First KisSplice publication:
Gustavo AT Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo and Vincent Lacroix KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.
BMC Bioinformatics 2012, 13(Suppl 6):S5
KisSplice Workflows and Applications to SNPs and AS
Helene Lopez-Maestre, Lilia Brinza, Camille Marchet, Janice Kielbassa, Sylvere Bastien, Mathilde Boutigny, David Monnin, Adil El Filali, Claudia Marcia Carareto, Cristina Vieira, Franck Picard, Natacha Kremer, Fabrice Vavre, Marie-France Sagot, Vincent Lacroix SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence Nucleic Acids Research, vol. 44 pp.1-13.
Clara Benoit-Pilven, Camille Marchet, Emilie Chautard, Leandro Lima, Marie-Pierre Lambert, Gustavo Sacomoto, Amandine Rey, Audric Cologne, Sophie Terrone, Louis Dulaurier, Jean-Baptiste Claude, Cyril F. Bourgeois, Didier Auboeuf, Vincent Lacroix Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data Scientific Reports, 8, Article Number: 4307 (2018)
Improvements of methods in KisSplice:
Etienne Birmele, Pierluigi Crescenzi, Rui Ferreira, Roberto Grossi, Vincent Lacroix, Andrea Marino, Nadia Pisanti, Gustavo AT Sacomoto and Marie-France Sagot, Efficient bubble enumeration in directed graphs.
Proceedings of 19th Conference on String Processing and Information Retrieval (SPIRE) 2012, Springer LNCS 7608, pages 118-129, 2012.
Gustavo AT Sacomoto, Vincent Lacroix and Marie-France Sagot A Polynomial Delay Algorithm for the Enumeration of Bubbles with Length Constraints in Directed Graphs, Algorithms for Molecular Biology, 10:20, 2015
Gustavo AT Sacomoto, Blerina Sinaimeri, Camille Marchet, Vincent Miele, Marie-France Sagot and Vincent Lacroix Navigating in a sea of repeats in RNA-seq without drowning Proceedings of 14th Workshop on Algorithms in Bioinformatics (WABI) 2014, Springer LNCS 8701, pages 82-96, 2014
Leandro Lima, Blerina Sinaimeri, Gustavo Sacomoto, Helene Lopez-Maestre, Camille Marchet, Vincent Miele, Marie-France Sagot and Vincent Lacroix. Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads. Algorithms for Molecular Biology, 2017, 12 (1), pp.2. <10.1186/s13015-017-0091-2>