Published in Nat Methods on November 11, 2012
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Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database. Curr Biol (2014) 1.32
Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq. Mol Cell Proteomics (2013) 1.20
Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences. J Proteome Res (2013) 1.14
Proteomics informed by transcriptomics reveals Hendra virus sensitizes bat cells to TRAIL-mediated apoptosis. Genome Biol (2014) 0.98
An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer. Mol Cell Proteomics (2015) 0.94
Ixodes scapularis and Ixodes ricinus tick cell lines respond to infection with tick-borne encephalitis virus: transcriptomic and proteomic analysis. Parasit Vectors (2015) 0.92
Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations. BMC Genomics (2014) 0.92
Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework. J Proteome Res (2014) 0.90
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Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data. Proteomics (2014) 0.86
The Role of Mass Spectrometry in the "Omics" Era. Curr Org Chem (2013) 0.85
Leveraging the complementary nature of RNA-Seq and shotgun proteomics data. Proteomics (2014) 0.84
Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis. Mol Cell Proteomics (2014) 0.84
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Immunology of bats and their viruses: challenges and opportunities. Viruses (2014) 0.82
Quantification of peptides from immunoglobulin constant and variable regions by LC-MRM MS for assessment of multiple myeloma patients. Proteomics Clin Appl (2014) 0.82
Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics. Mol Cell Proteomics (2015) 0.81
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MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms. Bioinformatics (2015) 0.79
Integrating genomic, transcriptomic, and interactome data to improve Peptide and protein identification in shotgun proteomics. J Proteome Res (2014) 0.78
Elucidation of the CHO Super-Ome (CHO-SO) by Proteoinformatics. J Proteome Res (2015) 0.78
Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy. J Proteome Res (2016) 0.78
Identification of Novel Short Ragweed Pollen Allergens Using Combined Transcriptomic and Immunoproteomic Approaches. PLoS One (2015) 0.78
The Adenovirus E4-ORF3 Protein Stimulates SUMOylation of General Transcription Factor TFII-I to Direct Proteasomal Degradation. MBio (2016) 0.78
Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti. BMC Genomics (2017) 0.78
Immunoglobulins: expanding the role for mass spectrometry in protein biomarker quantification. Clin Chem (2014) 0.76
Analysis of purified wild type and mutant adenovirus particles by SILAC based quantitative proteomics. J Gen Virol (2014) 0.76
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Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrum-Phytophthora capsici Phytopathosystem. Front Plant Sci (2016) 0.75
Utilising proteomic approaches to understand oncogenic human herpesviruses (Review). Mol Clin Oncol (2014) 0.75
Identification of Epstein-Barr Virus Replication Proteins in Burkitt's Lymphoma Cells. Pathogens (2015) 0.75
Proteomics informed by transcriptomics for characterising differential cellular susceptibility to Nelson Bay orthoreovirus infection. BMC Genomics (2017) 0.75
A proteomic insight into the midgut proteome of Ornithodoros moubata females reveals novel information on blood digestion in argasid ticks. Parasit Vectors (2017) 0.75
RNA splicing and splicing regulator changes in prostate cancer pathology. Hum Genet (2017) 0.75
Proteomics technique opens new frontiers in mobilome research. Mob Genet Elements (2017) 0.75
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21
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Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86
GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics (2005) 21.04
Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol (2010) 17.00
Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res (2011) 14.82
Widespread RNA and DNA sequence differences in the human transcriptome. Science (2011) 11.45
Adenovirus early region 4 encodes functions required for efficient DNA replication, late gene expression, and host cell shutoff. J Virol (1985) 4.35
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics (2010) 3.78
SKAR links pre-mRNA splicing to mTOR/S6K1-mediated enhanced translation efficiency of spliced mRNAs. Cell (2008) 3.43
Defining the transcriptome and proteome in three functionally different human cell lines. Mol Syst Biol (2010) 3.00
The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nat Biotechnol (2011) 2.87
A quantitative spatial proteomics analysis of proteome turnover in human cells. Mol Cell Proteomics (2011) 2.22
Late viral RNA export, rather than p53 inactivation, determines ONYX-015 tumor selectivity. Cancer Cell (2004) 2.05
The E1A 13S product of adenovirus 5 activates transcription of the cellular human HSP70 gene. Mol Cell Biol (1986) 1.81
Proteogenomics to discover the full coding content of genomes: a computational perspective. J Proteomics (2010) 1.71
Characterization of a cell type-specific enhancer found in the human papilloma virus type 18 genome. EMBO J (1987) 1.67
Relocalization of the Mre11-Rad50-Nbs1 complex by the adenovirus E4 ORF3 protein is required for viral replication. J Virol (2005) 1.63
Adenovirus ubiquitin-protein ligase stimulates viral late mRNA nuclear export. J Virol (2006) 1.37
Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing. Nucleic Acids Res (2010) 1.37
Strategic attack on host cell gene expression during adenovirus infection. J Virol (2003) 1.21
Proteomics analysis of the nucleolus in adenovirus-infected cells. Mol Cell Proteomics (2009) 1.16
The adenovirus E1b55K/E4orf6 complex induces degradation of the Bloom helicase during infection. J Virol (2010) 1.15
Advancing cell biology through proteomics in space and time (PROSPECTS). Mol Cell Proteomics (2012) 1.15
Proteomics technologies for the global identification and quantification of proteins. Adv Protein Chem Struct Biol (2010) 1.06
Biosynthesis of adenovirus type 2 i-leader protein. J Virol (1986) 0.99
The adenovirus type 5 i-leader open reading frame functions in cis to reduce the half-life of L1 mRNAs. J Virol (1990) 0.98
Serotype-specific inactivation of the cellular DNA damage response during adenovirus infection. J Virol (2010) 0.98
The transcriptome of the adenovirus infected cell. Virology (2012) 0.87
A proteogenomic survey of the Medicago truncatula genome. Mol Cell Proteomics (2012) 0.87
A proteomic approach to identify candidate substrates of human adenovirus E4orf6-E1B55K and other viral cullin-based E3 ubiquitin ligases. J Virol (2009) 0.86
Truncating the i-leader open reading frame enhances release of human adenovirus type 5 in glioma cells. Virol J (2011) 0.78
The zebrafish reference genome sequence and its relationship to the human genome. Nature (2013) 8.52
Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnol J (2014) 4.02
H7N9 influenza viruses are transmissible in ferrets by respiratory droplet. Science (2013) 3.33
Mapping the Arabidopsis organelle proteome. Proc Natl Acad Sci U S A (2006) 3.03
Protein-folding location can regulate manganese-binding versus copper- or zinc-binding. Nature (2008) 2.81
Tyrosine phosphorylation of mitochondrial pyruvate dehydrogenase kinase 1 is important for cancer metabolism. Mol Cell (2011) 2.61
Phosphoglycerate mutase 1 coordinates glycolysis and biosynthesis to promote tumor growth. Cancer Cell (2012) 2.39
The identification of ATP-citrate lyase as a protein kinase B (Akt) substrate in primary adipocytes. J Biol Chem (2002) 2.36
Pituitary homeobox 2 (PITX2) promotes thyroid carcinogenesis by activation of cyclin D2. Cell Cycle (2010) 2.29
i-Tracker: for quantitative proteomics using iTRAQ. BMC Genomics (2005) 2.22
A global analysis of SNX27-retromer assembly and cargo specificity reveals a function in glucose and metal ion transport. Nat Cell Biol (2013) 2.18
Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol (2003) 2.05
Challenging and changing gender attitudes among young men in Mumbai, India. Reprod Health Matters (2006) 1.77
Recent developments in public proteomic MS repositories and pipelines. Proteomics (2009) 1.72
Simple sequence repeat marker loci discovery using SSR primer. Bioinformatics (2004) 1.54
Protein kinase B phosphorylation of PIKfyve regulates the trafficking of GLUT4 vesicles. J Cell Sci (2004) 1.54
TreeVector: scalable, interactive, phylogenetic trees for the web. PLoS One (2010) 1.45
Identifying the important HIV-1 recombination breakpoints. PLoS Comput Biol (2008) 1.42
SNPServer: a real-time SNP discovery tool. Nucleic Acids Res (2005) 1.42
MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions. Mol Cell Proteomics (2008) 1.41
SNX17 protects integrins from degradation by sorting between lysosomal and recycling pathways. J Cell Biol (2012) 1.40
trans-Diaqua-bis-(1H-imidazole-4-carboxyl-ato-κN,O)nickel(II). Acta Crystallogr Sect E Struct Rep Online (2011) 1.40
Intraventricular craniopharyngioma: morphological analysis and outcome evaluation of 17 cases. Acta Neurochir (Wien) (2011) 1.40
Di-μ-chlorido-bis-{[2-(8-quinol-yloxy)-acetato-κN,O,O]copper(II)}. Acta Crystallogr Sect E Struct Rep Online (2008) 1.35
Public proteomic MS repositories and pipelines: available tools and biological applications. Proteomics (2007) 1.32
The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Mol Cell Proteomics (2013) 1.28
A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis. OMICS (2012) 1.25
Prospects for clinical application of electronic-nose technology to early detection of Mycobacterium tuberculosis in culture and sputum. J Clin Microbiol (2006) 1.20
GAPP: a fully automated software for the confident identification of human peptides from tandem mass spectra. J Proteome Res (2006) 1.19
Free computational resources for designing selected reaction monitoring transitions. Proteomics (2010) 1.17
Golgi localization of Syne-1. Mol Biol Cell (2003) 1.17
Crystal structure of human vacuolar protein sorting protein 29 reveals a phosphodiesterase/nuclease-like fold and two protein-protein interaction sites. J Biol Chem (2005) 1.17
Proteomics analysis of the nucleolus in adenovirus-infected cells. Mol Cell Proteomics (2009) 1.16
Identification and characterization of inhibitors of bacterial enoyl-acyl carrier protein reductase. Antimicrob Agents Chemother (2004) 1.13
Quantitative proteomic approach to study subcellular localization of membrane proteins. Nat Protoc (2006) 1.11
Photophysiology and albedo-changing potential of the ice algal community on the surface of the Greenland ice sheet. ISME J (2012) 1.11
Tyr26 phosphorylation of PGAM1 provides a metabolic advantage to tumours by stabilizing the active conformation. Nat Commun (2013) 1.08
Anatomical study of the arachnoid envelope over the pineal region. Neurosurgery (2011) 1.06
Mesenchymal stem cell-secreted superoxide dismutase promotes cerebellar neuronal survival. J Neurochem (2010) 1.05
The Herpesvirus Saimiri open reading frame 73 gene product interacts with the cellular protein p32. J Virol (2002) 1.05
Protein distribution during human erythroblast enucleation in vitro. PLoS One (2013) 1.04
Sequence determinants of breakpoint location during HIV-1 intersubtype recombination. Nucleic Acids Res (2006) 1.02
Comparison of novel decoy database designs for optimizing protein identification searches using ABRF sPRG2006 standard MS/MS data sets. J Proteome Res (2009) 1.02
Measuring global gene expression in polyploidy; a cautionary note from allohexaploid wheat. Funct Integr Genomics (2007) 1.01
Elucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity. Genome Biol (2014) 1.01
A variant of estrogen receptor-alpha, ER-alpha36 is expressed in human gastric cancer and is highly correlated with lymph node metastasis. Oncol Rep (2010) 1.00
NGFI-B nuclear orphan receptor Nurr1 interacts with p53 and suppresses its transcriptional activity. Mol Cancer Res (2009) 1.00
Evaluation of a gas sensor array and pattern recognition for the identification of bladder cancer from urine headspace. Analyst (2010) 0.99
MRMaid 2.0: mining PRIDE for evidence-based SRM transitions. OMICS (2012) 0.99
XAV939, a tankyrase 1 inhibitior, promotes cell apoptosis in neuroblastoma cell lines by inhibiting Wnt/β-catenin signaling pathway. J Exp Clin Cancer Res (2013) 0.99
Autologous transplantation of adipose-derived mesenchymal stem cells ameliorates streptozotocin-induced diabetic nephropathy in rats by inhibiting oxidative stress, pro-inflammatory cytokines and the p38 MAPK signaling pathway. Int J Mol Med (2012) 0.98
Evidence of recombination between divergent hepatitis E viruses. J Virol (2005) 0.98
Inhibition of cell proliferation and glucose uptake in human laryngeal carcinoma cells by antisense oligonucleotides against glucose transporter-1. Head Neck (2009) 0.98
Protein and peptide identification algorithms using MS for use in high-throughput, automated pipelines. Proteomics (2005) 0.97
Analysis of volatile organic compounds of bacterial origin in chronic gastrointestinal diseases. Inflamm Bowel Dis (2013) 0.97
MRMaid-DB: a repository of published SRM transitions. J Proteome Res (2010) 0.97
Novel molecular approaches to cystic fibrosis gene therapy. Biochem J (2005) 0.96
Phasic contractions of isolated human myometrium are associated with Rho-kinase (ROCK)-dependent phosphorylation of myosin phosphatase-targeting subunit (MYPT1). Mol Hum Reprod (2011) 0.96
Adenovirus core protein VII contains distinct sequences that mediate targeting to the nucleus and nucleolus, and colocalization with human chromosomes. J Gen Virol (2003) 0.95
Quantitative proteomics using SILAC coupled to LC-MS/MS reveals changes in the nucleolar proteome in influenza A virus-infected cells. J Proteome Res (2010) 0.95
Nucleolar protein upstream binding factor is sequestered into adenovirus DNA replication centres during infection without affecting RNA polymerase I location or ablating rRNA synthesis. J Cell Sci (2006) 0.95
A coaxial cable Fabry-Perot interferometer for sensing applications. Sensors (Basel) (2013) 0.95
Hypoxia inhibits the differentiation of mesenchymal stem cells into osteoblasts by activation of Notch signaling. Exp Mol Pathol (2012) 0.94
The interactome of the human respiratory syncytial virus NS1 protein highlights multiple effects on host cell biology. J Virol (2012) 0.94
Evidence for regulation of monomethyl mercury by nitrate in a seasonally stratified, eutrophic lake. Environ Sci Technol (2009) 0.93
Effect on the expression of MMP-2, MT-MMP in laryngeal carcinoma Hep-2 cell line by antisense glucose transporter-1. Arch Med Res (2012) 0.93
Effect of antisense oligodeoxynucleotides glucose transporter-1 on enhancement of radiosensitivity of laryngeal carcinoma. Int J Med Sci (2013) 0.93
Brassica ASTRA: an integrated database for Brassica genomic research. Nucleic Acids Res (2005) 0.93
Overexpression of the TXNDC5 protein in non-small cell lung carcinoma. Anticancer Res (2011) 0.92
The herpesvirus saimiri ORF73 gene product interacts with host-cell mitotic chromosomes and self-associates via its C terminus. J Gen Virol (2004) 0.92
Current perspectives and recommendations for the development of mass spectrometry methods for the determination of allergens in foods. J AOAC Int (2011) 0.92
Diversity and distribution of sulphate-reducing bacteria in human faeces from healthy subjects and patients with inflammatory bowel disease. FEMS Immunol Med Microbiol (2012) 0.91
The prometastatic ribosomal S6 kinase 2-cAMP response element-binding protein (RSK2-CREB) signaling pathway up-regulates the actin-binding protein fascin-1 to promote tumor metastasis. J Biol Chem (2013) 0.91
Expression of glucose transporter-1 and -3 in the head and neck carcinoma--the correlation of the expression with the biological behaviors. ORL J Otorhinolaryngol Relat Spec (2008) 0.91
Detection of humoral response using a recombinant heat shock protein 70, DnaK, of Mycoplasma haemofelis in experimentally and naturally hemoplasma-infected cats. Clin Vaccine Immunol (2010) 0.91
Core labeling of adenovirus with EGFP. Virology (2006) 0.91
RhoG protein regulates platelet granule secretion and thrombus formation in mice. J Biol Chem (2013) 0.90
Characterization of GPR56 protein and its suppressed expression in human pancreatic cancer cells. Mol Cell Biochem (2007) 0.90
Structure-based design, synthesis, and biological evaluation of irreversible human rhinovirus 3C protease inhibitors. Part 7: structure-activity studies of bicyclic 2-pyridone-containing peptidomimetics. Bioorg Med Chem Lett (2002) 0.90
Normal prion protein trafficking in cultured human erythroblasts. Blood (2007) 0.89
A role for transportin in the nuclear import of adenovirus core proteins and DNA. Traffic (2007) 0.89
The antiviral protein cyanovirin-N: the current state of its production and applications. Appl Microbiol Biotechnol (2010) 0.89
Confident protein identification using the average peptide score method coupled with search-specific, ab initio thresholds. Rapid Commun Mass Spectrom (2005) 0.89
Discovery of a potent respiratory syncytial virus RNA polymerase inhibitor. Bioorg Med Chem Lett (2013) 0.88
Biotemplated preparation of CdS nanoparticles/bacterial cellulose hybrid nanofibers for photocatalysis application. J Hazard Mater (2011) 0.87
Nucleolar proteomics and viral infection. Proteomics (2010) 0.87
Crystal structure of 3-hydroxyanthranilic acid 3,4-dioxygenase from Saccharomyces cerevisiae: a special subgroup of the type III extradiol dioxygenases. Protein Sci (2006) 0.87
1-(4-Amino-phenyl)-pyrrolidin-3-yl-amine and 6-(3-amino-pyrrolidin-1-yl)-pyridin-3-yl-amine derivatives as melanin-concentrating hormone receptor-1 antagonists. Bioorg Med Chem Lett (2005) 0.86
SNX15 links clathrin endocytosis to the PtdIns3P early endosome independently of the APPL1 endosome. J Cell Sci (2013) 0.86
Investigation of support vector machines and Raman spectroscopy for lymph node diagnostics. Analyst (2010) 0.86
In vitro dynamic visualization analysis of fluorescently labeled minor capsid protein IX and core protein V by simultaneous detection. J Mol Biol (2009) 0.86
Physical and structural basis for the strong interactions of the -ImPy- central pairing motif in the polyamide f-ImPyIm. Biochemistry (2006) 0.86