Publications 2017

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.

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.

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.

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.

Deciphering the demographic history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa.

Deciphering the demographic history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa.
Leblois R, Gautier M, Rohfritsch A, Foucaud J, Burban C, Galan M, Loiseau A, Sauné L, Branco M, Gharbi K, Vitalis R, Kerdelhué C. Mol Ecol. 2018 Jan;27(1):264-278. doi: 10.1111/mec.14411.

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.

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.

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.

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.

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 :

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 :

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 :

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 : .PDF :

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 : . PDF :

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 : .PDF :

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 : . PDF :

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 : . PDF :

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 : PDF :

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)

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: ; 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)

LZ78 Compression in Low Main Memory Space

Diego Arroyuelo, Rodrigo Canovas, Gonzalo Navarro, and Rajeev Raman.
Proc. SPIRE'17, Springer-Verlag,  LNCS vol. 10508,  p. 38-50, 2017.
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De novo assembly of viral quasispecies using overlap graphs

Baaijens J.A., Zine El Aabidine A., Rivals E., Schönhuth A.
Genome Research, 2017 [epub]

Likelihood-free model choice

Marin J-M, Pudlo P., Estoup A., Robert C.
Handbook of Approximate Bayesian Computation, Chapman and Hall/CRC, 2017

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

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

The combinatorics of overlapping genes

Lebre S., Gascuel O.
Journal of Theoretical Biology, Volume 415, 21 February 2017, Pages 90-101 2017

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