Resources

PanDaTox: The Pan Genomic Database of microbial genes that are Toxic to bacteria

Kimelman et al (2012). A vast collection of microbial genes that are toxic to bacteria. Genome Research, 22(4):802-9.

The E. coli RNA 3'end viewer

Dar et al (2018). High-resolution RNA 3’-ends mapping of bacterial rho-dependent transcripts Nucleic Acids Research, gky274.

Differential operonic decay viewer

Dar et al (2018). Extensive reshaping of bacterial operons by programmed mRNA decay PLoS Genet., 14(4): e1007354.

The Archaea RNA 3'end viewer

Dar et al (2016). Widespread formation of alternative 3’ UTR isoforms via transcription termination in archaea Nat. Microbiol. , 1, 16143.

The comparative transcriptome browser across the microbial tree of life

Cohen et al (2016). Comparative transcriptomics across the prokaryotic tree of life. Nucleic Acids Research, in press

PASIFIC: Prediction of riboregulators in bacterial 5'UTRs

Millman et al (2017). Computational prediction of regulatory, premature transcription termination in bacteriaNucleic Acids Research, 45(2):886-893 (2017).

The Pseudomonas aeruginosa Transcriptome Browser

Wurtzel et al (2012). The single-nucleotide resolution transcriptome of Pseudomonas aeruginosa grown in body temperature PLoS Pathogens, 8(9):e1002945 (2012).

The Listeria Transcriptome Browser

Wurtzel et al (2012). Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. Molecular Systems Biology, 8:583 (2012).

The Syn9 Transcriptome Browser

Doron et al (2015). Transcriptome dynamics of a broad host-range cyanophage and its hosts. The ISME Journal, in press (2015).

The Bdellovibrio Transcriptome Browser

Karunker et al (2013). A Global Transcriptional Switch between the Attack and Growth Forms of Bdellovibrio bacteriovorus. PLoS One, 8(4):e61850 (2013).

Human gut microbiome phage browser

Stern, Mick et al (2012). CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome Genome Research, 22(10):1985-94 (2012).

The Sulfolobus solfataricus Transcriptome Browser

Wurtzel et al (2010). A single-base resolution map of an archaeal transcriptome. Genome Research, 20(1):133-41.

Burkholderia RNA-seq data

Yoder-Himes et al (2009). Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. PNAS, 106(10):3976-3981.