- Mining regulatory 5'UTRs from cDNA deep sequencing datasetsJonathan Livny
The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
Nucleic Acids Res 38:1504-14. 2010..Our findings suggest that the number and diversity of pathways regulated by r5'UTRs has been underestimated and that deep sequencing-based transcriptomics will be extremely valuable in the search for novel r5'UTRs...
- Bioinformatic discovery of bacterial regulatory RNAs using SIPHTJonathan Livny
The Broad Institute of MIT and Harvard, Cambridge, MA, USA
Methods Mol Biol 905:3-14. 2012..Each locus is then annotated for numerous features that provide clues about its potential function and/or enable the most reliable candidates to be identified...
- How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?Brian J Haas
Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
BMC Genomics 13:734. 2012..A central challenge in designing RNA-Seq-based experiments is estimating a priori the number of reads per sample needed to detect and quantify thousands of individual transcripts with a large dynamic range of abundance...
- Identification of small RNAs in Francisella tularensisGuillaume Postic
INSERM U1002, Paris, France
BMC Genomics 11:625. 2010..Relatively little is known about the regulatory networks existing in this organism that allows it to survive in a wide array of environments and no sRNA regulators have been identified so far...
- Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomesGeorgia Giannoukos
Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
Genome Biol 13:R23. 2012..The resulting expression profiles were highly reproducible, enriched up to 40-fold for non-rRNA transcripts, and correlated well with profiles representing undepleted total RNA...