Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes

Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes

(2017) Joana C. Xavier et al.   METABOLIC ENGINEERING

Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis

(2017) Byoung-Mo Koo et al.   Cell Systems

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

The physiology and habitat of the last universal common ancestor

(2016) Madeline C. Weiss et al.   Nature Microbiology

Ancient horizontal gene transfer and the last common ancestors

(2015) Gregory P Fournier et al.   BMC EVOLUTIONARY BIOLOGY

Do genome-scale models need exact solvers or clearer standards?

(2015) A. Ebrahim et al.   Molecular Systems Biology

Essential Genes in the Core Genome of the Human Pathogen Streptococcus pyogenes

(2015) Yoann Le Breton et al.   Scientific Reports

Comparative analysis of essential genes in prokaryotic genomic islands

(2015) Xi Zhang et al.   Scientific Reports

Evolutionary conservation analysis between the essential and nonessential genes in bacterial genomes

(2015) Hao Luo et al.   Scientific Reports

Identification of genes required for the survival of B. fragilis using massive parallel sequencing of a saturated transposon mutant library

(2014) Yaligara Veeranagouda et al.   BMC GENOMICS

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Genome-Wide Saturation Mutagenesis of Burkholderia pseudomallei K96243 Predicts Essential Genes and Novel Targets for Antimicrobial Development

(2014) M. G. Moule et al.   mBio

Rescuing Auxotrophic Microorganisms with Nonenzymatic Chemistry

(2013) Yunmi Lee et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium

(2013) Lars Barquist et al.   NUCLEIC ACIDS RESEARCH

DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements: Table 1.

(2013) Hao Luo et al.   NUCLEIC ACIDS RESEARCH

Combining Functional and Structural Genomics to Sample the Essential Burkholderia Structome

(2013) Loren Baugh et al.   PLoS One

Genome Scanning for Conditionally Essential Genes in Salmonella enterica Serotype Typhimurium

(2012) Anita Khatiwara et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Out of fuzzy chemistry: from prebiotic chemistry to metabolic networks

(2012) Juli Peretó   CHEMICAL SOCIETY REVIEWS

Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis

(2012) J. Nogales et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coping with complexity in metabolic engineering

(2012) Joerg Mampel et al.   TRENDS IN BIOTECHNOLOGY

Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis

(2012) Yanjia J. Zhang et al.   PLoS Pathogens

The proteomic complexity and rise of the primordial ancestor of diversified life

(2011) Kyung Mo Kim et al.   BMC EVOLUTIONARY BIOLOGY

The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli

(2011) Colin T Archer et al.   BMC GENOMICS

In vivo and in silico determination of essential genes of Campylobacter jejuni

(2011) Aline Metris et al.   BMC GENOMICS

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

(2011) Caroline B Milne et al.   BMC Systems Biology

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

(2011) Ines Thiele et al.   BMC Systems Biology

An Experimentally Validated Genome-Scale Metabolic Reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228

(2011) Y.-C. Liao et al.   JOURNAL OF BACTERIOLOGY

The essential genome of a bacterium

(2011) B. Christen et al.   Molecular Systems Biology

OGEE: an online gene essentiality database

(2011) Wei-Hua Chen et al.   NUCLEIC ACIDS RESEARCH

Genome-Scale Identification of Resistance Functions in Pseudomonas aeruginosa Using Tn-seq

(2011) L. A. Gallagher et al.   mBio

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

High-Resolution Phenotypic Profiling Defines Genes Essential for Mycobacterial Growth and Cholesterol Catabolism

(2011) Jennifer E. Griffin et al.   PLoS Pathogens

OptFlux: an open-source software platform for in silico metabolic engineering

(2010) Isabel Rocha et al.   BMC Systems Biology

Characterizing the Metabolism of Dehalococcoides with a Constraint-Based Model

(2010) M. Ahsanul Islam et al.   PLoS Computational Biology

Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: A Tool for Data Analysis and Hypothesis Generation

(2010) Grigoriy E. Pinchuk et al.   PLoS Computational Biology

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH)

(2009) Roy R Chaudhuri et al.   BMC GENOMICS

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

(2009) Andrew L. Goodman et al.   Cell Host & Microbe

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

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

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Origin and evolution of metabolic pathways

(2009) Renato Fani et al.   Physics of Life Reviews

Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima

(2009) Y. Zhang et al.   SCIENCE

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

(2008) Juan Nogales et al.   BMC Systems Biology

Large-scale transposon mutagenesis ofMycoplasma pulmonis

(2008) Christopher T. French et al.   MOLECULAR MICROBIOLOGY

A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1

(2008) Véronique de Berardinis et al.   Molecular Systems Biology

A defined transposon mutant library and its use in identifying motility genes in Vibrio cholerae

(2008) D. E. Cameron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA