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KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.
Sacomoto GA, Kielbassa J, Chikhi R, Uricaru R, Antoniou P, Sagot MF, Peterlongo P, Lacroix V. Sacomoto GA, et al. Among authors: chikhi r. BMC Bioinformatics. 2012 Apr 19;13 Suppl 6(Suppl 6):S5. doi: 10.1186/1471-2105-13-S6-S5. BMC Bioinformatics. 2012. PMID: 22537044 Free PMC article.
Compareads: comparing huge metagenomic experiments.
Maillet N, Lemaitre C, Chikhi R, Lavenier D, Peterlongo P. Maillet N, et al. Among authors: chikhi r. BMC Bioinformatics. 2012;13 Suppl 19(Suppl 19):S10. doi: 10.1186/1471-2105-13-S19-S10. Epub 2012 Dec 19. BMC Bioinformatics. 2012. PMID: 23282463 Free PMC article.
DSK: k-mer counting with very low memory usage.
Rizk G, Lavenier D, Chikhi R. Rizk G, et al. Among authors: chikhi r. Bioinformatics. 2013 Mar 1;29(5):652-3. doi: 10.1093/bioinformatics/btt020. Epub 2013 Jan 16. Bioinformatics. 2013. PMID: 23325618 Free article.
GATB: Genome Assembly & Analysis Tool Box.
Drezen E, Rizk G, Chikhi R, Deltel C, Lemaitre C, Peterlongo P, Lavenier D. Drezen E, et al. Among authors: chikhi r. Bioinformatics. 2014 Oct 15;30(20):2959-61. doi: 10.1093/bioinformatics/btu406. Epub 2014 Jul 1. Bioinformatics. 2014. PMID: 24990603 Free PMC article.
Reference-free detection of isolated SNPs.
Uricaru R, Rizk G, Lacroix V, Quillery E, Plantard O, Chikhi R, Lemaitre C, Peterlongo P. Uricaru R, et al. Among authors: chikhi r. Nucleic Acids Res. 2015 Jan;43(2):e11. doi: 10.1093/nar/gku1187. Epub 2014 Nov 17. Nucleic Acids Res. 2015. PMID: 25404127 Free PMC article.
On the representation of de Bruijn graphs.
Chikhi R, Limasset A, Jackman S, Simpson JT, Medvedev P. Chikhi R, et al. J Comput Biol. 2015 May;22(5):336-52. doi: 10.1089/cmb.2014.0160. Epub 2015 Jan 28. J Comput Biol. 2015. PMID: 25629448
A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y.
Tomaszkiewicz M, Rangavittal S, Cechova M, Campos Sanchez R, Fescemyer HW, Harris R, Ye D, O'Brien PC, Chikhi R, Ryder OA, Ferguson-Smith MA, Medvedev P, Makova KD. Tomaszkiewicz M, et al. Among authors: chikhi r. Genome Res. 2016 Apr;26(4):530-40. doi: 10.1101/gr.199448.115. Epub 2016 Mar 2. Genome Res. 2016. PMID: 26934921 Free PMC article.
64 results