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Items: 26

1.

Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data.

Lima L, Marchet C, Caboche S, Da Silva C, Istace B, Aury JM, Touzet H, Chikhi R.

Brief Bioinform. 2019 Jun 24. pii: bbz058. doi: 10.1093/bib/bbz058. [Epub ahead of print]

PMID:
31232449
2.

Graph analysis of fragmented long-read bacterial genome assemblies.

Marijon P, Chikhi R, Varré JS.

Bioinformatics. 2019 Nov 1;35(21):4239-4246. doi: 10.1093/bioinformatics/btz219.

PMID:
30918948
3.

Practical dynamic de Bruijn graphs.

Crawford VG, Kuhnle A, Boucher C, Chikhi R, Gagie T.

Bioinformatics. 2018 Dec 15;34(24):4189-4195. doi: 10.1093/bioinformatics/bty500.

PMID:
29939217
4.

AllSome Sequence Bloom Trees.

Sun C, Harris RS, Chikhi R, Medvedev P.

J Comput Biol. 2018 May;25(5):467-479. doi: 10.1089/cmb.2017.0258. Epub 2018 Apr 5.

PMID:
29620920
5.

DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.

Audoux J, Philippe N, Chikhi R, Salson M, Gallopin M, Gabriel M, Le Coz J, Drouineau E, Commes T, Gautheret D.

Genome Biol. 2017 Dec 28;18(1):243. doi: 10.1186/s13059-017-1372-2.

6.

RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly.

Rangavittal S, Harris RS, Cechova M, Tomaszkiewicz M, Chikhi R, Makova KD, Medvedev P.

Bioinformatics. 2018 Apr 1;34(7):1125-1131. doi: 10.1093/bioinformatics/btx771.

7.

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC.

Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2.

8.

Compacting de Bruijn graphs from sequencing data quickly and in low memory.

Chikhi R, Limasset A, Medvedev P.

Bioinformatics. 2016 Jun 15;32(12):i201-i208. doi: 10.1093/bioinformatics/btw279.

9.

Giraffe genome sequence reveals clues to its unique morphology and physiology.

Agaba M, Ishengoma E, Miller WC, McGrath BC, Hudson CN, Bedoya Reina OC, Ratan A, Burhans R, Chikhi R, Medvedev P, Praul CA, Wu-Cavener L, Wood B, Robertson H, Penfold L, Cavener DR.

Nat Commun. 2016 May 17;7:11519. doi: 10.1038/ncomms11519.

10.

Assembly scaffolding with PE-contaminated mate-pair libraries.

Sahlin K, Chikhi R, Arvestad L.

Bioinformatics. 2016 Jul 1;32(13):1925-32. doi: 10.1093/bioinformatics/btw064. Epub 2016 Mar 2.

PMID:
27153683
11.

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.

Genome Res. 2016 Apr;26(4):530-40. doi: 10.1101/gr.199448.115. Epub 2016 Mar 2.

12.

Born from pre-eclamptic pregnancies predisposes infants to altered cortisol metabolism in the first postnatal year.

Broughton Pipkin F, Mistry HD, Roy C, Dick B, Waugh J, Chikhi R, Kurlak LO, Mohaupt MG.

Endocr Connect. 2015 Dec;4(4):233-41. doi: 10.1530/EC-15-0084. Epub 2015 Sep 16.

13.

On the representation of de Bruijn graphs.

Chikhi R, Limasset A, Jackman S, Simpson JT, Medvedev P.

J Comput Biol. 2015 May;22(5):336-52. doi: 10.1089/cmb.2014.0160. Epub 2015 Jan 28.

PMID:
25629448
14.

Reference-free detection of isolated SNPs.

Uricaru R, Rizk G, Lacroix V, Quillery E, Plantard O, Chikhi R, Lemaitre C, Peterlongo P.

Nucleic Acids Res. 2015 Jan;43(2):e11. doi: 10.1093/nar/gku1187. Epub 2014 Nov 17.

15.

MindTheGap: integrated detection and assembly of short and long insertions.

Rizk G, Gouin A, Chikhi R, Lemaitre C.

Bioinformatics. 2014 Dec 15;30(24):3451-7. doi: 10.1093/bioinformatics/btu545. Epub 2014 Aug 14.

16.

GATB: Genome Assembly & Analysis Tool Box.

Drezen E, Rizk G, Chikhi R, Deltel C, Lemaitre C, Peterlongo P, Lavenier D.

Bioinformatics. 2014 Oct 15;30(20):2959-61. doi: 10.1093/bioinformatics/btu406. Epub 2014 Jul 1.

17.

Space-efficient and exact de Bruijn graph representation based on a Bloom filter.

Chikhi R, Rizk G.

Algorithms Mol Biol. 2013 Sep 16;8(1):22. doi: 10.1186/1748-7188-8-22.

18.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.

Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.

19.

Informed and automated k-mer size selection for genome assembly.

Chikhi R, Medvedev P.

Bioinformatics. 2014 Jan 1;30(1):31-7. doi: 10.1093/bioinformatics/btt310. Epub 2013 Jun 3.

PMID:
23732276
20.

DSK: k-mer counting with very low memory usage.

Rizk G, Lavenier D, Chikhi R.

Bioinformatics. 2013 Mar 1;29(5):652-3. doi: 10.1093/bioinformatics/btt020. Epub 2013 Jan 16.

PMID:
23325618
21.

Compareads: comparing huge metagenomic experiments.

Maillet N, Lemaitre C, Chikhi R, Lavenier D, Peterlongo P.

BMC Bioinformatics. 2012;13 Suppl 19:S10. doi: 10.1186/1471-2105-13-S19-S10. Epub 2012 Dec 19.

22.

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.

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S5. doi: 10.1186/1471-2105-13-S6-S5.

23.

Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer.

Peterlongo P, Chikhi R.

BMC Bioinformatics. 2012 Mar 23;13:48. doi: 10.1186/1471-2105-13-48.

24.

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B.

Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16.

25.

Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking.

Kihara D, Sael L, Chikhi R, Esquivel-Rodriguez J.

Curr Protein Pept Sci. 2011 Sep;12(6):520-30.

PMID:
21787306
26.

Real-time ligand binding pocket database search using local surface descriptors.

Chikhi R, Sael L, Kihara D.

Proteins. 2010 Jul;78(9):2007-28. doi: 10.1002/prot.22715.

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