Papers Referencing SEQanswers

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Publications about SEQanswers and the SEQanswers WIKI:

Year Publication Title PubMed Publication Link
2012 Bioinformatics SEQanswers: An open access community for collaboratively decoding genomes http://www.ncbi.nlm.nih.gov/pubmed/22419780 http://bioinformatics.oxfordjournals.org/content/early/2012/03/13/bioinformatics.bts128.abstract
2011 Nucleic Acids Research The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis http://www.ncbi.nlm.nih.gov/pubmed/22086956 http://nar.oxfordjournals.org/content/early/2011/11/15/nar.gkr1058.abstract
  • Updated Figure 1 of SEQanswers paper in Bioinformatics. Date as of 20 March 2012

Figure01 2012-02.s.jpg

  • Cumulative number of Peer-reviewed articles and Book that cited SEQanswers. Date as of 27 Jan 2012

SEQwiki.citations.27.Jan.2012.2.png

  • This is a list of publications that have referenced SEQanswers.

This list also exists on the forums as well. [Depreciated]

Year Publication Lead Author Title PubMed Publication Link
2008 Nature Biotechnology Shendure Next-generation DNA sequencing http://www.ncbi.nlm.nih.gov/pubmed/18846087 http://www.nature.com/nbt/journal/v26/n10/abs/nbt1486.html
2009 Briefings in Bioinformatics Horner Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing http://www.ncbi.nlm.nih.gov/pubmed/19864250 http://bib.oxfordjournals.org/cgi/content/abstract/11/2/181
2009 Nature Biotechnology Trapnell How to map billions of short reads onto genomes. http://www.ncbi.nlm.nih.gov/pubmed/19430453 http://www.nature.com/nbt/journal/v27/n5/abs/nbt0509-455.html
2009 Nature Methods McPherson Next-generation gap http://www.ncbi.nlm.nih.gov/pubmed/19844227 http://www.nature.com/nmeth/journal/v6/n11s/full/nmeth.f.268.html
2009 Nature Methods Flicek Sense from sequence reads: methods for alignment and assembly http://www.ncbi.nlm.nih.gov/pubmed/19844229 http://www.nature.com/nmeth/journal/v6/n11s/full/nmeth.1376.html
2009 Nature Reviews Genetics Park ChIP-seq: advantages and challenges of a maturing technology http://www.ncbi.nlm.nih.gov/pubmed/19736561 http://www.nature.com/nrg/journal/v10/n10/abs/nrg2641.html
2009 Trends in Ecology & Evolution Rokas Harnessing genomics for evolutionary insights http://www.ncbi.nlm.nih.gov/pubmed/19201503 http://dx.doi.org/10.1016/j.tree.2008.11.004
2009 Nature Review Genetics Wang et. al. RNA-Seq: a revolutionary tool for transcriptomics http://www.ncbi.nlm.nih.gov/pubmed?term=19015660 http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html
2009 Book: Bioinformatics Matukumalli Sequence Based Gene Expression Analysis n/a http://www.springerlink.com/content/h451373705j60006/
2010 Nature Methods Nielsen Visualizing genomes: techniques and challenges http://www.ncbi.nlm.nih.gov/pubmed/20195257 http://www.nature.com/nmeth/journal/v7/n3s/full/nmeth.1422.html
2010 The Auk Lerner Prospects for the Use of Next-Generation Sequencing Methods in Ornithology n/a http://caliber.ucpress.net/doi/abs/10.1525/auk.2010.127.1.4
2010 Expert Rev Mol Diagn Corbett Great expectations: using massively parallel sequencing to solve inherited disorders http://www.ncbi.nlm.nih.gov/pubmed/20964599 http://www.expert-reviews.com/doi/abs/10.1586/erm.10.83
2010 Briefings in Bioinformatics Li & Homer A survey of sequence alignment algorithms for next-generation sequencing http://www.ncbi.nlm.nih.gov/pubmed/20460430 http://bib.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=20460430
2010 Briefings in Bioinformatics Huss Introduction into the analysis of high-throughput-sequencing based epigenome data http://www.ncbi.nlm.nih.gov/pubmed/20457755 http://bib.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=20457755
2010 PLoS Comput Biol Huttenhower A Quick Guide to Large-Scale Genomic Data Mining. http://www.ncbi.nlm.nih.gov/pubmed/20523745 http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000779
2010 Nucleic Acids Res. Zheng Titration-free massively parallel pyrosequencing using trace amounts of starting material http://www.ncbi.nlm.nih.gov/pubmed/20435675 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2910068/
2010 Genes Magi Bioinformatics for Next Generation Sequencing Data n/a http://www.mdpi.com/2073-4425/1/2/294/
2010 Genomics Inform Rhie A Simple GUI-based Sequencing Format Conversion Tool for the Three NGS Platforms. n/a http://www.genominfo.org/html/UploadFile/article8_201006.pdf
2010 Plant biology Bräutigam & Gowik What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research http://www.ncbi.nlm.nih.gov/pubmed/21040298 http://onlinelibrary.wiley.com/doi/10.1111/j.1438-8677.2010.00373.x/full
2010 Genome Biology Oshlack From RNA-seq reads to differential expression results http://www.ncbi.nlm.nih.gov/pubmed/21176179 http://genomebiology.com/2010/11/12/220/?mkt=260328&amp
2010 PLoS One Krueger Large Scale Loss of Data in Low-Diversity Illumina Sequencing Libraries Can Be Recovered by Deferred Cluster Calling http://www.ncbi.nlm.nih.gov/pubmed/21305042 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016607
2010 Eukaryotic Cell Nowrousian Next-Generation Sequencing Techniques for Eukaryotic Microorganisms: Sequencing-Based Solutions to Biological Problems http://www.ncbi.nlm.nih.gov/pubmed/20601439 http://ec.asm.org/cgi/content/full/9/9/1300
2011 Nature Review Genetics Nielsen Genotype and SNP calling from next-generation sequencing data http://www.ncbi.nlm.nih.gov/pubmed/21587300 http://www.nature.com/nrg/journal/v12/n6/full/nrg2986.html
2011 Methods in Molecular Biology Nielsen Outsourcing of experimental work http://www.ncbi.nlm.nih.gov/pubmed/21125500 http://www.springerlink.com/content/m946150214752254/#section=826553&page=3&locus=59
2011 BMC Genomics Blanca "ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence" http://www.ncbi.nlm.nih.gov/pubmed/21635747 http://www.biomedcentral.com/1471-2164/12/285/abstract
2011 Nature Methods Perkel Coding your way out of a problem http://www.ncbi.nlm.nih.gov/pubmed/21716280 http://www.nature.com/nmeth/journal/v8/n7/full/nmeth.1631.html
2011 BMC Genomics Kircher at al Addressing challenges in the production and analysis of Illumina sequencing data http://www.ncbi.nlm.nih.gov/pubmed/21801405 http://www.biomedcentral.com/1471-2164/12/382/abstract
2011 PLoS One Huang Rapid Screening of Complex DNA Samples by Single-Molecule Amplification and Sequencing http://www.ncbi.nlm.nih.gov/pubmed/21625543 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019723
2011 Molecular Ecology Resources Glenn Field guide to next-generation DNA sequencers http://www.ncbi.nlm.nih.gov/pubmed/21592312 http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2011.03024.x/full
2011 BMC Bioinformatics Deng SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data http://www.ncbi.nlm.nih.gov/pubmed/21714929 http://www.biomedcentral.com/1471-2105/12/267/abstract/
2011 Heredity Ekblom & Galindo Applications of next generation sequencing in molecular ecology of non-model organisms http://www.ncbi.nlm.nih.gov/pubmed/21139633 http://www.nature.com/hdy/journal/v107/n1/full/hdy2010152a.html
2011 Respirology Cullum The next generation: Using new sequencing technologies to analyse gene regulation http://www.ncbi.nlm.nih.gov/pubmed/21077988 http://onlinelibrary.wiley.com/doi/10.1111/j.1440-1843.2010.01899.x/full
2011 BMC Genomics Berninger Conserved generation of short products at piRNA loci http://www.ncbi.nlm.nih.gov/pubmed/21247452 http://www.biomedcentral.com/1471-2164/12/46/
2011 Journal of Genetics and Genomics Zhang The impact of next-generation sequencing on genomics http://www.ncbi.nlm.nih.gov/pubmed/21477781 http://www.sciencedirect.com/science/article/pii/S1673852711000300
2011 Nature Genetics Dassanayake The genome of the extremophile crucifer Thellungiella parvula http://www.ncbi.nlm.nih.gov/pubmed/21822265 http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.889.html
2011 Investigative Genetics Berglund et. al Next generation sequencing technologies and applications http://www.ncbi.nlm.nih.gov/pubmed/22115430 http://www.investigativegenetics.com/content/2/1/23/abstract
2011 Current Protocols in Bioinformatics Lincoln D. Stein An introduction to the informatics of "next-generation" sequencing http://www.ncbi.nlm.nih.gov/pubmed?term=22161566 http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1101s36/abstract
2011 Journal of Cereal Science Edwards et al DNA sequencing methods contributing to new directions in cereal research n/a http://www.sciencedirect.com/science/article/pii/S0733521011001330
2011 The HUGO Journal Moorthie et al Review of massively parallel DNA sequencing technologies n/a http://www.springerlink.com/content/g050l8u29m3m1mk6/fulltext.html
2011 PLoS ONE Haiminen et al Evaluation of Methods for De Novo Genome Assembly from High-Throughput Sequencing Reads Reveals Dependencies That Affect the Quality of the Results http://www.ncbi.nlm.nih.gov/pubmed?term=21915294 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0024182
2012 Book: Plant Fungal Pathogens Ronnie de Jonge In Silico Identification and Characterization of Effector Catalogs n/a http://www.springerlink.com/content/j537q1x22w2438x0/#section=1006190&page=1
2012 Book: Next-Generation MicroRNA Expression Profiling Technology Sarah Aldridge and James Hadfield Introduction to miRNA Profiling Technologies and Cross-Platform Comparison n/a http://www.springerlink.com/content/lkp634m127123422/#section=999805&page=1
2012 Book: Bioinformatics for High Throughput Sequencing Paszkiewicz et. al. High-Throughput Sequencing Data Analysis Software: Current State and Future Developments n/a http://www.springerlink.com/content/xm0p862qp4h287w0/
2012 Future Microbiology Schmieder Insights into antibiotic resistance through metagenomic approaches http://www.ncbi.nlm.nih.gov/pubmed/22191448 http://www.futuremedicine.com/doi/abs/10.2217/fmb.11.135
2012 Bioinformation Laczik et. al. Geno viewer, a SAM/BAM viewer tool view here http://www.bioinformation.net/008/97320630008107.pdf
2012 n/a yet (NOT included in above figure) Pomraning et. al. Library preparation for rapid genome Illumina sequencingl n/a YET https://shell.cgrb.oregonstate.edu/sites/default/files/Files/Docs/Illumina/barcodes/Pomraning2011MMiB_RapGenSeq.pdf
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