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Items: 1 to 20 of 36

1.

Antisense transcription is pervasive but rarely conserved in enteric bacteria.

Raghavan R, Sloan DB, Ochman H.

MBio. 2012 Aug 7;3(4). pii: e00156-12. doi: 10.1128/mBio.00156-12. Print 2012.

2.

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.

Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, Nusbaum C, Birren BW, Gnirke A.

Genome Biol. 2012;13(3):R23. doi: 10.1186/gb-2012-13-3-r23.

3.

Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.

Nicolas P, Mäder U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, Becher D, Bisicchia P, Botella E, Delumeau O, Doherty G, Denham EL, Fogg MJ, Fromion V, Goelzer A, Hansen A, Härtig E, Harwood CR, Homuth G, Jarmer H, Jules M, Klipp E, Le Chat L, Lecointe F, Lewis P, Liebermeister W, March A, Mars RA, Nannapaneni P, Noone D, Pohl S, Rinn B, Rügheimer F, Sappa PK, Samson F, Schaffer M, Schwikowski B, Steil L, Stülke J, Wiegert T, Devine KM, Wilkinson AJ, van Dijl JM, Hecker M, Völker U, Bessières P, Noirot P.

Science. 2012 Mar 2;335(6072):1103-6. doi: 10.1126/science.1206848.

4.

Genome-wide antisense transcription drives mRNA processing in bacteria.

Lasa I, Toledo-Arana A, Dobin A, Villanueva M, de los Mozos IR, Vergara-Irigaray M, Segura V, Fagegaltier D, Penadés JR, Valle J, Solano C, Gingeras TR.

Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20172-7. doi: 10.1073/pnas.1113521108. Epub 2011 Nov 28.

5.

Differential expression in RNA-seq: a matter of depth.

Tarazona S, García-Alcalde F, Dopazo J, Ferrer A, Conesa A.

Genome Res. 2011 Dec;21(12):2213-23. doi: 10.1101/gr.124321.111. Epub 2011 Sep 8.

6.

RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression.

Mandlik A, Livny J, Robins WP, Ritchie JM, Mekalanos JJ, Waldor MK.

Cell Host Microbe. 2011 Aug 18;10(2):165-74. doi: 10.1016/j.chom.2011.07.007.

7.

NanoRNAs prime transcription initiation in vivo.

Goldman SR, Sharp JS, Vvedenskaya IO, Livny J, Dove SL, Nickels BE.

Mol Cell. 2011 Jun 24;42(6):817-25. doi: 10.1016/j.molcel.2011.06.005.

8.

Genome-wide detection of novel regulatory RNAs in E. coli.

Raghavan R, Groisman EA, Ochman H.

Genome Res. 2011 Sep;21(9):1487-97. doi: 10.1101/gr.119370.110. Epub 2011 Jun 10.

9.
10.

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries.

Fisher S, Barry A, Abreu J, Minie B, Nolan J, Delorey TM, Young G, Fennell TJ, Allen A, Ambrogio L, Berlin AM, Blumenstiel B, Cibulskis K, Friedrich D, Johnson R, Juhn F, Reilly B, Shammas R, Stalker J, Sykes SM, Thompson J, Walsh J, Zimmer A, Zwirko Z, Gabriel S, Nicol R, Nusbaum C.

Genome Biol. 2011;12(1):R1. doi: 10.1186/gb-2011-12-1-r1. Epub 2011 Jan 4.

11.

Differential expression analysis for sequence count data.

Anders S, Huber W.

Genome Biol. 2010;11(10):R106. doi: 10.1186/gb-2010-11-10-r106. Epub 2010 Oct 27.

12.

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics.

He S, Wurtzel O, Singh K, Froula JL, Yilmaz S, Tringe SG, Wang Z, Chen F, Lindquist EA, Sorek R, Hugenholtz P.

Nat Methods. 2010 Oct;7(10):807-12. doi: 10.1038/nmeth.1507. Epub 2010 Sep 19.

PMID:
20852648
13.

Comprehensive comparative analysis of strand-specific RNA sequencing methods.

Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A.

Nat Methods. 2010 Sep;7(9):709-15. doi: 10.1038/nmeth.1491. Epub 2010 Aug 15.

14.

Widespread antisense transcription in Escherichia coli.

Dornenburg JE, Devita AM, Palumbo MJ, Wade JT.

MBio. 2010 May 18;1(1). pii: e00024-10. doi: 10.1128/mBio.00024-10.

15.

The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems.

Kim KS, Pelton JG, Inwood WB, Andersen U, Kustu S, Wemmer DE.

J Bacteriol. 2010 Aug;192(16):4089-102. doi: 10.1128/JB.00201-10. Epub 2010 Apr 16. Erratum in: J Bacteriol. 2011 Jan;193(1):326.

16.

The primary transcriptome of the major human pathogen Helicobacter pylori.

Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J.

Nature. 2010 Mar 11;464(7286):250-5. doi: 10.1038/nature08756. Epub 2010 Feb 17.

PMID:
20164839
17.

A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454.

Lennon NJ, Lintner RE, Anderson S, Alvarez P, Barry A, Brockman W, Daza R, Erlich RL, Giannoukos G, Green L, Hollinger A, Hoover CA, Jaffe DB, Juhn F, McCarthy D, Perrin D, Ponchner K, Powers TL, Rizzolo K, Robbins D, Ryan E, Russ C, Sparrow T, Stalker J, Steelman S, Weiand M, Zimmer A, Henn MR, Nusbaum C, Nicol R.

Genome Biol. 2010;11(2):R15. doi: 10.1186/gb-2010-11-2-r15. Epub 2010 Feb 5.

18.

Mining regulatory 5'UTRs from cDNA deep sequencing datasets.

Livny J, Waldor MK.

Nucleic Acids Res. 2010 Mar;38(5):1504-14. doi: 10.1093/nar/gkp1121. Epub 2009 Dec 7.

19.

Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity.

Sorek R, Cossart P.

Nat Rev Genet. 2010 Jan;11(1):9-16. doi: 10.1038/nrg2695. Epub 2009 Nov 24.

PMID:
19935729
20.

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome.

Albrecht M, Sharma CM, Reinhardt R, Vogel J, Rudel T.

Nucleic Acids Res. 2010 Jan;38(3):868-77. doi: 10.1093/nar/gkp1032. Epub 2009 Nov 18.

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