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Bibliography

Publications of the year

Articles in International Peer-Reviewed Journals

  • 1U. Ashraf, C. Benoit-Pilven, V. Lacroix, V. Navratil, N. Naffakh.

    Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing, in: Trends in Microbiology, December 2018.

    https://hal.inria.fr/hal-01964983
  • 2L. Beaudou, P. Dankelmann, F. Foucaud, M. A. Henning, A. Mary, A. Parreau.

    Bounding the Order of a Graph Using Its Diameter and Metric Dimension: A Study Through Tree Decompositions and VC Dimension, in: Siam Journal on Discrete Mathematics, April 2018, vol. 32, no 2, pp. 902 - 918. [ DOI : 10.1137/16M1097833 ]

    https://hal.archives-ouvertes.fr/hal-01848648
  • 3C. Benoit-Pilven, C. Marchet, E. Chautard, L. Lima, M.-P. Lambert, G. Sacomoto, A. Rey, A. Cologne, S. Terrone, L. Dulaurier, J.-B. Claude, C. Bourgeois, D. Auboeuf, V. Lacroix.

    Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data, in: Scientific Reports, December 2018, vol. 8, no 1. [ DOI : 10.1038/s41598-018-21770-7 ]

    https://hal.inria.fr/hal-01924204
  • 4S. Colella, N. Parisot, P. Simonet, K. Gaget, G. Duport, P. Baa-Puyoulet, Y. Rahbé, H. Charles, G. Febvay, P. Callaerts, F. Calevro.

    Bacteriocyte Reprogramming to Cope With Nutritional Stress in a Phloem Sap Feeding Hemipteran, the Pea Aphid Acyrthosiphon pisum, in: Frontiers in Physiology, 2018, vol. 9, 1498 p. [ DOI : 10.3389/fphys.2018.01498 ]

    https://hal.archives-ouvertes.fr/hal-01905508
  • 5D. Di Francesco Maesa, A. Marino, L. Ricci.

    Data-driven analysis of Bitcoin properties: exploiting the users graph, in: International Journal of Data Science and Analytics, August 2018, vol. 6, no 1, pp. 63-80.

    https://hal.inria.fr/hal-01964718
  • 6Y. Drouet, I. Treilleux, A. Viari, S. Léon, M. Devouassoux-Shisheboran, N. Voirin, C. de la Fouchardiere, B. Manship, A. Puisieux, C. Lasset, C. Moyret-Lalle.

    Integrated analysis highlights APC11 protein expression as a likely new independent predictive marker for colorectal cancer, in: Scientific Reports, December 2018, vol. 8, no 1. [ DOI : 10.1038/s41598-018-25631-1 ]

    https://hal.inria.fr/hal-01920572
  • 7O. Duron, P. Doublet, F. Vavre, D. Bouchon.

    The Importance of Revisiting Legionellales Diversity, in: Trends in Parasitology, December 2018, vol. 34, no 12, pp. 1027 - 1037. [ DOI : 10.1016/j.pt.2018.09.008 ]

    https://hal.archives-ouvertes.fr/hal-01933206
  • 8O. Duron, O. Morel, V. Noël, M. Buysse, F. Binetruy, R. Lancelot, E. Loire, C. Ménard, O. Bouchez, F. Vavre, L. Vial.

    Tick-Bacteria Mutualism Depends on B Vitamin Synthesis Pathways, in: Current Biology - CB, June 2018, vol. 28, no 12, pp. 1896 - 1902.e5. [ DOI : 10.1016/j.cub.2018.04.038 ]

    https://hal.archives-ouvertes.fr/hal-01933362
  • 9M. G. Ferrarini, S. G. Mucha, D. Parrot, G. Meiffren, J. F. R. Bachega, G. Comte, A. Zaha, M.-F. Sagot.

    Hydrogen peroxide production and myo-inositol metabolism as important traits for virulence of Mycoplasma hyopneumoniae, in: Molecular Microbiology, 2018, pp. 1-45. [ DOI : 10.1111/mmi.13957 ]

    https://hal.inria.fr/hal-01765751
  • 10A. D. Genova, G. A. Ruz, M.-F. Sagot, A. Maass.

    Fast-SG: an alignment-free algorithm for hybrid assembly, in: GigaScience, May 2018, vol. 7, no 5, pp. 1 - 15. [ DOI : 10.1093/gigascience/giy048 ]

    https://hal.inria.fr/hal-01842462
  • 11R. P. Grossi, G. Menconi, N. P. Pisanti, R. Trani, S. Vind.

    Motif trie: An efficient text index for pattern discovery with don't cares, in: Theoretical Computer Science, February 2018, vol. 710, pp. 74-87.

    https://hal.inria.fr/hal-01964717
  • 12L. Guio, C. Vieira, J. González.

    Stress affects the epigenetic marks added by natural transposable element insertions in Drosophila melanogaster, in: Scientific Reports, December 2018, vol. 8, no 1.

    https://hal.inria.fr/hal-01965035
  • 13K. Huber, V. Moulton, M.-F. Sagot, B. Sinaimeri.

    Exploring and Visualising Spaces of Tree Reconciliations, in: Systematic Biology, December 2018.

    https://hal.inria.fr/hal-01964682
  • 14K. Huber, V. Moulton, M.-F. Sagot, B. Sinaimeri.

    Geometric medians in reconciliation spaces, in: Information Processing Letters, 2018, vol. 136, pp. 96 - 101. [ DOI : 10.1016/j.ipl.2018.04.001 ]

    https://hal.inria.fr/hal-01842439
  • 15S. Huet, B. Tesson, J.-P. Jais, A. Feldman, L. Magnano, E. Thomas, A. Traverse-Glehen, B. Albaud, M. Carrère, L. Xerri, S. Ansell, L. Baseggio, C. Reyes, K. Tarte, S. Boyault, C. Haioun, B. Link, P. Feugier, A. Lopez-Guillermo, H. Tilly, P. Brice, S. Hayette, F. Jardin, F. Offner, P. Sujobert, D. Gentien, A. Viari, E. Campo, J. Cerhan, G. Salles.

    A gene-expression profiling score for prediction of outcome in patients with follicular lymphoma: a retrospective training and validation analysis in three international cohorts, in: Lancet Oncology, April 2018, vol. 19, no 4, pp. 549 - 561, Erratum in: Correction to Lancet Oncol 2018; 19: 549-61. [Lancet Oncol. 2018]. [ DOI : 10.1016/S1470-2045(18)30102-5 ]

    https://hal.archives-ouvertes.fr/hal-01788996
  • 16B. Ibrahim, K. Arkhipova, A. C. Andeweg, S. Posada-Céspedes, F. Enault, A. Gruber, E. Koonin, A. Kupczok, P. Lemey, A. C. McHardy, D. P. McMahon, B. E. Pickett, D. Robertson, R. H. Scheuermann, A. Zhernakova, M. P. Zwart, A. Schönhuth, B. E. Dutilh, M. Marz.

    Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting, in: Viruses, May 2018, vol. 10, no 5, 256 p. [ DOI : 10.3390/v10050256 ]

    https://hal.inria.fr/hal-01964743
  • 17M. Jaillard, L. Lima, M. Tournoud, P. Mahé, A. Van Belkum, V. Lacroix, L. Jacob.

    A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between k-mers and genetic events, in: PLoS Genetics, 2018, pp. 1-28. [ DOI : 10.1371/journal.pgen.1007758 ]

    https://hal.inria.fr/hal-01920359
  • 18I. Kyrkou, T. Pusa, L. Ellegaard-Jensen, M.-F. Sagot, L. H. Hansen.

    Pierce's Disease of Grapevines: A Review of Control Strategies and an Outline of an Epidemiological Model, in: Frontiers in Microbiology, September 2018, vol. 9, pp. 1-23. [ DOI : 10.3389/fmicb.2018.02141 ]

    https://hal.inria.fr/hal-01920527
  • 19E. Lerat, C. Goubert, S. Guirao-Rico, M. Merenciano, A.-B. Dufour, C. Vieira, J. González.

    Population specific dynamics and selection patterns of transposable element insertions in European natural populations, in: Molecular Ecology, 2018.

    https://hal.inria.fr/hal-01965027
  • 20G. A. Marais, J.-M. Gaillard, C. Vieira, I. Plotton, D. Sanlaville, F. Gueyffier, J.-F. Lemaître.

    Sex gap in aging and longevity: can sex chromosomes play a role?, in: Biology of Sex Differences, December 2018, vol. 9, no 1.

    https://hal.inria.fr/hal-01965036
  • 21T. 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. De 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. De Ridder, J. De 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, 2018, vol. 19, no 1, pp. 118-135. [ DOI : 10.1093/bib/bbw089 ]

    https://hal.inria.fr/hal-01390478
  • 22B. Menezes, J. Salces-Ortiz, H. Muller, N. Burlet, S. Martinez, M. Fablet, C. Vieira.

    An attempt to select non-genetic variation in resistance to starvation and reduced chill coma recovery time in Drosophila melanogaster, in: The Journal of Experimental Biology, December 2018, vol. 221, no 23, jeb186254.

    https://hal.inria.fr/hal-01965032
  • 23A. Monti, B. Sinaimeri.

    On variants of Vertex Geography on undirected graphs, in: Discrete Applied Mathematics, December 2018, vol. 251, pp. 268-275.

    https://hal.inria.fr/hal-01965197
  • 24D. P. Morton, W. W. Romeijnders, R. R. Schultz, L. Stougie.

    The stochastic programming heritage of Maarten van der Vlerk, in: Computational Management Science, October 2018, vol. 15, no 3-4, pp. 319 - 323. [ DOI : 10.1007/s10287-018-0335-8 ]

    https://hal.inria.fr/hal-01925979
  • 25R. Romba, O. Gnankine, S. F. Drabo, F. Tiendrébéogo, H. Henri, L. Mouton, F. Vavre.

    Abundance of Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae) and its parasitoids on vegetables and cassava plants in Burkina Faso (West Africa), in: Ecology and Evolution, 2018, vol. 8, no 12, pp. 6091-6103. [ DOI : 10.1002/ece3.4078 ]

    https://hal.archives-ouvertes.fr/hal-01916799
  • 26P. Simonet, K. Gaget, S. Balmand, M. Ribeiro Lopes, N. Parisot, K. Buhler, G. Duport, V. Vulsteke, G. Febvay, A. Heddi, H. Charles, P. Callaerts, F. Calevro.

    Bacteriocyte cell death in the pea aphid/ Buchnera symbiotic system, in: Proceedings of the National Academy of Sciences of the United States of America , February 2018, vol. 115, no 8, pp. E1819 - E1828. [ DOI : 10.1073/pnas.1720237115 ]

    https://hal.archives-ouvertes.fr/hal-01768487
  • 27F. Thomas, F. Vavre, T. Tissot, M. Vittecoq, M. Giraudeau, F. F. Bernex, D. Missé, F. Renaud, N. Raven, C. Beckmann, R. Hamede, P. Biro, B. Ujvari.

    Cancer Is Not (Only) a Senescence Problem, in: Trends in Cancer, March 2018, vol. 4, no 3, pp. 169 - 172. [ DOI : 10.1016/j.trecan.2018.01.002 ]

    https://hal.archives-ouvertes.fr/hal-01933408
  • 28L. Tonon, G. Fromont, S. Boyault, E. Thomas, A. Ferrari, A.-S. Sertier, J. Kielbassa, V. Le Texier, A. Kamoun, N. Elarouci, J. Irani, L. Multigner, I. I. Gut, M. Gut, P. Blanchet, A. De Reyniès, G. Cancel-Tassin, A. Viari, O. Cussenot.

    Mutational Profile of Aggressive, Localised Prostate Cancer from African Caribbean Men Versus European Ancestry Men, in: European Urology, September 2018, vol. 75, no 1, pp. 11-15. [ DOI : 10.1016/j.eururo.2018.08.026 ]

    https://hal.inria.fr/hal-01921597
  • 29L. Urbini, B. Sinaimeri, C. Matias, M.-F. Sagot.

    Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, May 2018, pp. 1-11. [ DOI : 10.1109/TCBB.2018.2838667 ]

    https://hal.inria.fr/hal-01842451
  • 30L. 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, 2018, vol. 64, no 4, pp. 621 - 637. [ DOI : 10.1093/sysbio/syv020 ]

    https://hal.inria.fr/hal-01599716
  • 31G. L. Wallau, C. Vieira, É. L. S. Loreto.

    Genetic exchange in eukaryotes through horizontal transfer: connected by the mobilome, in: Mobile DNA, December 2018, vol. 9, no 1.

    https://hal.inria.fr/hal-01965038

International Conferences with Proceedings

  • 32M. Alzamel, L. A. K. Ayad, G. Bernardini, R. P. Grossi, C. S. Iliopoulos, N. P. Pisanti, S. P. Pissis, G. Rosone.

    Degenerate String Comparison and Applications, in: Workshop on Algorithms in Bioinformatics (WABI), Helsinki, Finland, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, 2018, vol. 113. [ DOI : 10.4230/LIPIcs.WABI.2018.21 ]

    https://hal.inria.fr/hal-01964706
  • 33L. A. K. Ayad, G. Bernardini, R. P. Grossi, C. S. Iliopoulos, N. Pisanti, S. P. Pissis, G. Rosone.

    Longest Property-Preserved Common Factor, in: International Symposium on String Processing and Information Retrieval, Lima, Peru, 2018.

    https://hal.inria.fr/hal-01921603
  • 34J. A. Baaijens, B. Van Der Roest, J. Koester, L. Stougie, A. Schoenhuth.

    Full-length de novo viral quasispecies assembly through variation graph construction, in: RECOMB Satellite on Massively Parallel Sequencing (RECOMB-Seq), Paris, France, 2018. [ DOI : 10.1101/287177 ]

    https://hal.inria.fr/hal-01964730
  • 35S. Bhattacharya, M. Henzinger, G. F. Italiano.

    Design of Dynamic Algorithms via Primal-Dual Method, in: International Colloquium on Automata, Languages, and Programming (ICALP), Kyoto, Japan, Lecture Notes in Computer Science, 2018, vol. 9134, pp. 206-218, https://arxiv.org/abs/1604.05337.

    https://hal.inria.fr/hal-01964700
  • 36P. Bille, M. Berggreen Ettienne, R. P. Grossi, I. L. Gørtz, E. Rotenberg.

    Compressed Communication Complexity of Longest Common Prefixes, in: International Symposium on String Processing and Information Retrieval (SPIRE), Lima, Peru, Lecture Notes in Computer Science, 2018, vol. 11147, pp. 74-87.

    https://hal.inria.fr/hal-01964719
  • 37T. Bosman, M. Van Ee, Y. Jiao, A. Marchetti-Spaccamela, R. Ravi, L. Stougie.

    Approximation Algorithms for Replenishment Problems with Fixed Turnover Times, in: Latin American Symposium on Theoretical Informatics (LATIN), Buenos Aires, Argentina, Lecture Notes in Computer Science, 2018, vol. 10807, pp. 217-230, https://arxiv.org/abs/1712.05218.

    https://hal.inria.fr/hal-01964685
  • 38G. Bottazzi, G. F. Italiano, D. Spera.

    Preventing Ransomware Attacks Through File System Filter Drivers, in: Second Italian Conference on Cyber Security, Milan, Italy, 2018.

    https://hal.inria.fr/hal-01925958
  • 39N. Bousquet, A. Mary.

    Reconfiguration of graphs with connectivity constraints, in: International Workshop on Approximation and Online Algorithms (WAOA), Helsinki, Finland, Lecture Notes in Computer Science, 2018, vol. 11312, pp. 295-309, https://arxiv.org/abs/1809.05443.

    https://hal.inria.fr/hal-01964723
  • 40A. Conte, T. De Matteis, D. De Sensi, R. P. Grossi, A. Marino, L. P. Versari.

    D2K: Scalable Community Detection in Massive Networks via Small-Diameter k-Plexes, in: ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), London, United Kingdom, 2018, pp. 1272-1281.

    https://hal.inria.fr/hal-01964688
  • 41A. Conte, G. Ferraro, R. P. Grossi, A. Marino, K. Sadakane, T. Uno.

    Node Similarity with q -Grams for Real-World Labeled Networks, in: ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), London, United Kingdom, Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 2018, pp. 1282-1291. [ DOI : 10.1145/3219819.3220085 ]

    https://hal.inria.fr/hal-01964716
  • 42A. Conte, R. P. Grossi, A. Marino, R. Rizzi, T. Uno, L. P. Versari.

    Tight Lower Bounds for the Number of Inclusion-Minimal st-Cuts, in: International Workshop on Graph-Theoretic Concepts in Computer Science (WG), Cottbus, Germany, Lecture Notes in Computer Science, 2018, vol. 11159, pp. 100-110.

    https://hal.inria.fr/hal-01964710
  • 43A. Conte, R. P. Grossi, A. Marino, R. Rizzi, L. P. Versari.

    Listing Subgraphs by Cartesian Decomposition, in: International Symposium on Mathematical Foundations of Computer Science (MFCS), Dagstuhl, Germany, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, 2018, vol. 117, pp. 1868-8969. [ DOI : 10.4230/LIPIcs.MFCS.2018.84 ]

    https://hal.inria.fr/hal-01964703
  • 44A. Conte, R. P. Grossi, A. Marino, L. P. Versari.

    Finding Maximal Common Subgraphs via Time-Space Efficient Reverse Search, in: International Computing and Combinatorics Conference (COCOON), Qing Dao, China, Lecture Notes in Computer Science, 2018, vol. 10976, pp. 328-340.

    https://hal.inria.fr/hal-01964709
  • 45L. Georgiadis, G. F. Italiano, N. Parotsidis.

    Incremental Strong Connectivity and 2-Connectivity in Directed Graphs, in: Latin American Symposium on Theoretical Informatics, Buenos Aires, Argentina, 2018, https://arxiv.org/abs/1802.10189.

    https://hal.inria.fr/hal-01925953
  • 46R. P. Grossi, A. Marino, L. P. Versari.

    Efficient Algorithms for Listing k Disjoint st-Paths in Graphs, in: Latin American Symposium on Theoretical Informatics (LATIN), Buenos Aires, Argentina, Lecture Notes in Computer Science, 2018, vol. 10807, pp. 544-557.

    https://hal.inria.fr/hal-01964712
  • 47R. P. Grossi, L. P. Versari.

    Round-Hashing for Data Storage: Distributed Servers and External-Memory Tables, in: European Symposium on Algorithms (ESA), Helsinki, Finland, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, 2018, vol. 43, pp. 1 - 43. [ DOI : 10.4230/LIPIcs.ESA.2018.43 ]

    https://hal.inria.fr/hal-01964721
  • 48J. Holm, G. F. Italiano, A. Karczmarz, J. Łącki, E. Rotenberg.

    Decremental SPQR-trees for Planar Graphs, in: European Symposium on Algorithms, Helsinki, Finland, 2018, https://arxiv.org/abs/1806.10772.

    https://hal.inria.fr/hal-01925961
  • 49G. F. Italiano, Y. Manoussakis, K. T. Nguyen, H.-P. Pham.

    Maximum colorful cliques in vertex-colored graphs, in: COCOON 2018 - 24th International Computing and Combinatorics Conference, Qingdao, China, LNCS, Springer, July 2018, vol. 10976, pp. 480-491. [ DOI : 10.1007/978-3-319-94776-1_40 ]

    https://hal.archives-ouvertes.fr/hal-01827893
  • 50N. Olver, K. Pruhs, K. Schewior, R. Sitters, L. Stougie.

    The Itinerant List Update Problem, in: Workshop on Approximation and Online Algorithms (WAOA), Helsinki, Finland, 2018, pp. 310-326.

    https://hal.inria.fr/hal-01972562
  • 51N. Prezza, N. P. Pisanti, M. Sciortino, G. Rosone.

    Detecting Mutations by eBWT, in: Workshop on Algorithms in Bioinformatics, Helsinki, Finland, 2018, https://arxiv.org/abs/1805.01876. [ DOI : 10.4230/LIPIcs.CVIT.2016.23 ]

    https://hal.inria.fr/hal-01925950
  • 52B. Yin, M. Balvert, D. Zambrano, A. Schönhuth, S. Bohte.

    An image representation based convolutional network for DNA classification, in: International Conference on Learning Representations (ICLR), Vancouver, Canada, 2018, https://arxiv.org/abs/1806.04931 - Published at ICLR 2018, https://openreview.net/pdf?id=HJvvRoe0W.

    https://hal.inria.fr/hal-01964736

Conferences without Proceedings

  • 53G. F. Italiano, Y. Manoussakis, N. Kim Thang, H.-P. Pham.

    Maximum Colorful Cycles in Vertex-Colored Graphs, in: CSR 2018 - 13th International Computer Science Symposium in Russia, Moscow, Russia, Lecture Notes in Computer Science, Springer, June 2018, vol. 10846, pp. 106-117. [ DOI : 10.1007/978-3-319-90530-3_10 ]

    https://hal.archives-ouvertes.fr/hal-01762581

Other Publications



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