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Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

  • 1A. Cologne.

    Exploration of minor splicing function during embryonic development with the Taybi-Linder Syndrome (TALS) model, Université de Lyon, October 2019.

    https://tel.archives-ouvertes.fr/tel-02363211
  • 2L. Ishi Soares de Lima.

    De novo algorithms to identify patterns associated with biological events in de Bruijn graphs built from NGS data, Université de Lyon ; Università degli studi di Roma "Tor Vergata", April 2019.

    https://tel.archives-ouvertes.fr/tel-02280110
  • 3T. Pusa.

    Modélisation mathématique des impacts de l'environnement à l'aide de réseaux métaboliques et de la théorie des jeux, Université de Lyon ; Università degli studi La Sapienza (Rome), February 2019.

    https://tel.archives-ouvertes.fr/tel-02096971

Articles in International Peer-Reviewed Journals

  • 4V. Acuña, R. Grossi, G. F. Italiano, L. Lima, R. Rizzi, G. Sacomoto, M.-F. Sagot, B. Sinaimeri.

    On Bubble Generators in Directed Graphs, in: Algorithmica, 2019, pp. 1-19. [ DOI : 10.1007/s00453-019-00619-z ]

    https://hal.inria.fr/hal-02284946
  • 5N. Alcala, N. Leblay, A. Gabriel, L. Mangiante, D. Hervás, T. Giffon, A.-S. Sertier, A. Ferrari, J. Derks, A. Ghantous, T. Delhomme, A. Chabrier, C. Cuenin, B. Abedi-Ardekani, A. Boland, R. Olaso, V. Meyer, J. Altmuller, F. Le Calvez-Kelm, G. Durand, C. Voegele, S. Boyault, L. Moonen, N. Lemaître, P. Lorimier, A.-C. Toffart, A. Soltermann, J. Clement, J. Saenger, J. Field, M. Brevet, C. Blanc-Fournier, F. Galateau-Sallé, N. Le Stang, P. Russell, G. Wright, G. Sozzi, U. Pastorino, S. Lacomme, J. Vignaud, V. Hofman, P. Hofman, O. T. Brustugun, M. Lund-Iversen, V. Thomas de Montpreville, L. A. Muscarella, P. Graziano, H. H. Popper, J. Stojsic, J.-F. Deleuze, Z. Herceg, A. Viari, P. Nuernberg, G. Pelosi, A.-M. C. Dingemans, M. Milione, L. Roz, L. Brcic, M. Volante, M. Papotti, C. Caux, J. Sandoval, H. Hernandez-Vargas, E. Brambilla, E. Speel, N. Girard, S. Lantuejoul, J. McKay, M. Foll, L. Fernandez-Cuesta.

    Integrative and comparative genomic analyses identify clinically relevant pulmonary carcinoid groups and unveil the supra-carcinoids, in: Nature Communications, December 2019, vol. 10, no 1, pp. 1-21. [ DOI : 10.1038/s41467-019-11276-9 ]

    https://hal.inria.fr/hal-02339242
  • 6U. Ashraf, C. Benoit-Pilven, V. Lacroix, V. Navratil, N. Naffakh.

    Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing, in: Trends in Microbiology, 2019, vol. 27, no 3, pp. 268-281. [ DOI : 10.1016/j.tim.2018.11.004 ]

    https://hal.inria.fr/hal-01964983
  • 7J. A. Baaijens, A. Schönhuth.

    Overlap graph-based generation of haplotigs for diploids and polyploids, in: Bioinformatics, November 2019, vol. 35, no 21, pp. 4281-4289. [ DOI : 10.1093/bioinformatics/btz255 ]

    https://hal.inria.fr/hal-02344853
  • 8A. C. Baller, M. Van Ee, M. Hoogeboom, L. Stougie.

    Complexity of inventory routing problems when routing is easy, in: Networks, October 2019, pp. 1-11. [ DOI : 10.1002/net.21908 ]

    https://hal.inria.fr/hal-02422721
  • 9S. K. Baruah, V. Bonifaci, R. Bruni, A. Marchetti-Spaccamela.

    ILP models for the allocation of recurrent workloads upon heterogeneous multiprocessors, in: Journal of Scheduling, April 2019, vol. 22, no 2, pp. 195-209. [ DOI : 10.1007/s10951-018-0593-x ]

    https://hal.inria.fr/hal-02339161
  • 10G. Bernardini, P. Bonizzoni, L. Denti, M. Previtali, A. Schönhuth.

    MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants, in: iScience, 2019, vol. 18, pp. 20-27. [ DOI : 10.1016/j.isci ]

    https://hal.inria.fr/hal-02344254
  • 11G. Bernardini, N. Pisanti, S. Pissis, G. Rosone.

    Approximate pattern matching on elastic-degenerate text, in: Theoretical Computer Science, August 2019, pp. 1-30. [ DOI : 10.1016/j.tcs.2019.08.012 ]

    https://hal.inria.fr/hal-02298622
  • 12V. Bonifaci, A. Wiese, S. K. Baruah, A. Marchetti-Spaccamela, S. Stiller, L. Stougie.

    A Generalized Parallel Task Model for Recurrent Real-time Processes, in: ACM Transactions on Parallel Computing, June 2019, vol. 6, no 1, pp. 63-72. [ DOI : 10.1109/RTSS.2012.59 ]

    https://hal.inria.fr/hal-02347467
  • 13M. Bonnin, N. Fares, B. Testoni, Y. Estornes, K. Weber, B. Vanbervliet, L. Lefrancois, A. Garcia, A. Kfoury, F. Pez, I. Coste, P. Saintigny, A. Viari, K. Lang, B. Guey, V. Hervieu, B. Bancel, B. Bartoch, D. Durantel, T. Renno, P. Merle, S. Lebecque.

    Toll-like receptor 3 downregulation is an escape mechanism from apoptosis during hepatocarcinogenesis, in: Journal of Hepatology, October 2019, vol. 71, no 4, pp. 763-772. [ DOI : 10.1016/j.jhep.2019.05.031 ]

    https://hal.inria.fr/hal-02367101
  • 14T. Calamoneri, A. Monti, B. Sinaimeri.

    Co-divergence and tree topology, in: Journal of Mathematical Biology, August 2019, vol. 79, no 3, pp. 1149-1167. [ DOI : 10.1007/s00285-019-01385-w ]

    https://hal.inria.fr/hal-02298643
  • 15A. Cologne, C. Benoit-Pilven, A. Besson, A. Putoux, A. Campan-Fournier, M. B. Bober, C. E. De Die-Smulders, A. Paulussen, L. Pinson, A. Toutain, C. M. Roifman, A.-L. Leutenegger, S. Mazoyer, P. EDERY, V. Lacroix.

    New insights into minor splicing-a transcriptomic analysis of cells derived from TALS patients, in: RNA, 2019, pp. 1-21. [ DOI : 10.1261/rna.071423.119 ]

    https://hal.inria.fr/hal-02305628
  • 16M. Fablet, A. Jacquet, R. Rebollo, A. A. Haudry, C. Rey, J. Salces-Ortiz, P. Bajad, N. Burlet, M. Jantsch, M. P. Garcia Guerreiro, C. Vieira.

    Dynamic Interactions Between the Genome and an Endogenous Retrovirus: Tirant in Drosophila simulans Wild-Type Strains, in: G3, March 2019, vol. 9, no 3, pp. 855-865. [ DOI : 10.1534/g3.118.200789 ]

    https://hal.archives-ouvertes.fr/hal-02004384
  • 17L. Georgiadis, G. F. Italiano, A. Karanasiou.

    Approximating the smallest 2-vertex connected spanning subgraph of a directed graph, in: Theoretical Computer Science, September 2019, pp. 1-16. [ DOI : 10.1016/j.tcs.2019.09.040 ]

    https://hal.inria.fr/hal-02335015
  • 18L. Guillot, L. Delage, A. Viari, Y. Vandenbrouck, E. Com, A. A. Ritter, R. Lavigne, D. Marie, P. Peterlongo, P. Potin, C. Pineau.

    Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes, in: BMC Genomics, January 2019, vol. 20, no 1, 56 p. [ DOI : 10.1186/s12864-019-5431-9 ]

    https://hal.inria.fr/hal-01987197
  • 19E. Lerat, J. Casacuberta, C. Chaparro, C. Vieira.

    On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses, in: Genes, March 2019, vol. 10, no 4, 258 p. [ DOI : 10.3390/genes10040258 ]

    https://hal.archives-ouvertes.fr/hal-02093613
  • 20L. Lima, C. Marchet, S. Caboche, C. Da Silva, B. Istace, J.-M. Aury, H. Touzet, R. Chikhi.

    Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data, in: Briefings in Bioinformatics, June 2019, pp. 1-18. [ DOI : 10.1093/bib/bbz058 ]

    https://hal.archives-ouvertes.fr/hal-02394395
  • 21A. Lopez-Rincon, M. Martinez-Archundia, G. U. Martinez-Ruiz, A. Schönhuth, A. Tonda.

    Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection, in: BMC Bioinformatics, December 2019, vol. 20, no 1, pp. 1-17. [ DOI : 10.1186/s12859-019-3050-8 ]

    https://hal.inria.fr/hal-02344257
  • 22P. Marin, J. Genitoni, D. D. Barloy, S. Maury, P. Gibert, C. K. Ghalambor, C. Vieira.

    Biological Invasion: The Influence of the Hidden Side of the (Epi)Genome, in: Functional Ecology, 2019, pp. 1-55, forthcoming. [ DOI : 10.1111/1365-2435.13317 ]

    https://hal-agrocampus-ouest.archives-ouvertes.fr/hal-02063295
  • 23A. Marino, L. Versari, A. Conte, R. Grossi, G. Punzi, T. Uno.

    Polynomial-Delay Enumeration of Maximal Common Subsequences, in: SIAM Journal on Discrete Mathematics, October 2019, vol. 33, no 2, pp. 189-202. [ DOI : 10.1007/978-3-030-32686-9_14 ]

    https://hal.inria.fr/hal-02338458
  • 24A. Mary, Y. Strozecki.

    Efficient enumeration of solutions produced by closure operations, in: Discrete Mathematics and Theoretical Computer Science, June 2019, pp. 1-30, https://arxiv.org/abs/1712.03714 - 30 pages, 1 figure. Long version of the article arXiv:1509.05623 of the same name which appeared in STACS 2016. Final version for DMTCS journal. [ DOI : 10.23638/DMTCS-21-3-22 ]

    https://hal.inria.fr/hal-02373737
  • 25N. Prezza, N. Pisanti, M. Sciortino, G. Rosone.

    SNPs detection by eBWT positional clustering, in: Algorithms for Molecular Biology, December 2019, vol. 14, no 1, pp. 1-13. [ DOI : 10.1186/s13015-019-0137-8 ]

    https://hal.inria.fr/hal-02335605
  • 26T. Pusa, M. G. Ferrarini, R. Andrade, A. Mary, A. Marchetti-Spaccamela, L. Stougie, M.-F. Sagot.

    MOOMIN – Mathematical explOration of ’Omics data on a MetabolIc Network, in: Bioinformatics, August 2019, pp. 1-10. [ DOI : 10.1093/bioinformatics/btz584 ]

    https://hal.inria.fr/hal-02284835
  • 27T. Pusa, M. Wannagat, M.-F. Sagot.

    Metabolic Games, in: Frontiers in Applied Mathematics and Statistics, April 2019, vol. 5, pp. 1-13. [ DOI : 10.3389/fams.2019.00018 ]

    https://hal.inria.fr/hal-02336595
  • 28C. Sessegolo, C. Cruaud, C. Da Silva, A. Cologne, M. Dubarry, T. Derrien, V. Lacroix, J.-M. Aury.

    Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules, in: Scientific Reports, December 2019, vol. 9, no 1, pp. 1-12. [ DOI : 10.1038/s41598-019-51470-9 ]

    https://hal.inria.fr/hal-02335574
  • 29T. Shekarian, E. Sivado, A.-C. Jallas, S. Depil, J. Kielbassa, I. Janoueix-Lerosey, G. Hutter, N. Goutagny, C. Bergeron, A. Viari, S. Valsesia-Wittmann, C. Caux, A. Marabelle.

    Repurposing rotavirus vaccines for intratumoral immunotherapy can overcome resistance to immune checkpoint blockade, in: Science Translational Medicine, October 2019, vol. 11, no 515, eaat5025 p. [ DOI : 10.1126/scitranslmed.aat5025 ]

    https://hal.inria.fr/hal-02347852
  • 30M. Smid, S. M. Wilting, K. Uhr, F. G. Rodríguez-González, V. de Weerd, W. J. Prager-Van der Smissen, M. van der Vlugt-Daane, A. van Galen, S. Nik-Zainal, A. P. Butler, S. Martin, H. R. Davies, J. Staaf, M. J. van de Vijver, A. L. Richardson, G. MacGrogan, R. Salgado, G. G. Van den Eynden, C. A. Purdie, A. M. Thompson, C. Caldas, P. N. Span, F. C. Sweep, P. T. Simpson, S. R. Lakhani, S. Van Laere, C. Desmedt, A. Paradiso, J. Eyfjord, A. Broeks, A. Vincent-Salomon, A. P. Futreal, S. Knappskog, T. King, A. Viari, A.-L. Børresen-Dale, H. G. Stunnenberg, M. Stratton, J. A. Foekens, A. M. Sieuwerts, J. W. Martens.

    The circular RNome of primary breast cancer, in: Genome Research, March 2019, vol. 29, no 3, pp. 356-366. [ DOI : 10.1101/gr.238121.118 ]

    https://hal.inria.fr/hal-02338656
  • 31L. 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, January 2019, vol. 75, no 1, pp. 11-15. [ DOI : 10.1016/j.eururo.2018.08.026 ]

    https://hal.inria.fr/hal-01921597
  • 32O. Trédan, Q. Wang, D. Pissaloux, P. Cassier, A. De La Fouchardière, J. Fayette, F. Desseigne, I. Ray-Coquard, C. De La Fouchardière, D. Frappaz, P. E. Heudel, A. Bonneville-Levard, A. Flechon, M. Sarabi, P. Guibert, T. Bachelot, M. Pérol, B. You, N. Bonnin, O. Collard, C. Leyronnas, V. Attignon, C. Baudet, E. Sohier, J.-P. Villemin, A. Viari, S. Boyault, S. Lantuejoul, S. Paindavoine, I. Treillleux, C. Rodriguez, V. Agrapart, V. Corset, G. Garin, S. Chabaud, D. Perol, J.-Y. Blay.

    Molecular screening program to select molecular-based recommended therapies for metastatic cancer patients: analysis from the ProfiLER trial, in: Annals of Oncology, May 2019, vol. 30, no 5, pp. 757-765. [ DOI : 10.1093/annonc/mdz080 ]

    https://hal.inria.fr/hal-02367110
  • 33L. 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, 2019, pp. 1-11. [ DOI : 10.1109/TCBB.2018.2838667 ]

    https://hal.inria.fr/hal-01842451
  • 34B. Yin, M. Balvert, R. van der Spek, B. E. Dutilh, S. Bohte, J. Veldink, A. Schönhuth.

    Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype, in: Bioinformatics, July 2019, vol. 35, no 14, pp. i538-i547. [ DOI : 10.1093/bioinformatics/btz369 ]

    https://hal.inria.fr/hal-02344253

International Conferences with Proceedings

  • 35A. Abboud, L. Georgiadis, G. F. Italiano, R. Krauthgamer, N. Parotsidis, O. Trabelsi, P. Uznański, D. Wolleb-Graf.

    Faster Algorithms for All-Pairs Bounded Min-Cuts, in: ICALP 2019 - 46th International Colloquium on Automata, Languages and Programming, Patras, Greece, July 2019, pp. 1-15. [ DOI : 10.4230/LIPIcs.ICALP.2019.7 ]

    https://hal.inria.fr/hal-02335025
  • 36G. Bernardini, P. Gawrychowski, N. Pisanti, S. Pissis, G. Rosone.

    Even Faster Elastic-Degenerate String Matching via Fast Matrix Multiplication, in: ICALP 2019 - 46th International Colloquium on Automata, Languages and Programming, Patras, Greece, July 2019, pp. 1-15. [ DOI : 10.4230/LIPIcs.ICALP.2019.21 ]

    https://hal.inria.fr/hal-02298621
  • 37M. Bonamy, N. Bousquet, M. Heinrich, T. Ito, Y. Kobayashi, A. Mary, M. Mühlenthaler, K. Wasa.

    The Perfect Matching Reconfiguration Problem, in: MFCS 2019 - 44th International Symposium on Mathematical Foundations of Computer Science, Aachen, Germany, August 2019, pp. 1-14. [ DOI : 10.4230/LIPIcs.MFCS.2019.80 ]

    https://hal.inria.fr/hal-02335588
  • 38A. Conte, R. Grossi, M. M. Kanté, A. Marino, T. Uno, K. Wasa.

    Listing Induced Steiner Subgraphs as a Compact Way to Discover Steiner Trees in Graphs, in: MFCS 2019 - 44th International Symposium on Mathematical Foundations of Computer Science, Aachen, Germany, August 2019, pp. 1-14. [ DOI : 10.4230/LIPIcs.MFCS.2019.73 ]

    https://hal.inria.fr/hal-02335601
  • 39A. Conte, R. Grossi, A. Marino, L. Tattini, L. Versari.

    A Fast Discovery Algorithm for Large Common Connected Induced Subgraphs, in: WEPA 2019 - Workshop on Enumeration Problems & Applications, Awaji Island, Japan, October 2019, pp. 1-26.

    https://hal.inria.fr/hal-02338435
  • 40A. Conte, R. Grossi, G. Punzi, T. Uno.

    Polynomial-Delay Enumeration of Maximal Common Subsequences, in: SPIRE 2019 - 26th International Symposium on String Processing and Information Retrieval, Segovia, Spain, October 2019, pp. 189-202. [ DOI : 10.1007/978-3-030-32686-9_14 ]

    https://hal.inria.fr/hal-02338437
  • 41M. Equi, R. Grossi, V. Makinen.

    On the Complexity of Exact Pattern Matching in Graphs: Binary Strings and Bounded Degree, in: ICALP 2019 - 46th International Colloquium on Automata, Languages and Programming, Patras, Greece, July 2019, pp. 1-15.

    https://hal.inria.fr/hal-02338498
  • 42F. Geraci, R. Massidda, N. Pisanti.

    Technology and Species independent Simulation of Sequencing data and Genomic Variants, in: BIBE 2019 - 19th annual IEEE International Conference on BioInformatics and BioEngineering, Athens, Greece, IEEE, October 2019, pp. 1-8.

    https://hal.inria.fr/hal-02336600
  • 43N. Hjuler, G. F. Italiano, N. Parotsidis, D. Saulpic.

    Dominating Sets and Connected Dominating Sets in Dynamic Graphs, in: STACS 2019 - 36th International Symposium on Theoretical Aspects of Computer Science, Berlin, Germany, March 2019, pp. 1-17. [ DOI : 10.4230/LIPIcs.STACS.2019.35 ]

    https://hal.inria.fr/hal-02335028
  • 44G. F. Italiano, S. Lattanzi, V. Mirrokni, N. Parotsidis.

    Dynamic Algorithms for the Massively Parallel Computation Model, in: SPAA 2019 - 31st ACM Symposium on Parallelism in Algorithms and Architectures, Phoenix, France, ACM Press, June 2019, pp. 49-58, https://arxiv.org/abs/1905.09175. [ DOI : 10.1145/3323165.3323202 ]

    https://hal.inria.fr/hal-02335011

Scientific Books (or Scientific Book chapters)

  • 45N. Pisanti.

    Algorithms Foundations, in: Encyclopedia of Bioinformatics and Computational Biology, Elsevier, 2019, vol. 1, pp. 1-4. [ DOI : 10.1016/b978-0-12-809633-8.20315-4 ]

    https://hal.inria.fr/hal-01964689


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