核糖核酸测序 (Chinese Wikipedia)

Analysis of information sources in references of the Wikipedia article "核糖核酸测序" in Chinese language version.

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25nih.gov

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25doi.org

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3web.archive.org

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1bcgsc.ca

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1illumina.com

low place

1ebi.ac.uk

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1archive.org

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1arxiv.org

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archive.org

Patro R, Mount SM, Kingsford C. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature Biotechnology. May 2014, 32 (5): 462–4. PMC 4077321 . PMID 24752080. arXiv:1308.3700 . doi:10.1038/nbt.2862.

arxiv.org

Patro R, Mount SM, Kingsford C. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature Biotechnology. May 2014, 32 (5): 462–4. PMC 4077321 . PMID 24752080. arXiv:1308.3700 . doi:10.1038/nbt.2862.

bcgsc.ca

Ryan D. Morin, Matthew Bainbridge, Anthony Fejes, Martin Hirst, Martin Krzywinski, Trevor J. Pugh, Helen McDonald, Richard Varhol, Steven J.M. Jones, and Marco A. Marra. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. BioTechniques. 2008, 45 (1): 81–94 [2014-02-16]. PMID 18611170. doi:10.2144/000112900. （原始内容存档于2009-03-21）.

doi.org

Ryan D. Morin, Matthew Bainbridge, Anthony Fejes, Martin Hirst, Martin Krzywinski, Trevor J. Pugh, Helen McDonald, Richard Varhol, Steven J.M. Jones, and Marco A. Marra. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. BioTechniques. 2008, 45 (1): 81–94 [2014-02-16]. PMID 18611170. doi:10.2144/000112900. （原始内容存档于2009-03-21）.
Chu Y, Corey DR. RNA sequencing: platform selection, experimental design, and data interpretation. Nucleic Acid Ther. August 2012, 22 (4): 271–4. PMC 3426205 . PMID 22830413. doi:10.1089/nat.2012.0367.
Maher CA, Kumar-Sinha C, Cao X,; et al. Transcriptome sequencing to detect gene fusions in cancer. Nature. March 2009, 458 (7234): 97–101. PMC 2725402 . PMID 19136943. doi:10.1038/nature07638.
Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc. August 2012, 7 (8): 1534–50. PMC 3535016 . PMID 22836135. doi:10.1038/nprot.2012.086.
Qian F, Chung L, Zheng W; et al. Identification of Genes Critical for Resistance to Infection by West Nile Virus Using RNA-Seq Analysis. Viruses. 2013, 5 (7): 1664–81. PMID 23881275. doi:10.3390/v5071664.
Beane J, Vick J, Schembri F. Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq. Cancer Prev Res (Phila). June 2011, 4 (6): 803–17. PMC 3694393 . PMID 21636547. doi:10.1158/1940-6207.CAPR-11-0212.
Maher CA, Kumar-Sinha C, Cao X,; et al. Transcriptome sequencing to detect gene fusions in cancer. Nature. March 2009, 458 (7234): 97–101. PMC 2725402 . PMID 19136943. doi:10.1038/nature07638.
Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc. August 2012, 7 (8): 1534–50. PMC 3535016 . PMID 22836135. doi:10.1038/nprot.2012.086.
Qian F, Chung L, Zheng W; et al. Identification of Genes Critical for Resistance to Infection by West Nile Virus Using RNA-Seq Analysis. Viruses. 2013, 5 (7): 1664–81. PMID 23881275. doi:10.3390/v5071664.
Beane J, Vick J, Schembri F. Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq. Cancer Prev Res (Phila). June 2011, 4 (6): 803–17. PMC 3694393 . PMID 21636547. doi:10.1158/1940-6207.CAPR-11-0212.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology. May 2011, 29 (7): 644–52. PMC 3571712 . PMID 21572440. doi:10.1038/nbt.1883.
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research. May 2008, 18 (5): 821–9. PMC 2336801 . PMID 18349386. doi:10.1101/gr.074492.107.
Chang Z, Li G, Liu J, Zhang Y, Ashby C, Liu D, Cramer CL, Huang X. Bridger: a new framework for de novo transcriptome assembly using RNA-seq data. Genome Biology. February 2015, 16 (1): 30. PMC 4342890 . PMID 25723335. doi:10.1186/s13059-015-0596-2.
Li B, Fillmore N, Bai Y, Collins M, Thomson JA, Stewart R, Dewey CN. Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome Biology. December 2014, 15 (12): 553. PMC 4298084 . PMID 25608678. doi:10.1186/s13059-014-0553-5.
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. January 2013, 29 (1): 15–21. PMC 3530905 . PMID 23104886. doi:10.1093/bioinformatics/bts635.
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology. 2009, 10 (3): R25. PMC 2690996 . PMID 19261174. doi:10.1186/gb-2009-10-3-r25.
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. May 2009, 25 (9): 1105–11. PMC 2672628 . PMID 19289445. doi:10.1093/bioinformatics/btp120.
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols. March 2012, 7 (3): 562–78. PMC 3334321 . PMID 22383036. doi:10.1038/nprot.2012.016.
Liao Y, Smyth GK, Shi W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research. May 2013, 41 (10): e108. PMC 3664803 . PMID 23558742. doi:10.1093/nar/gkt214.
Kim, D; Langmead, B; Salzberg, SL. HISAT: a fast spliced aligner with low memory requirements.. Nature Methods. April 2015, 12 (4): 357–60. PMC 4655817 . PMID 25751142. doi:10.1038/nmeth.3317.
Patro R, Mount SM, Kingsford C. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature Biotechnology. May 2014, 32 (5): 462–4. PMC 4077321 . PMID 24752080. arXiv:1308.3700 . doi:10.1038/nbt.2862.
Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology. May 2016, 34 (5): 525–7. PMID 27043002. doi:10.1038/nbt.3519.
Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics. May 2005, 21 (9): 1859–75. PMID 15728110. doi:10.1093/bioinformatics/bti310.
Baruzzo G, Hayer KE, Kim EJ, Di Camillo B, FitzGerald GA, Grant GR. Simulation-based comprehensive benchmarking of RNA-seq aligners. Nature Methods. February 2017, 14 (2): 135–139. PMC 5792058 . PMID 27941783. doi:10.1038/nmeth.4106 （英语）.
Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, et al. Systematic evaluation of spliced alignment programs for RNA-seq data. Nature Methods. December 2013, 10 (12): 1185–91. PMC 4018468 . PMID 24185836. doi:10.1038/nmeth.2722 （英语）.

ebi.ac.uk

Oases: a transcriptome assembler for very short reads. [2019-02-16]. （原始内容存档于2018-11-29）.

illumina.com

De Novo Assembly Using Illumina Reads (PDF). [22 October 2016]. （原始内容存档 (PDF)于2020-09-24）.

nih.gov

ncbi.nlm.nih.gov

Ryan D. Morin, Matthew Bainbridge, Anthony Fejes, Martin Hirst, Martin Krzywinski, Trevor J. Pugh, Helen McDonald, Richard Varhol, Steven J.M. Jones, and Marco A. Marra. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. BioTechniques. 2008, 45 (1): 81–94 [2014-02-16]. PMID 18611170. doi:10.2144/000112900. （原始内容存档于2009-03-21）.
Chu Y, Corey DR. RNA sequencing: platform selection, experimental design, and data interpretation. Nucleic Acid Ther. August 2012, 22 (4): 271–4. PMC 3426205 . PMID 22830413. doi:10.1089/nat.2012.0367.
Maher CA, Kumar-Sinha C, Cao X,; et al. Transcriptome sequencing to detect gene fusions in cancer. Nature. March 2009, 458 (7234): 97–101. PMC 2725402 . PMID 19136943. doi:10.1038/nature07638.
Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc. August 2012, 7 (8): 1534–50. PMC 3535016 . PMID 22836135. doi:10.1038/nprot.2012.086.
Qian F, Chung L, Zheng W; et al. Identification of Genes Critical for Resistance to Infection by West Nile Virus Using RNA-Seq Analysis. Viruses. 2013, 5 (7): 1664–81. PMID 23881275. doi:10.3390/v5071664.
Beane J, Vick J, Schembri F. Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq. Cancer Prev Res (Phila). June 2011, 4 (6): 803–17. PMC 3694393 . PMID 21636547. doi:10.1158/1940-6207.CAPR-11-0212.
Maher CA, Kumar-Sinha C, Cao X,; et al. Transcriptome sequencing to detect gene fusions in cancer. Nature. March 2009, 458 (7234): 97–101. PMC 2725402 . PMID 19136943. doi:10.1038/nature07638.
Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc. August 2012, 7 (8): 1534–50. PMC 3535016 . PMID 22836135. doi:10.1038/nprot.2012.086.
Qian F, Chung L, Zheng W; et al. Identification of Genes Critical for Resistance to Infection by West Nile Virus Using RNA-Seq Analysis. Viruses. 2013, 5 (7): 1664–81. PMID 23881275. doi:10.3390/v5071664.
Beane J, Vick J, Schembri F. Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq. Cancer Prev Res (Phila). June 2011, 4 (6): 803–17. PMC 3694393 . PMID 21636547. doi:10.1158/1940-6207.CAPR-11-0212.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology. May 2011, 29 (7): 644–52. PMC 3571712 . PMID 21572440. doi:10.1038/nbt.1883.
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research. May 2008, 18 (5): 821–9. PMC 2336801 . PMID 18349386. doi:10.1101/gr.074492.107.
Chang Z, Li G, Liu J, Zhang Y, Ashby C, Liu D, Cramer CL, Huang X. Bridger: a new framework for de novo transcriptome assembly using RNA-seq data. Genome Biology. February 2015, 16 (1): 30. PMC 4342890 . PMID 25723335. doi:10.1186/s13059-015-0596-2.
Li B, Fillmore N, Bai Y, Collins M, Thomson JA, Stewart R, Dewey CN. Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome Biology. December 2014, 15 (12): 553. PMC 4298084 . PMID 25608678. doi:10.1186/s13059-014-0553-5.
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. January 2013, 29 (1): 15–21. PMC 3530905 . PMID 23104886. doi:10.1093/bioinformatics/bts635.
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology. 2009, 10 (3): R25. PMC 2690996 . PMID 19261174. doi:10.1186/gb-2009-10-3-r25.
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. May 2009, 25 (9): 1105–11. PMC 2672628 . PMID 19289445. doi:10.1093/bioinformatics/btp120.
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols. March 2012, 7 (3): 562–78. PMC 3334321 . PMID 22383036. doi:10.1038/nprot.2012.016.
Liao Y, Smyth GK, Shi W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research. May 2013, 41 (10): e108. PMC 3664803 . PMID 23558742. doi:10.1093/nar/gkt214.
Kim, D; Langmead, B; Salzberg, SL. HISAT: a fast spliced aligner with low memory requirements.. Nature Methods. April 2015, 12 (4): 357–60. PMC 4655817 . PMID 25751142. doi:10.1038/nmeth.3317.
Patro R, Mount SM, Kingsford C. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature Biotechnology. May 2014, 32 (5): 462–4. PMC 4077321 . PMID 24752080. arXiv:1308.3700 . doi:10.1038/nbt.2862.
Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology. May 2016, 34 (5): 525–7. PMID 27043002. doi:10.1038/nbt.3519.
Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics. May 2005, 21 (9): 1859–75. PMID 15728110. doi:10.1093/bioinformatics/bti310.
Baruzzo G, Hayer KE, Kim EJ, Di Camillo B, FitzGerald GA, Grant GR. Simulation-based comprehensive benchmarking of RNA-seq aligners. Nature Methods. February 2017, 14 (2): 135–139. PMC 5792058 . PMID 27941783. doi:10.1038/nmeth.4106 （英语）.
Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, et al. Systematic evaluation of spliced alignment programs for RNA-seq data. Nature Methods. December 2013, 10 (12): 1185–91. PMC 4018468 . PMID 24185836. doi:10.1038/nmeth.2722 （英语）.

web.archive.org

Ryan D. Morin, Matthew Bainbridge, Anthony Fejes, Martin Hirst, Martin Krzywinski, Trevor J. Pugh, Helen McDonald, Richard Varhol, Steven J.M. Jones, and Marco A. Marra. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. BioTechniques. 2008, 45 (1): 81–94 [2014-02-16]. PMID 18611170. doi:10.2144/000112900. （原始内容存档于2009-03-21）.
De Novo Assembly Using Illumina Reads (PDF). [22 October 2016]. （原始内容存档 (PDF)于2020-09-24）.
Oases: a transcriptome assembler for very short reads. [2019-02-16]. （原始内容存档于2018-11-29）.