Related references
Note: Only part of the references are listed.A Proteogenomic Resource Enabling Integrated Analysis of Listeria Genotype-Proteotype-Phenotype Relationships
Adithi R. Varadarajan et al.
JOURNAL OF PROTEOME RESEARCH (2020)
Enrichment and identification of small proteins in a simplified human gut microbiome
Hannes Petruschke et al.
JOURNAL OF PROTEOMICS (2020)
Pervasive functional translation of noncanonical human open reading frames
Jin Chen et al.
SCIENCE (2020)
Following the community development of SIHUMIx - a new intestinal in vitro model for bioreactor use
Jannike Lea Krause et al.
GUT MICROBES (2020)
Function is what counts: how microbial community complexity affects species, proteome and pathway coverage in metaproteomics
Patrick Lohmann et al.
EXPERT REVIEW OF PROTEOMICS (2020)
Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss
Sven-Bastiaan Haange et al.
MICROBIOME (2020)
Characterization of purified antimicrobial peptide produced by Pediococcus pentosaceus LJR1, and its application in preservation of white leg shrimp
Gothandam Ladha et al.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY (2020)
Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host
Duarte Gouveia et al.
NPJ BIOFILMS AND MICROBIOMES (2020)
The Leader Peptide peTrpL Forms Antibiotic-Containing Ribonucleoprotein Complexes for Posttranscriptional Regulation of Multiresistance Genes
Hendrik Melior et al.
MBIO (2020)
An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1
Adithi R. Varadarajan et al.
NPJ BIOFILMS AND MICROBIOMES (2020)
Identifying Small Proteins by Ribosome Profiling with Stalled Initiation Complexes
Jeremy Weaver et al.
MBIO (2019)
Development of an interspecies interaction model: An experiment on Clostridium cadaveris and Clostridium sporogenes under anaerobic condition
Taewoan Koo et al.
JOURNAL OF ENVIRONMENTAL MANAGEMENT (2019)
Assembly of long, error-prone reads using repeat graphs
Mikhail Kolmogorov et al.
NATURE BIOTECHNOLOGY (2019)
An Integrated Systems Approach Unveils New Aspects of Microoxia-Mediated Regulation in Bradyrhizobium diazoefficiens
Noemi Fernandez et al.
FRONTIERS IN MICROBIOLOGY (2019)
Metabolic Functions of Gut Microbes Associate With Efficacy of Tumor Necrosis Factor Antagonists in Patients With Inflammatory Bowel Diseases
Konrad Aden et al.
GASTROENTEROLOGY (2019)
Metaproteomic investigation to assess gut microbiota shaping in newborn mice: A combined taxonomic, functional and quantitative approach
Stefano Levi Mortera et al.
JOURNAL OF PROTEOMICS (2019)
Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes
Hila Sberro et al.
CELL (2019)
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
Daehwan Kim et al.
NATURE BIOTECHNOLOGY (2019)
uap: reproducible and robust HTS data analysis
Christoph Kaempf et al.
BMC BIOINFORMATICS (2019)
The Simplified Human Intestinal Microbiota (SIHUMIx) Shows High Structural and Functional Resistance against Changing Transit Times in In Vitro Bioreactors
Stephanie Serena Schaepe et al.
MICROORGANISMS (2019)
Metaproteomics of the human gut microbiota: Challenges and contributions to other OMICS
Ngom Issa Isaac et al.
CLINICAL MASS SPECTROMETRY (2019)
Deep learning improves antimicrobial peptide recognition
Daniel Veltri et al.
BIOINFORMATICS (2018)
Grasping the nettle: A bacterial invasin that targets immunoglobulin variable domains
Paul Barlow
JOURNAL OF BIOLOGICAL CHEMISTRY (2018)
Accurate detection of complex structural variations using single-molecule sequencing
Fritz J. Sedlazeck et al.
NATURE METHODS (2018)
Identifying New Small Proteins in Escherichia coli
Caitlin E. VanOrsdel et al.
PROTEOMICS (2018)
An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics
Ulrich Omasits et al.
GENOME RESEARCH (2017)
SgrT, a Small Protein That Packs a Sweet Punch
Medha Raina et al.
JOURNAL OF BACTERIOLOGY (2017)
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
Jaime Huerta-Cepas et al.
MOLECULAR BIOLOGY AND EVOLUTION (2017)
Quorum sensing integrates environmental cues, cell density and cell history to control bacterial competence
Stefany Moreno-Gamez et al.
NATURE COMMUNICATIONS (2017)
Small bacterial and phagic proteins: an updated view on a rapidly moving field
Melodie Duval et al.
CURRENT OPINION IN MICROBIOLOGY (2017)
Dysbiosis and the immune system
Maayan Levy et al.
NATURE REVIEWS IMMUNOLOGY (2017)
HYBRIDSPADES: an algorithm for hybrid assembly of short and long reads
Dmitry Antipov et al.
BIOINFORMATICS (2016)
Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data
Konstantin Okonechnikov et al.
BIOINFORMATICS (2016)
The quantitative and condition-dependent Escherichia coli proteome
Alexander Schmidt et al.
NATURE BIOTECHNOLOGY (2016)
Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules
Baptiste Mayjonade et al.
BIOTECHNIQUES (2016)
Multifaceted Interfaces of Bacterial Competition
Reed M. Stubbendieck et al.
JOURNAL OF BACTERIOLOGY (2016)
Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei
Liam Cassidy et al.
JOURNAL OF PROTEOME RESEARCH (2016)
Six alternative proteases for mass spectrometry-based proteomics beyond trypsin
Piero Giansanti et al.
NATURE PROTOCOLS (2016)
NCBI prokaryotic genome annotation pipeline
Tatiana Tatusova et al.
NUCLEIC ACIDS RESEARCH (2016)
Fast and sensitive mapping of nanopore sequencing reads with GraphMap
Ivan Sovic et al.
NATURE COMMUNICATIONS (2016)
Bacterial Communities: Interactions to Scale
Reed M. Stubbendieck et al.
FRONTIERS IN MICROBIOLOGY (2016)
The Phyre2 web portal for protein modeling, prediction and analysis
Lawrence A. Kelley et al.
NATURE PROTOCOLS (2015)
Navigating through metaproteomics data: A logbook of database searching
Thilo Muth et al.
PROTEOMICS (2015)
HTSeq-a Python framework to work with high-throughput sequencing data
Simon Anders et al.
BIOINFORMATICS (2015)
Small Proteins Can No Longer Be Ignored
Gisela Storz et al.
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 83 (2014)
Proteogenomics: concepts, applications and computational strategies
Alexey I. Nesvizhskii
NATURE METHODS (2014)
Ribosome profiling: new views of translation, from single codons to genome scale APPLICATIONS OF NEXT-GENERATION SEQUENCING - INNOVATION
Nicholas T. Ingolia
NATURE REVIEWS GENETICS (2014)
MS-GF plus makes progress towards a universal database search tool for proteomics
Sangtae Kim et al.
NATURE COMMUNICATIONS (2014)
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
Helga Thorvaldsdottir et al.
BRIEFINGS IN BIOINFORMATICS (2013)
Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome
Ulrich Omasits et al.
GENOME RESEARCH (2013)
Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics
Stephan A. Mueller et al.
JOURNAL OF PROTEOMICS (2013)
Small proteins: untapped area of potential biological importance
Mingming Su et al.
Frontiers in Genetics (2013)
Natural antimicrobial peptides from bacteria: characteristics and potential applications to fight against antibiotic resistance
M. Hassan et al.
JOURNAL OF APPLIED MICROBIOLOGY (2012)
Addressing Statistical Biases in Nucleotide-Derived Protein Databases for Proteogenomic Search Strategies
Paul Blakeley et al.
JOURNAL OF PROTEOME RESEARCH (2012)
Functional interactions between the gut microbiota and host metabolism
Valentina Tremaroli et al.
NATURE (2012)
A cross-platform toolkit for mass spectrometry and proteomics
Matthew C. Chambers et al.
NATURE BIOTECHNOLOGY (2012)
Human intestinal microbiota Characterization of a simplified and stable gnotobiotic rat model
Natalie Becker et al.
GUT MICROBES (2011)
Optimization of parameters for coverage of low molecular weight proteins
Stephan A. Mueller et al.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2010)
Bacterial Contact-Dependent Delivery Systems
Christopher S. Hayes et al.
ANNUAL REVIEW OF GENETICS, VOL 44 (2010)
Missing genes in the annotation of prokaryotic genomes
Andrew S. Warren et al.
BMC BIOINFORMATICS (2010)
Prodigal: prokaryotic gene recognition and translation initiation site identification
Doug Hyatt et al.
BMC BIOINFORMATICS (2010)
Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics
Danielle L. Swaney et al.
JOURNAL OF PROTEOME RESEARCH (2010)
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
Alexey I. Nesvizhskii
JOURNAL OF PROTEOMICS (2010)
PeptideClassifier for protein inference and targeted quantitative proteomics
Ermir Qeli et al.
NATURE BIOTECHNOLOGY (2010)
The Sequence Alignment/Map format and SAMtools
Heng Li et al.
BIOINFORMATICS (2009)
Circos: An information aesthetic for comparative genomics
Martin Krzywinski et al.
GENOME RESEARCH (2009)
Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics Simulations
Poonam Singhal et al.
BIOPHYSICAL JOURNAL (2008)
Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities
Marcel E. Dinger et al.
PLOS COMPUTATIONAL BIOLOGY (2008)
Semi-supervised learning for peptide identification from shotgun proteomics datasets
Lukas Kall et al.
NATURE METHODS (2007)
Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae
Boris Zybailov et al.
JOURNAL OF PROTEOME RESEARCH (2006)
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins
Edouard de Castro et al.
NUCLEIC ACIDS RESEARCH (2006)
Immunity, inflammation, and allergy in the gut
TT MacDonald et al.
SCIENCE (2005)
A combined transmembrane topology and signal peptide prediction method
L Käll et al.
JOURNAL OF MOLECULAR BIOLOGY (2004)
Multidimensional signatures in antimicrobial peptides
NY Yount et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
The crystal structure of MarR, a regulator of multiple antibiotic resistance, at 2.3 Å resolution
MN Alekshun et al.
NATURE STRUCTURAL BIOLOGY (2001)
Crystal structure of enteropathogenic Escherichia coli intimin-receptor complex
L Yu et al.
NATURE (2000)