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Bibliography

Publications of the year

Articles in International Peer-Reviewed Journals

  • 1R. Andonov, H. Djidjev, G. Klau, M. Boudic-Jamin, I. Wohlers.

    Automatic Classification of Protein Structure Using the Maximum Contact Map Overlap Metric, in: Algorithms and Combinatorics, December 2015, vol. 8, no 4. [ DOI : 10.3390/a8040850 ]

    https://hal.inria.fr/hal-01248543
  • 2A. C. Azevedo-Martins, A. C. L. Machado, C. C. Klein, L. Ciapina, L. Gonzaga, A. T. R. Vasconcelos, M.-F. Sagot, W. De Souza, M. Einicker-Lamas, A. Galina, M. C. M. Motta.

    Mitochondrial respiration and genomic analysis provide insight into the influence of the symbiotic bacterium on host trypanosomatid oxygen consumption, in: Parasitology, 2015, vol. 142, no 2, pp. 352-362. [ DOI : 10.1017/S0031182014001139 ]

    https://hal.inria.fr/hal-01073754
  • 3S. Baruah, V. Bonifaci, G. D'Angelo, H. Li, A. Marchetti-Spaccamela, S. Van Der Ster, L. Stougie.

    Preemptive Uniprocessor Scheduling of Mixed-Criticality Sporadic Task Systems, in: Journal of the ACM (JACM), May 2015, vol. 62, no 2, 14 p. [ DOI : 10.1145/2699435 ]

    https://hal.inria.fr/hal-01249091
  • 4C. Baudet, B. Donati, B. Sinaimeri, P. Crescenzi, C. Gautier, C. Matias, M.-F. Sagot.

    Cophylogeny Reconstruction via an Approximate Bayesian Computation, in: Systematic Biology, 2015, vol. 64, no 3, pp. 416-431. [ DOI : 10.1093/sysbio/syu129 ]

    https://hal.inria.fr/hal-01092972
  • 5M. Borassi, P. Crescenzi, M. Habib, W. A. Kosters, A. Marino, F. W. Takes.

    Fast diameter and radius BFS-based computation in (weakly connected) real-world graphs, in: Journal of Theoretical Computer Science (TCS), June 2015, vol. 586, pp. 59–80. [ DOI : 10.1016/j.tcs.2015.02.033 ]

    https://hal.inria.fr/hal-01248555
  • 6E. Bosi, B. Donati, M. Galardini, S. Brunetti, M.-F. Sagot, P. Lió, P. Crescenzi, R. Fani, M. Fondi.

    MeDuSa: A multi-draft based scaffolder, in: Bioinformatics (Oxford, England), March 2015, pii: btv171 [Epub ahead of print].

    https://hal.inria.fr/hal-01139506
  • 7L. Bulteau, G. Sacomoto, B. Sinaimeri.

    Computing an Evolutionary Ordering is Hard, in: Electronic Notes in Discrete Mathematics, 2015. [ DOI : 10.1016/j.endm.2015.07.043 ]

    https://hal.archives-ouvertes.fr/hal-01249259
  • 8S. Canzar, K. Elbassioni, G. W. Klau, J. Mestre.

    On Tree-Constrained Matchings and Generalizations, in: Algorithmica, January 2015, vol. 71, no 1. [ DOI : 10.1007/s00453-013-9785-0 ]

    https://hal.inria.fr/hal-01248542
  • 9R. Cijvat, S. Manegold, M. Kersten, G. W. Klau, A. Schönhuth, T. Marschall, Y. Zhang.

    Genome sequence analysis with MonetDB - A case study on Ebola virus diversity, in: Datenbank-Spektrum, November 2015, vol. 15, no 3. [ DOI : 10.1007/s13222-015-0198-x ]

    https://hal.inria.fr/hal-01248546
  • 10J. Correa, A. Marchetti-Spaccamela, J. Matuschke, L. Stougie, O. Svensson, V. Verdugo, J. Verschae.

    Strong LP formulations for scheduling splittable jobs on unrelated machines, in: Mathematical Programming, December 2015, vol. 154, no 1-2, pp. 305-328. [ DOI : 10.1007/s10107-014-0831-8 ]

    https://hal.inria.fr/hal-01249090
  • 11P. Crescenzi, D. Gildea, A. Marino, G. Rossi, G. Satta.

    Synchronous context-free grammars and optimal linear parsing strategies, in: Izvestia Rossiiskoi Akademii Nauk.Teoriya i Systemy Upravleniya / Journal of Computer and Systems Sciences International, November 2015, vol. 81, no 7, pp. 1333-1356. [ DOI : 10.1016/j.jcss.2015.04.003 ]

    https://hal.inria.fr/hal-01249108
  • 12M. Crochemore, R. Grossi, J. Kärkkäinen, G. M. Landau.

    Computing the Burrows–Wheeler transform in place and in small space, in: Journal of Discrete Algorithms, May 2015, vol. 32, pp. 44-52. [ DOI : 10.1016/j.jda.2015.01.004 ]

    https://hal.inria.fr/hal-01248855
  • 13P. DUMAS, F. Legeai, C. Lemaitre, E. Scaon, M. ORSUCCI, K. Labadie, S. Gimenez, A. L. Clamens, H. Henri, F. Vavre, J. M. Aury, P. Fournier, G. Kergoat, E. D'Alençon.

    Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species?, in: Genetica, 2015, vol. 143, no 3, pp. 305-316. [ DOI : 10.1007/s10709-015-9829-2 ]

    https://hal.archives-ouvertes.fr/hal-01208780
  • 14J. David, L. Lhote, A. Mary, F. Rioult.

    An average study of hypergraphs and their minimal transversals, in: Journal of Theoretical Computer Science (TCS), September 2015, vol. 596, pp. 124-141. [ DOI : 10.1016/j.tcs.2015.06.052 ]

    https://hal.archives-ouvertes.fr/hal-01086638
  • 15B. Donati, C. Baudet, B. Sinaimeri, P. Crescenzi, M.-F. Sagot.

    EUCALYPT: efficient tree reconciliation enumerator, in: Algorithms for Molecular Biology, January 2015, vol. 10, no 1, 11 p. [ DOI : 10.1186/s13015-014-0031-3 ]

    https://hal.inria.fr/hal-01092977
  • 16O. Duron, V. Noël, K. D. Mccoy, M. Bonazzi, K. Sidi-Boumedine, O. Morel, F. Vavre, L. Zenner, E. Jourdain, P. Durand, C. Arnathau, F. Renaud, J.-F. Trape, A. S. Biguezoton, J. Cremaschi, M. Dietrich, E. Léger, A. Appelgren, M. Dupraz, E. Gómez-Díaz, G. Diatta, G.-K. Dayo, H. Adakal, S. Zoungrana, L. Vial, C. Chevillon.

    The Recent Evolution of a Maternally-Inherited Endosymbiont of Ticks Led to the Emergence of the Q Fever Pathogen, Coxiella burnetii, in: PLoS Pathogens, May 2015, vol. 11, no 5. [ DOI : 10.1371/journal.ppat.1004892 ]

    https://hal.inria.fr/hal-01250470
  • 17M. Dyer, L. Stougie.

    Erratum to: Computational complexity of stochastic programming problems, in: Mathematical Programming, November 2015, vol. 153, no 2, pp. 723-725. [ DOI : 10.1007/s10107-015-0935-9 ]

    https://hal.inria.fr/hal-01249093
  • 18M. El-Kebir, J. Heringa, G. Klau.

    Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment, in: Algorithms and Combinatorics, December 2015, vol. 8, no 4. [ DOI : 10.3390/a8041035 ]

    https://hal.inria.fr/hal-01248544
  • 19M. El-Kebir, H. Soueidan, T. Hume, D. Beisser, M. Dittrich, T. Müller, G. Blin, J. Heringa, M. Nikolski, L. F. A. Wessels, G. W. Klau.

    xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model, in: Bioinformatics, 2015, vol. 31, no 19. [ DOI : 10.1093/bioinformatics/btv316 ]

    https://hal.inria.fr/hal-01248545
  • 20C. Goubert, L. Modolo, C. Vieira, C. ValienteMoro, P. Mavingui, M. Boulesteix.

    De novo assembly and annotation of the Asian tiger mosquito (Aedes albopictus) repeatome with dnaPipeTE from raw genomic reads and comparative analysis with the yellow fever mosquito (Aedes aegypti), in: Genome Biology and Evolution, March 2015, vol. 7, no 4, pp. 1192-205.

    https://hal.inria.fr/hal-01227710
  • 21E. Hellard, D. Fouchet, F. Vavre, D. Pontier.

    Parasite-Parasite Interactions in the Wild: How To Detect Them?, in: Trends in Parasitology, August 2015.

    https://hal.inria.fr/hal-01227711
  • 22S. Higashi, C. Fournier, C. Gautier, C. Gaspin, M.-F. Sagot.

    Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data, in: BMC Bioinformatics, 2015, vol. 16, no 1, 179 p. [ DOI : 10.1186/s12859-015-0594-0 ]

    https://hal.archives-ouvertes.fr/hal-01166487
  • 23A. Marchetti-Spaccamela, C. Rutten, S. Van Der Ster, A. Wiese.

    Assigning sporadic tasks to unrelated machines, in: Mathematical Programming, August 2015, vol. 152, no 1-2, pp. 247-274. [ DOI : 10.1007/s10107-014-0786-9 ]

    https://hal.inria.fr/hal-01249101
  • 24L. Mouton, O. Gnankiné, H. Henri, G. Terraz, G. Ketoh, T. Martin, F. Fleury, F. Vavre.

    Detection of genetically isolated entities within the Mediterranean species of Bemisia tabaci: new insights into the systematics of this worldwide pest, in: Pest Management Science, March 2015, vol. 71, no 3, pp. 452-458. [ DOI : 10.1002/ps.3834 ]

    https://hal.inria.fr/hal-01250472
  • 25M. Patterson, T. Marschall, N. Pisanti, L. Van Iersel, L. Stougie, G. W. Klau, A. Schönhuth.

    WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads, in: Journal of computational biology : a journal of computational molecular cell biology, May 2015, vol. 22, no 6, pp. 498-509. [ DOI : 10.1089/cmb.2014.0157 ]

    https://hal.inria.fr/hal-01225988
  • 26Y. Pirola, S. Zaccaria, R. Dondi, G. W. Klau, N. Pisanti, P. Bonizzoni.

    HapCol: accurate and memory-efficient haplotype assembly from long reads, in: Bioinformatics, 2015. [ DOI : 10.1093/bioinformatics/btv495 ]

    https://hal.inria.fr/hal-01225984
  • 27Q. Rao, P.-A. Rollat-Farnier, D.-T. Zhu, D. Santos-Garcia, F. J. Silva, A. Moya, A. Latorre, C. C. Klein, F. Vavre, M.-F. Sagot, S.-S. Liu, L. Mouton, X.-W. Wang.

    Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci, in: BMC Genomics, December 2015, vol. 16, 226 p. [ DOI : 10.1186/s12864-015-1379-6 ]

    https://hal.inria.fr/hal-01139508
  • 28A. C. Reimers, F. J. Bruggeman, B. G. Olivier, L. Stougie.

    Fast Flux Module Detection Using Matroid Theory, in: Journal of Computational Biology, May 2015, vol. 22, no 5. [ DOI : 10.1089/cmb.2014.0141 ]

    https://hal.inria.fr/hal-01227722
  • 29P.-A. Rollat-Farnier, D. Santos-Garcia, Q. Rao, M.-F. Sagot, F. J. Silva, H. Henri, E. Zchori-Fein, A. Latorre, A. Moya, V. Barbe, S.-S. Liu, X.-W. Wang, F. Vavre, L. Mouton.

    Two Host Clades, Two Bacterial Arsenals: Evolution through Gene Losses in Facultative Endosymbionts, in: Genome Biology and Evolution, 2015, vol. 7, no 3, pp. 839-855.

    https://hal.inria.fr/hal-01139507
  • 30G. Sacomoto, V. Lacroix, M. Sagot.

    A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs, in: Algorithms for Molecular Biology, 2015, 10 p. [ DOI : 10.1186/s13015-015-0046-4 ]

    https://hal.inria.fr/hal-01170399
  • 31F. Schalekamp, R. Sitters, S. Van Der Ster, L. Stougie, V. Verdugo, A. Van Zuylen.

    Split scheduling with uniform setup times, in: Journal of Scheduling, April 2015, vol. 18, no 2, pp. 119-129. [ DOI : 10.1007/s10951-014-0370-4 ]

    https://hal.inria.fr/hal-01249095

International Conferences with Proceedings

  • 32R. Andrade, E. Birmelé, A. Mary, T. Picchetti, M.-F. Sagot.

    Incremental complexity of a bi-objective hypergraph transversal problem, in: Fundamentals of Computation Theory (FCT2015), Gdansk, Poland, Fundamentals of Computation Theory (FCT2015), 2015, vol. 9210.

    https://hal.archives-ouvertes.fr/hal-01149392
  • 33S. K. Baruah, V. Bonifaci, A. Marchetti-Spaccamela.

    The Global EDF Scheduling of Systems of Conditional Sporadic DAG Tasks, in: ECRTS 2015 - Euromicro Conference on Real-Time Systems, Lund, Sweden, July 2015, pp. 222-231. [ DOI : 10.1109/ECRTS.2015.27 ]

    https://hal.inria.fr/hal-01249105
  • 34L. Bettini, P. Crescenzi.

    Java-Meets Eclipse - An IDE for Teaching Java Following the Object-later Approach, in: International Conference on Software Paradigm Trend (ICSOFT-PT), Colmar, France, September 2015, pp. 31-42. [ DOI : 10.5220/0005512600310042 ]

    https://hal.inria.fr/hal-01249109
  • 35P. Bonizzoni, R. Dondi, G. W. Klau, Y. Pirola, N. Pisanti, S. Zaccaria.

    On the Fixed Parameter Tractability and Approximability of the Minimum Error Correction Problem, in: 26th Annual Symposium on Combinatorial Pattern Matching (CPM), Ischia, Italy, June 2015. [ DOI : 10.1007/978-3-319-19929-0 ]

    https://hal.inria.fr/hal-01246260
  • 36M. Borassi, D. Coudert, P. Crescenzi, A. Marino.

    On Computing the Hyperbolicity of Real-World Graphs, in: 23rd Annual European Symposium on Algorithms (ESA), Patras, Greece, Lecture Notes in Computer Science, Springer, September 2015, vol. 9294, pp. 215-226. [ DOI : 10.1007/978-3-662-48350-3_19 ]

    https://hal.inria.fr/hal-01199860
  • 37S. Canzar, A. Sandro, D. Weese, R. Knut, K. Gunnar.

    CIDANE: Comprehensive Isoform Discovery and Abundance Estimation, in: Research in Computational Molecular Biology (RECOMB), Warsaw, Poland, April 2015, vol. 9029, pp. 60-84. [ DOI : 10.1007/978-3-319-16706-0_8 ]

    https://hal.inria.fr/hal-01248849
  • 38L. Chen, N. Megow, R. Rischke, L. Stougie.

    Stochastic and Robust Scheduling in the Cloud, in: Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM), Princeton, United States, August 2015, pp. 175-186. [ DOI : 10.4230/LIPIcs.APPROX-RANDOM.2015.175 ]

    https://hal.inria.fr/hal-01249100
  • 39L. Chen, N. Megow, R. Rischke, L. Stougie, J. Verschae.

    Optimal Algorithms and a PTAS for Cost-Aware Scheduling, in: Mathematical Foundations of Computer Science (MFCS), Milan, Italy, August 2015, vol. 9235, pp. 211-222. [ DOI : 10.1007/978-3-662-48054-0_18 ]

    https://hal.inria.fr/hal-01249098
  • 40P. Crescenzi, G. D'Angelo, S. Lorenzo, V. Yllka.

    Greedily Improving Our Own Centrality in A Network, in: Experimental Algorithms - SEA, Paris, France, June 2015, vol. 9125, pp. 43-55. [ DOI : 10.1007/978-3-319-20086-6_4 ]

    https://hal.inria.fr/hal-01248558
  • 41R. Grossi, C. S. Iliopoulos, R. Mercas, N. Pisanti, S. Pissis, A. Retha, F. Vayani.

    Circular Sequence Comparison with q-grams, in: 15th International Conference on Algorithms in BioInformatics (WABI), Atlanta, United States, September 2015. [ DOI : 10.1007/978-3-662-48221-6_15 ]

    https://hal.inria.fr/hal-01246271
  • 42M. M. Kanté, V. Limouzy, A. Mary, L. Nourine, T. Uno.

    Polynomial Delay Algorithm for Listing Minimal Edge Dominating Sets in Graphs, in: Algorithms and Data Structures (WADS), Victoria, Canada, August 2015, vol. 9214, pp. 446-457. [ DOI : 10.1007/978-3-319-21840-3_37 ]

    https://hal.inria.fr/hal-01248851
  • 43A. Melani, M. Bertogna, V. Bonifaci, A. Marchetti-Spaccamela, G. Buttazzo.

    Memory-processor co-scheduling in fixed priority systems, in: International Conference on Real Time and Networks Systems (RTNS), Lille, France, November 2015, pp. 87-96. [ DOI : 10.1145/2834848.2834854 ]

    https://hal.inria.fr/hal-01249107
  • 44A. Melani, V. Bonifaci, M. Bertogna, A. Marchetti-Spaccamela, G. Buttazzo.

    Response-Time Analysis of Conditional DAG Tasks in Multiprocessor Systems, in: ECRTS 2015 - Euromicro Conference on Real-Time Systems, Lund, Sweden, July 2015, pp. 211-221. [ DOI : 10.1109/ECRTS.2015.26 ]

    https://hal.inria.fr/hal-01249103
  • 45M. F. Zini, N. Pisanti, E. Biasci, A. Podda, V. Mey, F. Piras, G. L'Abbate, S. Marini, D. Fratta, S. Bonaretti, S. Trasciatti.

    Preclinical Tests for Cerebral Stroke, in: The 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM), Paris, France, August 2015. [ DOI : 10.1145/2808797.2808816 ]

    https://hal.inria.fr/hal-01246340


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