Publications 2017

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, 2017 [epub]
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