Promoter propagation in prokaryotes

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

Evolutionary rewiring and reprogramming of bacterial transcription regulation

(2011) Li Wang et al.   Journal of Genetics and Genomics

The Transposon-Like Correia Elements Encode Numerous Strong Promoters and Provide a Potential New Mechanism for Phase Variation in the Meningococcus

(2011) Azeem Siddique et al.   PLoS Genetics

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, L-1,2-Propanediol

(2010) D.-H. Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks

(2010) A. Kuzniar et al.   BIOINFORMATICS

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

The Effect of Mobile Element IS10 on Experimental Regulatory Evolution in Escherichia coli

(2010) D. M. Stoebel et al.   MOLECULAR BIOLOGY AND EVOLUTION

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

Comparative analysis of two Neisseria gonorrhoeae genome sequences reveals evidence of mobilization of Correia Repeat Enclosed Elements and their role in regulation

(2009) Lori AS Snyder et al.   BMC GENOMICS

Lateral genetic transfer: open issues

(2009) M. A. Ragan et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli

(2009) Alfredo Mendoza-Vargas et al.   PLoS One

Transcription factor function and promoter architecture govern the evolution of bacterial regulons

(2009) J. C. Perez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Novel Mechanism of Transposon-Mediated Gene Activation

(2009) Zhongge Zhang et al.   PLoS Genetics

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Evolution of Eukaryotic Transcription Circuits

(2008) B. B. Tuch et al.   SCIENCE

The Emergence and Fate of Horizontally Acquired Genes in Escherichia coli

(2008) Mark W. J. van Passel et al.   PLoS Computational Biology

Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years

(2007) M. J. Lercher et al.   MOLECULAR BIOLOGY AND EVOLUTION