Papers Referencing SEQanswers
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
- Cumulative number of Peer-reviewed articles and Book that cited SEQanswers. Date as of 27 Jan 2012
- 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& |
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 |