactome network. Science (2008) 10.65
Cytoscape Web: an interactive web-based network browser. Bioinformatics (2010) 10.03
Targets of the cyclin-dependent kinase Cdk1. Nature (2003) 8.05
FunSpec: a web-based cluster interpreter for yeast. BMC Bioinformatics (2002) 8.01
Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46
Protein kinases--the major drug targets of the twenty-first century? Nat Rev Drug Discov (2002) 7.38
Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell (2006) 6.42
A global protein kinase and phosphatase interaction network in yeast. Science (2010) 5.95
PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics (2004) 5.55
An in vivo map of the yeast protein interactome. Science (2008) 5.52
Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science (2009) 5.37
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Functional organization of the S. cerevisiae phosphorylation network. Cell (2009) 3.15
Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci Signal (2010) 2.95
Snf1 protein kinase regulates phosphorylation of the Mig1 repressor in Saccharomyces cerevisiae. Mol Cell Biol (1998) 2.69
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Combining chemical genetics and proteomics to identify protein kinase substrates. Proc Natl Acad Sci U S A (2005) 1.63
The high osmotic response and cell wall integrity pathways cooperate to regulate transcriptional responses to zymolyase-induced cell wall stress in Saccharomyces cerevisiae. J Biol Chem (2009) 1.46
The sequential activation of the yeast HOG and SLT2 pathways is required for cell survival to cell wall stress. Mol Biol Cell (2008) 1.45
The SNF1 kinase complex from Saccharomyces cerevisiae phosphorylates the transcriptional repressor protein Mig1p in vitro at four sites within or near regulatory domain 1. FEBS Lett (1999) 1.23
The Snf1 kinase controls glucose repression in yeast by modulating interactions between the Mig1 repressor and the Cyc8-Tup1 co-repressor. EMBO Rep (2004) 1.15
The high-osmolarity glycerol (HOG) and cell wall integrity (CWI) signalling pathways interplay: a yeast dialogue between MAPK routes. Yeast (2010) 1.04
Linking the kinome and phosphorylome--a comprehensive review of approaches to find kinase targets. Mol Biosyst (2008) 0.99
Cell integrity signaling activation in response to hyperosmotic shock in yeast. FEBS Lett (2005) 0.99
Mechanisms regulating the protein kinases of Saccharomyces cerevisiae. Eukaryot Cell (2007) 0.85
Global mapping of the yeast genetic interaction network. Science (2004) 21.34
The genetic landscape of a cell. Science (2010) 16.52
Population genomics of domestic and wild yeasts. Nature (2009) 11.79
In vivo enhancer analysis of human conserved non-coding sequences. Nature (2006) 10.60
Exploring genetic interactions and networks with yeast. Nat Rev Genet (2007) 5.67
Exploration of essential gene functions via titratable promoter alleles. Cell (2004) 5.21
The synthetic genetic interaction spectrum of essential genes. Nat Genet (2005) 3.06
Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genet (2006) 3.01
eSGA: E. coli synthetic genetic array analysis. Nat Methods (2008) 3.01
Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci Signal (2010) 2.95
Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol (2004) 2.81
Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods (2010) 2.67
Identifying transcription factor functions and targets by phenotypic activation. Proc Natl Acad Sci U S A (2006) 2.39
Chlorophyll breakdown in senescent Arabidopsis leaves. Characterization of chlorophyll catabolites and of chlorophyll catabolic enzymes involved in the degreening reaction. Plant Physiol (2005) 2.39
Direct regulation of Arp2/3 complex activity and function by the actin binding protein coronin. J Cell Biol (2002) 2.17
NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. BMC Bioinformatics (2009) 2.11
A high-definition view of functional genetic variation from natural yeast genomes. Mol Biol Evol (2014) 2.10
Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes. Proc Natl Acad Sci U S A (2008) 2.01
Systematic exploration of synergistic drug pairs. Mol Syst Biol (2011) 1.89
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet (2013) 1.68
Global gene deletion analysis exploring yeast filamentous growth. Science (2012) 1.67
The budding yeast nuclear envelope adjacent to the nucleolus serves as a membrane sink during mitotic delay. Curr Biol (2012) 1.65
An integrated approach to characterize genetic interaction networks in yeast metabolism. Nat Genet (2011) 1.62
Cellular pathways regulating responses to compatible and self-incompatible pollen in Brassica and Arabidopsis stigmas intersect at Exo70A1, a putative component of the exocyst complex. Plant Cell (2009) 1.62
Yeast Barcoders: a chemogenomic application of a universal donor-strain collection carrying bar-code identifiers. Nat Methods (2008) 1.56
Global map of SUMO function revealed by protein-protein interaction and genetic networks. Mol Cell (2009) 1.55
Pho85, a multifunctional cyclin-dependent protein kinase in budding yeast. Mol Microbiol (2007) 1.44
Evidence for widespread adaptive evolution of gene expression in budding yeast. Proc Natl Acad Sci U S A (2010) 1.44
Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. BMC Bioinformatics (2006) 1.44
DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Res (2009) 1.41
Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biol (2003) 1.40
Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis. J Cell Biol (2010) 1.36
Bringing order to protein disorder through comparative genomics and genetic interactions. Genome Biol (2011) 1.34
Good fat, essential cellular requirements for triacylglycerol synthesis to maintain membrane homeostasis in yeast. J Biol Chem (2009) 1.34
Components of the ESCRT pathway, DFG16, and YGR122w are required for Rim101 to act as a corepressor with Nrg1 at the negative regulatory element of the DIT1 gene of Saccharomyces cerevisiae. Mol Cell Biol (2005) 1.33
The EVERSHED receptor-like kinase modulates floral organ shedding in Arabidopsis. Development (2010) 1.28
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
Protein-protein interaction affinity plays a crucial role in controlling the Sho1p-mediated signal transduction pathway in yeast. Mol Cell (2004) 1.24
Putting genetic interactions in context through a global modular decomposition. Genome Res (2011) 1.24
Evolution of characterized phosphorylation sites in budding yeast. Mol Biol Evol (2010) 1.20
Activation of the Cdc42p GTPase by cyclin-dependent protein kinases in budding yeast. EMBO J (2007) 1.20
The SERK1 receptor-like kinase regulates organ separation in Arabidopsis flowers. Plant J (2010) 1.16
Proteome-wide discovery of evolutionary conserved sequences in disordered regions. Sci Signal (2012) 1.15
Dissecting BAR domain function in the yeast Amphiphysins Rvs161 and Rvs167 during endocytosis. Mol Biol Cell (2010) 1.14
SGAtools: one-stop analysis and visualization of array-based genetic interaction screens. Nucleic Acids Res (2013) 1.10
Q&A: epistasis. J Biol (2009) 1.10
Peroxisome proliferator-activated receptor (PPAR)-alpha activation prevents diabetes in OLETF rats: comparison with PPAR-gamma activation. Diabetes (2003) 1.10
Global functional map of the p23 molecular chaperone reveals an extensive cellular network. Mol Cell (2011) 1.09
The biologically relevant targets and binding affinity requirements for the function of the yeast actin-binding protein 1 Src-homology 3 domain vary with genetic context. Genetics (2007) 1.05
Exploring the yeast acetylome using functional genomics. Cell (2012) 1.05
High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome. BMC Genomics (2013) 1.03
Whole-genome analysis reveals that active heat shock factor binding sites are mostly associated with non-heat shock genes in Drosophila melanogaster. PLoS One (2011) 1.02
Functional analysis with a barcoder yeast gene overexpression system. G3 (Bethesda) (2012) 1.02
Mss11p is a transcription factor regulating pseudohyphal differentiation, invasive growth and starch metabolism in Saccharomyces cerevisiae in response to nutrient availability. Mol Microbiol (2003) 0.99
Linking the kinome and phosphorylome--a comprehensive review of approaches to find kinase targets. Mol Biosyst (2008) 0.99
Protein complexes are central in the yeast genetic landscape. PLoS Comput Biol (2011) 0.99
Phenotypic activation to discover biological pathways and kinase substrates. Cell Cycle (2006) 0.99
Quantitative modeling of triacylglycerol homeostasis in yeast--metabolic requirement for lipolysis to promote membrane lipid synthesis and cellular growth. FEBS J (2008) 0.99
Global analysis of SUMO chain function reveals multiple roles in chromatin regulation. J Cell Biol (2013) 0.98
Dual regulation by pairs of cyclin-dependent protein kinases and histone deacetylases controls G1 transcription in budding yeast. PLoS Biol (2009) 0.98
Clathrin light chain directs endocytosis by influencing the binding of the yeast Hip1R homologue, Sla2, to F-actin. Mol Biol Cell (2011) 0.98
A novel mechanism for SUMO system control: regulated Ulp1 nucleolar sequestration. Mol Cell Biol (2010) 0.97
The Arabidopsis ZED1 pseudokinase is required for ZAR1-mediated immunity induced by the Pseudomonas syringae type III effector HopZ1a. Proc Natl Acad Sci U S A (2013) 0.97
alpha-Lipoic acid prevents diabetes mellitus in diabetes-prone obese rats. Biochem Biophys Res Commun (2005) 0.96
Conserved rules govern genetic interaction degree across species. Genome Biol (2012) 0.95
Conserved regulators of nucleolar size revealed by global phenotypic analyses. Sci Signal (2013) 0.95
A genome-wide synthetic dosage lethality screen reveals multiple pathways that require the functioning of ubiquitin-binding proteins Rad23 and Dsk2. BMC Biol (2009) 0.94
Primate-specific evolution of an LDLR enhancer. Genome Biol (2006) 0.94
A picture is worth a thousand words: genomics to phenomics in the yeast Saccharomyces cerevisiae. FEBS Lett (2009) 0.94
Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs. Genome Res (2012) 0.93
Ubiquitin ligase Ufd2 is required for efficient degradation of Mps1 kinase. J Biol Chem (2011) 0.92
Polymorphism, divergence, and the role of recombination in Saccharomyces cerevisiae genome evolution. Mol Biol Evol (2011) 0.92
Ubiquitin chain elongation enzyme Ufd2 regulates a subset of Doa10 substrates. J Biol Chem (2010) 0.92
Sequencing and annotation of the Ophiostoma ulmi genome. BMC Genomics (2013) 0.91
Regulation of cell polarity through phosphorylation of Bni4 by Pho85 G1 cyclin-dependent kinases in Saccharomyces cerevisiae. Mol Biol Cell (2009) 0.90
Unsupervised clustering of subcellular protein expression patterns in high-throughput microscopy images reveals protein complexes and functional relationships between proteins. PLoS Comput Biol (2013) 0.88
Ranking insertion, deletion and nonsense mutations based on their effect on genetic information. BMC Bioinformatics (2011) 0.87
Restriction of histone gene transcription to S phase by phosphorylation of a chromatin boundary protein. Genes Dev (2011) 0.85
Bck2 acts through the MADS box protein Mcm1 to activate cell-cycle-regulated genes in budding yeast. PLoS Genet (2013) 0.84
Playing tag with the yeast proteome. Nat Biotechnol (2003) 0.83
Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis. PLoS One (2007) 0.83