Bonsai Bioinformatics

2015 [bib]

[1] Maude Pupin, Qassim Esmaeel, Areski Flissi, Yoann Dufresne, Philippe Jacques, and Valérie Leclère. Norine: a powerful resource for novel nonribosomal peptide discovery. Synthetic and Systems Biotechnology, December 2015. [ bib | DOI | http | http ]
[2] Yoann Dufresne, Laurent Noé, Valérie Leclère, and Maude Pupin. Smiles2Monomers: a link between chemical and biological structures for polymers. Journal of Cheminformatics, December 2015. [ bib | DOI | http | http ]
[3] Donald E. K. Martin and Laurent Noé. Faster exact distributions of pattern statistics through sequential elimination of states. Annals of the Institute of Statistical Mathematics, September 2015. [ bib | DOI | http ]
[4] Mihai Pop and Hélène Touzet, editors. Algorithms for bioinformatics, number 9289 in 15th International Workshop, WABI 2015, Atlanta, GA, USA, September 10-12, 2015, Proceedings, Atlanta, United States, September 2015. S. Aluru, Springer Verlag. [ bib | DOI | http ]
[5] Michaela Kotrova, Katerina Muzikova, Ester Mejstrikova, Michaela Novakova, Violeta Bakardjieva-Mihaylova, Karel Fiser, Jan Stuchly, Mathieu Giraud, Mikael Salson, Christiane Pott, Monika Brüggemann, Marc Füllgrabe, Jan Stary, Jan Trka, and Eva Fronkova. The predictive strength of next-generation sequencing MRD detection for relapse compared with current methods in childhood ALL. Blood, 126(8):1045--7, August 2015. [ bib | DOI | http ]
[6] Isabelle Guigon, Sylvain Legrand, Jean-Frédéric Berthelot, Mohcen Benmounah, and Helene Touzet. Finding and analysing microRNAs in plant genomes with miRkwood. In JOBIM 2015, Clermont-Ferrand, France, July 2015. [ bib | http ]
[7] Azadeh Saffarian, Mathieu Giraud, and Hélène Touzet. Modeling alternate RNA structures in genomic sequences. Journal of Computational Biology, 22(3):190--204, February 2015. [ bib | DOI | http ]
[8] Amandine Perrin, Jean-Stéphane Varré, Samuel Blanquart, and Aïda Ouangraoua. ProCARs: Progressive Reconstruction of Ancestral Gene Orders. BMC Genomics, 16(Suppl 5):S6, 2015. [ bib | DOI | http | http ]
[9] Tuan Tu Tran, Mathieu Giraud, and Jean-Stéphane Varré. Perfect Hashing Structures for Parallel Similarity Searches. In International Workshop on High Performance Computational Biology (HiCOMB 2015) / International Parallel and Distributed Processing Symposium (IPDPS 2015), pages 332--341, Hyderabad, India, 2015. [ bib | DOI | http ]
[10] Kristoffer Sahlin, Rayan Chikhi, and Lars Arvestad. Genome scaffolding with PE-contaminated mate-pair libraries. In WABI 2015, Atlanta, United States, 2015. [ bib | DOI | http ]
[11] Areski Flissi, Yoann Dufresne, Juraj Michalik, Laurie Tonon, Stéphane Janot, Laurent Noé, Philippe Jacques, Valérie Leclère, and Maude Pupin. Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing. Nucleic Acids Research, 2015. [ bib | DOI | http | http ]
[12] Evguenia Kopylova, Laurent Noé, Corinne Da Silva, Jean-Frédéric Berthelot, Adriana A. Alberti, Jean-Marc Aury, and Helene Touzet. Deciphering metatranscriptomic data. In Methods in Molecular Biology, volume 1269 of RNA Bioinformatics, pages 279--291. Springer, January 2015. [ bib | DOI | http ]

2014 [bib]

[1] Laurent Noé and Donald E. K. Martin. A Coverage Criterion for Spaced Seeds and Its Applications to Support Vector Machine String Kernels and k-Mer Distances. Journal of Computational Biology, 21(12):28, November 2014. [ bib | DOI | http | http ]
[2] Christophe Vroland, Mikael Salson, and Hélène Touzet. Lossless seeds for searching short patterns with high error rates. In International Workshop On Combinatorial Algorithms, Duluth, United States, October 2014. [ bib | http ]
[3] Amandine Perrin, Jean-Stéphane Varré, Samuel Blanquart, and Aïda Ouangraoua. ProCARs: Progressive Reconstruction of Ancestral Gene Orders. In ISCB-Latin America, Belo Horizonte, Brazil, October 2014. [ bib | http | http ]
[4] Azadeh Saffarian, Mathieu Giraud, and Hélène Touzet. Searching for alternate RNA structures in genomic sequences. In Computational Methods for Structural RNAs, CMSR'14, volume 1 of 1st workshop on Computational Methods for Structural RNAs, pages 13-24, Strasbourg, France, September 2014. [ bib | DOI | http | http ]
[5] Evguenia Kopylova, Laurent Noé, Pierre Pericard, Mikael Salson, and Helene Touzet. SortMeRNA 2: ribosomal RNA classification for taxonomic assignation. In Workshop on Recent Computational Advances in Metagenomics, ECCB 2014, Strasbourg, France, September 2014. [ bib | http ]
[6] Evguenia Kopylova, Laurent Noé, Pierre Pericard, and Helene Touzet. SortMeRNA 2: ribosomal RNA classification for taxonomic assignation . In Bioinformatics for Environmental Genomics, Lyon, France, May 2014. [ bib | http ]
[7] Martin Frith and Laurent Noé. Improved search heuristics find 20 000 new alignments between human and mouse genomes. Nucleic Acids Research, 42(7):e59, February 2014. [ bib | DOI | http ]
[8] Mathieu Giraud, Mikaël Salson, Marc Duez, Céline Villenet, Sabine Quief, Aurélie Caillault, Nathalie Grardel, Christophe Roumier, Claude Preudhomme, and Martin Figeac. Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing. BMC Genomics, 15(1):409, 2014. [ bib | DOI | http | http ]
[9] Robert Giegerich and Hélène Touzet. Modeling Dynamic Programming Problems over Sequences and Trees with Inverse Coupled Rewrite Systems. Algorithms, 7:62 - 144, 2014. [ bib | DOI | http | http ]
[10] Thibault Caradec, Maude Pupin, Aurélien Vanvlassenbroeck, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Philippe Jacques, and Valérie Leclère. Prediction of Monomer Isomery in Florine: A Workflow Dedicated to Nonribosomal Peptide Discovery. PLoS ONE, 9(1):e85667, January 2014. [ bib | DOI | http | http ]
[11] Ammar Abdo, Valérie Leclère, Philippe Jacques, Naomie Salim, and Maude Pupin. Prediction of New Bioactive Molecules using a Bayesian Belief Network. Journal of Chemical Information and Modeling, 54(1):30-36, January 2014. [ bib | DOI | http ]
[12] Bernd Reisinger, Josef Sperl, Alexandra Holinski, Veronika Schmid, Chitra Rajendran, Linn Carstensen, Sandra Schlee, Samuel Blanquart, Rainer Merkl, and Reinhard Sterner. Evidence for the Existence of Elaborate Enzyme Complexes in the Paleoarchean Era. Journal of the American Chemical Society, pages 122-9, January 2014. [ bib | DOI | http | http ]

2013 [bib]

[1] Bernd Reisinger, Josef Sperl, Alexandra Holinski, Veronika Schmid, Chitra Rajendran, Linn Carstensen, Sandra Schlee, Samuel Blanquart, Rainer Merkl, and Reinhard Sterner. Evidence for the existence of elaborate enzyme complexes in the paleoarchean era. Journal of the American Chemical Society, December 2013. [ bib | DOI | http ]
[2] Evguenia Kopylova. Algorithmes bio-informatiques pour l'analyse de données de séquençage à haut débit. These, Université Lille 1, December 2013. [ bib | http | .pdf ]
[3] Maude Pupin. Modèles bio-informatiques pour les peptides non-ribosomiques et leurs synthétases. Hdr, Université Lille 1, December 2013. [ bib | http | .pdf ]
[4] Mathieu Groussin, Bastien Boussau, Sandrine Charles, Samuel Blanquart, and Manolo Gouy. The molecular signal for the adaptation to cold temperature during early life on earth. Biol Lett, 9(5):20130608, October 2013. [ bib | DOI | http | .pdf ]
[5] Mathieu Giraud, Mikaël Salson, Marc Duez, Jean-Stéphane Varré, Céline Villenet, Sabine Quief, Aurélie Caillault, Nathalie Grardel, Christophe Roumier, Claude Preudhomme, and Martin Figeac. Suivi de la leucémie résiduelle par séquençage haut-débit. In JOBIM, Toulouse, France, July 2013. [ bib | http ]
[6] Yoann Dufresne, Valérie Leclère, Philippe Jacques, Laurent Noé, and Maude Pupin. Non Ribosomal Peptides : A monomeric puzz