Loss of Conserved Noncoding RNAs in Genomes of Bacterial Endosymbionts

Transcriptome-Based Analysis of the Pantoea stewartii Quorum-Sensing Regulon and Identification of EsaR Direct Targets

(2014) Revathy Ramachandran et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Widespread expression of conserved small RNAs in small symbiont genomes

(2014) Allison K Hansen et al.   ISME Journal

Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling

(2014) Stinus Lindgreen et al.   PLoS Computational Biology

Ends of the line for tmRNA-SmpB

(2014) Corey M. Hudson et al.   Frontiers in Microbiology

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

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

Database resources of the National Center for Biotechnology Information

(2013)   NUCLEIC ACIDS RESEARCH

Most RNAs regulating ribosomal protein biosynthesis in Escherichia coli are narrowly distributed to Gammaproteobacteria

(2013) Yang Fu et al.   NUCLEIC ACIDS RESEARCH

S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA

(2013) D. Matelska et al.   RNA

Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu

(2013) Kui Han et al.   Scientific Reports

Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist

(2012) Laura E Williams et al.   BMC GENOMICS

A Tight Link between Orthologs and Bidirectional Best Hits in Bacterial and Archaeal Genomes

(2012) Yuri I. Wolf et al.   Genome Biology and Evolution

Comparative transcriptomics of pathogenic and non-pathogenic Listeria species

(2012) Omri Wurtzel et al.   Molecular Systems Biology

The excludon: a new concept in bacterial antisense RNA-mediated gene regulation

(2012) Nina Sesto et al.   NATURE REVIEWS MICROBIOLOGY

Bacterial RNA thermometers: molecular zippers and switches

(2012) Jens Kortmann et al.   NATURE REVIEWS MICROBIOLOGY

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs

(2012) S. Will et al.   RNA

Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life

(2012) Marc P. Hoeppner et al.   PLoS Computational Biology

Multiple origins of endosymbiosis within the Enterobacteriaceae (γ-Proteobacteria): convergence of complex phylogenetic approaches

(2011) Filip Husník et al.   BMC BIOLOGY

Massive Genomic Decay in Serratia symbiotica, a Recently Evolved Symbiont of Aphids

(2011) Gaelen R. Burke et al.   Genome Biology and Evolution

Regulation by Small RNAs in Bacteria: Expanding Frontiers

(2011) Gisela Storz et al.   MOLECULAR CELL

Extreme genome reduction in symbiotic bacteria

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

Bacterial transcriptomics: what is beyond the RNA horiz-ome?

(2011) Marc Güell et al.   NATURE REVIEWS MICROBIOLOGY

Database resources of the National Center for Biotechnology Information

(2011) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

Sequence Conservation and Functional Constraint on Intergenic Spacers in Reduced Genomes of the Obligate Symbiont Buchnera

(2011) Patrick H. Degnan et al.   PLoS Genetics

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

(2011) Araceli Lamelas et al.   PLoS Genetics

Structural and operational complexity of the Geobacter sulfurreducens genome

(2010) Y. Qiu et al.   GENOME RESEARCH

Kinship in the SRP RNA family

(2010) Magnus Alm Rosenblad et al.   RNA Biology

Bacterial Small RNA Regulators: Versatile Roles and Rapidly Evolving Variations

(2010) S. Gottesman et al.   Cold Spring Harbor Perspectives in Biology

Massive comparative genomic analysis reveals convergent evolution of specialized bacteria

(2009) Vicky Merhej et al.   Biology Direct

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Regulatory RNAs in Bacteria

(2009) Lauren S. Waters et al.   CELL

The consequences of genetic drift for bacterial genome complexity

(2009) C.-H. Kuo et al.   GENOME RESEARCH

Impact of Genome Reduction on Bacterial Metabolism and Its Regulation

(2009) E. Yus et al.   SCIENCE

Transcriptome Complexity in a Genome-Reduced Bacterium

(2009) M. Guell et al.   SCIENCE

5′-End maturation of tRNA in Aquifex aeolicus

(2008) Michal Marszalkowski et al.   BIOLOGICAL CHEMISTRY

Towards deciphering the principles underlying an mRNA recognition code

(2008) Alexander Serganov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY