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Results: 1 to 20 of 40

1.

Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq.

Yi H, Cho YJ, Won S, Lee JE, Jin Yu H, Kim S, Schroth GP, Luo S, Chun J.

Nucleic Acids Res. 2011 Nov 1;39(20):e140. doi: 10.1093/nar/gkr617. Epub 2011 Aug 31.

PMID:
21880599
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
21843873
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

High-throughput illumina strand-specific RNA sequencing library preparation.

Zhong S, Joung JG, Zheng Y, Chen YR, Liu B, Shao Y, Xiang JZ, Fei Z, Giovannoni JJ.

Cold Spring Harb Protoc. 2011 Aug 1;2011(8):940-9. doi: 10.1101/pdb.prot5652. No abstract available.

PMID:
21807852
[PubMed - indexed for MEDLINE]
4.

Gut microbiome-host interactions in health and disease.

Kinross JM, Darzi AW, Nicholson JK.

Genome Med. 2011 Mar 4;3(3):14. doi: 10.1186/gm228.

PMID:
21392406
[PubMed]
Free PMC Article
5.

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries.

Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A.

Genome Biol. 2011;12(2):R18. doi: 10.1186/gb-2011-12-2-r18. Epub 2011 Feb 21.

PMID:
21338519
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
21205303
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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
[PubMed - indexed for MEDLINE]
8.

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.

PMID:
20711195
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

The microbiota and allergies/asthma.

Huffnagle GB.

PLoS Pathog. 2010 May 27;6(5):e1000549. doi: 10.1371/journal.ppat.1000549. No abstract available.

PMID:
20523892
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

A catalog of reference genomes from the human microbiome.

Human Microbiome Jumpstart Reference Strains Consortium, Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, FitzGerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D.

Science. 2010 May 21;328(5981):994-9. doi: 10.1126/science.1183605.

PMID:
20489017
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Dissecting the in vivo metabolic potential of two human gut acetogens.

Rey FE, Faith JJ, Bain J, Muehlbauer MJ, Stevens RD, Newgard CB, Gordon JI.

J Biol Chem. 2010 Jul 16;285(29):22082-90. doi: 10.1074/jbc.M110.117713. Epub 2010 May 5.

PMID:
20444704
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Bacillus anthracis genome organization in light of whole transcriptome sequencing.

Martin J, Zhu W, Passalacqua KD, Bergman N, Borodovsky M.

BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S10. doi: 10.1186/1471-2105-11-S3-S10.

PMID:
20438648
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing.

Camarena L, Bruno V, Euskirchen G, Poggio S, Snyder M.

PLoS Pathog. 2010 Apr 1;6(4):e1000834. doi: 10.1371/journal.ppat.1000834.

PMID:
20368969
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins.

Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, Niazi F, Affourtit J, Egholm M, Henrissat B, Knight R, Gordon JI.

Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7503-8. doi: 10.1073/pnas.1002355107. Epub 2010 Apr 2.

PMID:
20363958
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics.

Stewart FJ, Ottesen EA, DeLong EF.

ISME J. 2010 Jul;4(7):896-907. doi: 10.1038/ismej.2010.18. Epub 2010 Mar 11.

PMID:
20220791
[PubMed - indexed for MEDLINE]
16.

A human gut microbial gene catalogue established by metagenomic sequencing.

Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J; MetaHIT Consortium, Bork P, Ehrlich SD, Wang J.

Nature. 2010 Mar 4;464(7285):59-65. doi: 10.1038/nature08821.

PMID:
20203603
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity.

Filiatrault MJ, Stodghill PV, Bronstein PA, Moll S, Lindeberg M, Grills G, Schweitzer P, Wang W, Schroth GP, Luo S, Khrebtukova I, Yang Y, Thannhauser T, Butcher BG, Cartinhour S, Schneider DJ.

J Bacteriol. 2010 May;192(9):2359-72. doi: 10.1128/JB.01445-09. Epub 2010 Feb 26.

PMID:
20190049
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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
[PubMed - indexed for MEDLINE]
19.

Fast and accurate long-read alignment with Burrows-Wheeler transform.

Li H, Durbin R.

Bioinformatics. 2010 Mar 1;26(5):589-95. doi: 10.1093/bioinformatics/btp698. Epub 2010 Jan 15.

PMID:
20080505
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

A single-base resolution map of an archaeal transcriptome.

Wurtzel O, Sapra R, Chen F, Zhu Y, Simmons BA, Sorek R.

Genome Res. 2010 Jan;20(1):133-41. doi: 10.1101/gr.100396.109. Epub 2009 Nov 2.

PMID:
19884261
[PubMed - indexed for MEDLINE]
Free PMC Article

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