Format
Sort by

Send to

Choose Destination

Links from PubMed

Items: 20

1.

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.

Schulz MH, Zerbino DR, Vingron M, Birney E.

Bioinformatics. 2012 Apr 15;28(8):1086-92. doi: 10.1093/bioinformatics/bts094. Epub 2012 Feb 24.

2.

Next-generation transcriptome assembly.

Martin JA, Wang Z.

Nat Rev Genet. 2011 Sep 7;12(10):671-82. doi: 10.1038/nrg3068. Review.

PMID:
21897427
3.

RNA-Seq unleashed.

Iyer MK, Chinnaiyan AM.

Nat Biotechnol. 2011 Jul 11;29(7):599-600. doi: 10.1038/nbt.1915. No abstract available.

PMID:
21747384
4.
5.

Full-length transcriptome assembly from RNA-Seq data without a reference genome.

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.

Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883.

6.

Comparing de novo genome assembly: the long and short of it.

Narzisi G, Mishra B.

PLoS One. 2011 Apr 29;6(4):e19175. doi: 10.1371/journal.pone.0019175.

7.

Evaluation of next-generation sequencing software in mapping and assembly.

Bao S, Jiang R, Kwan W, Wang B, Ma X, Song YQ.

J Hum Genet. 2011 Jun;56(6):406-14. doi: 10.1038/jhg.2011.43. Epub 2011 Apr 28. Review.

PMID:
21525877
8.

A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.

Zhang W, Chen J, Yang Y, Tang Y, Shang J, Shen B.

PLoS One. 2011 Mar 14;6(3):e17915. doi: 10.1371/journal.pone.0017915.

9.

De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification.

Garg R, Patel RK, Tyagi AK, Jain M.

DNA Res. 2011 Feb;18(1):53-63. doi: 10.1093/dnares/dsq028. Epub 2011 Jan 7.

10.

De novo assembly and analysis of RNA-seq data.

Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu AL, Tam A, Zhao Y, Moore RA, Hirst M, Marra MA, Jones SJ, Hoodless PA, Birol I.

Nat Methods. 2010 Nov;7(11):909-12. doi: 10.1038/nmeth.1517. Epub 2010 Oct 10.

PMID:
20935650
11.

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data.

Cox MP, Peterson DA, Biggs PJ.

BMC Bioinformatics. 2010 Sep 27;11:485. doi: 10.1186/1471-2105-11-485.

12.

Optimization of de novo transcriptome assembly from next-generation sequencing data.

Surget-Groba Y, Montoya-Burgos JI.

Genome Res. 2010 Oct;20(10):1432-40. doi: 10.1101/gr.103846.109. Epub 2010 Aug 6.

13.

De novo assembly of human genomes with massively parallel short read sequencing.

Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J.

Genome Res. 2010 Feb;20(2):265-72. doi: 10.1101/gr.097261.109. Epub 2009 Dec 17.

14.

Investigation of biomass and lipids production with Neochloris oleoabundans in photobioreactor.

Pruvost J, Van Vooren G, Cogne G, Legrand J.

Bioresour Technol. 2009 Dec;100(23):5988-95. doi: 10.1016/j.biortech.2009.06.004. Epub 2009 Jun 26.

PMID:
19560349
15.

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead B, Trapnell C, Pop M, Salzberg SL.

Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4.

16.

Effects of nitrogen sources on cell growth and lipid accumulation of green alga Neochloris oleoabundans.

Li Y, Horsman M, Wang B, Wu N, Lan CQ.

Appl Microbiol Biotechnol. 2008 Dec;81(4):629-36. doi: 10.1007/s00253-008-1681-1. Epub 2008 Sep 16.

PMID:
18795284
17.

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Zerbino DR, Birney E.

Genome Res. 2008 May;18(5):821-9. doi: 10.1101/gr.074492.107. Epub 2008 Mar 18.

18.

KAAS: an automatic genome annotation and pathway reconstruction server.

Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W182-5. Epub 2007 May 25.

19.

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.

Li W, Godzik A.

Bioinformatics. 2006 Jul 1;22(13):1658-9. Epub 2006 May 26.

20.

TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.

Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J.

Bioinformatics. 2003 Mar 22;19(5):651-2.

Items per page

Supplemental Content

Write to the Help Desk