Publications 2017

Full Compressed Affix Tree Representations

R. Canovas, E. Rivals
Proceedings of  Data Compression Conference (DCC),  IEEE Computer Society Press, p. 102-111, 2017.                   URL : https://www.computer.org/csdl/proceedings/dcc/2017/6721/00/07921905.pdf

REHH 2.0: a reimplementation of the R package REHH to detect positive selection from haplotype structure

Gautier M., Klassmann A., Vitalis R.
Molecular Ecology Resources, Volume 17, January 2017, Pages 78-90 DOI: 10.1111/1755-0998.12634
URL : https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12634
PDF : https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.12634

Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time

Frachon L., Libourel C., Villoutreix R., Carrère S., Glorieux C., Huard-Chauveau C., Navascués M., Gay L., Vitalis R., Bron E., Amsellem L., Bouchez O., Vidal M., Le Corre V., Roby D., Bergelson J., Roux F.
Nature Ecology & Evolution, Volume 1, September 2017, Pages 1551-1561

DOI: 10.1038/s41559-017-0297-1
URL : https://www.nature.com/articles/s41559-017-0297-1

Rearrangement Moves on Rooted Phylogenetic Networks.

Philippe Gambette, Leo van Iersel, Mark Jones, Manuel Lafond, Fabio Pardi, Celine Scornavacca.
PLOS Computational Biology, 13(2017), no. 8, p e1005611.
URL: https://doi.org/10.1371/journal.pcbi.1005611

Inferring incomplete lineage sorting, duplications, transfers and losses with reconciliations.

Yao-ban Chan, Vincent Ranwez, Celine Scornavacca.
Journal of Theoretical Biology 432(2017), no. 2, pp 404-417.
https://doi.org/10.1016/j.jtbi.2017.08.008

Constructing a Consensus Phylogeny from a Leaf-Removal Distance

Cedric Chauve, Mark Jones, Manuel Lafond, Celine Scornavacca, Mathias Weller.
SPIRE 2017. LNCS vol. 10508, Springer International Publishing, 2017, pp. 129-143, 2017.
URL: https://link.springer.com/chapter/10.1007/978-3-319-67428-5_12
URL: https://arxiv.org/abs/1705.05295

Resampling: An improvement of importance sampling in varying population size models

Merle C, Leblois R, Rousset F, Pudlo P. Theor Popul Biol. 2017 Apr;114:70-87. doi: 10.1016/j.tpb.2016.09.002.
URL: https://www.sciencedirect.com/science/article/pii/S0040580916300557?via%3Dihub

Genetic structure and invasion history of the house mouse (Mus musculus domesticus) in Senegal, West Africa: a legacy of colonial and contemporary times

Lippens C, Estoup A, Hima MK, Loiseau A, Tatard C, Dalecky A, Bâ K, Kane M, Diallo M, Sow A, Niang Y, Piry S, Berthier K, Leblois R, Duplantier JM, Brouat C. Heredity (Edinb). 2017 Aug;119(2):64-75. doi: 10.1038/hdy.2017.18.
URL: https://www.nature.com/articles/hdy201718

Demographic inference through approximate-Bayesian-computation skyline plots.

Navascués M, Leblois R, Burgarella C. PeerJ. 2017 Jul 18;5:e3530. doi: 10.7717/peerj.3530. eCollection 2017.
URL: https://peerj.com/articles/3530/
PDF: https://peerj.com/articles/3530.pdf

A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes

Bonnet T, Leblois R, Rousset F, Crochet PA. Evolution. 2017 Sep;71(9):2140-2158. doi: 10.1111/evo.13296.

Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats

Wereszczuk A, Leblois R, Zalewski A. BMC Ecol. 2017 Dec 22;17(1):46. doi: 10.1186/s12898-017-0156-6.
URL: https://academic.oup.com/dote/advance-article-abstract/doi/10.1093/dote/dox128/4569321?redirectedFrom=fulltext

New insights into diagnosis and therapeutic options for proliferative hepatoblastoma

Hooks KB, Audoux J, Fazli H, Lesjean S, Ernault T, Senant ND, Leste-Lasserre T, Hagedorn M, Rousseau B, Danet C, Branchereau S, Brugières L, Taque S, Guettier C, Fabre M, Rullier A, Buendia MA, Commes T, Grosset CF, Raymond AA.
Hepatology. 2017 Nov 20. doi: 10.1002/hep.29672.
URL: http://onlinelibrary.wiley.com/doi/10.1002/hep.29672/abstract;jsessionid=8FDA69B2312B9B61B13F02033094F411.f02t02

DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition

Audoux J, Philippe N, Chikhi R, Salson M, Gallopin M, Gabriel M, Le Coz J, Drouineau E, Commes T, Gautheret D.
Genome Biol. 2017 Dec 28;18(1):243. doi: 10.1186/s13059-017-1372-2.
URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1372-2
PDF: https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-017-1372-2?site=genomebiology.biomedcentral.com

SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines

Audoux J, Salson M, Grosset CF, Beaumeunier S, Holder JM, Commes T, Philippe N.
BMC Bioinformatics. 2017 Sep 29;18(1):428. doi: 10.1186/s12859-017-1831-5.
URL: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1831-5
PDF: https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1831-5?site=bmcbioinformatics.biomedcentral.com

Virtual Plants Need Water Too: Functional-Structural Root System Models in the Context of Drought Tolerance Breeding

Ndour A., Vadez V., Pradal C., Lucas M. Frontiers in Plant Science, 8:1577, 2017. URL : https://doi.org/10.3389/fpls.2017.01577

Reshaping Plant Biology: Qualitative and Quantitative Descriptors for Plant Morphology.

Balduzzi M., Binder BM.., Bucksch A., Chang C., Hong L., Iyer-Pascuzzi A.S., Pradal C., Sparks E.E. Frontiers in Plant Science, 8:117, 2017. URL : https://doi.org/10.3389/fpls.2017.00117

Modelling interaction dynamics between two foliar pathogens in wheat: a multi-scale approach.

Garin G., Pradal C., Fournier C., Claessen D., Houlès V., Robert C. Annals of botany, 2017. URL : https://doi.org/10.1093/aob/mcx186

InfraPhenoGrid: A scientific workflow infrastructure for Plant Phenomics on the Grid.

Pradal C., Artzet S., Chopard J., Dupuis D., Fournier C., Mielewczik M., Negre V., Neveu P., Parigot D., Valduriez P., Cohen-Boulakia S. Future Generation Computer Systems, Elsevier, 67, 341-353, 2017. URL : https://doi.org/10.1016/j.future.2016.06.002 .PDF : https://hal.inria.fr/hal-01336655/document

Raw data queries during data-intensive parallel workflow execution

Silva V., Leite J., Camata J., De Oliveira D., Coutinho, A., Valduriez P., Mattoso M. Future Generation Computer Systems, Elsevier, 75, 402-422., 2017. URL : https://doi.org/10.1016/j.future.2017.01.016 . PDF : https://hal-lirmm.ccsd.cnrs.fr/lirmm-01445219/document

Scientific Workflow Scheduling with Provenance Data in a Multisite Cloud.

Liu J., Pacitti E., Valduriez P., Mattoso M. Transactions on Large-Scale Data- and Knowledge-Centered Systems, Springer, 33:80-112, 2017. URL : https://hal-lirmm.ccsd.cnrs.fr/lirmm-01620224 .PDF : https://hal-lirmm.ccsd.cnrs.fr/lirmm-01620224/document

DPiSAX: Massively Distributed Partitioned iSAX.

Yagoubi D-E., Akbarinia R., Masseglia F., Palpanas T. IEEE International Conference on Data Mining, pp.1-6, 2017. URL : https://hal-lirmm.ccsd.cnrs.fr/lirmm-01620125 . PDF : https://hal-lirmm.ccsd.cnrs.fr/lirmm-01620125/document

Spark Scalability Analysis in a Scientific Workflow.

Souza R., Silva V., Miranda P.,  Lima A., Valduriez P., Mattoso M. Brazilian Symposium on Databases, pp.1-6, 2017. Best paper award. URL : https://hal-lirmm.ccsd.cnrs.fr/lirmm-01620161 . PDF : https://hal-lirmm.ccsd.cnrs.fr/lirmm-01620161/document

Pre-processing and Indexing techniques for Constellation Queries in Big Data.

Khatibi A., Porto F., Rittmeyer J., Ogasawara E., Valduriez P., Shasha D. International Conference on Big Data Analytics and Knowledge Discovery, Springer, LNCS, pp.74-87, 2017. URL : https://hal-lirmm.ccsd.cnrs.fr/lirmm-01620398. PDF : https://hal-lirmm.ccsd.cnrs.fr/lirmm-01620398/document

Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities.

Cohen-Boulakia S., Belhajjame K., Collin C., Chopard J., Froidevaux C., Gaignard A., Hinsen K., Larmande P.,  Le Bras Y., Lemoine F., Mareuil F., Ménager H., Pradal C.,  Blanchet C. . Futur. Gener. Comput. Syst. 75 : 284-298. doi: 10.1016/j.future.2017.01.012

Developing data interoperability using standards: A wheat community use case

Dzale Yeumo E., Alaux M., Arnaud E., Aubin S., Baumann U., Buche P., Cooper L., Ćwiek-Kupczyńska H., Davey R.P., Fulss R.A., Jonquet C., Laporte M., Larmande P., Pommier C., Protonotarios V., Reverte C., Shrestha R., Subirats I., Venkatesan A., Whan A., Quesneville H. F1000Research 2017, 6:1843 doi: 10.12688/f1000research.12234.2. 2017.

Population genomics of picophytoplankton unveils novel chromosome hypervariability

Population genomics of picophytoplankton unveils novel chromosome hypervariability
R. Blanc-Mathieu, M. Krasovec, M. Hébrard, S. Yau, E. Desgranges, J. Martin, W. Schackwitz, A. Kuo, G. Salin, C. Donnadieu, Y. Desdevises, S. Sanchez-Ferandin, H. Moreau, E. Rivals, I. Grigoriev, N. Grimsley, AC Eyre-Walker, G. Piganeau
Science Advances 3(7), e1700239, doi: 10.1126/sciadv.1700239, 2017.

The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies

The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies
X. Argout, G. Martin, G. Droc, O. Fouet, K. Labadie, E. Rivals, J.M. Aury, C. Lanaud
BMC Genomics 18:730, DOI: 10.1186/s12864-017-4120-9 2017.

Fbw7α stability in M-phase requires its phosphorylation by PKC.

Zitouni, S., Mechali, F., Papin, C., Choquet, A., Roche, D. B., Baldin, V., Coux, O. & Bonne-Andréa, C.
PLoS ONE, 12(8): e0183500 (2017)
PDF:

Accurate Template Based Modelling in CASP12 using the IntFOLD4-TS, ModFOLD6 and ReFOLD methods

McGuffin, L.J., Shuid, A. N., Kempster, R., Maghrabi, A. H. A., Nealon, J. O., Salehe, B. R., Atkins, J. D., Roche, D. B.
PROTEINS: Structure, Function, and Bioinformatics, doi: 10.1002/prot.25360  (2017)
PDF: http://onlinelibrary.wiley.com/doi/10.1002/prot.25360/full ; DOI: 10.1002/prot.25360

Usage of a dataset of NMR resolved protein structures to test aggregation vs. solubility prediction algorithms

Roche, D. B., Villain, E. & Kajava, A. V..
Data C Protein Science, 26(9):1864-1869 (2017)
PDF: http://onlinelibrary.wiley.com/doi/10.1002/pro.3225/epdf

LZ78 Compression in Low Main Memory Space

Diego Arroyuelo, Rodrigo Canovas, Gonzalo Navarro, and Rajeev Raman.
  [abstract]
Proc. SPIRE'17, Springer-Verlag,  LNCS vol. 10508,  p. 38-50, 2017.
URL; https://link.springer.com/chapter/10.1007/978-3-319-67428-5_4 .
PDF : https://www.dcc.uchile.cl/~gnavarro/ps/spire17.2.pdf .

De novo assembly of viral quasispecies using overlap graphs

Baaijens J.A., Zine El Aabidine A., Rivals E., Schönhuth A.
Genome Research, 27: 835-848, 2017.
URL : http://genome.cshlp.org/content/early/2017/04/10/gr.215038.116

Likelihood-free model choice

Marin J-M, Pudlo P., Estoup A., Robert C.
Handbook of Approximate Bayesian Computation, Chapman and Hall/CRC, 2017
URL : https://arxiv.org/pdf/1503.07689.pdf

Ribo-seq enlightens codon usage bias

On the fixed parameter tractability of agreement-based phylogenetic distances

Bordewich M., Scornavacca C., Tokac N., Weller M.
Journal of Mathematical Biology 74:239-257, 2017
URL : http://link.springer.com/article/10.1007%2Fs00285-016-1023-3

Linking indexing data structures to de Bruijn graphs: Construction and update

The summary-likelihood method and its implementation in the Infusion package

Rousset F., Gouy A., Martinez-Almoyna C., Courtiol A.
Molecular Ecology Resources, 17:110–119, 2017
URL : http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12627/abstract
PDF : http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12627/pdf

The combinatorics of overlapping genes

Lebre S., Gascuel O.
Journal of Theoretical Biology, Volume 415, 21 February 2017, Pages 90-101 2017
URL : https://arxiv.org/abs/1602.04971
PDF : https://arxiv.org/ftp/arxiv/papers/1602/1602.04971.pdf

Accurate self-correction of errors in long reads using de Bruijn graphs

Salmela L., Walve R., Rivals E., Ukkonen E.
Bioinformatics, Volume 33, Issue 6, 15 March 2017, Pages 799–806, 2017
URL : https://doi.org/10.1093/bioinformatics/btw321
PDF : https://hal.archives-ouvertes.fr/lirmm-01385006/document

Publications

Deciphering the Routes of invasion of Drosophila suzukii by Means of ABC Random Forest
Antoine Fraimout, Vincent Debat, Simon Fellous, Ruth A. Hufbauer, Julien Foucaud, Pierre Pudlo, Jean-Michel Marin, Donald K. Price, Julien Cattel, Xiao Chen, Marindia Deprá, Pierre François Duyck, Christelle Guedot, Marc Kenis, Masahito T. Kimura, Gregory Loeb, Anne Loiseau, Isabel Martinez-Sañudo, Marta Pascual, Maxi Polihronakis Richmond, Peter Shearer, Nadia Singh, Koichiro Tamura,  Anne Xuéreb, Jinping Zhang and Arnaud Estoup
Molecular Biology and Evolution, Volume 34, Issue 4, 1 April 2017
Pages 980–996
URL : https://doi.org/10.1093/molbev/msx050