Published in Nucleic Acids Res on May 30, 2013
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Rtr1 is a dual specificity phosphatase that dephosphorylates Tyr1 and Ser5 on the RNA polymerase II CTD. J Mol Biol (2014) 0.89
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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
A novel cytoplasmic GTPase XAB1 interacts with DNA repair protein XPA. Nucleic Acids Res (2000) 1.23
Ser7 phosphorylation of the CTD recruits the RPAP2 Ser5 phosphatase to snRNA genes. Mol Cell (2011) 1.20
A human RNA polymerase II-containing complex associated with factors necessary for spliceosome assembly. J Biol Chem (2001) 1.12
MBDin, a novel MBD2-interacting protein, relieves MBD2 repression potential and reactivates transcription from methylated promoters. Mol Cell Biol (2003) 1.12
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Human GTPases associate with RNA polymerase II to mediate its nuclear import. Mol Cell Biol (2011) 1.05
Rtr1 is the Saccharomyces cerevisiae homolog of a novel family of RNA polymerase II-binding proteins. Eukaryot Cell (2008) 0.99
The yeast regulator of transcription protein Rtr1 lacks an active site and phosphatase activity. Nat Commun (2012) 0.96
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GTP-dependent binding and nuclear transport of RNA polymerase II by Npa3 protein. J Biol Chem (2011) 0.89
New insights into the biogenesis of nuclear RNA polymerases? Biochem Cell Biol (2010) 0.89
Importin-beta is a GDP-to-GTP exchange factor of Ran: implications for the mechanism of nuclear import. J Biol Chem (2009) 0.86
Expression, purification, crystallization and preliminary crystallographic analysis of the PAB0955 gene product. Acta Crystallogr Sect F Struct Biol Cryst Commun (2005) 0.86
A nuclear export sequence in GPN-loop GTPase 1, an essential protein for nuclear targeting of RNA polymerase II, is necessary and sufficient for nuclear export. Biochim Biophys Acta (2012) 0.81
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
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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
hnRNP proteins and splicing control. Adv Exp Med Biol (2007) 2.39
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
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
High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes. Methods (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
hnRNP I/PTB can antagonize the splicing repressor activity of SRp30c. RNA (2007) 1.19
Deletion of many yeast introns reveals a minority of genes that require splicing for function. Mol Biol Cell (2008) 1.19
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
Protein kinase C-dependent control of Bcl-x alternative splicing. Mol Cell Biol (2007) 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
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
Computational prediction of the localization of microRNAs within their pre-miRNA. Nucleic Acids Res (2013) 0.94
Long-range regulation is a major driving force in maintaining genome integrity. BMC Evol Biol (2009) 0.94
Interactions of a DNA-bound transcriptional activator with the TBP-TFIIA-TFIIB-promoter quaternary complex. J Biol Chem (2003) 0.93
FootPrinter3: phylogenetic footprinting in partially alignable sequences. Nucleic Acids Res (2006) 0.92
Computing chromosome conformation. Methods Mol Biol (2010) 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
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
Regulation of molecular chaperones through post-translational modifications: decrypting the chaperone code. Biochim Biophys Acta (2013) 0.90
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
New insights into the biogenesis of nuclear RNA polymerases? Biochem Cell Biol (2010) 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
Detection of locally over-represented GO terms in protein-protein interaction networks. J Comput Biol (2010) 0.85
Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania. BMC Bioinformatics (2008) 0.85
Genome-wide mouse mutagenesis reveals CD45-mediated T cell function as critical in protective immunity to HSV-1. PLoS Pathog (2013) 0.84
An N-ethyl-N-nitrosourea (ENU)-induced dominant negative mutation in the JAK3 kinase protects against cerebral malaria. PLoS One (2012) 0.83
Classifying leukemia types with chromatin conformation data. Genome Biol (2014) 0.83
A whole genome study and identification of specific carcinogenic regions of the human papilloma viruses. J Comput Biol (2009) 0.82
Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI). Biochem Cell Biol (2008) 0.81
Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry. J Proteome Res (2012) 0.80
The RPB2 flap loop of human RNA polymerase II is dispensable for transcription initiation and elongation. Mol Cell Biol (2011) 0.80
Genetic map refinement using a comparative genomic approach. J Comput Biol (2009) 0.79
Site-specific protein-DNA photocross-linking of purified complexes: topology of the RNA polymerase II transcription initiation complex. Methods Enzymol (2003) 0.78
Mapping association between long-range cis-regulatory regions and their target genes using synteny. J Comput Biol (2011) 0.77
Predicting site-specific human selective pressure using evolutionary signatures. Bioinformatics (2011) 0.77
Defining protein interactions that regulate disease progression. Expert Opin Ther Targets (2009) 0.76
A probabilistic model for sequence alignment with context-sensitive indels. J Comput Biol (2011) 0.76
Positional mapping and candidate gene analysis of the mouse Ccs3 locus that regulates differential susceptibility to carcinogen-induced colorectal cancer. PLoS One (2013) 0.76
SPARCS: a web server to analyze (un)structured regions in coding RNA sequences. Nucleic Acids Res (2013) 0.76
Use of site-specific protein-DNA photocrosslinking of purified complexes to analyze the topology of the RNA polymerase II transcription initiation complex. Methods Mol Biol (2009) 0.75
Increased subcutaneous adipose tissue expression of genes involved in glycerolipid-fatty acid cycling in obese insulin-resistant versus -sensitive individuals. J Clin Endocrinol Metab (2014) 0.75
StructMiner: a tool for alignment and detection of conserved secondary structure. Genome Inform (2004) 0.75