Publications
1.
Brown JW, Jossinet
F, Kachouri R, Lang F, Leontis NB, Steger G, Stombaugh J, Westhof E. (In
Preparation) RNA
sequence/structure alignments (an RNA Ontology Consortium contribution).
2.
Parisien M, Major F.
(2008) The MC-Fold – MC-Sym pipeline infers RNA structure from
sequence data. Nature 452:51-55. Abstract
3.
Smit S, Rother K,
Heringa J, Knight R. (2008) From
knotted to nested RNA structures: a variety of computational methods for
pseudoknot removal. Rna
4.
Richardson JS,
Schneider B, Murray LW, Kapral GJ, Immormino RM, Headd JJ, Richardson DC, Ham
D, Hershkovits E, Williams LD, Keating KS, Pyle AM, Micallef D, Westbrook J,
Berman HM. (2008) RNA backbone:
Consensus all-angle conformers and modular string nomenclature (an RNA
Ontology Consortium contribution).
Rna Abstract
5.
Sarver M, Zirbel CL,
Stombaugh J, Mokdad A, Leontis NB. (2008) FR3D: finding local and composite
recurrent structural motifs in RNA 3D structure. J Math Biol. Abstract
6.
Smith B, Ashburner
M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A,
Mungall CJ, OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA,
Scheuermann RH, Shah N, Whetzel PL, Lewis S. (2007) The OBO Foundry:
coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25:1251-1255. Abstract
7.
Kim N, Shin JS,
Elmetwaly S, Gan HH, Schlick T. (2007) RagPools: RNA-As-Graph-Pools—a
web server for assisting the design of structured RNA pools for in vitro
selection. Bioinformatics 23:2959-2960.
Abstract
8.
Lisi V, Major F.
(2007) A comparative analysis of the triloops in all high-resolution RNA
structures reveals sequence structure relationships. Rna 13:1537-1545. Abstract
9.
Laederach A. (2007) Informatics
challenges in structured RNA. Brief
Bioinform. 8:294-303. Abstract
10.
Jossinet F, Ludwig
TE, Westhof E. (2007) RNA structure: bioinformatic analysis. Curr Opin Microbiol. 10:279-285. Abstract
11.
Hamman C, Westhof E.
(2007) Searching genomes for ribozymes and riboswitches. Genome Biol. 8:210. Abstract
12.
Laederach A, Chan
JM, Schwartzman A, Willgohs E, Altman RB. (2007) Co-planar and Co-axial
orientations of RNA bases and helices.
Rna 13:643-650. Abstract
13.
Kim N, Gan HH,
Schlick T. (2007) A computational proposal for designing structured RNA
pools for in vitro selection of RNAs.
Rna 13:478:492. Abstract
14.
Leontis NB, Altman
RB, Berman HM, Brenner SE, Brown JW, Engelke DR, Harvey SC, Holbrook SR,
Jossinet F, Lewis SE, Major F, Mathews DH, Richardson JS, Williamson JR,
Westhof E. (2006) The RNA Ontology Consortium: an open invitation to the RNA
community. Rna 12:533-541. Abstract
15.
St-Onge K, Thibault
P, Hamel S, Major F. (2007) Modeling RNA tertiary structure motifs by
graph-grammars. Nucleic Acids Res.
35:1726-1736. Abstract
16.
Marck C,
Kachouri-Lafond R, Lafontaine I, Westhof E, Dujon B, Grosjean H. (2006) The
RNA polymerase III-dependent family of genes in hemiascomycetes: comparative
RNomics, decoding strategies, transcription and evolutionary implications. Nucleic Acids Res. 34:1816-1835. Abstract