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Items: 7

1.

Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data.

Benoit-Pilven C, Marchet C, Chautard E, Lima L, Lambert MP, Sacomoto G, Rey A, Cologne A, Terrone S, Dulaurier L, Claude JB, Bourgeois CF, Auboeuf D, Lacroix V.

Sci Rep. 2018 Mar 9;8(1):4307. doi: 10.1038/s41598-018-21770-7.

2.

Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads.

Lima L, Sinaimeri B, Sacomoto G, Lopez-Maestre H, Marchet C, Miele V, Sagot MF, Lacroix V.

Algorithms Mol Biol. 2017 Feb 22;12:2. doi: 10.1186/s13015-017-0091-2. eCollection 2017.

3.

Colib'read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads.

Le Bras Y, Collin O, Monjeaud C, Lacroix V, Rivals É, Lemaitre C, Miele V, Sacomoto G, Marchet C, Cazaux B, Zine El Aabidine A, Salmela L, Alves-Carvalho S, Andrieux A, Uricaru R, Peterlongo P.

Gigascience. 2016 Feb 11;5:9. doi: 10.1186/s13742-015-0105-2. eCollection 2016.

4.

A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs.

Sacomoto G, Lacroix V, Sagot MF.

Algorithms Mol Biol. 2015 Jun 27;10:20. doi: 10.1186/s13015-015-0046-4. eCollection 2015.

5.

Using cascading Bloom filters to improve the memory usage for de Brujin graphs.

Salikhov K, Sacomoto G, Kucherov G.

Algorithms Mol Biol. 2014 Feb 24;9(1):2. doi: 10.1186/1748-7188-9-2.

6.

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.

7.

Lossless filter for multiple repeats with bounded edit distance.

Peterlongo P, Sacomoto GA, do Lago AP, Pisanti N, Sagot MF.

Algorithms Mol Biol. 2009 Jan 30;4:3. doi: 10.1186/1748-7188-4-3.

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