Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow
出版年份 2016 全文链接
标题
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow
作者
关键词
-
出版物
Nature Communications
Volume 7, Issue -, Pages 11778
出版商
Springer Nature
发表日期
2016-06-02
DOI
10.1038/ncomms11778
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- A note on the false discovery rate of novel peptides in proteogenomics
- (2015) Kun Zhang et al. BIOINFORMATICS
- Tissue-Based Proteogenomics Reveals that Human Testis Endows Plentiful Missing Proteins
- (2015) Yao Zhang et al. JOURNAL OF PROTEOME RESEARCH
- Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification
- (2015) Gilbert S. Omenn et al. JOURNAL OF PROTEOME RESEARCH
- Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer
- (2015) Sunghee Woo et al. JOURNAL OF PROTEOME RESEARCH
- A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets
- (2015) Mikhail M. Savitski et al. MOLECULAR & CELLULAR PROTEOMICS
- Tissue-based map of the human proteome
- (2015) M. Uhlen et al. SCIENCE
- Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species
- (2015) Hadas Hezroni et al. Cell Reports
- HTSeq--a Python framework to work with high-throughput sequencing data
- (2014) S. Anders et al. BIOINFORMATICS
- Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes
- (2014) Iakes Ezkurdia et al. HUMAN MOLECULAR GENETICS
- Non-model organisms, a species endangered by proteogenomics
- (2014) Jean Armengaud et al. Journal of Proteomics
- A draft map of the human proteome
- (2014) Min-Sik Kim et al. NATURE
- Mass-spectrometry-based draft of the human proteome
- (2014) Mathias Wilhelm et al. NATURE
- A promoter-level mammalian expression atlas
- (2014) NATURE
- Proteogenomics: concepts, applications and computational strategies
- (2014) Alexey I Nesvizhskii NATURE METHODS
- Database resources of the National Center for Biotechnology Information
- (2014) NUCLEIC ACIDS RESEARCH
- UniProt: a hub for protein information
- (2014) NUCLEIC ACIDS RESEARCH
- Proteogenomics
- (2014) PROTEOMICS
- Proteogenomics in microbiology: Taking the right turn at the junction of genomics and proteomics
- (2014) Veronika Kucharova et al. PROTEOMICS
- MS-GF+ makes progress towards a universal database search tool for proteomics
- (2014) Sangtae Kim et al. Nature Communications
- Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions
- (2013) Jainab Khatun et al. BMC GENOMICS
- Fast and Accurate Database Searches with MS-GF+Percolator
- (2013) Viktor Granholm et al. JOURNAL OF PROTEOME RESEARCH
- Proteogenomic Analysis of Human Chromosome 9-Encoded Genes from Human Samples and Lung Cancer Tissues
- (2013) Jung-Mo Ahn et al. JOURNAL OF PROTEOME RESEARCH
- High Performance Computational Analysis of Large-scale Proteome Data Sets to Assess Incremental Contribution to Coverage of the Human Genome
- (2013) Nadin Neuhauser et al. JOURNAL OF PROTEOME RESEARCH
- Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics
- (2013) Linn Fagerberg et al. MOLECULAR & CELLULAR PROTEOMICS
- Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells
- (2013) Charlotte Stadler et al. NATURE METHODS
- HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics
- (2013) Rui M M Branca et al. NATURE METHODS
- RefSeq: an update on mammalian reference sequences
- (2013) Kim D. Pruitt et al. NUCLEIC ACIDS RESEARCH
- Ensembl 2014
- (2013) Paul Flicek et al. NUCLEIC ACIDS RESEARCH
- TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
- (2013) Daehwan Kim et al. GENOME BIOLOGY
- A quantitative atlas of polyadenylation in five mammals
- (2012) Adnan Derti et al. GENOME RESEARCH
- GENCODE: The reference human genome annotation for The ENCODE Project
- (2012) J. Harrow et al. GENOME RESEARCH
- Addressing Statistical Biases in Nucleotide-Derived Protein Databases for Proteogenomic Search Strategies
- (2012) Paul Blakeley et al. JOURNAL OF PROTEOME RESEARCH
- Enhanced Peptide Identification by Electron Transfer Dissociation Using an Improved Mascot Percolator
- (2012) James C. Wright et al. MOLECULAR & CELLULAR PROTEOMICS
- Landscape of transcription in human cells
- (2012) Sarah Djebali et al. NATURE
- A cross-platform toolkit for mass spectrometry and proteomics
- (2012) Matthew C Chambers et al. NATURE BIOTECHNOLOGY
- The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
- (2012) Juan Antonio Vizcaíno et al. NUCLEIC ACIDS RESEARCH
- PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions
- (2011) M. F. Lin et al. BIOINFORMATICS
- Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome
- (2011) M. Brosch et al. GENOME RESEARCH
- Target-Decoy Approach and False Discovery Rate: When Things May Go Wrong
- (2011) Nitin Gupta et al. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
- neXtProt: a knowledge platform for human proteins
- (2011) L. Lane et al. NUCLEIC ACIDS RESEARCH
- Comprehensive proteomics
- (2010) Martin Beck et al. CURRENT OPINION IN BIOTECHNOLOGY
- Towards a knowledge-based Human Protein Atlas
- (2010) Mathias Uhlen et al. NATURE BIOTECHNOLOGY
- Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
- (2010) Mitchell Guttman et al. NATURE BIOTECHNOLOGY
- BLAST+: architecture and applications
- (2009) Christiam Camacho et al. BMC BIOINFORMATICS
- Improvements to the Percolator Algorithm for Peptide Identification from Shotgun Proteomics Data Sets
- (2009) Marina Spivak et al. JOURNAL OF PROTEOME RESEARCH
- Accurate and Sensitive Peptide Identification with Mascot Percolator
- (2009) Markus Brosch et al. JOURNAL OF PROTEOME RESEARCH
- Identifying protein-coding genes in genomic sequences
- (2009) Jennifer Harrow et al. GENOME BIOLOGY
- Mapping and quantifying mammalian transcriptomes by RNA-Seq
- (2008) Ali Mortazavi et al. NATURE METHODS
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started