SAINT: probabilistic scoring of affinity purification-mass spectrometry data.

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34

Global landscape of HIV-human protein complexes. Nature (2011) 3.70

A protein complex network of Drosophila melanogaster. Cell (2011) 3.31

SLC38A9 is a component of the lysosomal amino acid sensing machinery that controls mTORC1. Nature (2015) 2.01

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nat Methods (2015) 1.77

Inhibition of the Mitochondrial Protease ClpP as a Therapeutic Strategy for Human Acute Myeloid Leukemia. Cancer Cell (2015) 1.70

The linear ubiquitin-specific deubiquitinase gumby regulates angiogenesis. Nature (2013) 1.70

The functional interactome landscape of the human histone deacetylase family. Mol Syst Biol (2013) 1.63

Post-translational modifications regulate class IIa histone deacetylase (HDAC) function in health and disease. Mol Cell Proteomics (2015) 1.49

The Hippo signaling pathway interactome. Science (2013) 1.42

Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics. Elife (2015) 1.41

Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS. Nat Methods (2013) 1.30

Mass-spectrometric exploration of proteome structure and function. Nature (2016) 1.28

SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software. J Proteomics (2013) 1.27

Multidimensional proteomics for cell biology. Nat Rev Mol Cell Biol (2015) 1.26

Structure-function analysis of core STRIPAK Proteins: a signaling complex implicated in Golgi polarization. J Biol Chem (2011) 1.26

Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis. Proteomics (2011) 1.24

Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5. Proteomics (2011) 1.24

Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics (2012) 1.21

Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry. Mol Cell Proteomics (2015) 1.21

Sirtuin 4 is a lipoamidase regulating pyruvate dehydrogenase complex activity. Cell (2014) 1.20

SAINT-MS1: protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments. J Proteome Res (2012) 1.20

Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT. Curr Protoc Bioinformatics (2012) 1.20

Computational mass spectrometry-based proteomics. PLoS Comput Biol (2011) 1.18

A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface. Cell (2015) 1.14

Defining the protein-protein interaction network of the human hippo pathway. Mol Cell Proteomics (2013) 1.14

Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. Mol Syst Biol (2015) 1.12

Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. Mol Syst Biol (2011) 1.12

Artemisinins Target GABAA Receptor Signaling and Impair α Cell Identity. Cell (2016) 1.10

GSK3β controls epithelial-mesenchymal transition and tumor metastasis by CHIP-mediated degradation of Slug. Oncogene (2013) 1.03

C9orf72 Dipeptide Repeats Impair the Assembly, Dynamics, and Function of Membrane-Less Organelles. Cell (2016) 1.03

Modulation of the chromatin phosphoproteome by the Haspin protein kinase. Mol Cell Proteomics (2014) 1.02

Proteomic profiling of the human cytomegalovirus UL35 gene products reveals a role for UL35 in the DNA repair response. J Virol (2011) 1.01

Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nat Methods (2015) 1.00

ZNF750 interacts with KLF4 and RCOR1, KDM1A, and CTBP1/2 chromatin regulators to repress epidermal progenitor genes and induce differentiation genes. Genes Dev (2014) 0.98

Interactions of the Antiviral Factor Interferon Gamma-Inducible Protein 16 (IFI16) Mediate Immune Signaling and Herpes Simplex Virus-1 Immunosuppression. Mol Cell Proteomics (2015) 0.98

Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. Anal Chem (2012) 0.98

TRIM32 Senses and Restricts Influenza A Virus by Ubiquitination of PB1 Polymerase. PLoS Pathog (2015) 0.98

Mapping the protein interaction network of the human COP9 signalosome complex using a label-free QTAX strategy. Mol Cell Proteomics (2012) 0.98

Proteomic profiling of the TRAF3 interactome network reveals a new role for the ER-to-Golgi transport compartments in innate immunity. PLoS Pathog (2012) 0.95

BioID-based Identification of Skp Cullin F-box (SCF)β-TrCP1/2 E3 Ligase Substrates. Mol Cell Proteomics (2015) 0.95

Proteomic approaches to the study of papillomavirus-host interactions. Virology (2013) 0.94

Fundamentals of protein interaction network mapping. Mol Syst Biol (2015) 0.93

High-throughput analysis of peptide-binding modules. Proteomics (2012) 0.93

Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data. Curr Protoc Bioinformatics (2012) 0.92

A computational framework for boosting confidence in high-throughput protein-protein interaction datasets. Genome Biol (2012) 0.92

Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc (2014) 0.92

The deca-GX3 proteins Yae1-Lto1 function as adaptors recruiting the ABC protein Rli1 for iron-sulfur cluster insertion. Elife (2015) 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

Interrogating the Plasmodium Sporozoite Surface: Identification of Surface-Exposed Proteins and Demonstration of Glycosylation on CSP and TRAP by Mass Spectrometry-Based Proteomics. PLoS Pathog (2016) 0.91

Triple SILAC to determine stimulus specific interactions in the Wnt pathway. J Proteome Res (2011) 0.91

A global S. cerevisiae small ubiquitin-related modifier (SUMO) system interactome. Mol Syst Biol (2013) 0.90

The functional interactome of PYHIN immune regulators reveals IFIX is a sensor of viral DNA. Mol Syst Biol (2015) 0.90

Substrate trapping proteomics reveals targets of the βTrCP2/FBXW11 ubiquitin ligase. Mol Cell Biol (2014) 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

Technologies and approaches to elucidate and model the virulence program of salmonella. Front Microbiol (2011) 0.88

Proteomic analysis of the human cyclin-dependent kinase family reveals a novel CDK5 complex involved in cell growth and migration. Mol Cell Proteomics (2014) 0.87

Network Analysis Identifies Mitochondrial Regulation of Epidermal Differentiation by MPZL3 and FDXR. Dev Cell (2015) 0.87

Histone deacetylases in herpesvirus replication and virus-stimulated host defense. Viruses (2013) 0.87

Beyond hairballs: The use of quantitative mass spectrometry data to understand protein-protein interactions. FEBS Lett (2012) 0.86

Identification of Regulatory and Cargo Proteins of Endosomal and Secretory Pathways in Arabidopsis thaliana by Proteomic Dissection. Mol Cell Proteomics (2015) 0.86

Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST. Curr Protoc Bioinformatics (2015) 0.85

Incorporating DNA shearing in standard affinity purification allows simultaneous identification of both soluble and chromatin-bound interaction partners. J Proteomics (2014) 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

Identification of protein interactions involved in cellular signaling. Mol Cell Proteomics (2013) 0.84

The ecdysone receptor coactivator Taiman links Yorkie to transcriptional control of germline stem cell factors in somatic tissue. Dev Cell (2015) 0.83

Comparative interaction networks: bridging genotype to phenotype. Adv Exp Med Biol (2012) 0.83

Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. Nat Immunol (2016) 0.83

Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity. Cell Rep (2015) 0.82

Conserved abundance and topological features in chromatin-remodeling protein interaction networks. EMBO Rep (2014) 0.82

TRAF1 Coordinates Polyubiquitin Signaling to Enhance Epstein-Barr Virus LMP1-Mediated Growth and Survival Pathway Activation. PLoS Pathog (2015) 0.81

Mapping the H(+) (V)-ATPase interactome: identification of proteins involved in trafficking, folding, assembly and phosphorylation. Sci Rep (2015) 0.81

The interactome of the atypical phosphatase Rtr1 in Saccharomyces cerevisiae. Mol Biosyst (2014) 0.81

ROCS: a reproducibility index and confidence score for interaction proteomics studies. BMC Bioinformatics (2012) 0.81

PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data. J Proteome Res (2014) 0.81

From pathways to networks: connecting dots by establishing protein-protein interaction networks in signaling pathways using affinity purification and mass spectrometry. Proteomics (2014) 0.81

Discovery of host-viral protein complexes during infection. Methods Mol Biol (2013) 0.80

Reinvestigation of aminoacyl-tRNA synthetase core complex by affinity purification-mass spectrometry reveals TARSL2 as a potential member of the complex. PLoS One (2013) 0.80

Identification of SUMO-2/3-modified proteins associated with mitotic chromosomes. Proteomics (2015) 0.80

Interactome analysis of AMP-activated protein kinase (AMPK)-α1 and -β1 in INS-1 pancreatic beta-cells by affinity purification-mass spectrometry. Sci Rep (2014) 0.80

Predicting physical interactions between protein complexes. Mol Cell Proteomics (2013) 0.80

CALML5 is a ZNF750- and TINCR-induced protein that binds stratifin to regulate epidermal differentiation. Genes Dev (2015) 0.79

Depot specific differences in the adipogenic potential of precursors are mediated by collagenous extracellular matrix and Flotillin 2 dependent signaling. Mol Metab (2016) 0.78

The lysine methyltransferase SMYD3 interacts with hepatitis C virus NS5A and is a negative regulator of viral particle production. Virology (2014) 0.78

Stable association of RNAi machinery is conserved between the cytoplasm and nucleus of human cells. RNA (2016) 0.78

Proteomics of yeast telomerase identified Cdc48-Npl4-Ufd1 and Ufd4 as regulators of Est1 and telomere length. Nat Commun (2015) 0.78

Identifying binary protein-protein interactions from affinity purification mass spectrometry data. BMC Genomics (2015) 0.78

Building and exploring an integrated human kinase network: global organization and medical entry points. J Proteomics (2014) 0.78

From Raw Data to Biological Discoveries: A Computational Analysis Pipeline for Mass Spectrometry-Based Proteomics. J Am Soc Mass Spectrom (2015) 0.78

Human antiviral protein IFIX suppresses viral gene expression during HSV-1 infection and is counteracted by virus-induced proteasomal degradation. Mol Cell Proteomics (2017) 0.78

ZMPSTE24 defends against influenza and other pathogenic viruses. J Exp Med (2017) 0.78

Defining the Protein-Protein Interaction Network of the Human Protein Tyrosine Phosphatase Family. Mol Cell Proteomics (2016) 0.78

APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data. J Proteome Res (2016) 0.77

Spotlite: web application and augmented algorithms for predicting co-complexed proteins from affinity purification--mass spectrometry data. J Proteome Res (2014) 0.77

Decoding protein networks during virus entry by quantitative proteomics. Virus Res (2015) 0.77

Proteomic approaches to uncovering virus-host protein interactions during the progression of viral infection. Expert Rev Proteomics (2016) 0.77

Mass spectrometry-based shotgun proteomic analysis of C. elegans protein complexes. WormBook (2014) 0.77

Dual action antifungal small molecule modulates multidrug efflux and TOR signaling. Nat Chem Biol (2016) 0.77

Myotubularin-related proteins 3 and 4 interact with polo-like kinase 1 and centrosomal protein of 55 kDa to ensure proper abscission. Mol Cell Proteomics (2015) 0.77

Functional and structural properties of a novel protein and virulence factor (Protein sHIP) in Streptococcus pyogenes. J Biol Chem (2014) 0.77

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom (1994) 45.51

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29

Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77

The BioGRID Interaction Database: 2008 update. Nucleic Acids Res (2007) 11.83

Defining the human deubiquitinating enzyme interaction landscape. Cell (2009) 11.39

Network organization of the human autophagy system. Nature (2010) 11.38

Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol (2007) 8.16

A global protein kinase and phosphatase interaction network in yeast. Science (2010) 5.95

Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods (2007) 5.10

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

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Cell Biol (2010) 3.61

Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc Natl Acad Sci U S A (2008) 3.23

Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis. Nat Biotechnol (2009) 3.01

An integrated mass spectrometric and computational framework for the analysis of protein interaction networks. Nat Biotechnol (2007) 2.59

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Database (Oxford) (2010) 2.47

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66

Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem (2002) 35.30

BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41

The genetic landscape of a cell. Science (2010) 16.52

A comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet (2006) 12.45

The BioGRID Interaction Database: 2008 update. Nucleic Acids Res (2007) 11.83

Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet (2001) 10.48

Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. Am J Hum Genet (2002) 10.12

The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science (2008) 8.52

The BioGRID Interaction Database: 2011 update. Nucleic Acids Res (2010) 8.46

The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03

The PeptideAtlas project. Nucleic Acids Res (2006) 7.87

Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46

Systematic identification of pathways that couple cell growth and division in yeast. Science (2002) 6.95

p53-mediated activation of miRNA34 candidate tumor-suppressor genes. Curr Biol (2007) 6.87

An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression. Cancer Cell (2010) 6.76

Osprey: a network visualization system. Genome Biol (2003) 6.23

The BioGRID interaction database: 2013 update. Nucleic Acids Res (2012) 6.09

A global protein kinase and phosphatase interaction network in yeast. Science (2010) 5.95

Structural basis for phosphodependent substrate selection and orientation by the SCFCdc4 ubiquitin ligase. Cell (2003) 5.72

Histone recognition and large-scale structural analysis of the human bromodomain family. Cell (2012) 5.15

A guided tour of the Trans-Proteomic Pipeline. Proteomics (2010) 5.09

A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev (2004) 5.08

Wilms tumor suppressor WTX negatively regulates WNT/beta-catenin signaling. Science (2007) 5.08

PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods (2011) 5.01

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol (2004) 4.91

How cells coordinate growth and division. Curr Biol (2004) 4.81

A hitchhiker's guide to the cullin ubiquitin ligases: SCF and its kin. Biochim Biophys Acta (2004) 4.53

Human Plasma PeptideAtlas. Proteomics (2005) 4.52

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34

A mechanism for cell-cycle regulation of MAP kinase signaling in a yeast differentiation pathway. Cell (2007) 4.21

The BTB protein MEL-26 is a substrate-specific adaptor of the CUL-3 ubiquitin-ligase. Nature (2003) 4.18

A rapamycin-sensitive signaling pathway contributes to long-term synaptic plasticity in the hippocampus. Proc Natl Acad Sci U S A (2001) 4.16

The GRID: the General Repository for Interaction Datasets. Genome Biol (2003) 4.09

CDK activity antagonizes Whi5, an inhibitor of G1/S transcription in yeast. Cell (2004) 4.04

An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. Proc Natl Acad Sci U S A (2009) 3.82

Molecular profiling of non-small cell lung cancer and correlation with disease-free survival. Cancer Res (2002) 3.68

Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol (2006) 3.44

Phosphorylation of eucaryotic translation initiation factor 4B Ser422 is modulated by S6 kinases. EMBO J (2004) 3.29

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods (2012) 3.17

Significance analysis of spectral count data in label-free shotgun proteomics. Mol Cell Proteomics (2008) 3.12

Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains. Mol Cell (2012) 3.08

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics (2011) 3.03

HAUS, the 8-subunit human Augmin complex, regulates centrosome and spindle integrity. Curr Biol (2009) 2.98

iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics (2011) 2.88

Chemical genetics reveals a complex functional ground state of neural stem cells. Nat Chem Biol (2007) 2.88

Calorie restriction alters mitochondrial protein acetylation. Aging Cell (2009) 2.73

Suprafacial orientation of the SCFCdc4 dimer accommodates multiple geometries for substrate ubiquitination. Cell (2007) 2.69

Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods (2010) 2.67

Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol (2006) 2.66

A PP2A phosphatase high density interaction network identifies a novel striatin-interacting phosphatase and kinase complex linked to the cerebral cavernous malformation 3 (CCM3) protein. Mol Cell Proteomics (2008) 2.56

The size of the nucleus increases as yeast cells grow. Mol Biol Cell (2007) 2.55

Experimental protein mixture for validating tandem mass spectral analysis. OMICS (2002) 2.54

Biophysical studies of eIF4E cap-binding protein: recognition of mRNA 5' cap structure and synthetic fragments of eIF4G and 4E-BP1 proteins. J Mol Biol (2002) 2.53

Non-canonical inhibition of DNA damage-dependent ubiquitination by OTUB1. Nature (2010) 2.47

Functional genomics and proteomics: charting a multidimensional map of the yeast cell. Trends Cell Biol (2003) 2.46

Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci Signal (2010) 2.36

False discovery rates and related statistical concepts in mass spectrometry-based proteomics. J Proteome Res (2007) 2.36

An allosteric inhibitor of the human Cdc34 ubiquitin-conjugating enzyme. Cell (2011) 2.35

Evolutionary and physiological importance of hub proteins. PLoS Comput Biol (2006) 2.34

Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics. J Proteome Res (2007) 2.33

Temporal regulation of EGF signalling networks by the scaffold protein Shc1. Nature (2013) 2.33

Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase. Structure (2010) 2.33

Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nat Biotechnol (2011) 2.26

ProHits: integrated software for mass spectrometry-based interaction proteomics. Nat Biotechnol (2010) 2.22

PP4 is a gamma H2AX phosphatase required for recovery from the DNA damage checkpoint. EMBO Rep (2008) 2.09

Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. J Proteome Res (2007) 2.09

Type III secretion effectors of the IpaH family are E3 ubiquitin ligases. Cell Host Microbe (2007) 2.08

Global gene expression analysis reveals evidence for decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin. J Invest Dermatol (2009) 2.06

Activation of GCN2 in UV-irradiated cells inhibits translation. Curr Biol (2002) 2.02

Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor. Proc Natl Acad Sci U S A (2008) 2.00

Eukaryotic translation initiation factor 4E availability controls the switch between cap-dependent and internal ribosomal entry site-mediated translation. Mol Cell Biol (2005) 1.99

Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells. Science (2009) 1.91

An allosteric inhibitor of substrate recognition by the SCF(Cdc4) ubiquitin ligase. Nat Biotechnol (2010) 1.88

Combinations of antibiotics and nonantibiotic drugs enhance antimicrobial efficacy. Nat Chem Biol (2011) 1.84

Still stratus not altocumulus: further evidence against the date/party hub distinction. PLoS Biol (2007) 1.84

The rate of cell growth is governed by cell cycle stage. Genes Dev (2009) 1.82