Indispensability of Horizontally Transferred Genes and Its Impact on Bacterial Genome Streamlining

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

(2015) Socorro Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes

(2015) Chuan Ku et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Colony-live —a high-throughput method for measuring microbial colony growth kinetics— reveals diverse growth effects of gene knockouts in Escherichia coli

(2014) Rikiya Takeuchi et al.   BMC MICROBIOLOGY

LESS IS MORE: SELECTIVE ADVANTAGES CAN EXPLAIN THE PREVALENT LOSS OF BIOSYNTHETIC GENES IN BACTERIA

(2014) Glen D'Souza et al.   EVOLUTION

Implications of streamlining theory for microbial ecology

(2014) Stephen J Giovannoni et al.   ISME Journal

Bacillus subtilis and Escherichia coli essential genes and minimal cell factories after one decade of genome engineering

(2014) M. Juhas et al.   MICROBIOLOGY-SGM

Conditional DNA repair mutants enable highly precise genome engineering

(2014) Ákos Nyerges et al.   NUCLEIC ACIDS RESEARCH

The Heat Shock Factor A4A Confers Salt Tolerance and Is Regulated by Oxidative Stress and the Mitogen-Activated Protein Kinases MPK3 and MPK6

(2014) I. Perez-Salamo et al.   PLANT PHYSIOLOGY

Genome-wide analysis captures the determinants of the antibiotic cross-resistance interaction network

(2014) Viktória Lázár et al.   Nature Communications

Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction

(2014) George C. diCenzo et al.   PLoS Genetics

Genome architecture and global gene regulation in bacteria: making progress towards a unified model?

(2013) Charles J. Dorman   NATURE REVIEWS MICROBIOLOGY

Synthetic tolerance: three noncoding small RNAs, DsrA, ArcZ and RprA, acting supra-additively against acid stress

(2013) S. M. Gaida et al.   NUCLEIC ACIDS RESEARCH

Roles ofrpoS-activating small RNAs in pathways leading to acid resistance ofEscherichia coli

(2013) Geunu Bak et al.   MicrobiologyOpen

EcoGene 3.0

(2012) Jindan Zhou et al.   NUCLEIC ACIDS RESEARCH

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Repeated, Selection-Driven Genome Reduction of Accessory Genes in Experimental Populations

(2012) Ming-Chun Lee et al.   PLoS Genetics

Selection-Driven Gene Loss in Bacteria

(2012) Sanna Koskiniemi et al.   PLoS Genetics

Extreme genome reduction in symbiotic bacteria

(2011) John P. McCutcheon et al.   NATURE REVIEWS MICROBIOLOGY

Coexisting/Coexpressing Genomic Libraries (CoGeL) identify interactions among distantly located genetic loci for developing complex microbial phenotypes

(2011) Sergios A. Nicolaou et al.   NUCLEIC ACIDS RESEARCH

Condition-Dependent Cell Volume and Concentration of Escherichia coli to Facilitate Data Conversion for Systems Biology Modeling

(2011) Benjamin Volkmer et al.   PLoS One

Bacterial Chromosome Organization and Segregation

(2010) E. Toro et al.   Cold Spring Harbor Perspectives in Biology

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Genetic Architecture of Intrinsic Antibiotic Susceptibility

(2009) Hany S. Girgis et al.   PLoS One