Tristan Braquelaire, Marie Gasparoux, Mathieu Raffinot and Raluca Uricaru, On the Shortest Common Superstring of NGS Reads TAMC 2017
2016
Justine Rudewicz, Hayssam Soueidan, Raluca Uricaru, Hervé Bonnefoi, Richard Iggo, Jonas Bergh and Macha Nikolski, ‘’MICADo – looking for mutations in targeted PacBio cancer data: an alignment-free method.’’ Frontiers in genetics, vol. 7, p. 214, 2016.
Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Eric Rivals, Claire Lemaitre, Vincent Miele, Gustavo Sacomoto, Camille Marchet, Bastien Cazaux, Amal Zine El Aabidine, Leena Salmela, Susete Alves-Carvalho, Alexan Andrieux, Raluca Uricaru and Pierre Peterlongo, Colib'read on Galaxy: A tools suite dedicated to biological information extraction from raw NGS reads GigaScience Journal, doi:10.1186/s13742-015-0105-2, 2016
2015
Gaëtan Benoit, Claire Lemaitre, Dominique Lavenier, Erwan Drezen, Thibault Dayris, Raluca Uricaru and Guillaume Rizk, Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph BMC Bioinformatics Journal, doi:10.1186/s12859-015-0709-7, 2015
Gaëtan Benoit, Claire Lemaitre, Dominique Lavenier, Erwan Drezen, Thibault Dayris, Raluca Uricaru and Guillaume Rizk, Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph WABI 2015
Raluca Uricaru, Célia Michotey, Hélène Chiapello and Eric Rivals, YOC, a new strategy for pairwise alignment of collinear genomes BMC Bioinformatics Journal, doi:10.1186/s12859-015-0530-3, 2015
2014
Patricia Thébault, Romain Bourqui, William Benchimol, Christine Gaspin, Pascal Sirand-Pugnet, Raluca Uricaru and Isabelle Dutour, Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks Briefings in Bioinformatics Journal, doi:10.1093/bib/bbu045, 2014
Raluca Uricaru, Guillaume Rizk, Vincent Lacroix, Elsa Quillery, Olivier Plantard, Rayan Chikhi, Claire Lemaitre and Pierre Peterlongo, Reference-free detection of isolated SNPs Nucleic Acids Research Journal, doi:10.1093/nar/gku1187, 2014
2012
Gustavo Akio Sacamoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo, Vincent Lacroix, KisSplice: de-novo calling alternative splicing events from RNA-seq data BMC Bioinformatics Journal, vol. 13, suppl. 6, 2012
2011
Raluca Uricaru, Alban Mancheron, Eric Rivals, Novel definition and algorithm for chaining fragments with proportional overlaps (paper) Journal of Computational Biology, vol. 18, no. 9, pages 1141-1154, 2011
Alban Mancheron, Raluca Uricaru, Eric Rivals, An alternative approach to multiple genome comparison Nucleic Acids Research Journal, vol. 39, no. 15, pages e101, doi:10.1093/nar/gkr177, 2011
2010
Raluca Uricaru, Algorithmes de comparaison de génomes appliqués aux génomes bactériens (manuscript) PhD manuscript
Raluca Uricaru, Alban Mancheron, Eric Rivals, Novel definition and algorithm for chaining fragments with proportional overlaps (paper) Proceedings of the 8th RECOMB Comparative Genomics, 2010, pages 161-172
Eric Rivals, Alban Mancheron, Raluca Uricaru, Reliable bacterial genome comparison tools (paper) ERCIM News, 2010, Vol. 82, pages 17–18
2009
Raluca Uricaru, Célia Michotey, Laurent Noé, Hélène Chiapello, Eric Rivals, Improved sensitivity and reliability of anchor based genome alignment JOBIM Conference, 2009, Nantes (website)
2007
Raluca Uricaru, Laurent Bréhélin, Eric Rivals, A new type of Hidden Markov Models to predict complex domain architecture in protein sequences (paper) JOBIM Conference, 2007, Marseille (website)
2006
Raluca Uricaru, Laurent Bréhélin, Eric Rivals, A new type of Hidden Markov Models to predict complex motif organization in protein sequences (abstract) Poster, Integrative Post Genomics (IPG), 2006, Lyon (website)
Raluca Uricaru, Hidden Markov Models for the Detection of Motif Repeats in Protein Sequences (report) Master Thesis, École Normale Supérieure of Lyon
2005
Raluca Uricaru, Liviu Ciortuz, Genic Interaction Extraction from Medline Abstracts - A Case Study (report) Scientific Annals of Cuza University
Slides for scientific talks and ANR project meetings
Raluca Uricaru, Algorithmes de comparaison de génomes appliqués aux génomes bactériens (slides) PhD defence, 2010, Montpellier
Raluca Uricaru, Novel definition and algorithm for chaining fragments with proportional overlaps (slides) RECOMB Comparative Genomics Conference, 2010, Ottawa (website)
Raluca Uricaru, New method for improved sensitivity and reliability of anchor based genome alignment (slides) ALPHY-GTGC Workshop, 2010, Marseille
Raluca Uricaru, Trapezoid graphs, independent sets, and whole genome comparisons (slides) JGA 2009 and GTSEQ 2010 Workshops
Raluca Uricaru, Improved sensitivity and reliability of anchor based genome alignment (slides) JOBIM Conference, 2009, Nantes (website)
Raluca Uricaru, Accuracy of the anchor-based strategy for genome alignment (slides) ANR projects PlasmoExplore and CoCoGEN meetings, 2008
Raluca Uricaru, A new type of Hidden Markov Models to predict complex domain architecture in protein sequences (slides) JOBIM Conference, 2007, Marseille (website)
Raluca Uricaru, Un nouveau type de Modèles de Markov Cachés (MMC) capables de prédire des architectures de domaines complexes dans les séquences protéiques. Applications à l’agent de la malaria (slides) ANR project PlasmoExplore meeting, 2007, Paris