Published in Methods on May 18, 2009
HSP90 and its R2TP/Prefoldin-like cochaperone are involved in the cytoplasmic assembly of RNA polymerase II. Mol Cell (2010) 2.07
A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. PLoS Genet (2013) 1.37
Integrated metabolo-proteomic approach to decipher the mechanisms by which wheat QTL (Fhb1) contributes to resistance against Fusarium graminearum. PLoS One (2012) 1.28
Establishment of a protein frequency library and its application in the reliable identification of specific protein interaction partners. Mol Cell Proteomics (2009) 1.24
The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II. Mol Cell Proteomics (2010) 1.23
Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics (2012) 1.21
Defining the budding yeast chromatin-associated interactome. Mol Syst Biol (2010) 1.19
Dysferlin interacts with tubulin and microtubules in mouse skeletal muscle. PLoS One (2010) 1.06
Modeling contaminants in AP-MS/MS experiments. J Proteome Res (2010) 1.03
Regulation of androgen receptor-mediated transcription by RPB5 binding protein URI/RMP. Mol Cell Biol (2011) 1.02
Mass spectrometry and biochemical analysis of RNA polymerase II: targeting by protein phosphatase-1. Mol Cell Biochem (2010) 1.00
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. Anal Chem (2012) 0.98
Quality control for unfolded proteins at the plasma membrane. J Cell Biol (2010) 0.96
Transcription factor IIS cooperates with the E3 ligase UBR5 to ubiquitinate the CDK9 subunit of the positive transcription elongation factor B. J Biol Chem (2010) 0.96
Integrated regulation of PIKK-mediated stress responses by AAA+ proteins RUVBL1 and RUVBL2. Nucleus (2012) 0.94
Recessive mutations in POLR1C cause a leukodystrophy by impairing biogenesis of RNA polymerase III. Nat Commun (2015) 0.92
Drosophila Spag is the homolog of RNA polymerase II-associated protein 3 (RPAP3) and recruits the heat shock proteins 70 and 90 (Hsp70 and Hsp90) during the assembly of cellular machineries. J Biol Chem (2014) 0.92
Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. Mol Cell Proteomics (2012) 0.92
Analysis of URI nuclear interaction with RPB5 and components of the R2TP/prefoldin-like complex. PLoS One (2013) 0.89
Proteomic and 3D structure analyses highlight the C/D box snoRNP assembly mechanism and its control. J Cell Biol (2014) 0.89
New insights into the biogenesis of nuclear RNA polymerases? Biochem Cell Biol (2010) 0.89
Predicting direct protein interactions from affinity purification mass spectrometry data. Algorithms Mol Biol (2010) 0.86
Nuclear import of RNA polymerase II is coupled with nucleocytoplasmic shuttling of the RNA polymerase II-associated protein 2. Nucleic Acids Res (2013) 0.84
The interactome of the atypical phosphatase Rtr1 in Saccharomyces cerevisiae. Mol Biosyst (2014) 0.81
Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes. PLoS Comput Biol (2011) 0.80
Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry. J Proteome Res (2012) 0.80
Substrate recognition and function of the R2TP complex in response to cellular stress. Front Genet (2015) 0.79
Proteomic analysis of mitotic RNA polymerase II reveals novel interactors and association with proteins dysfunctional in disease. Mol Cell Proteomics (2011) 0.77
Proteomic and Genomic Analyses of the Rvb1 and Rvb2 Interaction Network upon Deletion of R2TP Complex Components. Mol Cell Proteomics (2016) 0.76
Mapping the disease protein interactome: toward a molecular medicine GPS to accelerate drug and biomarker discovery. J Proteome Res (2010) 0.76
Colorectal cancer cells display chaperone dependency for the unconventional prefoldin URI1. Oncotarget (2016) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis (1999) 45.01
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods (2007) 25.29
A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol (1999) 25.13
The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods (2001) 15.37
Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol (2007) 8.16
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
Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods (2006) 3.37
Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc Natl Acad Sci U S A (2008) 3.23
VisANT: an integrative framework for networks in systems biology. Brief Bioinform (2008) 2.85
LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated. Nucleic Acids Res (2008) 2.38
Fast-response proteomics by accelerated in-gel digestion of proteins. Anal Chem (2003) 2.32
Control of nutrient-sensitive transcription programs by the unconventional prefoldin URI. Science (2003) 2.15
Molecular chaperone Hsp90 stabilizes Pih1/Nop17 to maintain R2TP complex activity that regulates snoRNA accumulation. J Cell Biol (2008) 1.92
S6K1-mediated disassembly of mitochondrial URI/PP1gamma complexes activates a negative feedback program that counters S6K1 survival signaling. Mol Cell (2007) 1.66
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
RMP, a novel RNA polymerase II subunit 5-interacting protein, counteracts transactivation by hepatitis B virus X protein. Mol Cell Biol (1998) 1.39
Molecular cloning of novel Monad binding protein containing tetratricopeptide repeat domains. FEBS Lett (2008) 0.92
Identification and characterization of multi-species conserved sequences. Genome Res (2003) 10.18
Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat Genet (2009) 4.72
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
Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biol (2005) 4.48
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res (2006) 4.32
Reconstructing contiguous regions of an ancestral genome. Genome Res (2006) 3.68
PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics (2004) 3.63
Genome-wide orchestration of cardiac functions by the orphan nuclear receptors ERRalpha and gamma. Cell Metab (2007) 3.00
Phylo: a citizen science approach for improving multiple sequence alignment. PLoS One (2012) 2.64
A probabilistic approach for SNP discovery in high-throughput human resequencing data. Genome Res (2009) 2.55
Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics (2004) 2.50
LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated. Nucleic Acids Res (2008) 2.38
PReMod: a database of genome-wide mammalian cis-regulatory module predictions. Nucleic Acids Res (2006) 2.27
Evolutionarily conserved sequence elements that positively regulate IFN-gamma expression in T cells. Proc Natl Acad Sci U S A (2004) 2.21
The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts. Genome Biol (2014) 2.01
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling. BMC Bioinformatics (2011) 1.78
The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet (2013) 1.69
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet (2013) 1.68
Chromatin conformation signatures of cellular differentiation. Genome Biol (2009) 1.68
Ordered conformational changes in damaged DNA induced by nucleotide excision repair factors. J Biol Chem (2004) 1.59
Structural perspective on mutations affecting the function of multisubunit RNA polymerases. Microbiol Mol Biol Rev (2006) 1.51
BH3-ligand regulates access of MCL-1 to its E3 ligase. FEBS Lett (2005) 1.49
Amino acid substitutions that specifically impair the transcriptional activity of papillomavirus E2 affect binding to the long isoform of Brd4. Virology (2006) 1.47
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
S-nitrosylation of beta-catenin by eNOS-derived NO promotes VEGF-induced endothelial cell permeability. Mol Cell (2010) 1.38
A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. PLoS Genet (2013) 1.37
The three-dimensional architecture of Hox cluster silencing. Nucleic Acids Res (2010) 1.36
Exact and heuristic algorithms for the Indel Maximum Likelihood Problem. J Comput Biol (2007) 1.35
Photo-cross-linking of a purified preinitiation complex reveals central roles for the RNA polymerase II mobile clamp and TFIIE in initiation mechanisms. Mol Cell Biol (2004) 1.32
The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II. Mol Cell Proteomics (2010) 1.23
Effects of echo time on diffusion quantification of brain white matter at 1.5 T and 3.0 T. Magn Reson Med (2009) 1.17
On the inference of parsimonious indel evolutionary scenarios. J Bioinform Comput Biol (2006) 1.14
A human RNA polymerase II-containing complex associated with factors necessary for spliceosome assembly. J Biol Chem (2001) 1.12
Seeder: discriminative seeding DNA motif discovery. Bioinformatics (2008) 1.10
Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment. Genome Biol (2013) 1.06
Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase. Biochim Biophys Acta (2010) 1.06
Highly enriched CD133(+)CD44(+) stem-like cells with CD133(+)CD44(high) metastatic subset in HCT116 colon cancer cells. Clin Exp Metastasis (2011) 1.05
Human papillomavirus E1 helicase interacts with the WD repeat protein p80 to promote maintenance of the viral genome in keratinocytes. J Virol (2007) 1.04
A flexible ancestral genome reconstruction method based on gapped adjacencies. BMC Bioinformatics (2012) 1.03
Modeling contaminants in AP-MS/MS experiments. J Proteome Res (2010) 1.03
Genomic location of the human RNA polymerase II general machinery: evidence for a role of TFIIF and Rpb7 at both early and late stages of transcription. Biochem J (2008) 1.03
Ancestors 1.0: a web server for ancestral sequence reconstruction. Bioinformatics (2009) 1.01
Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase. BMC Biophys (2012) 0.99
Computational analysis of whole-genome differential allelic expression data in human. PLoS Comput Biol (2010) 0.99
Detecting non-coding selective pressure in coding regions. BMC Evol Biol (2007) 0.98
Interaction of RNA polymerase II fork loop 2 with downstream non-template DNA regulates transcription elongation. J Biol Chem (2011) 0.96
Transcription factor IIS cooperates with the E3 ligase UBR5 to ubiquitinate the CDK9 subunit of the positive transcription elongation factor B. J Biol Chem (2010) 0.96
Sheathless capillary electrophoresis-tandem mass spectrometry for top-down characterization of Pyrococcus furiosus proteins on a proteome scale. Anal Chem (2014) 0.95
Mass spectrometry-based metabolomics application to identify quantitative resistance-related metabolites in barley against Fusarium head blight. Mol Plant Pathol (2010) 0.94
Long-range regulation is a major driving force in maintaining genome integrity. BMC Evol Biol (2009) 0.94
Computational prediction of the localization of microRNAs within their pre-miRNA. Nucleic Acids Res (2013) 0.94
Interactions of a DNA-bound transcriptional activator with the TBP-TFIIA-TFIIB-promoter quaternary complex. J Biol Chem (2003) 0.93
ERCC5 promoter polymorphisms at -763 and +25 predict the response to oxaliplatin-based chemotherapy in patients with advanced colorectal cancer. Cancer Biol Ther (2009) 0.92
FootPrinter3: phylogenetic footprinting in partially alignable sequences. Nucleic Acids Res (2006) 0.92
Novel effects of chromosome Y on cardiac regulation, chromatin remodeling, and neonatal programming in male mice. Endocrinology (2013) 0.91
Computing chromosome conformation. Methods Mol Biol (2010) 0.90
Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fish. PLoS One (2011) 0.90
Site-directed mutagenesis, purification and assay of Saccharomyces cerevisiae RNA polymerase II. Protein Expr Purif (2009) 0.90
Hox in motion: tracking HoxA cluster conformation during differentiation. Nucleic Acids Res (2013) 0.90
Regulation of molecular chaperones through post-translational modifications: decrypting the chaperone code. Biochim Biophys Acta (2013) 0.90
New insights into the biogenesis of nuclear RNA polymerases? Biochem Cell Biol (2010) 0.89
Rapid development of sensitive, high-throughput, quantitative and highly selective mass spectrometric targeted immunoassays for clinically important proteins in human plasma and serum. Clin Biochem (2013) 0.89
Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees. BMC Bioinformatics (2007) 0.89
The highly conserved glutamic acid 791 of Rpb2 is involved in the binding of NTP and Mg(B) in the active center of human RNA polymerase II. Nucleic Acids Res (2005) 0.88
Predicting direct protein interactions from affinity purification mass spectrometry data. Algorithms Mol Biol (2010) 0.86
Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania. BMC Bioinformatics (2008) 0.85
Detection of locally over-represented GO terms in protein-protein interaction networks. J Comput Biol (2010) 0.85
Identification of bottlenecks in Escherichia coli engineered for the production of CoQ(10). Metab Eng (2011) 0.85
Nuclear import of RNA polymerase II is coupled with nucleocytoplasmic shuttling of the RNA polymerase II-associated protein 2. Nucleic Acids Res (2013) 0.84
Genome-wide mouse mutagenesis reveals CD45-mediated T cell function as critical in protective immunity to HSV-1. PLoS Pathog (2013) 0.84
Photocycloadditions of substituted oxazoles with isoquinoline-1,3,4-trione--chemo-, regio-, diastereoselectivities and transformation of the photocycloadducts. Org Biomol Chem (2013) 0.83