Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

• 1A. Julien-Laferrière.
  
  Models and algorithms applied to metabolism: From revealing the responses to perturbations towards the design of microbial consortia , Université Lyon 1 - Claude Bernard, December 2016.
  
  https://hal.inria.fr/tel-01394113
• 2M. Wannagat.
  
  Study of the evolution of symbiosis at the metabolic level using models from game theory and economics, Université de Lyon, July 2016.
  
  https://hal.inria.fr/tel-01394107

Articles in International Peer-Reviewed Journals

• 3R. Andrade, M. Wannagat, C. C. Klein, V. Acuña, A. Marchetti-Spaccamela, P. V. Milreu, L. Stougie, M.-F. Sagot.
  
  Enumeration of minimal stoichiometric precursor sets in metabolic networks, in: Algorithms for Molecular Biology, December 2016, vol. 11, n^o 1, 25 p. [ DOI : 10.1186/s13015-016-0087-3 ]
  
  https://hal.inria.fr/hal-01368653
• 4P. Baa-Puyoulet, N. Parisot, G. Febvay, J. Huerta-Cepas, A. F. Vellozo, T. Gabaldon, F. Calevro, H. Charles, S. Colella.
  
  ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods, in: Database - The journal of Biological Databases and Curation, 2016. [ DOI : 10.1093/database/baw081 ]
  
  https://hal.inria.fr/hal-01352558
• 5P. Bonizzoni, R. Dondi, G. W. Klau, Y. Pirola, N. Pisanti, S. Zaccaria.
  
  On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes, in: Journal of Computational Biology, 2016, vol. 23, n^o 9, pp. 718 - 736. [ DOI : 10.1089/cmb.2015.0220 ]
  
  https://hal.inria.fr/hal-01388448
• 6M. Borassi, P. Crescenzi, M. Habib.
  
  Into the Square: On the Complexity of Some Quadratic-time Solvable Problems, in: Electronic Notes in Theoretical Computer Science, 2016, vol. 322, pp. 51-67. [ DOI : 10.1016/j.entcs.2016.03.005 ]
  
  https://hal.inria.fr/hal-01390131
• 7T. Calamoneri, B. Sinaimeri.
  
  Pairwise Compatibility Graphs: A Survey, in: SIAM Review, 2016, vol. 58, n^o 3, pp. 445 - 460. [ DOI : 10.1137/140978053 ]
  
  https://hal.inria.fr/hal-01388533
• 8S. Canzar, S. Andreotti, D. W. Weese, K. Reinert, G. W. Klau.
  
  CIDANE: comprehensive isoform discovery and abundance estimation, in: Genome Biology, 2016, vol. 17, 16 p. [ DOI : 10.1186/s13059-015-0865-0 ]
  
  https://hal.inria.fr/hal-01397539
• 9A. Clementi, P. Crescenzi, C. Doerr, P. Fraigniaud, F. Pasquale, R. Silvestri.
  
  Rumor Spreading in Random Evolving Graphs, in: Random Structures and Algorithms, March 2016, vol. 48, n^o 2, pp. 290-312. [ DOI : 10.1002/rsa.20586 ]
  
  https://hal.inria.fr/hal-01390133
• 10P. Crescenzi, G. D'Angelo, L. Severini, Y. Velaj.
  
  Greedily Improving Our Own Closeness Centrality in a Network, in: ACM Transactions on Knowledge Discovery from Data (TKDD), August 2016, vol. 11, n^o 1, pp. 1-32. [ DOI : 10.1145/2953882 ]
  
  https://hal.inria.fr/hal-01390134
• 11M. Crochemore, C. Epifanio, R. Grossi, F. Mignosi.
  
  Linear-size suffix tries, in: Theoretical Computer Science, 2016, vol. 638, pp. 171 - 178. [ DOI : 10.1016/j.tcs.2016.04.002 ]
  
  https://hal.inria.fr/hal-01388452
• 12A. Ferrari, V. Vincent-Salomon, X. Pivot, A.-S. Sertier, T. Thomas, L. Tonon, S. Boyault, E. Mulugeta, I. Treilleux, G. Macgrogan, L. Arnould, J. Kielbassa, V. Le Texier, H. Blanché, J.-F. Deleuze, J. Jacquemier, M.-C. Mathieu, F. Penault-Llorca, F. Bibeau, M. Mariani, C. Mannina, J.-Y. Pierga, O. Trédan, H. Bonnefoi, G. Romieu, P. Fumoleau, S. Delaloge, M. Rios, J.-M. Ferrero, C. Tarpin, C. Bouteille, F. Calvo, I. G. Gut, M. Gut, S. Martin, S. Nik-Zainal, M. R. Stratton, I. Pauporté, P. Saintigny, D. Birnbaum, A. Viari, G. Thomas.
  
  A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers, in: Nature Communications, 2016, vol. 7. [ DOI : 10.1038/ncomms12222 ]
  
  https://hal.inria.fr/hal-01388446
• 13M. G. Ferrarini, F. M. Siqueira, S. G. Mucha, T. L. Palama, É. Jobard, B. Elena-Herrmann, A. T. Ribeiro de Vasconcelos, F. Tardy, I. S. Schrank, A. Zaha, M.-F. Sagot.
  
  Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling, in: BMC Genomics, December 2016, vol. 17, n^o 1, 353 p. [ DOI : 10.1186/s12864-016-2644-z ]
  
  https://hal.inria.fr/hal-01315893
• 14F. Freyermuth, F. Rau, Y. Kokunai, T. Linke, C. Sellier, M. Nakamori, Y. Kino, L. Arandel, A. Jollet, C. Thibault, M. Philipps, S. Vicaire, B. Jost, B. Udd, J. W. Day, D. Duboc, K. Wahbi, T. Matsumura, H. Fujimura, H. Mochizuki, F. Deryckere, T. Kimura, N. Nukina, S. Ishiura, V. Lacroix, A. Campan-Fournier, V. Navratil, E. Chautard, D. Auboeuf, M. Horie, K. Imoto, K.-Y. Lee, M. S. Swanson, A. L. de Munain, S. Inada, H. Itoh, K. Nakazawa, T. Ashihara, E. Wang, T. Zimmer, D. Furling, M. P. Takahashi, N. Charlet-Berguerand.
  
  Splicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy, in: Nature Communications, 2016, vol. 7. [ DOI : 10.1038/ncomms11067 ]
  
  https://hal.inria.fr/hal-01388496
• 15R. Grossi, C. S. Iliopoulos, R. Mercas, N. Pisanti, S. P. Pissis, A. Retha, F. Vayani.
  
  Circular sequence comparison: algorithms and applications, in: Algorithms for Molecular Biology, 2016, vol. 11, n^o 1. [ DOI : 10.1186/s13015-016-0076-6 ]
  
  https://hal.inria.fr/hal-01388449
• 16A. Julien-Laferrière, L. Bulteau, D. Parrot, A. Marchetti-Spaccamela, L. Stougie, S. Vinga, A. Mary, M.-F. Sagot.
  
  A Combinatorial Algorithm for Microbial Consortia Synthetic Design, in: Scientific Reports, July 2016. [ DOI : 10.1038/srep29182 ]
  
  https://hal.archives-ouvertes.fr/hal-01344296
• 17Y. Le Bras, O. Collin, C. MONJEAUD, V. Lacroix, E. Rivals, C. Lemaitre, V. Miele, G. Sacomoto, C. Marchet, B. Cazaux, A. Zine El Aabidine, L. Salmela, S. Alves-Carvalho, A. Andrieux, R. Uricaru, P. Peterlongo.
  
  Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads, in: GigaScience, February 2016, vol. 5, n^o 1. [ DOI : 10.1186/s13742-015-0105-2 ]
  
  https://hal.inria.fr/hal-01280238
• 18H. Lopez-Maestre, L. Brinza, C. Marchet, J. Kielbassa, S. Bastien, M. Boutigny, D. Monnin, A. El Filali, C. M. Carareto, C. Vieira, F. Picard, N. Kremer, F. Vavre, M.-F. Sagot, V. Lacroix.
  
  SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence, in: Nucleic Acids Research, 2016. [ DOI : 10.1093/nar/gkw655 ]
  
  https://hal.inria.fr/hal-01352586
• 19T. Marschall, M. Marz, T. Abeel, L. Dijkstra, B. E. Dutilh, A. Ghaffaari, P. Kersey, W. P. Kloosterman, V. Makinen, A. M. Novak, B. Paten, D. Porubsky, E. Rivals, C. Alkan, J. A. Baaijens, P. I. W. D. Bakker, V. Boeva, R. J. P. Bonnal, F. Chiaromonte, R. Chikhi, F. D. Ciccarelli, R. Cijvat, E. Datema, C. M. V. Duijn, E. E. Eichler, C. Ernst, E. Eskin, E. Garrison, M. El-Kebir, G. W. Klau, J. O. Korbel, E.-W. Lameijer, B. Langmead, M. Martin, P. Medvedev, J. C. Mu, P. Neerincx, K. Ouwens, P. Peterlongo, N. Pisanti, S. Rahmann, B. Raphael, K. Reinert, D. d. Ridder, J. d. Ridder, M. Schlesner, O. Schulz-Trieglaff, A. D. Sanders, S. Sheikhizadeh, C. Shneider, S. Smit, D. Valenzuela, J. Wang, L. Wessels, Y. Zhang, V. Guryev, F. Vandin, K. Ye, A. Schönhuth.
  
  Computational pan-genomics: status, promises and challenges, in: Briefings in Bioinformatics, October 2016. [ DOI : 10.1093/bib/bbw089 ]
  
  https://hal.inria.fr/hal-01390478
• 20A. May, B. W. Brandt, M. El-Kebir, G. W. Klau, E. Zaura, W. Crielaard, J. Heringa, S. Abeln.
  
  metaModules identifies key functional subnetworks in microbiome-related disease, in: Bioinformatics, 2016, vol. 32, n^o 11, pp. 1678 - 1685. [ DOI : 10.1093/bioinformatics/btv526 ]
  
  https://hal.inria.fr/hal-01388508
• 21S. Nik-Zainal, H. R. Davies, J. Staaf, M. Ramakrishna, D. Glodzik, X. Zou, I. Martincorena, L. B. Alexandrov, S. Martin, D. C. Wedge, P. Van Loo, Y. S. Ju, M. Smid, A. B. Brinkman, S. Morganella, M. R. Aure, O. C. Lingjærde, A. Langerød, M. Ringnér, S.-M. Ahn, S. Boyault, J. E. Brock, A. Broeks, A. Butler, C. Desmedt, L. Dirix, S. Dronov, A. Fatima, J. A. Foekens, M. Gerstung, G. K. J. Hooijer, S. J. Jang, D. R. Jones, H.-Y. Kim, T. A. King, S. Krishnamurthy, H. J. Lee, J.-Y. Lee, Y. Li, S. Mclaren, A. Menzies, V. Mustonen, S. O’Meara, I. Pauporté, X. Pivot, C. A. Purdie, K. Raine, K. Ramakrishnan, F. G. Rodríguez-González, G. Romieu, A. M. Sieuwerts, P. Simpson, R. Shepherd, L. Stebbings, O. A. Stefansson, J. Teague, S. Tommasi, I. Treilleux, G. G. Van den Eynden, P. Vermeulen, A. Vincent-Salomon, L. Yates, C. Caldas, L. v. Veer, A. Tutt, S. Knappskog, B. K. T. Tan, J. Jonkers, Å. Borg, N. T. Ueno, C. Sotiriou, A. Viari, P. A. Futreal, P. J. Campbell, P. N. Span, S. Van Laere, S. R. Lakhani, J. E. Eyfjord, A. M. Thompson, E. Birney, H. G. Stunnenberg, M. J. Van De Vijver, J. W. M. Martens, A.-L. Børresen-Dale, A. L. Richardson, G. Kong, G. Thomas, M. R. Stratton.
  
  Landscape of somatic mutations in 560 breast cancer whole-genome sequences, in: Nature, 2016, vol. 534, n^o 7605, pp. 47 - 54. [ DOI : 10.1038/nature17676 ]
  
  https://hal.inria.fr/hal-01388447
• 22Y. Pirola, S. Zaccaria, R. Dondi, G. W. Klau, N. Pisanti, P. Bonizzoni.
  
  HapCol: accurate and memory-efficient haplotype assembly from long reads, in: Bioinformatics, 2016. [ DOI : 10.1093/bioinformatics/btv495 ]
  
  https://hal.inria.fr/hal-01225984
• 23G. Rodrigues Galvao, C. Baudet, Z. Dias.
  
  Sorting Circular Permutations by Super Short Reversals, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, January 2016. [ DOI : 10.1109/TCBB.2016.2515594 ]
  
  https://hal.inria.fr/hal-01317003
• 24V. Romero-Soriano, N. Burlet, D. Vela, A. Fontdevila, C. Vieira, M. P. Garciá Guerreiro.
  
  Drosophila Females Undergo Genome Expansion after Interspecific Hybridization, in: Genome Biology and Evolution, February 2016, vol. 8, n^o 3, pp. 556-561. [ DOI : 10.1093/gbe/evw024 ]
  
  https://hal.inria.fr/hal-01352572
• 25P. Simonet, G. Duport, K. Gaget, M. Weiss-Gayet, S. Colella, G. Febvay, H. Charles, J. Viñuelas, A. Heddi, F. Calevro.
  
  Direct flow cytometry measurements reveal a fine-tuning of symbiotic cell dynamics according to the host developmental needs in aphid symbiosis, in: Scientific Reports, 2016, vol. 6, 19967 p. [ DOI : 10.1038/srep19967 ]
  
  https://hal.inria.fr/hal-01352561
• 26P. Simonet, K. Gaget, N. Parisot, G. Duport, M. Rey, G. Febvay, H. Charles, P. Callaerts, S. Colella, F. Calevro.
  
  Disruption of phenylalanine hydroxylase reduces adult lifespan and fecundity, and impairs embryonic development in parthenogenetic pea aphids, in: Scientific Reports, 2016, vol. 6. [ DOI : 10.1038/srep34321 ]
  
  https://hal.inria.fr/hal-01388523
• 27F. M. Siqueira, G. Loss de Morais, S. Higashi, L. Scherer Beier, G. Merker Breyer, C. Padoan De Sá Godinho, M.-F. Sagot, I. Silveira Schrank, A. Zaha, A. T. Ribeiro de Vasconcelos.
  
  Mycoplasma non-coding RNA: identification of small RNAs and targets, in: BMC Genomics, 2016, vol. 23, pp. 1289 - 26. [ DOI : 10.1186/s12864-016-3061-z ]
  
  https://hal.inria.fr/hal-01393122
• 28M. Smid, F. G. Rodríguez-González, A. M. Sieuwerts, R. Salgado, W. J. C. Prager-Van der Smissen, M. v. d. Vlugt-Daane, A. van Galen, S. Nik-Zainal, J. Staaf, A. B. Brinkman, M. J. Van De Vijver, A. L. Richardson, A. Fatima, K. Berentsen, A. Butler, S. Martin, H. R. Davies, R. Debets, M. E. M.-V. Gelder, C. H. M. van Deurzen, G. Macgrogan, G. G. G. M. Van den Eynden, C. Purdie, A. M. Thompson, C. Caldas, P. N. Span, P. T. Simpson, S. R. Lakhani, S. Van Laere, C. Desmedt, M. Ringnér, S. Tommasi, J. Eyford, A. Broeks, A. Vincent-Salomon, P. A. Futreal, S. Knappskog, T. A. King, G. Thomas, A. Viari, A. Langerød, A.-L. Børresen-Dale, E. Birney, H. G. Stunnenberg, M. Stratton, J. A. Foekens, J. W. M. Martens.
  
  Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration, in: Nature Communications, 2016, vol. 7. [ DOI : 10.1038/ncomms12910 ]
  
  https://hal.inria.fr/hal-01388445
• 29L. Urbini, C. Matias, M.-F. Sagot, B. Sinaimeri.
  
  Robustness of the Parsimonious Reconciliation Method in Cophylogeny, in: Springer - Lecture Notes in Computer Science (LNCS), June 2016, vol. 9702, 12 p. [ DOI : 10.1007/978-3-319-38827-4_10 ]
  
  https://hal.inria.fr/hal-01349773
• 30A. Veríssimo, A. L. Oliveira, M.-F. Sagot, S. Vinga.
  
  DegreeCox – a network-based regularization method for survival analysis, in: BMC Bioinformatics, December 2016, vol. 17, n^o Suppl 16, pp. 109-121. [ DOI : 10.1186/s12859-016-1310-4 ]
  
  https://hal.inria.fr/hal-01415968

International Conferences with Proceedings

• 31E. Bergamini, M. Borassi, P. Crescenzi, A. Marino, H. Meyerhenke.
  
  Computing Top-k Closeness Centrality Faster in Unweighted Graphs, in: Eighteenth Workshop on Algorithm Engineering and Experiments, ALENEX 2016, Arlington, United States, 2016. [ DOI : 10.1137/1.9781611974317.6 ]
  
  https://hal.inria.fr/hal-01390137
• 32V. Bonifaci, B. Brandenburg, G. D'Angelo, A. Marchetti-Spaccamela.
  
  Multiprocessor Real-Time Scheduling with Hierarchical Processor Affinities, in: 28th Euromicro Conference on Real-Time Systems, ECRTS 2016, Toulouse, France, IEEE Computer Society, July 2016, pp. 237-247. [ DOI : 10.1109/ECRTS.2016.24 ]
  
  https://hal.inria.fr/hal-01397807
• 33R. Bruni, A. Marchetti-Spaccamela, S. K. Baruah, V. Bonifaci.
  
  ILP-Based Approaches to Partitioning Recurrent Workloads Upon Heterogeneous Multiprocessors ILP-based approaches to partitioning recurrent workloads upon heterogeneous multiprocessors, in: 28th Euromicro Conference on Real-Time Systems, ECRTS 2016, Toulouse, France, IEEE Computer Society, July 2016, pp. 215-225. [ DOI : 10.1109/ECRTS.2016.10 ]
  
  https://hal.inria.fr/hal-01397810
• 34K. Böhmová, M. Mihalák, T. Pröger, G. Sacomoto, M.-F. Sagot, P. Widmayer.
  
  Computing and Listing st-Paths in Subway Networks, in: CSR 2016 - 11th International Computer Science Symposium in Russia, St. Petersburg, Russia, A. S. Kulikov, G. J. Woeginger (editors), Lecture Notes in Computer Science, Springer, June 2016, vol. 9691, pp. 102-116. [ DOI : 10.1007/978-3-319-34171-2_8 ]
  
  https://hal.inria.fr/hal-01348869
• 35T. Calamoneri, M. Gastaldello, A. Mary, B. Sinaimeri, M.-F. Sagot.
  
  On Maximal Chain Subgraphs and Covers of Bipartite Graphs, in: Combinatorial Algorithms - 27th International Workshop, IWOCA 2016, Helsinki, Finland, Lecture Notes in Computer Science, 2016, vol. 9843, pp. 137-150. [ DOI : 10.1007/978-3-319-44543-4_11 ]
  
  https://hal.inria.fr/hal-01388546
• 36F. Cambi, P. Crescenzi, L. Pagli.
  
  Analyzing and Comparing On-Line News Sources via (Two-Layer) Incremental Clustering, in: 8th International Conference on Fun with Algorithms, FUN 2016, La Maddalena, Italy, June 2016. [ DOI : 10.4230/LIPIcs.FUN.2016.9 ]
  
  https://hal.inria.fr/hal-01390139
• 37A. Conte, R. Grossi, A. Marino.
  
  Clique covering of large real-world networks, in: 31st Annual ACM Symposium on Applied Computing (SAC 2016), Pisa, Italy, ACM, April 2016. [ DOI : 10.1145/2851613.2851816 ]
  
  https://hal.inria.fr/hal-01388477
• 38A. Conte, R. Grossi, A. Marino, R. Rizzi.
  
  Listing Acyclic Orientations of Graphs with Single and Multiple Sources, in: LATIN 2016: Theoretical Informatics - 12th Latin American Symposium, Ensenada, Mexico, E. Kranakis, G. Navarro, E. Chávez (editors), Lecture Notes in Computer Science, Springer, April 2016, vol. 9644, pp. 319-333. [ DOI : 10.1007/978-3-662-49529-2_24 ]
  
  https://hal.inria.fr/hal-01388470
• 39A. Conte, R. Grossi, A. Marino, R. Rizzi, L. Versari.
  
  Directing Road Networks by Listing Strong Orientations, in: Combinatorial Algorithms - 27th International Workshop, IWOCA 2016, Helsinki, Finland, V. Mäkinen, S. J. Puglisi, L. Salmela (editors), Lecture Notes in Computer Science, Springer, August 2016, vol. 9843. [ DOI : 10.1007/978-3-319-44543-4_7 ]
  
  https://hal.inria.fr/hal-01388476
• 40A. Conte, R. Grossi, A. Marino, L. Versari.
  
  Sublinear-Space Bounded-Delay Enumeration for Massive Network Analytics: Maximal Cliques *, in: 43rd International Colloquium on Automata, Languages, and Programming (ICALP 2016), Schloss Dagstuhl, Germany, July 2016, vol. 148, pp. 1 - 148. [ DOI : 10.4230/LIPIcs.ICALP.2016.148 ]
  
  https://hal.inria.fr/hal-01388461
• 41A. Mary, Y. Strozecki.
  
  Efficient Enumeration of Solutions Produced by Closure Operations, in: 33rd Symposium on Theoretical Aspects of Computer Science, STACS 2016, Orléans, France, LIPIcs, February 2016, vol. 47. [ DOI : 10.4230/LIPIcs.STACS.2016.52 ]
  
  https://hal.inria.fr/hal-01388505
• 42C. Massimo, R. Grossi, R. Rizzi.
  
  New Bounds for Approximating Extremal Distances in Undirected Graphs, in: Twenty-Seventh Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 2016, Arlington, United States, SIAM, January 2016. [ DOI : 10.1137/1.9781611974331.ch27 ]
  
  https://hal.inria.fr/hal-01388484

Other Publications

• 43M. G. Ferrarini, F. M. Siqueira, S. G. Mucha, T. L. Palama, E. E. Jobard, B. E. Herrmann, A. T. Ribeiro de Vasconcelos, F. F. Tardy, I. S. Schrank, A. Zaha, M.-F. Sagot.
  
  Metabolic Investigation of the Mycoplasmas from the Swine Respiratory Tract, September 2016, JOBIM 2016, Poster. [ DOI : 10.1186/s12864-016-2644-z ]
  
  https://hal.inria.fr/hal-01394118
• 44A. Julien-Laferrière, L. Bulteau, D. Parrot, A. Marchetti-Spaccamela, L. Stougie, S. Vinga, A. Mary, M.-F. Sagot.
  
  MultiPus: Conception de communautés microbiennes pour la production de composés d'intérêt, June 2016, Jobim, Poster.
  
  https://hal.inria.fr/hal-01394119