An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics
出版年份 2017 全文链接
标题
An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics
作者
关键词
-
出版物
GENOME RESEARCH
Volume 27, Issue 12, Pages 2083-2095
出版商
Cold Spring Harbor Laboratory
发表日期
2017-11-16
DOI
10.1101/gr.218255.116
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。- Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-term chronic infection of cystic fibrosis lungs
- (2017) Amy Huei-Yi Lee et al. GENOME RESEARCH
- Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis – a rich resource to identify new transcripts, proteins and to study gene regulation
- (2016) Jelena Čuklina et al. BMC GENOMICS
- MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms
- (2015) Franziska Zickmann et al. BIOINFORMATICS
- Quantitative proteogenomics of human pathogens using DIA-MS
- (2015) Lars Malmström et al. Journal of Proteomics
- The quantitative and condition-dependent Escherichia coli proteome
- (2015) Alexander Schmidt et al. NATURE BIOTECHNOLOGY
- Mass spectrometrists should search only for peptides they care about
- (2015) William Stafford Noble NATURE METHODS
- One-hour proteome analysis in yeast
- (2015) Alicia L Richards et al. Nature Protocols
- eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
- (2015) Jaime Huerta-Cepas et al. NUCLEIC ACIDS RESEARCH
- Small Proteins Can No Longer Be Ignored
- (2014) Gisela Storz et al. Annual Review of Biochemistry
- PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations
- (2014) A. Tovchigrechko et al. BIOINFORMATICS
- Proteome-wide identification of predominant subcellular protein localizations in a bacterial model organism
- (2014) Daniel J. Stekhoven et al. Journal of Proteomics
- Improved prediction of peptide detectability for targeted proteomics using a rank-based algorithm and organism-specific data
- (2014) Ermir Qeli et al. Journal of Proteomics
- Non-model organisms, a species endangered by proteogenomics
- (2014) Jean Armengaud et al. Journal of Proteomics
- Proteogenomics: concepts, applications and computational strategies
- (2014) Alexey I Nesvizhskii NATURE METHODS
- Ribosome profiling: new views of translation, from single codons to genome scale
- (2014) Nicholas T. Ingolia NATURE REVIEWS GENETICS
- The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification
- (2014) T.B.K. Reddy et al. NUCLEIC ACIDS RESEARCH
- Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences
- (2014) W. Nasser et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- High-throughput parallel proteogenomics: A bacterial case study
- (2014) Brett Chapman et al. 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
- Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains
- (2014) Nikos C. Kyrpides et al. PLOS BIOLOGY
- Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approach
- (2013) Esteban Marcellin et al. BMC GENOMICS
- Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome
- (2013) Ulrich Omasits et al. GENOME RESEARCH
- MScDB: A Mass Spectrometry-centric Protein Sequence Database for Proteomics
- (2013) Harald Marx et al. JOURNAL OF PROTEOME RESEARCH
- Tools to Covisualize and Coanalyze Proteomic Data with Genomes and Transcriptomes: Validation of Genes and Alternative mRNA Splicing
- (2013) Chi Nam Ignatius Pang et al. JOURNAL OF PROTEOME RESEARCH
- Peppy: Proteogenomic Search Software
- (2013) Brian A. Risk et al. JOURNAL OF PROTEOME RESEARCH
- Deep Coverage of theEscherichia coliProteome Enables the Assessment of False Discovery Rates in Simple Proteogenomic Experiments
- (2013) Karsten Krug et al. MOLECULAR & CELLULAR PROTEOMICS
- Proteogenomic Analysis ofBradyrhizobium japonicumUSDA110 Using Genosuite, an Automated Multi-algorithmic Pipeline
- (2013) Dhirendra Kumar et al. MOLECULAR & CELLULAR PROTEOMICS
- Proteomics Analysis ofPsychotriaLeaf Nodule Symbiosis: Improved Genome Annotation and Metabolic Predictions
- (2013) Aurelien L. Carlier et al. MOLECULAR PLANT-MICROBE INTERACTIONS
- Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
- (2013) Chen-Shan Chin et al. NATURE METHODS
- Bartonella henselaetrimeric autotransporter adhesin BadA expression interferes with effector translocation by the VirB/D4 type IV secretion system
- (2012) Yun-Yueh Lu et al. CELLULAR MICROBIOLOGY
- Addressing Statistical Biases in Nucleotide-Derived Protein Databases for Proteogenomic Search Strategies
- (2012) Paul Blakeley et al. JOURNAL OF PROTEOME RESEARCH
- Proto-genes and de novo gene birth
- (2012) Anne-Ruxandra Carvunis et al. NATURE
- The human microbiome: at the interface of health and disease
- (2012) Ilseung Cho et al. NATURE REVIEWS GENETICS
- MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data
- (2012) David Vallenet et al. NUCLEIC ACIDS RESEARCH
- The rhizosphere microbiome and plant health
- (2012) Roeland L. Berendsen et al. TRENDS IN PLANT SCIENCE
- Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data
- (2011) Xiaojing Wang et al. JOURNAL OF PROTEOME RESEARCH
- System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap
- (2011) Nagarjuna Nagaraj et al. MOLECULAR & CELLULAR PROTEOMICS
- The essential genome of a bacterium
- (2011) B. Christen et al. Molecular Systems Biology
- Integrative genomics viewer
- (2011) James T Robinson et al. NATURE BIOTECHNOLOGY
- The evolutionary origin of orphan genes
- (2011) Diethard Tautz et al. NATURE REVIEWS GENETICS
- NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
- (2011) K. D. Pruitt et al. NUCLEIC ACIDS RESEARCH
- Proteogenomic Analysis of Bacteria and Archaea: A 46 Organism Case Study
- (2011) Eli Venter et al. PLoS One
- MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes
- (2010) Gustavo A. de Souza et al. BIOINFORMATICS
- Missing genes in the annotation of prokaryotic genomes
- (2010) Andrew S Warren et al. BMC BIOINFORMATICS
- Prodigal: prokaryotic gene recognition and translation initiation site identification
- (2010) Doug Hyatt et al. BMC BIOINFORMATICS
- Lipoproteins of Bacterial Pathogens
- (2010) A. Kovacs-Simon et al. INFECTION AND IMMUNITY
- Proteogenomics to discover the full coding content of genomes: A computational perspective
- (2010) Natalie Castellana et al. Journal of Proteomics
- Proteogenomic Analysis of Polymorphisms and Gene Annotation Divergences in Prokaryotes using a Clustered Mass Spectrometry-Friendly Database
- (2010) Gustavo A. de Souza et al. MOLECULAR & CELLULAR PROTEOMICS
- PeptideClassifier for protein inference and targeted quantitative proteomics
- (2010) Ermir Qeli et al. NATURE BIOTECHNOLOGY
- GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
- (2010) Amrita Pati et al. NATURE METHODS
- Genome annotation: man versus machine
- (2010) Nicola K. Petty NATURE REVIEWS MICROBIOLOGY
- Generating and navigating proteome maps using mass spectrometry
- (2010) Christian H. Ahrens et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Proteogenomics
- (2010) Santosh Renuse et al. PROTEOMICS
- IMG ER: a system for microbial genome annotation expert review and curation
- (2009) Victor M. Markowitz et al. BIOINFORMATICS
- Genome reannotation of Escherichia coli CFT073 with new insights into virulence
- (2009) Chengwei Luo et al. BMC GENOMICS
- The comprehensive microbial resource
- (2009) Tanja Davidsen et al. NUCLEIC ACIDS RESEARCH
- Evaluation of Three Automated Genome Annotations for Halorhabdus utahensis
- (2009) Peter Bakke et al. PLoS One
- Identification and Functional Characterization of N-Terminally Acetylated Proteins in Drosophila melanogaster
- (2009) Sandra Goetze et al. PLOS BIOLOGY
- Alliance of Proteomics and Genomics to Unravel the Specificities of Sahara Bacterium Deinococcus deserti
- (2009) Arjan de Groot et al. PLoS Genetics
- Prokaryotic Gene Finding Based on Physicochemical Characteristics of Codons Calculated from Molecular Dynamics Simulations
- (2008) Poonam Singhal et al. BIOPHYSICAL JOURNAL
- The RAST Server: Rapid Annotations using Subsystems Technology
- (2008) Ramy K Aziz et al. BMC GENOMICS
- Small membrane proteins found by comparative genomics and ribosome binding site models
- (2008) Matthew R. Hemm et al. MOLECULAR MICROBIOLOGY
- Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities
- (2008) Marcel E. Dinger et al. PLoS Computational Biology
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAsk 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