-
1
-
-
79957665988
-
Microarrays, deep sequencing and the true measure of the transcriptome
-
Available: Accessed 22 July 2012
-
Malone JH, Oliver B (2011) Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biol 9: 34. Available: http://www. pubmedcentral.nih. gov/articlerender.fcgi?artid= 3104486&tool= pmcentrez&rendertype= abstract. Accessed 22 July 2012.
-
(2011)
BMC Biol
, vol.9
, pp. 34
-
-
Malone, J.H.1
Oliver, B.2
-
2
-
-
79959212998
-
Landscape of next-generation sequencing technologies
-
Available: Accessed 24 July 2012
-
Niedringhaus TP, Milanova D, Kerby MB, Snyder MP, Barron AE (2011) Landscape of next-generation sequencing technologies. Anal Chem 83: 4327-4341. Available: http://www.pubmedcentral.nih.gov/articlerender. fcgi?artid =3437308&tool =pmcentrez&rendertype = abstract. Accessed 24 July 2012.
-
(2011)
Anal Chem
, vol.83
, pp. 4327-4341
-
-
Niedringhaus, T.P.1
Milanova, D.2
Kerby, M.B.3
Snyder, M.P.4
Barron, A.E.5
-
3
-
-
57749195712
-
RNA-Seq: A revolutionary tool for transcriptomics
-
Available: Accessed 13 July 2012
-
Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63. Available: http://www. pubmedcentral.nih.gov/articlerender.fcgi?artid = 2949280&tool = pmcentrez& rendertype = abstract. Accessed 13 July 2012.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
4
-
-
74949137952
-
A single-base resolution map of an archaeal transcriptome
-
Available
-
Wurtzel O, Sapra R, Chen F, Zhu Y, Simmons B, et al. (2010) A single-base resolution map of an archaeal transcriptome. Genome Res 20: 133-141. Available: http://www.ncbi.nlm.nih.gov/pubmed/19884261.
-
(2010)
Genome Res
, vol.20
, pp. 133-141
-
-
Wurtzel, O.1
Sapra, R.2
Chen, F.3
Zhu, Y.4
Simmons, B.5
-
5
-
-
84875457350
-
Bacterial small RNA-based negative regulation: Hfq and its accomplices
-
Available: Accessed 13 August 2013
-
De Lay N, Schu DJ, Gottesman S (2013) Bacterial small RNA-based negative regulation: Hfq and its accomplices. J Biol Chem 288: 7996-8003. Available: http://www.ncbi.nlm.nih.gov/pubmed/23362267. Accessed 13 August 2013.
-
(2013)
J Biol Chem
, vol.288
, pp. 7996-8003
-
-
De Lay, N.1
Schu, D.J.2
Gottesman, S.3
-
6
-
-
84872543206
-
A decade of riboswitches
-
Available: Accessed 15 August 2013
-
Serganov A, Nudler E (2013) A decade of riboswitches. Cell 152: 17-24. Available: http://www.ncbi.nlm.nih.gov/pubmed/23332744. Accessed 15 August 2013.
-
(2013)
Cell
, vol.152
, pp. 17-24
-
-
Serganov, A.1
Nudler, E.2
-
7
-
-
84555203309
-
Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000
-
Available: Accessed 23 May 2012
-
Filiatrault MJ, Stodghill PV, Myers CR, Bronstein PA, Butcher BG, et al. (2011) Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. PLoS One 6: e29335. Available: http://dx.plos.org/10.1371/journal.pone.0029335. Accessed 23 May 2012.
-
(2011)
PLoS One
, vol.6
-
-
Filiatrault, M.J.1
Stodghill, P.V.2
Myers, C.R.3
Bronstein, P.A.4
Butcher, B.G.5
-
8
-
-
84862813786
-
Genome-wide dynamic transcriptional profiling in Clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution RNA-Seq
-
Available: Accessed 12 March 2013
-
Wang Y, Li X, Mao Y, Blaschek HP (2012) Genome-wide dynamic transcriptional profiling in Clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution RNA-Seq. BMC Genomics 13: 102. Available: http://www.biomedcentral.com/1471-2164/13/102. Accessed 12 March 2013.
-
(2012)
BMC Genomics
, vol.13
, pp. 102
-
-
Wang, Y.1
Li, X.2
Mao, Y.3
Blaschek, H.P.4
-
9
-
-
84884737727
-
RNA-Seq of Bacillus licheniformis: Active regulatory RNA features expressed within a productive fermentation
-
Available: Accessed 1 October 2013
-
Wiegand S, Dietrich S, Hertel R, Bongaerts J, Evers S, et al. (2013) RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation. BMC Genomics 14: 667. Available: http://www. biomedcentral.com/1471-2164/14/667. Accessed 1 October 2013.
-
(2013)
BMC Genomics
, vol.14
, pp. 667
-
-
Wiegand, S.1
Dietrich, S.2
Hertel, R.3
Bongaerts, J.4
Evers, S.5
-
10
-
-
0034764307
-
SSAHA: A fast search method for large DNA databases
-
Available: Accessed 29 January 2013
-
Ning Z, Cox AJ, Mullikin JC (2001) SSAHA: a fast search method for large DNA databases. Genome Res 11: 1725-1729. Available: http://genome.cshlp. org/content/11/10/1725. Accessed 29 January 2013.
-
(2001)
Genome Res
, vol.11
, pp. 1725-1729
-
-
Ning, Z.1
Cox, A.J.2
Mullikin, J.C.3
-
11
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Available: Accessed 4 October 2012
-
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359. Available: http://www.ncbi.nlm.nih.gov/pubmed/22388286. Accessed 4 October 2012.
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
12
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Available: Accessed 28 January 2013
-
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760. Available: http://bioinformatics.oxfordjournals.org/content/25/14/1754.long. Accessed 28 January 2013.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
13
-
-
84857188863
-
Artemis: An integrated platform for visualization and analysis of high-throughput sequence-based experimental data
-
Available: Accessed 23 September 2013
-
Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA (2012) Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 28: 464-469. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid = 3278759&tool = pmcentrez& rendertype = abstract. Accessed 23 September 2013.
-
(2012)
Bioinformatics
, vol.28
, pp. 464-469
-
-
Carver, T.1
Harris, S.R.2
Berriman, M.3
Parkhill, J.4
McQuillan, J.A.5
-
14
-
-
84860425080
-
SAMSCOPE: An OpenGL based real-time interactive scale-free SAM viewer
-
bts122-. doi:10.1093/bioinformatics/bts122
-
Popendorf K, Sakakibara Y (2012) SAMSCOPE: An OpenGL based real-time interactive scale-free SAM viewer. Bioinformatics: bts122-. doi:10.1093/ bioinformatics/bts122.
-
(2012)
Bioinformatics
-
-
Popendorf, K.1
Sakakibara, Y.2
-
15
-
-
84875634162
-
Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration
-
Available: Accessed 17 September 2013
-
Thorvaldsdóttir H, Robinson JT, Mesirov JP (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14: 178-192. Available: http://www.pubmedcentral. nih.gov/articlerender.fcgi?artid = 3603213&tool = pmcentrez&rendertype = abstract. Accessed 17 September 2013.
-
(2013)
Brief Bioinform
, vol.14
, pp. 178-192
-
-
Thorvaldsdóttir, H.1
Robinson, J.T.2
Mesirov, J.P.3
-
16
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Available: Accessed 28 January 2013
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079. Available: http://bioinformatics.oxfordjournals.org/content/25/16/2078.long. Accessed 28 January 2013.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
-
17
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Available: Accessed 10 July 2011
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628. Available: http://dx.doi.org/10.1038/nmeth.1226. Accessed 10 July 2011.
-
(2008)
Nat Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
18
-
-
83455238345
-
GC-Content Normalization for RNA-Seq Data
-
Available: Accessed 19 December 2011
-
Risso D, Schwartz K, Sherlock G, Dudoit S (2011) GC-Content Normalization for RNA-Seq Data. BMC Bioinformatics 12: 480. Available: http://www. biomedcentral.com/1471-2105/12/480. Accessed 19 December 2011.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 480
-
-
Risso, D.1
Schwartz, K.2
Sherlock, G.3
Dudoit, S.4
-
19
-
-
77955883388
-
Biases in Illumina transcriptome sequencing caused by random hexamer priming
-
Available: Accessed 4 March 2013
-
Hansen KD, Brenner SE, Dudoit S (2010) Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res 38: e131. Available: http://nar.oxfordjournals.org/content/38/12/e131.long. Accessed 4 March 2013.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Hansen, K.D.1
Brenner, S.E.2
Dudoit, S.3
-
20
-
-
80052973462
-
Prospects for riboswitch discovery and analysis
-
Available: Accessed 13 August 2013
-
Breaker RR (2011) Prospects for riboswitch discovery and analysis. Mol Cell 43: 867-879. Available: http://www.ncbi.nlm.nih.gov/pubmed/21925376. Accessed 13 August 2013.
-
(2011)
Mol Cell
, vol.43
, pp. 867-879
-
-
Breaker, R.R.1
-
21
-
-
77955298482
-
baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
-
Available: Accessed 8 March 2012
-
Hardcastle TJ, Kelly KA (2010) baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 11: 422. Available: http://www.biomedcentral.com/1471-2105/11/422. Accessed 8 March 2012.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 422
-
-
Hardcastle, T.J.1
Kelly, K.A.2
-
22
-
-
77956295988
-
The Genome Analysis Toolkit: A MapReduce framework for analyzing nextgeneration DNA sequencing data
-
Available: Accessed 17 September 2013
-
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing nextgeneration DNA sequencing data. Genome Res 20: 1297-1303. Available: http://www.pubmedcentral. nih.gov/articlerender.fcgi?artid = 2928508&tool = pmcentrez&rendertype = abstract. Accessed 17 September 2013.
-
(2010)
Genome Res
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
Hanna, M.2
Banks, E.3
Sivachenko, A.4
Cibulskis, K.5
-
23
-
-
13444252847
-
Rfam: Annotating non-coding RNAs in complete genomes
-
Available: Accessed 9 August 2012
-
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, et al. (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 33: D121-4. Available: http://www.pubmedcentral.nih.gov/articlerender. fcgi?artid = 540035&tool = pmcentrez&rendertype = abstract. Accessed 9 August 2012.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Griffiths-Jones, S.1
Moxon, S.2
Marshall, M.3
Khanna, A.4
Eddy, S.R.5
-
24
-
-
84859048706
-
The Transcriptome Analysis and Comparison Explorer - T-ACE: A platform-independent, graphical tool to process large RNAseq data sets of non-model organisms
-
Available: Accessed 19 March 2012
-
Philipp EER, Kraemer L, Mountfort D, Schilhabel M, Schreiber S, et al. (2012) The Transcriptome Analysis and Comparison Explorer - T-ACE: a platform-independent, graphical tool to process large RNAseq data sets of non-model organisms. Bioinformatics 28: 777-783. Available: http:// bioinformatics. oxfordjournals.org/cgi/content/abstract/28/6/777. Accessed 19 March 2012.
-
(2012)
Bioinformatics
, vol.28
, pp. 777-783
-
-
Philipp, E.E.R.1
Kraemer, L.2
Mountfort, D.3
Schilhabel, M.4
Schreiber, S.5
-
25
-
-
84899412279
-
Using Tablet for visual exploration of second-generation sequencing data
-
bbs012-. Available: Accessed 25 March 2012
-
Milne I, Stephen G, Bayer M, Cock PJA, Pritchard L, et al. (2012) Using Tablet for visual exploration of second-generation sequencing data. Brief Bioinform: bbs012-. Available: http://bib.oxfordjournals.org/cgi/content/ abstract/bbs012v1. Accessed 25 March 2012.
-
(2012)
Brief Bioinform
-
-
Milne, I.1
Stephen, G.2
Bayer, M.3
Cock, P.J.A.4
Pritchard, L.5
-
26
-
-
77949425194
-
The primary transcriptome of the major human pathogen Helicobacter pylori
-
Available: Accessed 31 October 2012
-
Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, et al. (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464: 250-255. Available: http://dx.doi.org/10.1038/nature08756. Accessed 31 October 2012.
-
(2010)
Nature
, vol.464
, pp. 250-255
-
-
Sharma, C.M.1
Hoffmann, S.2
Darfeuille, F.3
Reignier, J.4
Findeiss, S.5
-
27
-
-
84858400338
-
Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions
-
Available: Accessed 14 November 2012
-
Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, et al. (2012) Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res 40: 2020-2031. Available: http://nar.oxfordjournals.org/content/40/5/2020.long. Accessed 14 November 2012.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 2020-2031
-
-
Schmidtke, C.1
Findeiss, S.2
Sharma, C.M.3
Kuhfuss, J.4
Hoffmann, S.5
-
28
-
-
79952174199
-
An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803
-
doi:10.1073/pnas.1015154108/-/DCSupplemental
-
Mitschke J, Georg J, Scholz I, Sharma CM, Dienst D, et al. (2011) An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. PNAS 108: 1-6. doi:10.1073/pnas. 1015154108/-/DCSupplemental.www.pnas.org/cgi/doi/10.1073/pnas.1015154108.
-
(2011)
PNAS
, vol.108
, pp. 1-6
-
-
Mitschke, J.1
Georg, J.2
Scholz, I.3
Sharma, C.M.4
Dienst, D.5
|