Insights from 20 years of bacterial genome sequencing

Efficiently gap-filling reaction networks

(2014) Mario Latendresse   BMC BIOINFORMATICS

Quantum coupled mutation finder: predicting functionally or structurally important sites in proteins using quantum Jensen-Shannon divergence and CUDA programming

(2014) Mehmet Gültas et al.   BMC BIOINFORMATICS

Using MLST to study bacterial variation: prospects in the genomic era

(2014) Keith A Jolley et al.   Future Microbiology

The Diversity of Prokaryotic DDE Transposases of the Mutator Superfamily, Insertion Specificity, and Association with Conjugation Machineries

(2014) Romain Guérillot et al.   Genome Biology and Evolution

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

(2014) J. Chun et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

The quest for a unified view of bacterial land colonization

(2014) Hao Wu et al.   ISME Journal

Intracellular Concentrations of 65 Species of Transcription Factors with Known Regulatory Functions in Escherichia coli

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

Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples

(2014) H. Hasman et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Benchmarking of Methods for Genomic Taxonomy

(2014) M. V. Larsen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Diverse Bacterial Microcompartment Organelles

(2014) C. Chowdhury et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Bacterial Genome Instability

(2014) E. Darmon et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria

(2014) R. Louwen et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A first look at the Oxford Nanopore MinION sequencer

(2014) Alexander S. Mikheyev et al.   Molecular Ecology Resources

Alterations of the human gut microbiome in liver cirrhosis

(2014) Nan Qin et al.   NATURE

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data

(2014) Manuel Garcia-Albornoz et al.   NUCLEIC ACIDS RESEARCH

Low-Bandwidth and Non-Compute Intensive Remote Identification of Microbes from Raw Sequencing Reads

(2014) Laurent Gautier et al.   PLoS One

Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica

(2014) Pimlapas Leekitcharoenphon et al.   PLoS One

The Whole Set of Constitutive Promoters Recognized by RNA Polymerase RpoD Holoenzyme of Escherichia coli

(2014) Tomohiro Shimada et al.   PLoS One

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

(2014) Shanrong Zhao et al.   PLoS One

Development and Evaluation of a Panel of Filovirus Sequence Capture Probes for Pathogen Detection by Next-Generation Sequencing

(2014) Jeffrey W. Koehler et al.   PLoS One

Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms

(2014) Rolf S. Kaas et al.   PLoS One

Predicting microbial growth

(2014) J. Monk et al.   SCIENCE

Supersize me: how whole-genome sequencing and big data are transforming epidemiology

(2014) Rowland R. Kao et al.   TRENDS IN MICROBIOLOGY

Unprecedented High-Resolution View of Bacterial Operon Architecture Revealed by RNA Sequencing

(2014) T. Conway et al.   mBio

The primary transcriptome of the marine diazotroph Trichodesmium erythraeum IMS101

(2014) Ulrike Pfreundt et al.   Scientific Reports

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

(2014) Nikos C. Kyrpides et al.   PLOS BIOLOGY

Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue

(2014) Fredrik H. Karlsson et al.   PLoS Computational Biology

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer

(2014) Joshua Quick et al.   GigaScience

Sigma factors in a thousandE. coligenomes

(2013) Helen Cook et al.   ENVIRONMENTAL MICROBIOLOGY

Software platforms to facilitate reconstructing genome-scale metabolic networks

(2013) Joshua J. Hamilton et al.   ENVIRONMENTAL MICROBIOLOGY

Small, Smaller, Smallest: The Origins and Evolution of Ancient Dual Symbioses in a Phloem-Feeding Insect

(2013) Gordon M. Bennett et al.   Genome Biology and Evolution

Pathoscope: Species identification and strain attribution with unassembled sequencing data

(2013) O. E. Francis et al.   GENOME RESEARCH

Marine metaproteomics: Current status and future directions

(2013) Da-Zhi Wang et al.   Journal of Proteomics

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

(2013) D. McCloskey et al.   Molecular Systems Biology

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments

(2013) Leon Eyrich Jessen et al.   NUCLEIC ACIDS RESEARCH

MetaRef: a pan-genomic database for comparative and community microbial genomics

(2013) Katherine Huang et al.   NUCLEIC ACIDS RESEARCH

Comparative genomics of defense systems in archaea and bacteria

(2013) Kira S. Makarova et al.   NUCLEIC ACIDS RESEARCH

IMG 4 version of the integrated microbial genomes comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Bacterial genomes in epidemiology--present and future

(2013) N. J. Croucher et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Taxonomic Classification of Bacterial 16S rRNA Genes Using Short Sequencing Reads: Evaluation of Effective Study Designs

(2013) Orna Mizrahi-Man et al.   PLoS One

A Genomic Redefinition of Pseudomonas avellanae species

(2013) Marco Scortichini et al.   PLoS One

PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data

(2013) Salvatore Cosentino et al.   PLoS One

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

(2013) J. M. Monk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

Veillonella, Firmicutes: Microbes disguised as Gram negatives

(2013) Tammi Vesth et al.   Standards in Genomic Sciences

Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges

(2013) Sara El-Metwally et al.   PLoS Computational Biology

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

Construction and completion of flux balance models from pathway databases

(2012) Mario Latendresse et al.   BIOINFORMATICS

snpTree - a web-server to identify and construct SNP trees from whole genome sequence data

(2012) Pimlapas Leekitcharoenphon et al.   BMC GENOMICS

Genomic variation in Salmonella enterica core genes for epidemiological typing

(2012) Pimlapas Leekitcharoenphon et al.   BMC GENOMICS

Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes

(2012) Rolf S Kaas et al.   BMC GENOMICS

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

(2012) M. V. Larsen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches

(2012) Ramiro Logares et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study

(2012) Simon R Harris et al.   LANCET INFECTIOUS DISEASES

Large Variations in Bacterial Ribosomal RNA Genes

(2012) K. Lim et al.   MOLECULAR BIOLOGY AND EVOLUTION

A framework for human microbiome research

(2012)   NATURE

Gut microbiota composition correlates with diet and health in the elderly

(2012) Marcus J. Claesson et al.   NATURE

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Genomic approaches to studying the human microbiota

(2012) George M. Weinstock   NATURE

Dual RNA-seq of pathogen and host

(2012) Alexander J. Westermann et al.   NATURE REVIEWS MICROBIOLOGY

Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak

(2012) Claudio U. Köser et al.   NEW ENGLAND JOURNAL OF MEDICINE

Analyzing large biological datasets with association networks

(2012) Tatiana V. Karpinets et al.   NUCLEIC ACIDS RESEARCH

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

(2012) Daniel R. Mende 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

Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria

(2012) Julien Jorda et al.   PROTEIN SCIENCE

Bistability in Atomic-Scale Antiferromagnets

(2012) S. Loth et al.   SCIENCE

Next-Generation Digital Information Storage in DNA

(2012) G. M. Church et al.   SCIENCE

Impact of Small Repeat Sequences on Bacterial Genome Evolution

(2011) Nicholas Delihas   Genome Biology and Evolution

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

(2011) O. Popa et al.   GENOME RESEARCH

Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems

(2011) K. S. Makarova et al.   JOURNAL OF BACTERIOLOGY

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

(2011) I. Pagani et al.   NUCLEIC ACIDS RESEARCH

Normal gut microbiota modulates brain development and behavior

(2011) R. D. Heijtz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Serratia symbiotica from the Aphid Cinara cedri: A Missing Link from Facultative to Obligate Insect Endosymbiont

(2011) Araceli Lamelas et al.   PLoS Genetics

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

(2010) A. Y. Pei et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Analysis of intra-genomic GC content homogeneity within prokaryotes

(2010) Jon Bohlin et al.   BMC GENOMICS

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

Genome update: the 1000th genome - a cautionary tale

(2010) K. Lagesen et al.   MICROBIOLOGY-SGM

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Genome Erosion in a Nitrogen-Fixing Vertically Transmitted Endosymbiotic Multicellular Cyanobacterium

(2010) Liang Ran et al.   PLoS One

In Silico Prediction of Human Pathogenicity in the γ-Proteobacteria

(2010) Massimo Andreatta et al.   PLoS One

CRISPR/Cas, the Immune System of Bacteria and Archaea

(2010) P. Horvath et al.   SCIENCE

Advances in molecular and “-omics” technologies to gauge microbial communities and bioremediation at xenobiotic/anthropogen contaminated sites

(2009) Chirayu Desai et al.   BIORESOURCE TECHNOLOGY

Genome assembly reborn: recent computational challenges

(2009) M. Pop   BRIEFINGS IN BIOINFORMATICS

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

(2009) P. D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

The transcription unit architecture of the Escherichia coli genome

(2009) Byung-Kwan Cho et al.   NATURE BIOTECHNOLOGY

TerraGenome: a consortium for the sequencing of a soil metagenome

(2009) Timothy M. Vogel et al.   NATURE REVIEWS MICROBIOLOGY

Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution

(2009) S.-R. Jun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea

(2008) Z. M.-P. Lee et al.   NUCLEIC ACIDS RESEARCH

A Standard MIGS/MIMS Compliant XML Schema: Toward the Development of the Genomic Contextual Data Markup Language (GCDML)

(2008) Renzo Kottmann et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea

(2007) Rotem Sorek et al.   NATURE REVIEWS MICROBIOLOGY