Explaining microbial phenotypes on a genomic scale: GWAS for microbes

Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation

(2012) Jonathan L Klassen et al.   BMC GENOMICS

PhenoLink - a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains

(2012) Jumamurat R Bayjanov et al.   BMC GENOMICS

The automatic annotation of bacterial genomes

(2012) E. J. Richardson et al.   BRIEFINGS IN BIOINFORMATICS

Comparison of antibiotic susceptibility of old and currentSerratia

(2012) Ester Fusté et al.   Future Microbiology

Quality of prokaryote genome assembly: Indispensable issues of factors affecting prokaryote genome assembly quality

(2012) Adriana R. Carneiro et al.   GENE

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

(2012) Kathryn E Holt et al.   NATURE GENETICS

Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing

(2012) Simon R Harris et al.   NATURE GENETICS

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

(2012) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

(2012) Sajia Akhter et al.   NUCLEIC ACIDS RESEARCH

Effect of garlic powder on the growth of commensal bacteria from the gastrointestinal tract

(2012) Angela Filocamo et al.   PHYTOMEDICINE

Modulation of Lactobacillus plantarum Gastrointestinal Robustness by Fermentation Conditions Enables Identification of Bacterial Robustness Markers

(2012) Hermien van Bokhorst-van de Veen et al.   PLoS One

Transcriptomes Reveal Genetic Signatures Underlying Physiological Variations Imposed by Different Fermentation Conditions in Lactobacillus plantarum

(2012) Peter A. Bron et al.   PLoS One

The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation

(2012) Konstantinos Mavromatis et al.   PLoS One

Discovery of a hapE Mutation That Causes Azole Resistance in Aspergillus fumigatus through Whole Genome Sequencing and Sexual Crossing

(2012) Simone M. T. Camps et al.   PLoS One

Metagenomics and future perspectives in virus discovery

(2012) John L Mokili et al.   Current Opinion in Virology

Joint Analysis of Multiple Metagenomic Samples

(2012) Yael Baran et al.   PLoS Computational Biology

Listeria monocytogenes Mutants with Altered Growth Phenotypes at Refrigeration Temperature and High Salt Concentrations

(2011) Laurel S. Burall et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Defining the structure of the general stress regulon of Bacillus subtilis using targeted microarray analysis and random forest classification

(2011) P. Nannapaneni et al.   MICROBIOLOGY-SGM

Evidence for several waves of global transmission in the seventh cholera pandemic

(2011) Ankur Mutreja et al.   NATURE

Ranking causal variants and associated regions in genome-wide association studies by the support vector machine and random forest

(2011) Usman Roshan et al.   NUCLEIC ACIDS RESEARCH

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

iPath2.0: interactive pathway explorer

(2011) Takuji Yamada et al.   NUCLEIC ACIDS RESEARCH

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Towards the Human Colorectal Cancer Microbiome

(2011) Julian R. Marchesi et al.   PLoS One

Growth of Acinetobacter baumannii in Pellicle Enhanced the Expression of Potential Virulence Factors

(2011) Sara Marti et al.   PLoS One

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays

(2011) Roland J. Siezen et al.   Microbial Biotechnology

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Class prediction for high-dimensional class-imbalanced data

(2010) Rok Blagus et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Identification of Lactobacillus plantarum genes modulating the cytokine response of human peripheral blood mononuclear cells

(2010) Saskia van Hemert et al.   BMC MICROBIOLOGY

Sample Size Calculation and Power Analysis: A Quick Review

(2010) Karen Fitzner et al.   DIABETES EDUCATOR

A screening methodology based on Random Forests to improve the detection of gene–gene interactions

(2010) Lizzy De Lobel et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Progress and Promise of Genome-Wide Association Studies for Human Complex Trait Genetics

(2010) B. E. Stranger et al.   GENETICS

The proof and measurement of association between two things

(2010) C Spearman   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Genomics-driven Reconstruction ofAcinetobacterNAD Metabolism

(2010) Leonardo Sorci et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

GenBank

(2010) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Identification of Genetic Loci in Lactobacillus plantarum That Modulate the Immune Response of Dendritic Cells Using Comparative Genome Hybridization

(2010) Marjolein Meijerink et al.   PLoS One

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Cryptic prophages help bacteria cope with adverse environments

(2010) Xiaoxue Wang et al.   Nature Communications

Genome (re-)annotation and open-source annotation pipelines

(2010) Roland J. Siezen et al.   Microbial Biotechnology

Metabolic Capacity of Sinorhizobium (Ensifer) meliloti Strains as Determined by Phenotype MicroArray Analysis

(2009) E. G. Biondi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly

(2009) Bas E. Dutilh et al.   BIOINFORMATICS

Predictor correlation impacts machine learning algorithms: implications for genomic studies

(2009) K. K. Nicodemus et al.   BIOINFORMATICS

PanCGH: a genotype-calling algorithm for pangenome CGH data

(2009) Jumamurat R. Bayjanov et al.   BIOINFORMATICS

Horizontal Gene Transfer of the Secretome Drives the Evolution of Bacterial Cooperation and Virulence

(2009) Teresa Nogueira et al.   CURRENT BIOLOGY

Phenotypic and genomic diversity ofLactobacillus plantarumstrains isolated from various environmental niches

(2009) Roland J. Siezen et al.   ENVIRONMENTAL MICROBIOLOGY

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Automatic policing of biochemical annotations using genomic correlations

(2009) Tzu-Lin Hsiao et al.   Nature Chemical Biology

Sense from sequence reads: methods for alignment and assembly

(2009) Paul Flicek et al.   NATURE METHODS

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

In the news

(2009)   NATURE REVIEWS MICROBIOLOGY

Quantifying environmental adaptation of metabolic pathways in metagenomics

(2009) T. A. Gianoulis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Variable selection for large p small n regression models with incomplete data: Mapping QTL with epistases

(2008) Min Zhang et al.   BMC BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

The minimum information about a genome sequence (MIGS) specification

(2008) Dawn Field et al.   NATURE BIOTECHNOLOGY

Comparing whole genomes using DNA microarrays

(2008) David Gresham et al.   NATURE REVIEWS GENETICS

Signature, a web server for taxonomic characterization of sequence samples using signature genes

(2008) B. E. Dutilh et al.   NUCLEIC ACIDS RESEARCH

STRING 8--a global view on proteins and their functional interactions in 630 organisms

(2008) L. J. Jensen et al.   NUCLEIC ACIDS RESEARCH

Conservation of divergent transcription in fungi

(2008) Philip R. Kensche et al.   TRENDS IN GENETICS

High-Throughput Phenotypic Characterization of Pseudomonas aeruginosa Membrane Transport Genes

(2008) Daniel A. Johnson et al.   PLoS Genetics

Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution

(2007) P. R Kensche et al.   Journal of the Royal Society Interface