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Items: 18

1.

CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts.

Zaharia A, Labedan B, Froidevaux C, Denise A.

BMC Bioinformatics. 2019 Jan 10;20(1):19. doi: 10.1186/s12859-018-2542-2.

2.

Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families.

Reinharz V, Soulé A, Westhof E, Waldispühl J, Denise A.

Nucleic Acids Res. 2018 May 4;46(8):3841-3851. doi: 10.1093/nar/gky197.

3.

GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization.

Boudard M, Barth D, Bernauer J, Denise A, Cohen J.

Bioinformatics. 2017 Aug 15;33(16):2479-2486. doi: 10.1093/bioinformatics/btx175.

PMID:
28398456
4.

GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.

Boudard M, Bernauer J, Barth D, Cohen J, Denise A.

PLoS One. 2015 Aug 27;10(8):e0136444. doi: 10.1371/journal.pone.0136444. eCollection 2015.

5.

A meta-approach for improving the prediction and the functional annotation of ortholog groups.

Pereira C, Denise A, Lespinet O.

BMC Genomics. 2014;15 Suppl 6:S16. doi: 10.1186/1471-2164-15-S6-S16. Epub 2014 Oct 17.

6.

Mechanisms for U2AF to define 3' splice sites and regulate alternative splicing in the human genome.

Shao C, Yang B, Wu T, Huang J, Tang P, Zhou Y, Zhou J, Qiu J, Jiang L, Li H, Chen G, Sun H, Zhang Y, Denise A, Zhang DE, Fu XD.

Nat Struct Mol Biol. 2014 Nov;21(11):997-1005. doi: 10.1038/nsmb.2906. Epub 2014 Oct 19.

7.

An algorithmic game-theory approach for coarse-grain prediction of RNA 3D structure.

Lamiable A, Quessette F, Vial S, Barth D, Denise A.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Jan-Feb;10(1):193-9. doi: 10.1109/TCBB.2012.148.

PMID:
23702555
8.

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.

9.

Automated prediction of three-way junction topological families in RNA secondary structures.

Lamiable A, Barth D, Denise A, Quessette F, Vial S, Westhof E.

Comput Biol Chem. 2012 Apr;37:1-5. doi: 10.1016/j.compbiolchem.2011.11.001. Epub 2012 Jan 11.

PMID:
22326420
10.

Counting RNA pseudoknotted structures.

Saule C, Régnier M, Steyaert JM, Denise A.

J Comput Biol. 2011 Oct;18(10):1339-51. doi: 10.1089/cmb.2010.0086. Epub 2011 May 6.

11.

Regulation of splicing enhancer activities by RNA secondary structures.

Liu W, Zhou Y, Hu Z, Sun T, Denise A, Fu XD, Zhang Y.

FEBS Lett. 2010 Nov 5;584(21):4401-7. doi: 10.1016/j.febslet.2010.09.039. Epub 2010 Oct 1.

12.

Alignments of RNA structures.

Blin G, Denise A, Dulucq S, Herrbach C, Touzet H.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Apr-Jun;7(2):309-22. doi: 10.1109/TCBB.2008.28.

13.

VARNA: Interactive drawing and editing of the RNA secondary structure.

Darty K, Denise A, Ponty Y.

Bioinformatics. 2009 Aug 1;25(15):1974-5. doi: 10.1093/bioinformatics/btp250. Epub 2009 Apr 27.

14.

Automated motif extraction and classification in RNA tertiary structures.

Djelloul M, Denise A.

RNA. 2008 Dec;14(12):2489-97. doi: 10.1261/rna.1061108. Epub 2008 Oct 28.

15.

Adding pyrrolysine to the Escherichia coli genetic code.

Namy O, Zhou Y, Gundllapalli S, Polycarpo CR, Denise A, Rousset JP, Söll D, Ambrogelly A.

FEBS Lett. 2007 Nov 13;581(27):5282-8. Epub 2007 Oct 23.

16.

GenRGenS: software for generating random genomic sequences and structures.

Ponty Y, Termier M, Denise A.

Bioinformatics. 2006 Jun 15;22(12):1534-5. Epub 2006 Mar 30.

PMID:
16574695
17.

A pairwise alignment algorithm which favors clusters of blocks.

Nédélec E, Moncion T, Gassiat E, Bossard B, Duchateau-Nguyen G, Denise A, Termier M.

J Comput Biol. 2005;12(1):33-47.

PMID:
15725732
18.

Towards a computational model for -1 eukaryotic frameshifting sites.

Bekaert M, Bidou L, Denise A, Duchateau-Nguyen G, Forest JP, Froidevaux C, Hatin I, Rousset JP, Termier M.

Bioinformatics. 2003 Feb 12;19(3):327-35.

PMID:
12584117

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