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RResolver: efficient short-read repeat resolution within ABySS.
Nikolić V, Afshinfard A, Chu J, Wong J, Coombe L, Nip KM, Warren RL, Birol I. Nikolić V, et al. Among authors: birol i. BMC Bioinformatics. 2022 Jun 21;23(1):246. doi: 10.1186/s12859-022-04790-z. BMC Bioinformatics. 2022. PMID: 35729491 Free PMC article.
ABySS: a parallel assembler for short read sequence data.
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. Simpson JT, et al. Among authors: birol i. Genome Res. 2009 Jun;19(6):1117-23. doi: 10.1101/gr.089532.108. Epub 2009 Feb 27. Genome Res. 2009. PMID: 19251739 Free PMC article.
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. Bioinformatics. 2009 Nov 1;25(21):2872-7. doi: 10.1093/bioinformatics/btp367. Epub 2009 Jun 15. Bioinformatics. 2009. PMID: 19528083
Complete genomic landscape of a recurring sporadic parathyroid carcinoma.
Kasaian K, Wiseman SM, Thiessen N, Mungall KL, Corbett RD, Qian JQ, Nip KM, He A, Tse K, Chuah E, Varhol RJ, Pandoh P, McDonald H, Zeng T, Tam A, Schein J, Birol I, Mungall AJ, Moore RA, Zhao Y, Hirst M, Marra MA, Walker BA, Jones SJ. Kasaian K, et al. Among authors: birol i. J Pathol. 2013 Jul;230(3):249-60. doi: 10.1002/path.4203. J Pathol. 2013. PMID: 23616356
Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.
Birol I, Raymond A, Jackman SD, Pleasance S, Coope R, Taylor GA, Yuen MM, Keeling CI, Brand D, Vandervalk BP, Kirk H, Pandoh P, Moore RA, Zhao Y, Mungall AJ, Jaquish B, Yanchuk A, Ritland C, Boyle B, Bousquet J, Ritland K, Mackay J, Bohlmann J, Jones SJ. Birol I, et al. Bioinformatics. 2013 Jun 15;29(12):1492-7. doi: 10.1093/bioinformatics/btt178. Epub 2013 May 22. Bioinformatics. 2013. PMID: 23698863 Free PMC article.
Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies.
Swanson L, Robertson G, Mungall KL, Butterfield YS, Chiu R, Corbett RD, Docking TR, Hogge D, Jackman SD, Moore RA, Mungall AJ, Nip KM, Parker JD, Qian JQ, Raymond A, Sung S, Tam A, Thiessen N, Varhol R, Wang S, Yorukoglu D, Zhao Y, Hoodless PA, Sahinalp SC, Karsan A, Birol I. Swanson L, et al. Among authors: birol i. BMC Genomics. 2013 Aug 14;14:550. doi: 10.1186/1471-2164-14-550. BMC Genomics. 2013. PMID: 23941359 Free PMC article.
Kleat: cleavage site analysis of transcriptomes.
Birol I, Raymond A, Chiu R, Nip KM, Jackman SD, Kreitzman M, Docking TR, Ennis CA, Robertson AG, Karsan A. Birol I, et al. Pac Symp Biocomput. 2015:347-58. Pac Symp Biocomput. 2015. PMID: 25592595 Free PMC article.
162 results