-
1
-
-
0038267065
-
Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: Regulation of the central metabolic pathways
-
Blencke HM, Homuth G, Ludwig H, Mader U, Hecker M, Stulke J. Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metabol Eng. 2003;5(2):133-49.
-
(2003)
Metabol Eng.
, vol.5
, Issue.2
, pp. 133-149
-
-
Blencke, H.M.1
Homuth, G.2
Ludwig, H.3
Mader, U.4
Hecker, M.5
Stulke, J.6
-
2
-
-
33646825213
-
Evidence supporting predicted metabolic pathways for Vibrio cholera: Gene expression data and clinical tests
-
Accessed November 15, 2012
-
Shi J, Romero PR, Schoolnik GK, Spormann AM, Karp PD. Evidence supporting predicted metabolic pathways for Vibrio cholera: gene expression data and clinical tests. Nucleic Acids Res. 2006;34(8):2438-44. Accessed November 15, 2012.
-
(2006)
Nucleic Acids Res.
, vol.34
, Issue.8
, pp. 2438-2444
-
-
Shi, J.1
Romero, P.R.2
Schoolnik, G.K.3
Spormann, A.M.4
Karp, P.D.5
-
3
-
-
74949137952
-
A single-base resolution map of an archaeal transcriptome
-
Wurtzel O, Sapra R, Chen F, Zhu Y, Simmons BA, Sorek R. A single-base resolution map of an archaeal transcriptome. Genome Res. 2010;20: 133-41.
-
(2010)
Genome Res.
, vol.20
, pp. 133-141
-
-
Wurtzel, O.1
Sapra, R.2
Chen, F.3
Zhu, Y.4
Simmons, B.A.5
Sorek, R.6
-
4
-
-
77952274420
-
Bacilus anthracis genome organization in light of whole transcriptome sequencing
-
Martin J, Zhu W, Passalacqua KD, Bergman N, Borodovsku M. Bacilus anthracis genome organization in light of whole transcriptome sequencing. BMC Bioinformatics. 2010;11(Suppl 3):S10.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.SUPPL. 3
-
-
Martin, J.1
Zhu, W.2
Passalacqua, K.D.3
Bergman, N.4
Borodovsku, M.5
-
5
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Method. 2008;5(7):621-8.
-
(2008)
Nat Method
, vol.5
, Issue.7
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
6
-
-
42749087226
-
Highly integrated single-base resolution maps of the epigenome in Arabidopsis
-
Lister R, O'Malley RC, Tonti-Filippini J, etal. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008;133(3): 523-36.
-
(2008)
Cell
, vol.133
, Issue.3
, pp. 523-536
-
-
Lister, R.1
O'Malley, R.C.2
Tonti-Filippini, J.3
-
7
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C, Williams BA, Pertea G, etal. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28:511-5.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
-
8
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11:R106.
-
(2010)
Genome Biol.
, vol.11
-
-
Anders, S.1
Huber, W.2
-
9
-
-
77955343193
-
Cloud-scale RNA-sequencing differential expression analysis with Myrna
-
Langmead B, Hansen K, Leek J. Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol. 2010;11:R83.
-
(2010)
Genome Biol.
, vol.11
-
-
Langmead, B.1
Hansen, K.2
Leek, J.3
-
10
-
-
35748945758
-
A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes
-
Kingsford C, Delcher AL, Salzberg SL. A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes. Mol Biol Evol. 2007;24(9):2091-8.
-
(2007)
Mol Biol Evol.
, vol.24
, Issue.9
, pp. 2091-2098
-
-
Kingsford, C.1
Delcher, A.L.2
Salzberg, S.L.3
-
11
-
-
0242496945
-
Degradation of stable RNA in bacteria
-
Deutscher MP. Degradation of stable RNA in bacteria. Journal of Biological Chemistry. 2003;278:45041-4.
-
(2003)
Journal of Biological Chemistry
, vol.278
, pp. 45041-45044
-
-
Deutscher, M.P.1
-
13
-
-
81755177792
-
Sequence-based analysis uncovers as abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis
-
Arnvig KB, Comas I, Thomson NR, etal. Sequence-based analysis uncovers as abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis. PLoS Pathog. 2011;7(11):e1002342.
-
(2011)
PLoS Pathog.
, vol.7
, Issue.11
-
-
Arnvig, K.B.1
Comas, I.2
Thomson, N.R.3
-
14
-
-
77954038036
-
Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing
-
Camarena L, Bruno V, Euskirchen G, Poggio S, Snyder M. Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing. PLoS Pathog. 2010;6(4):e10000834.
-
(2010)
PLoS Pathog.
, vol.6
, Issue.4
-
-
Camarena, L.1
Bruno, V.2
Euskirchen, G.3
Poggio, S.4
Snyder, M.5
-
15
-
-
80053460594
-
Quantitative RNA-seq analysis of the transcriptome of Campylobacter jejuni
-
Chaudhuri RR, Yu L, Kanji A, etal. Quantitative RNA-seq analysis of the transcriptome of Campylobacter jejuni. Microbiology. 2011;157(10): 2922-32.
-
(2011)
Microbiology
, vol.157
, Issue.10
, pp. 2922-2932
-
-
Chaudhuri, R.R.1
Yu, L.2
Kanji, A.3
-
16
-
-
64549149245
-
Experimental discovery of sRNAs in Vibrio cholera by direct cloning, 5S/tRNA deplation and parallel sequencing
-
Liu JM, Livny J, Lawrence MS, Kimball MD, Waldor MK, Camilli A. Experimental discovery of sRNAs in Vibrio cholera by direct cloning, 5S/tRNA deplation and parallel sequencing. Nucleic Acids Res. 2009;37:e46.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Liu, J.M.1
Livny, J.2
Lawrence, M.S.3
Kimball, M.D.4
Waldor, M.K.5
Camilli, A.6
-
17
-
-
80051915419
-
RNA-seq-based monitoring of infection-linked changes in Vibrio cholera gene expression
-
Mandlik A, Livny J, Robins WP, Ritchie JM, Mekalanos JJ, Waldor MK. RNA-seq-based monitoring of infection-linked changes in Vibrio cholera gene expression. Cell Host Microbe. 2011;10(2):165-74.
-
(2011)
Cell Host Microbe.
, vol.10
, Issue.2
, pp. 165-174
-
-
Mandlik, A.1
Livny, J.2
Robins, W.P.3
Ritchie, J.M.4
Mekalanos, J.J.5
Waldor, M.K.6
-
18
-
-
68249102779
-
A strand-specific RNA-seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi
-
Perkins TT, Kingaley RA, Fookes MC, etal. A strand-specific RNA-seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet. 2009;5:e10000569.
-
(2009)
PLoS Genet.
, vol.5
-
-
Perkins, T.T.1
Kingaley, R.A.2
Fookes, M.C.3
-
19
-
-
77949425194
-
The primary transcriptome of the major human pathogen Helicobacter pylori
-
Sharma CM, Hoffmann S, Darfeuille F, etal. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature. 2010;464:250-5.
-
(2010)
Nature
, vol.464
, pp. 250-255
-
-
Sharma, C.M.1
Hoffmann, S.2
Darfeuille, F.3
-
20
-
-
62649160909
-
Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing
-
Yoder-Himes DR, Chain PS, Zhu Y, etal. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci U S A. 2009;106:3976-81.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 3976-3981
-
-
Yoder-Himes, D.R.1
Chain, P.S.2
Zhu, Y.3
-
21
-
-
84875100451
-
-
Novocraft. Accessed November 15, 2012
-
Hercus C. Novoalign. Novocraft. http://www.novocraft.com. Accessed November 15, 2012.
-
Novoalign
-
-
Hercus, C.1
-
22
-
-
62349130698
-
Ultrafast and memory efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
-
(2009)
Genome Biol.
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
23
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler Transform
-
Li H, Durban R. Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics. 2009;25:1754-60.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durban, R.2
-
24
-
-
40049104732
-
SOAP: Short oligonucleotide alignment program
-
Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics. 2008;24(5):713-4.
-
(2008)
Bioinformatics
, vol.24
, Issue.5
, pp. 713-714
-
-
Li, R.1
Li, Y.2
Kristiansen, K.3
Wang, J.4
-
25
-
-
67650711615
-
SOAP2: An improved ultrafast tool for short read alignment
-
Li R, Yu C, Li Y, etal. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009;25(15):1966-7.
-
(2009)
Bioinformatics
, vol.25
, Issue.15
, pp. 1966-1967
-
-
Li, R.1
Yu, C.2
Li, Y.3
-
26
-
-
79960023926
-
-
Sourceforge. net. Accessed November 15, 2012
-
Maq: mapping and assembly with qualities. Sourceforge. net. http://maq.sourceforge.net. Accessed November 15, 2012.
-
Maq: Mapping and assembly with qualities
-
-
-
28
-
-
70949102952
-
Next generation sequencing of microbial transcriptomes: Challenges and opportunities
-
Van Vliet AHM. Next generation sequencing of microbial transcriptomes: challenges and opportunities. FEMS Microbiol Lett. 2010;302:1-7.
-
(2010)
FEMS Microbiol Lett.
, vol.302
, pp. 1-7
-
-
Van Vliet, A.H.M.1
-
29
-
-
34147132825
-
Identifying bacterial genes and endosymbiont DNA with Glimmer
-
Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23(6): 673-9.
-
(2007)
Bioinformatics
, vol.23
, Issue.6
, pp. 673-679
-
-
Delcher, A.L.1
Bratke, K.A.2
Powers, E.C.3
Salzberg, S.L.4
-
30
-
-
0030854739
-
tRNAscan-SE: A program for improved detections of transfer RNA genes in genomic sequence
-
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detections of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25(5): 955-64.
-
(1997)
Nucleic Acids Res.
, vol.25
, Issue.5
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
31
-
-
34250665888
-
RNAmmer: Consistent and rapid annotation of ribosomal RNA genes
-
Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Research. 2007;35(9):3100-8.
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.9
, pp. 3100-3108
-
-
Lagesen, K.1
Hallin, P.2
Rodland, E.A.3
Staerfeldt, H.H.4
Rognes, T.5
Ussery, D.W.6
-
32
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357-9.
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
33
-
-
0142125272
-
Transcription of sigma54-dependent but not sigma28-dependent flageller genes in Campylobacter jejuni is associated with formation of the flagellar secretory apparatus
-
Hendrixson DR, DiRita VJ. Transcription of sigma54-dependent but not sigma28-dependent flageller genes in Campylobacter jejuni is associated with formation of the flagellar secretory apparatus. Molecular Microbiology. 2003;50:687-702.
-
(2003)
Molecular Microbiology
, vol.50
, pp. 687-702
-
-
Hendrixson, D.R.1
DiRita, V.J.2
-
34
-
-
1942533529
-
The FlgS/FlgR two-component signal transduction system regulates the fla regulon in Camppylobacter jejuni
-
Wosten MM, Wagenaar JA, van Putten JP. The FlgS/FlgR two-component signal transduction system regulates the fla regulon in Camppylobacter jejuni. J Biol Chem. 2004;279:16214-22.
-
(2004)
J Biol Chem.
, vol.279
, pp. 16214-16222
-
-
Wosten, M.M.1
Wagenaar, J.A.2
van Putten, J.P.3
|