Pool-seq driven proteogenomic database for Group G Streptococcus.
暂无分享,去创建一个
J. Kere | M. Varjosalo | C. Kolmeder | S. Keskitalo | R. Vuento | T. Jokiranta | R. Weldatsadik | J. Flatt | J. Vuopio | N. Datta | K. Haapasalo | S. Wilkman
[1] E. Kristiansson,et al. Proteotyping bacteria: Characterization, differentiation and identification of pneumococcus and other species within the Mitis Group of the genus Streptococcus by tandem mass spectrometry proteomics , 2018, PloS one.
[2] A. Pain,et al. Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates. , 2017, Journal of proteome research.
[3] J. Kere,et al. Sequence analysis of pooled bacterial samples enables identification of strain variation in group A streptococcus , 2017, Scientific Reports.
[4] Davide Heller,et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences , 2015, Nucleic Acids Res..
[5] Lars Malmström,et al. Quantitative proteogenomics of human pathogens using DIA-MS. , 2015, Journal of proteomics.
[6] A. Nesvizhskii. Proteogenomics: concepts, applications and computational strategies , 2014, Nature Methods.
[7] J. Armengaud,et al. Non-model organisms, a species endangered by proteogenomics. , 2014, Journal of proteomics.
[8] S. Rantala,et al. Streptococcus dysgalactiae subsp. equisimilis bacteremia: an emerging infection , 2014, European Journal of Clinical Microbiology & Infectious Diseases.
[9] California Jack Cassidy,et al. An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes in Zea mays* , 2013, Molecular & Cellular Proteomics.
[10] B. Maček,et al. Deep Coverage of the Escherichia coli Proteome Enables the Assessment of False Discovery Rates in Simple Proteogenomic Experiments* , 2013, Molecular & Cellular Proteomics.
[11] Brian L. Frey,et al. Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq* , 2013, Molecular & Cellular Proteomics.
[12] S. Hubbard,et al. Addressing Statistical Biases in Nucleotide-Derived Protein Databases for Proteogenomic Search Strategies , 2012, Journal of proteome research.
[13] Derrick E. Fouts,et al. PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species , 2012, Nucleic acids research.
[14] Gabor T. Marth,et al. Haplotype-based variant detection from short-read sequencing , 2012, 1207.3907.
[15] R. Vuento,et al. Distribution of emm types in invasive and non-invasive group A and G streptococci , 2012, European Journal of Clinical Microbiology & Infectious Diseases.
[16] Roger Karlsson,et al. Strain-level typing and identification of bacteria using mass spectrometry-based proteomics. , 2012, Journal of proteome research.
[17] S. W. Long,et al. Bacterial genomics in infectious disease and the clinical pathology laboratory. , 2012, Archives of pathology & laboratory medicine.
[18] Bing Zhang,et al. Protein identification using customized protein sequence databases derived from RNA-Seq data. , 2012, Journal of proteome research.
[19] H. Hakonarson,et al. SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data , 2011, Nucleic acids research.
[20] James C. Wright,et al. Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome. , 2011, Genome research.
[21] M. DePristo,et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.
[22] W. Pao,et al. A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics* , 2011, Molecular & Cellular Proteomics.
[23] L. Käll,et al. Quality assessments of peptide–spectrum matches in shotgun proteomics , 2011, Proteomics.
[24] M. Mann,et al. Andromeda: a peptide search engine integrated into the MaxQuant environment. , 2011, Journal of proteome research.
[25] Martin Ester,et al. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes , 2010, Bioinform..
[26] Dexter T. Duncan,et al. CanProVar: a human cancer proteome variation database , 2010, Human mutation.
[27] J. Buhmann,et al. Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry* , 2009, Molecular & Cellular Proteomics.
[28] R. Vuento,et al. Predictors of mortality in beta-hemolytic streptococcal bacteremia: a population-based study. , 2009, The Journal of infection.
[29] M. Mann,et al. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.
[30] Yong-Hwan Lee,et al. SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry , 2008, Nucleic Acids Res..
[31] David R. Riley,et al. Comparative genomics: the bacterial pan-genome. , 2008, Current opinion in microbiology.
[32] Blagoy Blagoev,et al. A mass spectrometry–friendly database for cSNP identification , 2007, Nature Methods.
[33] R. Hendrickson,et al. Detection and validation of non-synonymous coding SNPs from orthogonal analysis of shotgun proteomics data. , 2007, Journal of proteome research.
[34] Patrick G. A. Pedrioli,et al. A high-quality catalog of the Drosophila melanogaster proteome , 2007, Nature Biotechnology.
[35] R. Guigó,et al. Improving gene annotation using peptide mass spectrometry. , 2007, Genome research.
[36] R. Aebersold,et al. Dynamic Spectrum Quality Assessment and Iterative Computational Analysis of Shotgun Proteomic Data , 2006, Molecular & Cellular Proteomics.
[37] Jaideep P. Sundaram,et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[38] Robertson Craig,et al. TANDEM: matching proteins with tandem mass spectra. , 2004, Bioinformatics.
[39] Jacob D. Jaffe,et al. Proteogenomic mapping as a complementary method to perform genome annotation , 2004, Proteomics.
[40] D. Creasy,et al. Error tolerant searching of uninterpreted tandem mass spectrometry data , 2002, Proteomics.
[41] Qunhua Li,et al. Modes of inference for evaluating the confidence of peptide identifications. , 2008, Journal of proteome research.
[42] William Stafford Noble,et al. Posterior error probabilities and false discovery rates: two sides of the same coin. , 2008, Journal of proteome research.