Published in Mol Cell Proteomics on February 17, 2010
Proteogenomics to discover the full coding content of genomes: a computational perspective. J Proteomics (2010) 1.71
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Loss of the tumor suppressor BAP1 causes myeloid transformation. Science (2012) 2.69
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Association of C-terminal ubiquitin hydrolase BRCA1-associated protein 1 with cell cycle regulator host cell factor 1. Mol Cell Biol (2009) 2.26
Compressing genomic sequence fragments using SlimGene. J Comput Biol (2011) 2.10
Autophosphorylated CaMKIIalpha acts as a scaffold to recruit proteasomes to dendritic spines. Cell (2010) 2.02
A covering method for detecting genetic associations between rare variants and common phenotypes. PLoS Comput Biol (2010) 1.98
Ubiquitin binding modulates IAP antagonist-stimulated proteasomal degradation of c-IAP1 and c-IAP2(1). Biochem J (2009) 1.94
Deubiquitinase USP37 is activated by CDK2 to antagonize APC(CDH1) and promote S phase entry. Mol Cell (2011) 1.92
Phosphorylation of NLRC4 is critical for inflammasome activation. Nature (2012) 1.92
Searching genomes for noncoding RNA using FastR. IEEE/ACM Trans Comput Biol Bioinform (2006) 1.90
COP1 is a tumour suppressor that causes degradation of ETS transcription factors. Nature (2011) 1.83
Peptide sequence tags for fast database search in mass-spectrometry. J Proteome Res (2005) 1.74
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Experimental selection of hypoxia-tolerant Drosophila melanogaster. Proc Natl Acad Sci U S A (2011) 1.60
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics (2011) 1.58
Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach. Mol Cell Proteomics (2010) 1.53
Protein identification using top-down. Mol Cell Proteomics (2011) 1.50
Ubiquitin ligase RNF146 regulates tankyrase and Axin to promote Wnt signaling. PLoS One (2011) 1.46
Improved quantitative mass spectrometry methods for characterizing complex ubiquitin signals. Mol Cell Proteomics (2010) 1.43
Phosphorylation-dependent activity of the deubiquitinase DUBA. Nat Struct Mol Biol (2012) 1.42
Ubiquitin binding to A20 ZnF4 is required for modulation of NF-κB signaling. Mol Cell (2010) 1.41
Robustness of inference of haplotype block structure. J Comput Biol (2003) 1.38
QNet: a tool for querying protein interaction networks. J Comput Biol (2008) 1.32
Expansion of the mycobacterial "PUPylome". Mol Biosyst (2009) 1.31
Accurate annotation of peptide modifications through unrestrictive database search. J Proteome Res (2007) 1.30
Evidence for large inversion polymorphisms in the human genome from HapMap data. Genome Res (2006) 1.29
Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis. J Proteome Res (2008) 1.28
Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies. Genome Res (2004) 1.28
Targeted mass spectrometric strategy for global mapping of ubiquitination on proteins. Rapid Commun Mass Spectrom (2007) 1.21
Orthologous repeats and mammalian phylogenetic inference. Genome Res (2005) 1.20
Death-receptor activation halts clathrin-dependent endocytosis. Proc Natl Acad Sci U S A (2006) 1.18
A decomposition theory for phylogenetic networks and incompatible characters. J Comput Biol (2007) 1.17
Shotgun protein sequencing by tandem mass spectra assembly. Anal Chem (2004) 1.15
Fast and accurate alignment of multiple protein networks. J Comput Biol (2009) 1.14
Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level. Genome Biol (2010) 1.12
De novo proteomic sequencing of a monoclonal antibody raised against OX40 ligand. Anal Biochem (2006) 1.12
Glycan shifting on hepatitis C virus (HCV) E2 glycoprotein is a mechanism for escape from broadly neutralizing antibodies. J Mol Biol (2013) 1.11
OTUB1 modulates c-IAP1 stability to regulate signalling pathways. EMBO J (2013) 1.09
The double-histone-acetyltransferase complex ATAC is essential for mammalian development. Mol Cell Biol (2008) 1.09
Resurrection of a clinical antibody: template proteogenomic de novo proteomic sequencing and reverse engineering of an anti-lymphotoxin-α antibody. Proteomics (2011) 1.08
B and T lymphocyte attenuator regulates B cell receptor signaling by targeting Syk and BLNK. J Immunol (2009) 1.08
Proteogenomic database construction driven from large scale RNA-seq data. J Proteome Res (2013) 1.08
Microwave-assisted proteomics. Mass Spectrom Rev (2007) 1.07
Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders. Am J Hum Genet (2013) 1.06
Mass spectrometric contributions to the practice of phosphorylation site mapping through 2003: a literature review. Mol Cell Proteomics (2005) 1.05
Comparative analysis of techniques to purify plasma membrane proteins. J Biomol Tech (2010) 1.05
A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements. Bioinformatics (2006) 1.04
Unrestrictive identification of post-translational modifications through peptide mass spectrometry. Nat Protoc (2006) 1.03
Peptide substrate profiling defines fibroblast activation protein as an endopeptidase of strict Gly(2)-Pro(1)-cleaving specificity. FEBS Lett (2006) 1.00
Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance. BMC Genomics (2010) 1.00
Furin-cleaved proprotein convertase subtilisin/kexin type 9 (PCSK9) is active and modulates low density lipoprotein receptor and serum cholesterol levels. J Biol Chem (2012) 0.99
Automated querying and identification of novel peptides using MALDI mass spectrometric imaging. J Proteome Res (2011) 0.97
Virmid: accurate detection of somatic mutations with sample impurity inference. Genome Biol (2013) 0.97
Optimization of primer design for the detection of variable genomic lesions in cancer. Bioinformatics (2007) 0.96
On the design of clone-based haplotyping. Genome Biol (2013) 0.95
Phosphorylation of Dishevelled by protein kinase RIPK4 regulates Wnt signaling. Science (2013) 0.95
An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays. Mol Cell Proteomics (2013) 0.95
Strobe sequence design for haplotype assembly. BMC Bioinformatics (2011) 0.94
AMASS: algorithm for MSI analysis by semi-supervised segmentation. J Proteome Res (2011) 0.94
Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes. BMC Genomics (2010) 0.94
Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes. Genome Biol (2014) 0.94
RAPID detection of gene-gene interactions in genome-wide association studies. Bioinformatics (2010) 0.94
Identification of longitudinally dynamic biomarkers in Alzheimer's disease cerebrospinal fluid by targeted proteomics. Mol Neurodegener (2014) 0.93
Polyubiquitination of insulin-like growth factor I receptor (IGF-IR) activation loop promotes antibody-induced receptor internalization and down-regulation. J Biol Chem (2011) 0.93
Using Genome Query Language to uncover genetic variation. Bioinformatics (2013) 0.93
Accurate mass spectrometry based protein quantification via shared peptides. J Comput Biol (2012) 0.92