Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

• 1H. Lopez-Maestre.
  
  Analyses and methods for transcriptomic data from non-model species: Variation in the expression of transposable elements (and genes) and nucleotide variants, Université Claude Bernard Lyon 1, February 2017.
  
  https://hal.inria.fr/tel-01575640
• 2L. Urbini.
  
  Models and algorithms to study the common evolutionary history of hosts and symbionts, Université Claude Bernard - Lyon I, October 2017.
  
  https://hal.inria.fr/tel-01673445

Articles in International Peer-Reviewed Journals

• 3M. Bailly-Bechet, P. Martins-Simões, G. Szöllősi, G. Mialdea, M.-F. Sagot, S. Charlat.
  
  How Long Does Wolbachia Remain on Board?, in: Molecular Biology and Evolution, 2017, vol. 34, pp. 1183 - 1193. [ DOI : 10.1093/molbev/msx073 ]
  
  https://hal.inria.fr/hal-01524867
• 4L. Beaudou, A. Mary, L. Nourine.
  
  Algorithms for k-meet-semidistributive lattices, in: Theoretical Computer Science, 2017, vol. 658, pp. 391 - 398. [ DOI : 10.1016/j.tcs.2015.10.029 ]
  
  https://hal.inria.fr/hal-01571243
• 5A. Conte, R. Grossi, A. Marino, R. Rizzi.
  
  Efficient enumeration of graph orientations with sources, in: Discrete Applied Mathematics, August 2017. [ DOI : 10.1016/j.dam.2017.08.002 ]
  
  https://hal.inria.fr/hal-01609009
• 6H. Davies, D. Glodzik, S. Morganella, L. R. Yates, J. Staaf, X. Zou, M. Ramakrishna, S. Martin, S. Boyault, A. M. Sieuwerts, P. T. Simpson, T. A. King, K. Raine, J. E. Eyfjord, G. Kong, Å. Borg, E. Birney, H. G. Stunnenberg, M. J. van de Vijver, A. Børresen-Dale, J. W. M. Martens, P. N. Span, S. R. Lakhani, A. Vincent-Salomon, C. Sotiriou, A. Tutt, A. M. Thompson, S. Van Laere, A. L. Richardson, A. Viari, P. J. Campbell, M. R. Stratton, S. Nik-Zainal.
  
  HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures, in: Nature Medicine, 2017, vol. 23, n^o 4, pp. 517 - 525. [ DOI : 10.1038/nm.4292 ]
  
  https://hal.inria.fr/hal-01525050
• 7H. Davies, S. Morganella, C. A. Purdie, S. J. Jang, E. Borgen, H. Russnes, D. Glodzik, X. Zou, A. Viari, A. L. Richardson, A.-L. Børresen-Dale, A. Thompson, J. E. Eyfjord, G. Kong, M. R. Stratton, S. Nik-Zainal.
  
  Whole-Genome Sequencing Reveals Breast Cancers with Mismatch Repair Deficiency, in: Cancer Research, 2017, vol. 77, n^o 18, pp. 4755-4762. [ DOI : 10.1158/0008-5472.CAN-17-1083 ]
  
  https://hal.inria.fr/hal-01599736
• 8A. Dudnik, F. Almeida, R. Andrade, B. Avila, P. Bañados, B. Diane, J.-E. Bassard, M. Benkoulouche, M. Bott, A. Braga, D. Breitel, R. Brennan, L. Bulteau, C. Chanforan, I. Costa, R. S. C. Costa, M. Doostmohammadi, N. Faria, C. Feng, R. Ferro, A. Fernandes, P. Ferreira, A. Foito, S. Freitag, C. Jardim, G. Garcia, P. Gaspar, J. Godinho-Pereira, B. Hamberger, A. Hartmann, H. Heider, S. Li, A. Julien-Laferrière, N. Kallscheuer, W. Kerbe, O. P. Kuipers, N. Love, A. Marchetti-Spaccamela, J. Marienhagen, C. Martin, A. Mary, V. Mazurek, C. Meinhart, D. M. Sevillano, R. Menezes, M. Naesby, M. H. H. Nørholm, F. T. Okkels, J. Oliveira, M. Ottens, D. Parrot, L. Pei, I. Rocha, R. Rosado-Ramos, C. Rousseau, M.-F. Sagot, C. Nunes dos Santos, M. Schmidt, T. Shelenga, L. Shepherd, A. Rita Silva, M. Henriques Da Silva, O. Simon, S. G. Stahlhut, A. Solopova, A. Sorokin, D. Stewart, L. Stougie, M. Trick, S. Su, V. Thole, O. Tikhonova, P. Vain, A. Veríssimo, A. Vila-Santa, S. Vinga, M. Vogt, L. Wang, L. Wang, W. Wei, S. Youssef, A. Rute, J. Förster.
  
  BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits, in: Phytochemistry Reviews, 2017, pp. 1-36. [ DOI : 10.1007/s11101-017-9532-2 ]
  
  https://hal.inria.fr/hal-01673596
• 9O. Duron, F. Binetruy, V. Noël, J. Cremaschi, K. McCoy, C. Arnathau, O. Plantard, J. Goolsby, A. Pérez de León, D. Heylen, A. R. van Oosten, Y. Gottlieb, G. Baneth, A. Guglielmone, A. Estrada-Peña, M. Opara, L. Zenner, F. Vavre, C. Chevillon.
  
  Evolutionary changes in symbiont community structure in ticks, in: Molecular Ecology, 2017, vol. 26, n^o 11, pp. 2905–2921. [ DOI : 10.1111/mec.14094 ]
  
  https://hal.inria.fr/hal-01523998
• 10J.-P. Foy, L. Bazire, S. Ortiz-Cuaran, S. Deneuve, J. Kielbassa, E. Thomas, A. Viari, A. Puisieux, P. Goudot, C. Bertolus, N. Foray, Y. Kirova, P. Verrelle, P. Saintigny.
  
  A 13-gene expression-based radioresistance score highlights the heterogeneity in the response to radiation therapy across HPV-negative HNSCC molecular subtypes, in: BMC Medicine, December 2017, vol. 15, n^o 1, pp. 703 - 719. [ DOI : 10.1186/s12916-017-0929-y ]
  
  https://hal.inria.fr/hal-01599731
• 11P. Foy, C. Bertolus, M.-C. Michallet, S. Deneuve, R. Incitti, N. Bendriss-Vermare, M.-A. Albaret, S. Ortiz-Cuaran, E. Thomas, A. Colombe, C. Py, N. Gadot, J.-P. Michot, J. Fayette, A. Viari, B. Van Den Eynde, P. Goudot, M. Devouassoux-Shisheboran, A. Puisieux, C. Caux, P. Zrounba, S. Lantuejoul, P. Saintigny.
  
  The immune microenvironment of HPV-negative oral squamous cell carcinoma from never-smokers and never-drinkers patients suggests higher clinical benefit of IDO1 and PD1/PD-L1 blockade, in: Annals of Oncology, April 2017, vol. 28, n^o 8, pp. 1934–1941. [ DOI : 10.1093/annonc/mdx210 ]
  
  https://hal.inria.fr/hal-01560943
• 12D. Glodzik, S. Morganella, H. Davies, P. T. Simpson, Y. Li, X. Zou, J. Diez-Perez, J. Staaf, L. B. Alexandrov, M. Smid, A. B. Brinkman, I. H. Rye, H. Russnes, K. Raine, C. A. Purdie, S. R. Lakhani, 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, A. Viari, D. Easton, G. Evan, P. J. Campbell, M. R. Stratton, S. Nik-Zainal.
  
  A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers, in: Nature Genetics, 2017, vol. 49, n^o 3, pp. 341 - 348. [ DOI : 10.1038/ng.3771 ]
  
  https://hal.inria.fr/hal-01525728
• 13C. Goubert, H. Henri, G. Minard, C. Valiente Moro, P. Mavingui, C. Vieira, M. Boulesteix.
  
  High-Throughput Sequencing of Transposable Element Insertions Suggests Adaptive Evolution of the Invasive Asian Tiger Mosquito Towards Temperate Environments, in: Molecular Ecology, 2017, pp. 1-14. [ DOI : 10.1111/mec.14184 ]
  
  https://hal.inria.fr/hal-01546749
• 14R. Grossi, G. Menconi, N. Pisanti, R. Trani, S. Vind.
  
  Fast Output-Sensitive Pattern Discovery in Massive Sequences using the Motif Trie, in: Theoretical Computer Science, 2017, 25 p. [ DOI : 10.1016/j.tcs.2017.04.012 ]
  
  https://hal.inria.fr/hal-01525745
• 15A. Hartmann, A. Vila-Santa, N. Kallscheuer, M. Vogt, A. Julien-Laferrière, M.-F. Sagot, J. Marienhagen, S. Vinga.
  
  OptPipe - a pipeline for optimizing metabolic engineering targets, in: BMC Systems Biology, December 2017, vol. 11, pp. 1-9. [ DOI : 10.1186/s12918-017-0515-0 ]
  
  https://hal.inria.fr/hal-01672905
• 16S. Huet, E. Szafer-Glusman, B. Tesson, L. Xerri, W. J. Fairbrother, K. Mukhyala, C. Bolen, E. Punnoose, L. Tonon, C. Chassagne-Clément, P. Feugier, A. Viari, F. Jardin, G. Salles, P. Sujobert.
  
  BCL2 mutations do not confer adverse prognosis in follicular lymphoma patients treated with rituximab, in: American Journal of Hematology, 2017, vol. 92, n^o 6, pp. 515 - 519. [ DOI : 10.1002/ajh.24701 ]
  
  https://hal.inria.fr/hal-01524901
• 17S. Huet, L. Xerri, B. Tesson, S. Mareschal, S. Taix, L. Mescam-Mancini, E. Sohier, C. Carrère, J. Lazarovici, O. Casasnovas, L. Tonon, S. Boyault, S. Hayette, C. Haioun, B. Fabiani, A. Viari, F. Jardin, G. Salles.
  
  EZH2 alterations in follicular lymphoma: biological and clinical correlations, in: Blood Cancer Journal, 2017, vol. 7, n^o 4. [ DOI : 10.1038/bcj.2017.32 ]
  
  https://hal.inria.fr/hal-01566524
• 18Y. S. Ju, I. Martincorena, M. Gerstung, M. Petljak, L. B. Alexandrov, R. Rahbari, D. C. Wedge, H. R. Davies, M. Ramakrishna, A. Fullam, S. Martin, C. Alder, N. Patel, S. Gamble, S. O’Meara, D. D. Giri, T. Sauer, S. E. Pinder, C. A. Purdie, Å. Borg, H. Stunnenberg, M. Van De Vijver, B. K. T. Tan, C. Caldas, A. Tutt, N. T. Ueno, L. J. van ’t Veer, J. W. M. Martens, C. Sotiriou, S. Knappskog, P. N. Span, S. R. Lakhani, J. E. Eyfjörd, A.-L. Børresen-Dale, A. Richardson, A. M. Thompson, A. Viari, M. E. Hurles, S. Nik-Zainal, P. J. Campbell, M. R. Stratton.
  
  Somatic mutations reveal asymmetric cellular dynamics in the early human embryo, in: Nature, 2017, vol. 543, n^o 7647, pp. 714 - 718. [ DOI : 10.1038/nature21703 ]
  
  https://hal.inria.fr/hal-01525712
• 19E. LERAT, M. Fablet, L. Modolo, H. Lopez-Maestre, C. Vieira.
  
  TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes, in: Nucleic Acids Research, 2017, vol. 45, 13 p. [ DOI : 10.1093/nar/gkw953 ]
  
  https://hal.inria.fr/hal-01524877
• 20T. Lefébure, C. Morvan, F. Malard, C. François, L. Konecny-Dupré, L. Guéguen, M. Weiss-Gayet, A. Seguin-Orlando, L. Ermini, C. D. Sarkissian, N. P. Charrier, D. Eme, F. Mermillod-Blondin, L. Duret, C. Vieira, L. Orlando, C. J. Douady.
  
  Less effective selection leads to larger genomes, in: Genome Research, 2017, vol. 27, pp. 1016-1028. [ DOI : 10.1101/gr.212589.116 ]
  
  https://hal.inria.fr/hal-01544879
• 21L. Lima, B. Sinaimeri, G. Sacomoto, H. Lopez-Maestre, C. Marchet, V. Miele, M.-F. Sagot, V. Lacroix.
  
  Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads, in: Algorithms for Molecular Biology, December 2017, vol. 12, n^o 1, 2 p. [ DOI : 10.1186/s13015-017-0091-2 ]
  
  https://hal.inria.fr/hal-01474524
• 22H. Lopez-Maestre, E. A. G. Carnelossi, V. Lacroix, N. Burlet, B. Mugat, S. Chambeyron, C. M. A. Carareto, C. Vieira.
  
  Identification of misexpressed genetic elements in hybrids between Drosophila-related species, in: Scientific Reports, 2017, vol. 7, 40618 p.
  
  https://hal.archives-ouvertes.fr/hal-01524879
• 23A. Malizia, K. A. Olsen, T. Turchi, P. Crescenzi.
  
  An ant-colony based approach for real-time implicit collaborative information seeking, in: Information Processing and Management, 2017, vol. 53, n^o 3, pp. 608 - 623. [ DOI : 10.1016/j.ipm.2016.12.005 ]
  
  https://hal.inria.fr/hal-01525753
• 24A. Melani, M. Bertogna, V. Bonifaci, A. Marchetti-Spaccamela, G. Buttazzo.
  
  Schedulability Analysis of Conditional Parallel Task Graphs in Multicore Systems, in: IEEE Transactions on Computers, 2017, vol. 66, n^o 2, pp. 339-353. [ DOI : 10.1109/TC.2016.2584064 ]
  
  https://hal.inria.fr/hal-01556802
• 25A. Melani, M. Bertogna, R. Davis, V. Bonifaci, A. Marchetti-Spaccamela, G. Buttazzo.
  
  Exact Response Time Analysis for Fixed Priority Memory-Processor Co-Scheduling, in: IEEE Transactions on Computers, 2017, vol. 66, pp. 631 - 646. [ DOI : 10.1109/TC.2016.2614819 ]
  
  https://hal.inria.fr/hal-01556792
• 26D. Monnin, N. Kremer, E. Desouhant, F. Vavre.
  
  Impact of Wolbachia on oxidative stress sensitivity in the parasitic wasp Asobara japonica, in: PLoS ONE, 2017, vol. 5, 10 p. [ DOI : 10.1371/journal.pone.0175974.s002 ]
  
  https://hal.inria.fr/hal-01523927
• 27G. Rodrigues Galvao, C. Baudet, Z. Dias.
  
  Sorting Circular Permutations by Super Short Reversals, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017, vol. 14, n^o 3, pp. 620-633. [ DOI : 10.1109/TCBB.2016.2515594 ]
  
  https://hal.inria.fr/hal-01317003
• 28G. Tolosa, L. Becchetti, E. Feuerstein, A. Marchetti-Spaccamela.
  
  Performance Improvements for Search Systems using an Integrated Cache of Lists+Intersections, in: Information Retrieval Journal, 2017, vol. 20, n^o 3, pp. 172-198. [ DOI : 10.1007/978-3-319-11918-2_22 ]
  
  https://hal.inria.fr/hal-01528536
• 29L. Van Iersel, S. Kelk, G. Stamoulis, L. Stougie, O. Boes.
  
  On Unrooted and Root-Uncertain Variants of Several Well-Known Phylogenetic Network Problems, in: Algorithmica, 2017, vol. 64, n^o 4, pp. 621 - 637. [ DOI : 10.1093/sysbio/syv020 ]
  
  https://hal.inria.fr/hal-01599716

International Conferences with Proceedings

• 30V. Acuna, R. Grossi, G. F. Italiano, L. Lima, R. Rizzi, G. Sacomoto, M.-F. Sagot, B. Sinaimeri.
  
  On Bubble Generators in Directed Graphs, in: WG 2017 - 43rd International Workshop on Graph-Theoretic Concepts in Computer Science, Eindhoven, Netherlands, Lecture Notes in Computer Science, Springer, June 2017, vol. 10520, pp. 18-31. [ DOI : 10.1007/978-3-319-68705-6_2 ]
  
  https://hal.inria.fr/hal-01647516
• 31G. Bernardini, N. Pisanti, S. Pissis, G. Rosone.
  
  Pattern Matching on Elastic-Degenerate Text with Errors, in: SPIRE 2017 - 24th International Symposium on String Processing and Information Retrieval, Palermo, Italy, SPIRE 2017: String Processing and Information Retrieval, Springer, September 2017, vol. 10508, pp. 74-90. [ DOI : 10.1007/978-3-319-67428-5_7 ]
  
  https://hal.inria.fr/hal-01673585
• 32A. Bjelde, Y. Disser, J. Hackfeld, C. Hansknecht, M. Lipmann, J. Meißner, K. Schewior, M. Schlöter, L. Stougie.
  
  Tight Bounds for Online TSP on the Line, in: ACM-SIAM Symposium on Discrete Algorithms (SODA), Barcelona, Spain, January 2017, pp. 994 - 1005. [ DOI : 10.1137/1.9781611974782.63 ]
  
  https://hal.inria.fr/hal-01549685
• 33M. Borassi, P. Crescenzi, L. Trevisan.
  
  An Axiomatic and an Average-Case Analysis of Algorithms and Heuristics for Metric Properties of Graphs, in: SODA 2017 - Twenty-Eighth Annual ACM-SIAM Symposium on Discrete Algorithms, Barcelona, Spain, Proceedings of the Proceedings of the Twenty-Eighth Annual ACM-SIAM Symposium on Discrete Algorithms, January 2017, pp. 920 - 939. [ DOI : 10.1137/1.9781611974782.58 ]
  
  https://hal.inria.fr/hal-01525752
• 34N. Bousquet, A. Mary, A. Parreau.
  
  Token Jumping in minor-closed classes, in: Fundamentals of Computation Theory (FCT 2017), Bordeaux, France, R. Klasing, M. Zeitoun (editors), Lecture Notes in Computer Science, Springer, September 2017, vol. 10472, pp. 136-149, https://arxiv.org/abs/1706.09608. [ DOI : 10.1007/978-3-662-55751-8_12 ]
  
  https://hal.archives-ouvertes.fr/hal-01634505
• 35A. Conte, R. Grossi, A. Marino, L. Tattini, L. Versari.
  
  A Fast Algorithm for Large Common Connected Induced Subgraphs, in: AlCoB 2017: 4th International Conference on Algorithms for Computational Biology, Aveiro, Portugal, June 2017, vol. 37, pp. 828 - 74. [ DOI : 10.1021/ci9601675 ]
  
  https://hal.inria.fr/hal-01555996
• 36A. Conte, R. Grossi, A. Marino, T. Uno, L. P. Versari.
  
  Listing Maximal Independent Sets with Minimal Space and Bounded Delay, in: International Symposium on String Processing and Information Retrieval (SPIRE), Palermo, Italy, G. Fici, M. Sciortino, R. Venturini (editors), Lecture Notes in Computer Science, Springer, September 2017, vol. 10508, n^o 1-2, pp. 144-160. [ DOI : 10.1007/978-3-319-67428-5_13 ]
  
  https://hal.inria.fr/hal-01609012
• 37R. P. Grossi, C. S. Iliopoulos, C. Liu, N. P. Pisanti, S. P. Pissis, A. Retha, G. Rosone, F. Vayani, L. P. Versari.
  
  On-line pattern matching on similar texts, in: 28th Annual Symposium on Combinatorial Pattern Matching (CPM'17), Varsovie, Poland, 2017, pp. 7 - 8. [ DOI : 10.4230/LIPIcs.CPM.2017.07 ]
  
  https://hal.inria.fr/hal-01526650

Scientific Popularization

• 38P. Saintigny, P. Foy, A. Ferrari, P. Cassier, A. Viari, A. Puisieux.
  
  Apport et défis des Big Data en cancérologie, in: Bulletin du Cancer, 2017, vol. 104, n^o 3, pp. 281 - 287. [ DOI : 10.1016/j.bulcan.2016.10.020 ]
  
  https://hal.inria.fr/hal-01525736

Other Publications

• 39C. Benoit-Pilven, C. Marchet, E. Chautard, L. Lima, M.-P. Lambert, G. Sacomoto, A. Rey, C. Bourgeois, D. Auboeuf, V. Lacroix.
  
  Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data, November 2017, working paper or preprint. [ DOI : 10.1101/074807 ]
  
  https://hal.archives-ouvertes.fr/hal-01643169