CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains

TSSAR: TSS annotation regime for dRNA-seq data

(2014) Fabian Amman et al.   BMC BIOINFORMATICS

An Infection-Relevant Transcriptomic Compendium for Salmonella enterica Serovar Typhimurium

(2013) Carsten Kröger et al.   Cell Host & Microbe

CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems

(2013) Sita J. Lange et al.   NUCLEIC ACIDS RESEARCH

Comparative genomics boosts target prediction for bacterial small RNAs

(2013) P. R. Wright et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates

(2013) Gaurav Dugar et al.   PLoS Genetics

DAVID-WS: a stateful web service to facilitate gene/protein list analysis

(2012) X. Jiao et al.   BIOINFORMATICS

Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA

(2012) Colin P. Corcoran et al.   MOLECULAR MICROBIOLOGY

CARNA--alignment of RNA structure ensembles

(2012) D. A. Sorescu et al.   NUCLEIC ACIDS RESEARCH

Global or local? Predicting secondary structure and accessibility in mRNAs

(2012) Sita J. Lange et al.   NUCLEIC ACIDS RESEARCH

Rfam 11.0: 10 years of RNA families

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

An archaeal sRNA targeting cis - and trans -encoded mRNAs via two distinct domains

(2012) Dominik Jäger et al.   NUCLEIC ACIDS RESEARCH

Accessibility and conservation: General features of bacterial small RNA–mRNA interactions?

(2012) Andreas Richter et al.   RNA Biology

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Regulatory RNAs in cyanobacteria: developmental decisions, stress responses and a plethora of chromosomally encoded cis-antisense RNAs

(2011) Jens Georg et al.   BIOLOGICAL CHEMISTRY

Regulation by Small RNAs in Bacteria: Expanding Frontiers

(2011) Gisela Storz et al.   MOLECULAR CELL

RNApredator: fast accessibility-based prediction of sRNA targets

(2011) Florian Eggenhofer et al.   NUCLEIC ACIDS RESEARCH

sTarPicker: A Method for Efficient Prediction of Bacterial sRNA Targets Based on a Two-Step Model for Hybridization

(2011) Xiaomin Ying et al.   PLoS One

An experimentally anchored map of transcriptional start sites in the model cyanobacteriumSynechocystissp. PCC6803

(2011) Jan Mitschke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bioinformatic prediction and experimental verification of sRNAs in the haloarchaeonHaloferax volcanii

(2011) Julia Babski et al.   RNA Biology

Genome-wide identification of human microRNAs located in leukemia-associated genomic alterations

(2010) D. T. Starczynowski et al.   BLOOD

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA

(2010) C. Smith et al.   NUCLEIC ACIDS RESEARCH

Computational prediction of sRNAs and their targets in bacteria

(2010) Rolf Backofen 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

Seed-based IntaRNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1

(2009) Andreas S. Richter et al.   BIOINFORMATICS

Biocomputational prediction of non-coding RNAs in model cyanobacteria

(2009) Björn Voß et al.   BMC GENOMICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions

(2008) Anke Busch et al.   BIOINFORMATICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS