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ABySS-Explorer: visualizing genome sequence assemblies.
Nielsen CB, Jackman SD, Birol I, Jones SJ. Nielsen CB, et al. IEEE Trans Vis Comput Graph. 2009 Nov-Dec;15(6):881-8. doi: 10.1109/TVCG.2009.116. IEEE Trans Vis Comput Graph. 2009. PMID: 19834150
De novo transcriptome assembly with ABySS.
Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, Horsman DE, Connors JM, Gascoyne RD, Marra MA, Jones SJ. Birol I, et al. Among authors: nielsen cb. Bioinformatics. 2009 Nov 1;25(21):2872-7. doi: 10.1093/bioinformatics/btp367. Epub 2009 Jun 15. Bioinformatics. 2009. PMID: 19528083
Spark: a navigational paradigm for genomic data exploration.
Nielsen CB, Younesy H, O'Geen H, Xu X, Jackson AR, Milosavljevic A, Wang T, Costello JF, Hirst M, Farnham PJ, Jones SJ. Nielsen CB, et al. Genome Res. 2012 Nov;22(11):2262-9. doi: 10.1101/gr.140665.112. Epub 2012 Sep 7. Genome Res. 2012. PMID: 22960372 Free PMC article.
ChAsE: chromatin analysis and exploration tool.
Younesy H, Nielsen CB, Lorincz MC, Jones SJ, Karimi MM, Möller T. Younesy H, et al. Among authors: nielsen cb. Bioinformatics. 2016 Nov 1;32(21):3324-3326. doi: 10.1093/bioinformatics/btw382. Epub 2016 Jul 4. Bioinformatics. 2016. PMID: 27378294 Free PMC article.
Visualizing genomes: techniques and challenges.
Nielsen CB, Cantor M, Dubchak I, Gordon D, Wang T. Nielsen CB, et al. Nat Methods. 2010 Mar;7(3 Suppl):S5-S15. doi: 10.1038/nmeth.1422. Epub 2010 Feb 25. Nat Methods. 2010. PMID: 20195257 Review.
Conserved role of intragenic DNA methylation in regulating alternative promoters.
Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF. Maunakea AK, et al. Nature. 2010 Jul 8;466(7303):253-7. doi: 10.1038/nature09165. Nature. 2010. PMID: 20613842 Free PMC article.
Points of view: Representing the genome.
Nielsen C, Wong B. Nielsen C, et al. Nat Methods. 2012 May;9(5):423. doi: 10.1038/nmeth.1992. Nat Methods. 2012. PMID: 22803197 No abstract available.
203 results