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Items: 18

1.

SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups.

Jammali S, Aguilar JD, Kuitche E, Ouangraoua A.

BMC Bioinformatics. 2019 Mar 29;20(Suppl 3):133. doi: 10.1186/s12859-019-2647-2.

2.

OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes.

Brunet MA, Brunelle M, Lucier JF, Delcourt V, Levesque M, Grenier F, Samandi S, Leblanc S, Aguilar JD, Dufour P, Jacques JF, Fournier I, Ouangraoua A, Scott MS, Boisvert FM, Roucou X.

Nucleic Acids Res. 2019 Jan 8;47(D1):D403-D410. doi: 10.1093/nar/gky936.

3.

aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences.

Glouzon JS, Ouangraoua A.

Bioinformatics. 2018 Jul 1;34(13):i70-i78. doi: 10.1093/bioinformatics/bty234.

4.

Reconstructing protein and gene phylogenies using reconciliation and soft-clustering.

Kuitche E, Lafond M, Ouangraoua A.

J Bioinform Comput Biol. 2017 Dec;15(6):1740007. doi: 10.1142/S0219720017400078. Epub 2017 Oct 19.

PMID:
29169277
5.

Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins.

Samandi S, Roy AV, Delcourt V, Lucier JF, Gagnon J, Beaudoin MC, Vanderperre B, Breton MA, Motard J, Jacques JF, Brunelle M, Gagnon-Arsenault I, Fournier I, Ouangraoua A, Hunting DJ, Cohen AA, Landry CR, Scott MS, Roucou X.

Elife. 2017 Oct 30;6. pii: e27860. doi: 10.7554/eLife.27860.

6.

Gene Tree Construction and Correction Using SuperTree and Reconciliation.

Lafond M, Chauve C, El-Mabrouk N, Ouangraoua A.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Sep-Oct;15(5):1560-1570. doi: 10.1109/TCBB.2017.2720581. Epub 2017 Jun 27.

PMID:
28678712
7.

Aligning coding sequences with frameshift extension penalties.

Jammali S, Kuitche E, Rachati A, Bélanger F, Scott M, Ouangraoua A.

Algorithms Mol Biol. 2017 Mar 31;12:10. doi: 10.1186/s13015-017-0101-4. eCollection 2017.

8.

The SCJ Small Parsimony Problem for Weighted Gene Adjacencies.

Luhmann N, Lafond M, Thevenin A, Ouangraoua A, Wittler R, Chauve C.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Jan 31. doi: 10.1109/TCBB.2017.2661761. [Epub ahead of print]

PMID:
28166504
9.

Reconstructing a SuperGeneTree minimizing reconciliation.

Lafond M, Ouangraoua A, El-Mabrouk N.

BMC Bioinformatics. 2015;16 Suppl 14:S4. doi: 10.1186/1471-2105-16-S14-S4. Epub 2015 Oct 2.

10.

ProCARs: Progressive Reconstruction of Ancestral Gene Orders.

Perrin A, Varré JS, Blanquart S, Ouangraoua A.

BMC Genomics. 2015;16 Suppl 5:S6. doi: 10.1186/1471-2164-16-S5-S6. Epub 2015 May 26.

11.

On the identification of conflicting contiguities in ancestral genome reconstruction.

Ouangraoua A, Raffinot M.

J Comput Biol. 2014 Jan;21(1):64-79. doi: 10.1089/cmb.2013.0086. Epub 2013 Oct 9.

PMID:
24106802
12.

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms.

Allali J, Saule C, Chauve C, d'Aubenton-Carafa Y, Denise A, Drevet C, Ferraro P, Gautheret D, Herrbach C, Leclerc F, de Monte A, Ouangraoua A, Sagot MF, Termier M, Thermes C, Touzet H.

Adv Bioinformatics. 2012;2012:893048. doi: 10.1155/2012/893048. Epub 2012 May 23.

13.

Genome dedoubling by DCJ and reversal.

Thomas A, Varré JS, Ouangraoua A.

BMC Bioinformatics. 2011 Oct 5;12 Suppl 9:S20. doi: 10.1186/1471-2105-12-S9-S20.

14.

Theory and practice of ultra-perfection.

Ouangraoua A, Bergeron A, Swenson KM.

J Comput Biol. 2011 Sep;18(9):1219-30. doi: 10.1089/cmb.2011.0086.

PMID:
21899427
15.

A 2-approximation for the minimum duplication speciation problem.

Ouangraoua A, Swenson KM, Chauve C.

J Comput Biol. 2011 Sep;18(9):1041-53. doi: 10.1089/cmb.2011.0108.

PMID:
21899414
16.

Reconstructing the architecture of the ancestral amniote genome.

Ouangraoua A, Tannier E, Chauve C.

Bioinformatics. 2011 Oct 1;27(19):2664-71. doi: 10.1093/bioinformatics/btr461. Epub 2011 Aug 16.

PMID:
21846735
17.

Combinatorial structure of genome rearrangements scenarios.

Ouangraoua A, Bergeron A.

J Comput Biol. 2010 Sep;17(9):1129-44. doi: 10.1089/cmb.2010.0126.

PMID:
20874400
18.

Yeast ancestral genome reconstructions: the possibilities of computational methods II.

Chauve C, Gavranovic H, Ouangraoua A, Tannier E.

J Comput Biol. 2010 Sep;17(9):1097-112. doi: 10.1089/cmb.2010.0092.

PMID:
20874398

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