A local transcriptome assembler for SNPs, indels and AS events

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, 2016.

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

Application of KisSplice in pathological contexts:

Audric Cologne, Clara Benoit-Pilven, Alicia Besson, Audrey Putoux, Amandine Campan-Fournier, Michael B Bober, Christine EM De Die-Smulders, Aimee DC Paulussen, Lucile Pinson, Annick Toutain, Chaim M Roifman, Anne-Louise Leutenegger, Sylvie Mazoyer, Patrick Edery, Vincent Lacroix
New insights into minor splicing—a transcriptomic analysis of cells derived from TALS patients
RNA, vol 25, 9, 2019

Usama Ashraf, Clara Benoit-Pilven, Vincent Navratil, Cécile Ligneau, Guillaume Fournier, Sandie Munier, Odile Sismeiro, Jean-Yves Coppée, Vincent Lacroix, Nadia Naffakh
Influenza virus infection induces widespread alterations of host cell splicing
NAR Genomics and Bioinformatics, vol 2, 4, 2020

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>