Mentions of SEQanswers in the Literature

[steven]

FYI, here is a -probably non exhaustive- draft list i compiled of SEQanswers citations in scientific peer-reviewed literature:

Year	Publication	Lead Author	Title	PubMed	Publication Link
2008	Nature Biotechnology	Shendure	Next-generation DNA sequencing	PubMed Link	Link
2009	Briefings in Bioinformatics	Horner	Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing	PubMed Link	Link
2009	Nature Biotechnology	Trapnell	How to map billions of short reads onto genomes.	PubMed Link	Link
2009	Nature Methods	McPherson	Next-generation gap	PubMed Link	Link
2009	Nature Methods	Flicek	Sense from sequence reads: methods for alignment and assembly	PubMed Link	Link
2009	Nature Reviews Genetics	Park	ChIP-seq: advantages and challenges of a maturing technology	PubMed Link	Link
2009	Trends in Ecology & Evolution	Rokas	Harnessing genomics for evolutionary insights	PubMed Link	Link
2009	Book: Bioinformatics	Matukumalli	Sequence Based Gene Expression Analysis	n/a	Link
2010	Nature Methods	Nielsen	Visualizing genomes: techniques and challenges	n/a	Link
2010	The Auk	Lerner	Prospects for the Use of Next-Generation Sequencing Methods in Ornithology	n/a	Link

I think it's the first time i see articles referring to an internet forum, or at least so many of them.
Please don't hesitate to complete/correct/comment/etc
cheers,
s.

[ECO]

Compiled all that you found, as well as a couple more, and couldn't resist making it pretty.

Also put it on SEQwiki: The_Greatest_Papers_in_the_World.

[steven]

Two more:

Heng Li and Nils Homer
A survey of sequence alignment algorithms for next-generation sequencing
Briefings in Bioinformatics Advance Access published on May 11, 2010.
Pubmed

Mikael Huss
Introduction into the analysis of high-throughput-sequencing based epigenome data
Briefings in Bioinformatics Advance Access published on May 10, 2010.
Pubmed

[shine88]

good post for the beginer

[NeuroGenXtics]

Please excuse the shameless self promotion.
Corbett M, Gecz J.
Great expectations: using massively parallel sequencing to solve inherited disorders.
Expert Rev Mol Diagn. 2010 Oct;10(7):833-6.
Pubmed

[steven]

More:

Huttenhower C, Hofmann O (2010)
A Quick Guide to Large-Scale Genomic Data Mining.
PLoS Comput Biol 6(5): e1000779. doi:10.1371/journal.pcbi.1000779

Zheng Z, Advani A, Melefors O, Glavas S, Nordström H, Ye W, Engstrand L, Andersson AF.
Titration-free massively parallel pyrosequencing using trace amounts of starting material. Nucleic Acids Res. 2010 Jul;38(13):e137. Epub 2010 Apr 30. PubMed PMID: 20435675

(added to the wiki )

[steven]

Wow.. according to Google scholar, there are 17+ papers or so that are not yet listed in the wiki table!

I don't have time to update the wiki yet, but here are the links:

http://www.springerlink.com/content/...age=3&locus=59
http://www.biomedcentral.com/1471-2164/12/285/abstract
http://onlinelibrary.wiley.com/doi/1...9.ch22/summary
http://www.nature.com/nmeth/journal/....1631_BX1.html
http://www.mdpi.com/2073-4425/1/2/294/
http://www.genominfo.org/html/Upload...le8_201006.pdf
http://onlinelibrary.wiley.com/doi/1...0.00373.x/full
http://www.plosone.org/article/info%...l.pone.0016607
http://www.biomedcentral.com/1471-2164/12/382/abstract
http://genomebiology.com/2010/11/12/220/?mkt=260328&amp
http://www.plosone.org/article/info%...l.pone.0019723
http://www.biomedcentral.com/1471-2105/12/267/abstract/
http://onlinelibrary.wiley.com/doi/1...1.03024.x/full
http://onlinelibrary.wiley.com/doi/1...0.01899.x/full
http://www.nature.com/hdy/journal/v1...y2010152a.html
http://www.biomedcentral.com/1471-2164/12/46/

I only looked for papers since 2010.

[steven]

By the way, Google Scholar features a nice Alert system.. what about setting up another Newsbot to get an automatic post each time a paper cites "SEQanswers"?

[marcowanger]

Some more

http://www.nature.com/nmeth/journal/...meth.1631.html
http://www.springerlink.com/index/M946150214752254.pdf
http://www.biomedcentral.com/1471-2164/12/382/abstract
http://www.biomedcentral.com/1471-2164/12/46/
http://www.akademiai.com/index/K76G173700718605.pdf

[marcowanger]

Originally Posted by steven

By the way, Google Scholar features a nice Alert system.. what about setting up another Newsbot to get an automatic post each time a paper cites "SEQanswers"?

It seems it only works for person

http://scholar.google.com/citations?view_op=new_profile

[ECO]

Newsbot runs on RSS feeds, which Google (lamely) doesn't provide for Scholar Alerts...but there are several workarounds I will try to get going...

Great list guys, thanks for finding all these!