Publications
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“Application of RNA-seq to reveal the transcript profile in bacteria”, vol. 10. pp. 1707-1718, 2011.
, Albrecht M, Sharma CM, Reinhardt R, Vogel J, et al. (2010). Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome. Nucleic Acids Res. 38: 868-877.
http://dx.doi.org/10.1093/nar/gkp1032
PMid:19923228 PMCid:2817459
Anders S and Huber W (2010). Differential expression analysis for sequence count data. Genome Biol. 11: R106.
http://dx.doi.org/10.1186/gb-2010-11-10-r106
PMid:20979621
Anonymous (2011). Applied Biosystems by Life Technologies. Available at [http://www.appliedbiosystems.com.br]. Accessed May 26, 2011.
Beaume M, Hernandez D, Docquier M, Delucinge-Vivier C, et al. (2011). Orientation and expression of methicillin-resistant Staphylococcus aureus small RNAs by direct multiplexed measurements using the nCounter of NanoString technology. J. Microbiol. Methods 84: 327-334.
http://dx.doi.org/10.1016/j.mimet.2010.12.025
PMid:21195730
Bejerano-Sagie M and Xavier KB (2007). The role of small RNAs in quorum sensing. Curr. Opin. Microbiol. 10: 189-198.
http://dx.doi.org/10.1016/j.mib.2007.03.009
PMid:17387037
Bentley SD (2011). Identification, variation and transcription of pneumococcal repeat sequences. BMC Genom. 12: 120.
http://dx.doi.org/10.1186/1471-2164-12-120
PMid:21333003 PMCid:3049150
Brantl S (2007). Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr. Opin. Microbiol. 10: 102-109.
http://dx.doi.org/10.1016/j.mib.2007.03.012
PMid:17387036
Bullard JH, Purdom E, Hansen KD and Dudoit S (2010). Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11: 94.
http://dx.doi.org/10.1186/1471-2105-11-94
PMid:20167110 PMCid:2838869
Camarena L, Bruno V, Euskirchen G, Poggio S, et al. (2010). Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing. PLoS Pathog. 6: e1000834.
http://dx.doi.org/10.1371/journal.ppat.1000834
PMid:20368969 PMCid:2848557
Chen Y, Souaiaia T and Chen T (2009). PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics 25: 2514-2521.
http://dx.doi.org/10.1093/bioinformatics/btp486
PMid:19675096 PMCid:2752623
Chevreux B, Pfisterer T, Drescher B, Driesel AJ, et al. (2004). Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 14: 1147-1159.
http://dx.doi.org/10.1101/gr.1917404
PMid:15140833 PMCid:419793
Clement NL, Snell Q, Clement MJ, Hollenhorst PC, et al. (2010). The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing. Bioinformatics 26: 38-45.
http://dx.doi.org/10.1093/bioinformatics/btp614
PMid:19861355
Croucher NJ, Vernikos GS, Parkhill J and Bentley SD (2011). Identification, variation and transcription of pneumococcal repeat sequences. BMC Genom. 12: 120.
http://dx.doi.org/10.1186/1471-2164-12-120
PMid:21333003 PMCid:3049150
Drevinek P, Holden MT, Ge Z, Jones AM, et al. (2008). Gene expression changes linked to antimicrobial resistance, oxidative stress, iron depletion and retained motility are observed when Burkholderia cenocepacia grows in cystic fibrosis sputum. BMC Infect. Dis. 8: 121.
http://dx.doi.org/10.1186/1471-2334-8-121
PMid:18801206 PMCid:2559838
Filiatrault MJ, Stodghill PV, Bronstein PA, Moll S, et al. (2010). Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity. J. Bacteriol. 192: 2359-2372.
http://dx.doi.org/10.1128/JB.01445-09
PMid:20190049 PMCid:2863471
Goncalves A, Tikhonov A, Brazma A and Kapushesky M (2011). A pipeline for RNA-seq data processing and quality assessment. Bioinformatics 27: 867-869.
http://dx.doi.org/10.1093/bioinformatics/btr012
PMid:21233166 PMCid:3051320
Guell M, van Noort V, Yus E, Chen WH, et al. (2009). Transcriptome complexity in a genome-reduced bacterium. Science 326: 1268-1271.
http://dx.doi.org/10.1126/science.1176951
PMid:19965477
Hall N (2007). Advanced sequencing technologies and their wider impact in microbiology. J. Exp. Biol. 210: 1518-1525.
http://dx.doi.org/10.1242/jeb.001370
PMid:17449817
Homer N, Merriman B and Nelson SF (2009). BFAST: an alignment tool for large scale genome resequencing. PLoS One 4: e7767.
http://dx.doi.org/10.1371/journal.pone.0007767
PMid:19907642 PMCid:2770639
Isabella VM and Clark VL (2011). Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae. BMC Genom. 12: 51.
http://dx.doi.org/10.1186/1471-2164-12-51
PMid:21251255 PMCid:3032703
Li H and Durbin R (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
http://dx.doi.org/10.1093/bioinformatics/btp324
PMid:19451168 PMCid:2705234
Li R, Li Y, Kristiansen K and Wang J (2008). SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713- 714.
http://dx.doi.org/10.1093/bioinformatics/btn025
PMid:18227114
Li R, Yu C, Li Y, Lam TW, et al. (2009). SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967. Koide T, Reiss DJ, Bare JC, Pang WL, et al. (2009). Prevalence of transcription promoters within archaeal operons and coding sequences. Mol. Syst. Biol. 5: 285.
http://dx.doi.org/10.1038/msb.2009.54
Langmead B, Trapnell C, Pop M and Salzberg SL (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10: R25.
http://dx.doi.org/10.1186/gb-2009-10-3-r25
PMid:19261174 PMCid:2690996
Langmead B, Hansen KD and Leek JT (2010). Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol. 11: R83.
http://dx.doi.org/10.1186/gb-2010-11-8-r83
PMid:20701754 PMCid:2945785
MacLean D, Jones JD and Studholme DJ (2009). Application of ânext-generationâ sequencing technologies to microbial genetics. Nat. Rev. Microbiol. 7: 287-296.
PMid:19287448
Mane SP, Evans C, Cooper KL, Crasta OR, et al. (2009). Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing. BMC Genom. 10: 264.
http://dx.doi.org/10.1186/1471-2164-10-264
PMid:19523228 PMCid:2707382
Marioni JC, Mason CE, Mane SM, Stephens M, et al. (2008). RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18: 1509-1517.
http://dx.doi.org/10.1101/gr.079558.108
PMid:18550803 PMCid:2527709
Martin J, Zhu W, Passalacqua KD, Bergman N, et al. (2010). Bacillus anthracis genome organization in light of whole transcriptome sequencing. BMC Bioinformatics 11 (Suppl 3): S10.
http://dx.doi.org/10.1186/1471-2105-11-S3-S10
PMid:20438648 PMCid:2863060
Moody DE (2001). Genomics techniques: an overview of methods for the study of gene expression. J. Anim. Sci. 79 (Suppl E): E128-E135.
Morozova O and Marra MA (2008). Applications of next-generation sequencing technologies in functional genomics. Genomics 92: 255-264.
http://dx.doi.org/10.1016/j.ygeno.2008.07.001
PMid:18703132
Mortazavi A, Williams BA, McCue K, Schaeffer L, et al. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5: 621-628.
http://dx.doi.org/10.1038/nmeth.1226
PMid:18516045
Nagalakshmi U, Wang Z, Waern K, Shou C, et al. (2008). The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349.
http://dx.doi.org/10.1126/science.1158441
PMid:18451266 PMCid:2951732
NCBI (2011). National Center for Biotechnology Information. Available at [http://www.ncbi.nlm.nih.gov/genomes]. Accessed June 30, 2011.
Oliver HF, Orsi RH, Ponnala L, Keich U, et al. (2009). Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs. BMC Genom. 10: 641.
http://dx.doi.org/10.1186/1471-2164-10-641
PMid:20042087 PMCid:2813243
Oshlack A and Wakefield MJ (2009). Transcript length bias in RNA-seq data confounds systems biology. Biol. Direct. 4: 14.
http://dx.doi.org/10.1186/1745-6150-4-14
PMid:19371405 PMCid:2678084
Oshlack A, Robinson MD and Young MD (2010). From RNA-seq reads to differential expression results. Genome Biol. 11: 220.
http://dx.doi.org/10.1186/gb-2010-11-12-220
PMid:21176179
Passalacqua KD, Varadarajan A, Ondov BD, Okou DT, et al. (2009). Structure and complexity of a bacterial transcriptome. J. Bacteriol. 191: 3203-3211.
http://dx.doi.org/10.1128/JB.00122-09
PMid:19304856 PMCid:2687165
Perkins TT, Kingsley RA, Fookes MC, Gardner PP, et al. (2009). A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet. 5: e1000569.
http://dx.doi.org/10.1371/journal.pgen.1000569
PMid:19609351 PMCid:2704369
Philippe N, Boureux A, Brehelin L, Tarhio J, et al. (2009). Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity. Nucleic Acids Res. 37: e104.
http://dx.doi.org/10.1093/nar/gkp492
PMid:19531739 PMCid:2731892
Roberts A, Trapnell C, Donaghey J, Rinn JL, et al. (2011). Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol. 12: R22.
http://dx.doi.org/10.1186/gb-2011-12-3-r22
PMid:21410973 PMCid:3129672
Robinson MD and Oshlack A (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11: R25.
http://dx.doi.org/10.1186/gb-2010-11-3-r25
PMid:20196867 PMCid:2864565
Rumble SM, Lacroute P, Dalca AV, Fiume M, et al. (2009). SHRiMP: accurate mapping of short color-space reads. PLoS Comput. Biol. 5: e1000386.
http://dx.doi.org/10.1371/journal.pcbi.1000386
PMid:19461883 PMCid:2678294
Schatz MC (2009). CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics 25: 1363-1369.
http://dx.doi.org/10.1093/bioinformatics/btp236
PMid:19357099 PMCid:2682523
Sharma CM, Hoffmann S, Darfeuille F, Reignier J, et al. (2010). The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464: 250-255.
http://dx.doi.org/10.1038/nature08756
PMid:20164839
Shendure J and Ji H (2008). Next-generation DNA sequencing. Nat. Biotechnol. 26: 1135-1145.
http://dx.doi.org/10.1038/nbt1486
PMid:18846087
Siezen RJ, Wilson G and Todt T (2010). Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays. Microb. Biotechnol. 3: 125-130.
http://dx.doi.org/10.1111/j.1751-7915.2010.00166.x
PMid:21255314
Sorek R and Cossart P (2010). Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat. Rev. Genet. 11: 9-16.
http://dx.doi.org/10.1038/nrg2695
PMid:19935729
Teng X and Xiao H (2009). Perspectives of DNA microarray and next-generation DNA sequencing technologies. Sci. China C Life Sci. 52: 7-16.
http://dx.doi.org/10.1007/s11427-009-0012-9
PMid:19152079
Toledo-Arana A, Repoila F and Cossart P (2007). Small noncoding RNAs controlling pathogenesis. Curr. Opin. Microbiol. 10: 182-188.
http://dx.doi.org/10.1016/j.mib.2007.03.004
PMid:17383223
Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, et al. (2009). The Listeria transcriptional landscape from saprophytism to virulence. Nature 459: 950-956.
http://dx.doi.org/10.1038/nature08080
PMid:19448609
van Vliet AH (2010). Next generation sequencing of microbial transcriptomes: challenges and opportunities. FEMS Microbiol. Lett. 302: 1-7.
http://dx.doi.org/10.1111/j.1574-6968.2009.01767.x
PMid:19735299
Wang Z, Gerstein M and Snyder M (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10: 57-63.
http://dx.doi.org/10.1038/nrg2484
PMid:19015660 PMCid:2949280
Weese D, Emde AK, Rausch T, Döring A, et al. (2009). RazerS - fast read mapping with sensitivity control. Genome Res. 19: 1646-1654.
http://dx.doi.org/10.1101/gr.088823.108
PMid:19592482 PMCid:2752123
Wu TD and Nacu S (2010). Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26: 873-881.
http://dx.doi.org/10.1093/bioinformatics/btq057
PMid:20147302 PMCid:2844994
Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, et al. (2009). Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc. Natl. Acad. Sci. U. S. A. 106: 3976-3981.
http://dx.doi.org/10.1073/pnas.0813403106
PMid:19234113 PMCid:2645912