Mutant phenotypes for thousands of bacterial genes of unknown function

PaperBLAST: Text Mining Papers for Information about Homologs

(2017) Morgan N. Price et al.   mSystems

Validating regulatory predictions from diverse bacteria with mutant fitness data

(2017) Shiori Sagawa et al.   PLoS One

Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri

(2016) Brian J. Vaccaro et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome

(2016) Tim van Opijnen et al.   PLoS Pathogens

Molybdenum Availability Is Key to Nitrate Removal in Contaminated Groundwater Environments

(2015) Michael P. Thorgersen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Functional characterization of two SOS-regulated genes involved in mitomycin C resistance in Caulobacter crescentus

(2015) Carina O. Lopes-Kulishev et al.   DNA REPAIR

Escherichia coli radD (yejH)gene: a novel function involved in radiation resistance and double-strand break repair

(2015) Stefanie H. Chen et al.   MOLECULAR MICROBIOLOGY

COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps

(2015) Yi-Chien Chang et al.   NUCLEIC ACIDS RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

The essential gene set of a photosynthetic organism

(2015) Benjamin E. Rubin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Novel Mechanism for Scavenging of Hypochlorite Involving a Periplasmic Methionine-Rich Peptide and Methionine Sulfoxide Reductase

(2015) Ryan A. Melnyk et al.   mBio

Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons

(2015) Kelly M. Wetmore et al.   mBio

grofit: Fitting Biological Growth Curves withR

(2015) Matthias Kahm et al.   Journal of Statistical Software

Carbohydrate Catabolism in Phaeobacter inhibens DSM 17395, a Member of the Marine Roseobacter Clade

(2014) Katharina Wiegmann et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5′ flap DNA: basis of interstrand cross-link repair by FAN1

(2014) Gwang Hyeon Gwon et al.   GENES & DEVELOPMENT

Towards an Informative Mutant Phenotype for Every Bacterial Gene

(2014) A. Deutschbauer et al.   JOURNAL OF BACTERIOLOGY

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Functional Genomics with a Comprehensive Library of Transposon Mutants for the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20

(2014) J. V. Kuehl et al.   mBio

The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20

(2014) Morgan N. Price et al.   Frontiers in Microbiology

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Bacterial Adaptation through Loss of Function

(2013) Alison K. Hottes et al.   PLoS Genetics

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A hybrid approach for the automated finishing of bacterial genomes

(2012) Ali Bashir et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

TIGRFAMs and Genome Properties in 2013

(2012) Daniel H. Haft et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

An Integrated Pipeline for de Novo Assembly of Microbial Genomes

(2012) Andrew Tritt et al.   PLoS One

Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride

(2011) J. L. Baker et al.   SCIENCE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions

(2011) Adam Deutschbauer et al.   PLoS Genetics

Effect of the Deletion of qmoABC and the Promoter-Distal Gene Encoding a Hypothetical Protein on Sulfate Reduction in Desulfovibrio vulgaris Hildenborough

(2010) G. M. Zane et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Phenotypic Landscape of a Bacterial Cell

(2010) Robert J. Nichols et al.   CELL

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action

(2010) Maureen E Hillenmeyer et al.   GENOME BIOLOGY

Quantitative phenotyping via deep barcode sequencing

(2009) A. M. Smith et al.   GENOME RESEARCH

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

(2009) G. C. Langridge et al.   GENOME RESEARCH

d-Xylose Degradation Pathway in the Halophilic ArchaeonHaloferax volcanii

(2009) Ulrike Johnsen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms

(2009) Tim van Opijnen et al.   NATURE METHODS

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

(2009) Alexandra M. Schnoes et al.   PLoS Computational Biology

Cloning, expression, purification and characterization of the stress kinase YeaG from Escherichia coli

(2008) Jihen Tagourti et al.   PROTEIN EXPRESSION AND PURIFICATION

Morphological plasticity as a bacterial survival strategy

(2007) Sheryl S. Justice et al.   NATURE REVIEWS MICROBIOLOGY