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This page will indicate the publications related to the MIRI project published between Jan. 1st 2009 and June 30th, 2013.

International journals

V. Acuña, A. Marchetti-Spaccamela, M.-F. Sagot, L. Stougie. A note on the complexity of finding and enumerating elementary modes. BioSystems, 99(3):210-214, 2010.

C. Baudet, C. Lemaitre, D. Zanoni, C. Gautier, E. Tannier, M.-F. Sagot. Cassis: precise detection of rearrangement breakpoints, Bioinformatics, 26(15):1897-1898, 2010.

L. Cottret, P.V. Milreu, V. Acuña, A. Marchetti-Spaccamela, L. Stougie, H. Charles, M.-F. Sagot. Graph based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata, PLoS Computational Biology, 6(9):307-316, 2010.

N. Mendes, A.T. Freitas, A.T. Vasconcelos, M.-F. Sagot. Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi, BMC Genomics, 11:529, 2010.

L. Cottret, D. Wildridge, F. Vinson, M.P. Barrett, H. Charles, M.-F. Sagot, F. Jourdan. MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic Acids Research, 2010, 38 (Web Server issue), pp. W132-137

Y.-P. Deniélou, M.-F. Sagot, F. Boyer, A. Viari. Bacterial syntenies: An exact approach with gene quorum, BMC Bioinformatics, 12:193, 2011.

P. Simões, G. Mialdea, D. Reiss, M.-F. Sagot, S. Charlat. Wolbachia detection: An assessment of standard PCR Protocols. Molecular Ecology Resources, 11:567-572, 2011.

A.F. Vellozo, A. Véron, P. Baa-Puyoulet, J. Huerta-Cepas, L. Cottret, G. Febvay, F. Calevro, Y. Rahbé, A.E. Douglas, T. Gabaldon, M.-F. Sagot, H. Charles, S. Colella. CycADS: An annotation database system to ease the development and update of BioCyc databases, Database, in press, 2011.

I. Nor, D. Hermelin, S. Charlat, J. Engelstadter, M. Reuter, O. Duron, M.-F. Sagot. Mod/Resc Parsimony Inference: Theory and application. Inf. Comput., 213: 23-32, 2012.

V. Acuña, E. Birmelé, L. Cottret, P. Crescenzi, F. Jourdan, V. Lacroix, A. Marchetti-Spaccamela, A. Marino, P.V. Milreu, M.-F. Sagot, L. Stougie. Telling Stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets. Theor. Comput. Sci., 457:1-9, 2012.

C.C. Klein, L. Cottret, J. Kielbassa, H. Charles, C. Gautier, A.T.R. Vasconcelos, V. Lacroix, M.-F. Sagot. Exploration of the core metabolism of symbiotic bacteria. BMC Genomics, 13(1):438, 2012.

C. Baudet, Z. Dias, M.-F. Sagot. Sampling solution traces for the problem of sorting permutations by signed reversals. Algorithms for Molecular Biology, 7(1):18, 2012.

N.D. Mendes, S. Heyne, A.T. Freitas, M.-F. Sagot, R. Backofen. Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches. Bioinformatics, 28(23):3034-3041, 2012

V. Acuña, P.V. Milreu, L. Cottret, A. Marchetti-Spaccamela, L. Stougie; M.-F. Sagot. Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks. Bioinformatics, 28(19):2474-2483, 2012.

G. Sacomoto, J. Kielbassa, R. Chikhi, R. Uricaru, P. Antoniou, M.-F. Sagot, P. Peterlongo, V. Lacroix. KisSplice: de-novo calling alternative splicing events from RNA-seq data BMC Bioinformatics, 13(Suppl 6):S5, 2012.

C. Klein, A. Marino, M.-F. Sagot, P.V. Milreu, M. Brilli. Structural and dynamical analysis of biological networks. Briefings in Functional Genomics, 11(6):420-433, 2012.

M. Brilli, P. Liò, V. Lacroix. M.-F. Sagot. Short and long-term genome stability analysis of prokaryotic genomes. BMC Genomics, 14:309, 2013.

I. Nor, J. Engelstädter, O. Duron, M. Reuter, M.-F. Sagot, S. Charlat. On the genetic architecture of cytoplasmic incompatibility: inference from phenotypic data. American Naturalist, 182(1):15-24, 2013.

M. Federico, P. Peterlongo, N. Pisanti, M.-F. Sagot. Rime: Repeat identification Discrete Applied Mathematics, in press, 2013.

M.C.M. Motta, A.C.A Martins, S. Sant'Anna De Souza, C.M.C. Catta-Preta, R. Silva, C.C. Klein, et al. Predicting the proteins of Angomonas deanei, Strigomonas culicis and their respective endosymbionts reveals new aspects of the trypanosomatidae family. PLoS ONE, 8(4):e60209, 2013.

International indexed conferences

Y.-P. Deniélou, F. Boyer, M.-F. Sagot, A. Viari. Multiple alignment of biological networks: A flexible approach. in Combinatorial Pattern Matching 2009, Lecture Notes in Computer Science, volume 5542, pages 173-185, 2009.

I. Nor, D. Hermelin, S. Charlat, J. Engelstadter, M. Reuter, O. Duron, M.-F. Sagot. Mod/Resc Parsimony Inference. in Combinatorial Pattern Matching 2010, Lecture Notes in Computer Science, vol. 6129, pages 202-213, 2010.

P. Milreu, V. Acuña, E. Birmelé, P. Crescenzi, A. Marchetti-Spaccamela, M.-F. Sagot, L. Stougie and V. Lacroix Enumerating chemical organisations in consistent metabolic networks: Complexity and algorithms. WABI'2010, LNBI/LNCS, vol. 6293, pages 226-237, 2010.

P. Peterlongo, N. Schnel, N. Pisanti, M.-F. Sagot, V. Lacroix. Identifying SNPs without a reference genome by comparing raw reads, SPIRE, Lecture Notes in Computer Science, vol. 6393, pp.147-158, 2011.

A. Freire, V. Acuña, P. Crescenzi, C. Ferreira, V. Lacroix, P.V. Milreu, E. Moreno, M.-F. Sagot. Minimum ratio cover of matrix columns by extreme rays of its induced cone. ISCO'12, Lecture Notes in Computer Science, vol. 7422, pages 165-177, 2012.

E. Birmelé, P. Crescenzi, R. Ferreira, R. Grossi, V. Lacroix, A. Marino, N. Pisanti, G. Sacomoto, M.-F. Sagot. Efficient bubble enumeration in directed graphs, SPIRE'2012, Lecture Notes in Computer Science, in press, 2012.

M. Borassi, P. Crescenzi, V. Lacroix, A. Marino. M.-F. Sagot, P. Vieira Milreu. Telling Stories Fast. Symposium Experimental Algorithms (SEA), Lecture Notes in Computer Science, vol. 7933, pages 200-211, 2013.

G.A.T. Sacomoto, V. Lacroix, M.-F. Sagot. A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data. Workshop on Algorithms in Bioinformatics (WABI), LNBI/LNCS in press, 2013.

Workshop without proceedings

V. Acuña, E. Birmelé, L. Cottret, P. Crescenzi, F. Jourdan, V. Lacroix, A. Marchetti-Spaccamela, A. Marino, P. Milreu, M.-F. Sagot, L Stougie. Telling stories. Workshop of ICALP Graph Algorithms and Applications, 2011.

PhD manuscript

V. Acuña. Models and algorithms for metabolic networks: elementary modes and precursor sets. Reviewers: Pierluigi Crescenzi (Univ. Florence, Italy) and Khaled Elbassioni (Max-Planck Saarbrücken, Germany); PhD supervisors: Marie-France Sagot and Christian Gautier.

N. Mendes. Efficient algorithms for the identification of miRNA motifs in DNA sequences, Reviewers: Christine Gaspin (MIA-INRA Toulouse, France) and Ana Maria Pires Parente (Departement Mathematics, Instituto Superior Técnico Lisbon, Portugal); PhD supervisors: Marie-France Sagot and Ana Teresa Freitas (INESC-ID, Lisbon, Portugal).

P. Simões. Génétique et Évolution des interactions Hôtes-Parasites, Reviewers: Claudio Bandi (University of Milan, Italy), Didier Bouchon (Écologie et Biologie des Interactions, CNRS UMR 7267 and University of Poitier, France); PhD Supervisors: Sylvain Charlat (LBBE, UCBL) and Marie-Frane Sagot.

P.V. Milreu. Enumerating Functional Substructures of Genome-Scale Metabolic Networks: Stories, Precursors and Organisations, Reviewers: Joseph J. Heijnen (TU Delft, The Netherlands), Steffen Klamt (Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany), Peter Widmeyer (ETHZ, Switzerland); PhD Supervisors: Christian Gautier, Vincent Lacroix and Marie-France Sagot.


P.V. Milreu, C.C. Klein, L. Cottret, V. Acuña, E. Birmelé, M. Borassi, C. Junot, A. Marchetti-Spaccamela, A. Marino, L. Stougie, F. Jourdan, P. Crescenzi, V. Lacroix, M.-F. Sagot. Telling metabolic stories to explore metabolomics data: A case study on the Yeast response to cadmium exposure.

J.M.P. Alves, C.C. Klein, F.M. da Silva, A.G. Costa-Martins, M.G. Serrano, G.A. Buck, A.T.R. Vasconcelos, M.-F. Sagot, M.M.G. Teixeira, M.C.M. Motta and E.P. Camargo. Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers.

C.C. Klein, J.M.P. Alves, M.G. Serrano, G.A. Buck, A.T.R. Vasconcelos, M.-F. Sagot, M.M.G. Teixeira and E.P. Camargo, M.C.M. Motta. Biosynthesis of vitamins and cofactors in bacterium-harbouring trypanosomatids depends on the symbiotic association as revealed by genomic analyses.

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