Published in Mol Cell Proteomics on December 05, 2011
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34
The functional interactome landscape of the human histone deacetylase family. Mol Syst Biol (2013) 1.63
Increased expression of LDL receptor-related protein 1 during human cytomegalovirus infection reduces virion cholesterol and infectivity. Cell Host Microbe (2012) 1.59
Evidence for a genetic and physical interaction between nonstructural proteins NS1 and NS4B that modulates replication of West Nile virus. J Virol (2012) 1.43
Sirtuin activators and inhibitors. Biofactors (2012) 1.19
Kinesin-3 mediates axonal sorting and directional transport of alphaherpesvirus particles in neurons. Cell Host Microbe (2012) 1.14
Regulation of Akt signaling by sirtuins: its implication in cardiac hypertrophy and aging. Circ Res (2014) 1.06
Sirtuin regulation in aging and injury. Biochim Biophys Acta (2015) 0.98
Aurora B-dependent regulation of class IIa histone deacetylases by mitotic nuclear localization signal phosphorylation. Mol Cell Proteomics (2012) 0.91
A Functional Proteomics Perspective of DBC1 as a Regulator of Transcription. J Proteomics Bioinform (2013) 0.86
A complex of YlbF, YmcA and YaaT regulates sporulation, competence and biofilm formation by accelerating the phosphorylation of Spo0A. Mol Microbiol (2013) 0.84
Discovery of host-viral protein complexes during infection. Methods Mol Biol (2013) 0.80
Probing phosphorylation-dependent protein interactions within functional domains of histone deacetylase 5 (HDAC5). Proteomics (2014) 0.76
SIRT7 Is an RNA-Activated Protein Lysine Deacylase. ACS Chem Biol (2016) 0.75
Interactomic analysis of REST/NRSF and implications of its functional links with the transcription suppressor TRIM28 during neuronal differentiation. Sci Rep (2016) 0.75
Computational framework for analysis of prey-prey associations in interaction proteomics identifies novel human protein-protein interactions and networks. J Proteome Res (2012) 0.75
Approaches for Studying the Subcellular Localization, Interactions, and Regulation of Histone Deacetylase 5 (HDAC5). Methods Mol Biol (2016) 0.75
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem (2002) 35.30
A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem (2003) 29.58
Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics (2010) 26.76
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res (2010) 18.73
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics (2010) 13.35
A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science (1996) 12.64
Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell (1990) 12.50
Histone deacetylases (HDACs): characterization of the classical HDAC family. Biochem J (2003) 11.27
The Sir2 family of protein deacetylases. Annu Rev Biochem (2004) 9.28
Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem Biophys Res Commun (2000) 9.09
Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell (2010) 8.79
Genomic instability and aging-like phenotype in the absence of mammalian SIRT6. Cell (2006) 8.48
SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev (1997) 7.81
Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Nature (1999) 7.47
Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: a molecular model for the formation of heterochromatin in yeast. Cell (1995) 7.20
Evolutionarily conserved and nonconserved cellular localizations and functions of human SIRT proteins. Mol Biol Cell (2005) 6.79
Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell (2009) 6.54
Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res (2006) 6.43
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep (2008) 6.10
An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev (1997) 6.00
Evidence that a complex of SIR proteins interacts with the silencer and telomere-binding protein RAP1. Genes Dev (1994) 5.21
c-Myc binds to human ribosomal DNA and stimulates transcription of rRNA genes by RNA polymerase I. Nat Cell Biol (2005) 4.89
Transcription-linked acetylation by Gcn5p of histones H3 and H4 at specific lysines. Nature (1996) 4.70
The biochemistry of sirtuins. Annu Rev Biochem (2006) 4.32
Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast. Genes Dev (1997) 4.31
Crystal structure of the heterodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA. Nature (1995) 4.08
c-Myc associates with ribosomal DNA and activates RNA polymerase I transcription. Nat Cell Biol (2005) 3.79
The nucleolar remodeling complex NoRC mediates heterochromatin formation and silencing of ribosomal gene transcription. Nat Genet (2002) 3.58
Crystal structure of a SIR2 homolog-NAD complex. Cell (2001) 3.57
Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle. Cell (1989) 3.51
Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development. J Proteome Res (2009) 3.44
Mutations in ATRX, encoding a SWI/SNF-like protein, cause diverse changes in the pattern of DNA methylation. Nat Genet (2000) 3.24
The chromatin-remodeling enzyme ACF is an ATP-dependent DNA length sensor that regulates nucleosome spacing. Nat Struct Mol Biol (2006) 3.05
Fluorescent proteins as proteomic probes. Mol Cell Proteomics (2005) 2.98
A genetic screen for ribosomal DNA silencing defects identifies multiple DNA replication and chromatin-modulating factors. Mol Cell Biol (1999) 2.80
Sirt7 increases stress resistance of cardiomyocytes and prevents apoptosis and inflammatory cardiomyopathy in mice. Circ Res (2008) 2.51
Mammalian Sir2 homolog SIRT7 is an activator of RNA polymerase I transcription. Genes Dev (2006) 2.47
Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet (2011) 2.38
The chromatin remodeling complex NoRC targets HDAC1 to the ribosomal gene promoter and represses RNA polymerase I transcription. EMBO J (2002) 2.36
Human Rif1, ortholog of a yeast telomeric protein, is regulated by ATM and 53BP1 and functions in the S-phase checkpoint. Genes Dev (2004) 2.33
A position-effect control for gene transposition: state of expression of yeast mating-type genes affects their ability to switch. Cell (1981) 2.33
Mutations in the chromatin-associated protein ATRX. Hum Mutat (2008) 2.12
A housekeeper with power of attorney: the rRNA genes in ribosome biogenesis. Cell Mol Life Sci (2007) 1.98
Growth factor signaling regulates elongation of RNA polymerase I transcription in mammals via UBF phosphorylation and r-chromatin remodeling. Mol Cell (2006) 1.97
ATRX encodes a novel member of the SNF2 family of proteins: mutations point to a common mechanism underlying the ATR-X syndrome. Hum Mol Genet (1996) 1.91
I-DIRT, a general method for distinguishing between specific and nonspecific protein interactions. J Proteome Res (2005) 1.87
Reconstitution of recombinant chromatin establishes a requirement for histone-tail modifications during chromatin assembly and transcription. Genes Dev (2001) 1.73
Structure and biochemical functions of SIRT6. J Biol Chem (2011) 1.67
Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome. Proteomics (2010) 1.64
The chromatin remodelling complex WSTF-SNF2h interacts with nuclear myosin 1 and has a role in RNA polymerase I transcription. EMBO Rep (2006) 1.59
Nuclear import of histone deacetylase 5 by requisite nuclear localization signal phosphorylation. Mol Cell Proteomics (2010) 1.52
X-ray scattering indicates that the leucine zipper is a coiled coil. Proc Natl Acad Sci U S A (1991) 1.51
The WSTF-SNF2h chromatin remodeling complex interacts with several nuclear proteins in transcription. J Biol Chem (2006) 1.36
Involvement of SIRT7 in resumption of rDNA transcription at the exit from mitosis. J Cell Sci (2009) 1.22
The chromatin remodeling complex NoRC and TTF-I cooperate in the regulation of the mammalian rRNA genes in vivo. Nucleic Acids Res (2004) 1.16
Sirt7-dependent inhibition of cell growth and proliferation might be instrumental to mediate tissue integrity during aging. J Physiol Pharmacol (2008) 1.15
Structure of histone deacetylases: insights into substrate recognition and catalysis. Structure (2001) 1.11
Conjugation of magnetic beads for immunopurification of protein complexes. Cold Spring Harb Protoc (2011) 1.10
Affinity purification of protein complexes. Cold Spring Harb Protoc (2011) 1.06
Regulation of rRNA synthesis in human and mouse cells is not determined by changes in active gene count. Cell Cycle (2006) 0.94
Proteasomal ATPases are associated with rDNA: the ubiquitin proteasome system plays a direct role in RNA polymerase I transcription. Biochim Biophys Acta (2008) 0.94
Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell (2010) 8.79
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34
Induction of autophagy in axonal dystrophy and degeneration. J Neurosci (2006) 3.28
DJ-1 gene deletion reveals that DJ-1 is an atypical peroxiredoxin-like peroxidase. Proc Natl Acad Sci U S A (2007) 2.87
A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. Mol Cell Proteomics (2011) 2.34
Acetylation modulates cellular distribution and DNA sensing ability of interferon-inducible protein IFI16. Proc Natl Acad Sci U S A (2012) 1.88
Structural profiling of endogenous S-nitrosocysteine residues reveals unique features that accommodate diverse mechanisms for protein S-nitrosylation. Proc Natl Acad Sci U S A (2010) 1.87
Human cytomegalovirus protein UL38 inhibits host cell stress responses by antagonizing the tuberous sclerosis protein complex. Cell Host Microbe (2008) 1.85
Systematic discovery of structural elements governing stability of mammalian messenger RNAs. Nature (2012) 1.80
Cell-cycle-dependent phosphorylation of the nuclear pore Nup107-160 subcomplex. Proc Natl Acad Sci U S A (2007) 1.64
The functional interactome landscape of the human histone deacetylase family. Mol Syst Biol (2013) 1.63
Increased expression of LDL receptor-related protein 1 during human cytomegalovirus infection reduces virion cholesterol and infectivity. Cell Host Microbe (2012) 1.59
Nuclear import of histone deacetylase 5 by requisite nuclear localization signal phosphorylation. Mol Cell Proteomics (2010) 1.52
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
A targeted spatial-temporal proteomics approach implicates multiple cellular trafficking pathways in human cytomegalovirus virion maturation. Mol Cell Proteomics (2009) 1.48
Human cytomegalovirus tegument protein pUL83 inhibits IFI16-mediated DNA sensing for immune evasion. Cell Host Microbe (2013) 1.44
Evidence for a genetic and physical interaction between nonstructural proteins NS1 and NS4B that modulates replication of West Nile virus. J Virol (2012) 1.43
Immunoglobulins against tyrosine-nitrated epitopes in coronary artery disease. Circulation (2012) 1.42
Identification of staphylococcal nuclease domain-containing 1 (SND1) as a Metadherin-interacting protein with metastasis-promoting functions. J Biol Chem (2011) 1.33
DNA replication through hard-to-replicate sites, including both highly transcribed RNA Pol II and Pol III genes, requires the S. pombe Pfh1 helicase. Genes Dev (2012) 1.28
The free and bound forms of Lpp occupy distinct subcellular locations in Escherichia coli. Mol Microbiol (2011) 1.27
Resolving the composition of protein complexes using a MALDI LTQ Orbitrap. J Am Soc Mass Spectrom (2009) 1.20
Co-compartmentalization of the astroglial glutamate transporter, GLT-1, with glycolytic enzymes and mitochondria. J Neurosci (2011) 1.18
Mass spectrometric and computational analysis of cytokine-induced alterations in the astrocyte secretome. Proteomics (2009) 1.17
Human cytomegalovirus UL29/28 protein interacts with components of the NuRD complex which promote accumulation of immediate-early RNA. PLoS Pathog (2010) 1.16
Kinesin-3 mediates axonal sorting and directional transport of alphaherpesvirus particles in neurons. Cell Host Microbe (2012) 1.14
Genetic and physiological activation of osmosensitive gene expression mimics transcriptional signatures of pathogen infection in C. elegans. PLoS One (2010) 1.13
Proteomic studies of a single CNS synapse type: the parallel fiber/purkinje cell synapse. PLoS Biol (2009) 1.11
Conjugation of magnetic beads for immunopurification of protein complexes. Cold Spring Harb Protoc (2011) 1.10
Sirtuin 7 plays a role in ribosome biogenesis and protein synthesis. Mol Cell Proteomics (2013) 1.08
Affinity purification of protein complexes. Cold Spring Harb Protoc (2011) 1.06
The nuclear basket proteins Mlp1p and Mlp2p are part of a dynamic interactome including Esc1p and the proteasome. Mol Biol Cell (2013) 1.06
Global analysis of Cdc14 phosphatase reveals diverse roles in mitotic processes. J Biol Chem (2010) 1.04
Glycoproteins gE and gI are required for efficient KIF1A-dependent anterograde axonal transport of alphaherpesvirus particles in neurons. J Virol (2013) 1.03
The response regulator SprE (RssB) is required for maintaining poly(A) polymerase I-degradosome association during stationary phase. J Bacteriol (2010) 1.01
Mechanistic investigations of the pseudouridine synthase RluA using RNA containing 5-fluorouridine. Biochemistry (2006) 1.01
Tcf21 regulates the specification and maturation of proepicardial cells. Development (2013) 0.98
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. Anal Chem (2012) 0.98
Proteomic profiling of cardiac tissue by isolation of nuclei tagged in specific cell types (INTACT). Development (2014) 0.92
Guanidination chemistry for qualitative and quantitative proteomics. Rapid Commun Mass Spectrom (2006) 0.91
Aurora B-dependent regulation of class IIa histone deacetylases by mitotic nuclear localization signal phosphorylation. Mol Cell Proteomics (2012) 0.91
The Caenorhabditis elegans mucin-like protein OSM-8 negatively regulates osmosensitive physiology via the transmembrane protein PTR-23. PLoS Genet (2011) 0.91
An unexpectedly high degree of specialization and a widespread involvement in sterol metabolism among the C. elegans putative aminophospholipid translocases. BMC Dev Biol (2008) 0.90
Thiouracil cross-linking mass spectrometry: a cell-based method to identify host factors involved in viral amplification. J Virol (2013) 0.89
A proteomic perspective of Sirtuin 6 (SIRT6) phosphorylation and interactions and their dependence on its catalytic activity. Mol Cell Proteomics (2013) 0.88
Histone deacetylases in herpesvirus replication and virus-stimulated host defense. Viruses (2013) 0.87
Complementary proteomic analysis of protein complexes. Methods Mol Biol (2012) 0.86
Proteomic identification of S-nitrosylated Golgi proteins: new insights into endothelial cell regulation by eNOS-derived NO. PLoS One (2012) 0.85
A complex of YlbF, YmcA and YaaT regulates sporulation, competence and biofilm formation by accelerating the phosphorylation of Spo0A. Mol Microbiol (2013) 0.84
A proteomic perspective of inbuilt viral protein regulation: pUL46 tegument protein is targeted for degradation by ICP0 during herpes simplex virus type 1 infection. Mol Cell Proteomics (2013) 0.84
Integrating Lys-N proteolysis and N-terminal guanidination for improved fragmentation and relative quantification of singly-charged ions. J Am Soc Mass Spectrom (2010) 0.83
Immunoisolation of protein complexes from Xenopus. Methods Mol Biol (2012) 0.81
A Gro/TLE-NuRD corepressor complex facilitates Tbx20-dependent transcriptional repression. J Proteome Res (2013) 0.81
The life cycle and pathogenesis of human cytomegalovirus infection: lessons from proteomics. Expert Rev Proteomics (2014) 0.80
Discovery of host-viral protein complexes during infection. Methods Mol Biol (2013) 0.80
A mass spectrometry view of stable and transient protein interactions. Adv Exp Med Biol (2014) 0.80
Complex formation and processing of the minor transformation pilins of Bacillus subtilis. Mol Microbiol (2013) 0.80
Hemagglutinating activity of Curcuma plants. Fitoterapia (2006) 0.79
Virology meets Proteomics. Proteomics (2015) 0.77
Probing phosphorylation-dependent protein interactions within functional domains of histone deacetylase 5 (HDAC5). Proteomics (2014) 0.76
Nitric oxide counteracts the hyperoxia-induced proliferation and proinflammatory responses of mouse astrocytes. Free Radic Biol Med (2011) 0.76
Zingipain, A cysteine protease from Zingiber ottensii Valeton rhizomes with antiproliferative activities against fungi and human malignant cell lines. Prep Biochem Biotechnol (2011) 0.75
A novel α-glucosidase inhibitor protein from the rhizomes of Zingiber ottensii valeton. Appl Biochem Biotechnol (2010) 0.75