Team, Visitors, External Collaborators
Overall Objectives
Research Program
Application Domains
Highlights of the Year
New Software and Platforms
New Results
Partnerships and Cooperations
Dissemination
Bibliography
XML PDF e-pub
PDF e-Pub


Bibliography

Major publications by the team in recent years
[1]
P. Almeida, C. Gonçalves, S. Teixeira, D. Libkind, M. Bontrager, I. Masneu-Pomarède, W. Albertin, P. Durrens, D. J. Sherman, P. Marullo, C. Todd Hittinger, P. Gonçalves, J. P. Sampaio.
A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum., in: Nature Communications, 2014, vol. 5, 4044 p. [ DOI : 10.1038/ncomms5044 ]
https://hal.inria.fr/hal-01002466
[2]
R. Assar, M. A. Montecino, A. Maass, D. J. Sherman.
Modeling acclimatization by hybrid systems: Condition changes alter biological system behavior models, in: BioSystems, June 2014, vol. 121, pp. 43-53. [ DOI : 10.1016/j.biosystems.2014.05.007 ]
https://hal.inria.fr/hal-01002987
[3]
D. J. Sherman, T. Martin, M. Nikolski, C. Cayla, J.-L. Souciet, P. Durrens.
Genolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes., in: Nucleic Acids Research, 2009, vol. 37, pp. D550-D554. [ DOI : 10.1093/nar/gkn859 ]
https://hal.inria.fr/inria-00341578
Publications of the year

Articles in International Peer-Reviewed Journals

[4]
B. Bailet, A. Bouchez, A. A. Franc, J.-M. Frigerio, F. Keck, S.-M. Karjalainen, F. Rimet, S. Schneider, M. Kahlert.
Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status, in: Metabarcoding and Metagenomics, June 2019, vol. 3. [ DOI : 10.3897/mbmg.3.34002 ]
https://hal.inria.fr/hal-02432989
[5]
H. Caron, J. Molino, D. Sabatier, P. P. Léger, P. Chaumeil, C. Scotti-Saintagne, J.-M. Frigerio, I. Scotti, A. A. Franc, R. J. Petit.
Chloroplast DNA variation in a hyperdiverse tropical tree community, in: Ecology and Evolution, March 2019, vol. 9, no 8, pp. 4897-4905. [ DOI : 10.1002/ece3.5096 ]
https://hal.umontpellier.fr/hal-02108230
[6]
A. A. Franc, P. Blanchard, O. Coulaud.
Nonlinear mapping and distance geometry, in: Optimization Letters, May 2019. [ DOI : 10.1007/s11590-019-01431-y ]
https://hal.inria.fr/hal-02124882
[7]
P. Marullo, P. Durrens, E. Peltier, M. Bernard, C. Mansour, D. Dubourdieu.
Natural allelic variations of Saccharomyces cerevisiae impact stuck fermentation due to the combined effect of ethanol and temperature; a QTL-mapping study, in: BMC Genomics, December 2019, vol. 20, no 1. [ DOI : 10.1186/s12864-019-5959-8 ]
https://hal.archives-ouvertes.fr/hal-02378470
[8]
N. D. P. Peyrard, S. De Givry, A. A. Franc, S. Robin, R. R. Sabbadin, T. Schiex, M. Vignes.
Exact or approximate inference in graphical models: why the choice is dictated by the treewidth, and how variable elimination can be exploited, in: Australian and New Zealand Journal of Statistics, June 2019, vol. 61, no 2, pp. 89-133. [ DOI : 10.1111/anzs.12257 ]
https://hal.inria.fr/hal-02433018

Internal Reports

[9]
S. Kanchan.
In silico comparative function prediction of enzymes, applied to fatty acid metabolism in microalgae : Final Report, Inria Bordeaux Sud-Ouest, December 2019.
https://hal.inria.fr/hal-02431250
References in notes
[10]
R. Alur.
SIGPLAN Notices, in: Generating Embedded Software from Hierarchical Hybrid Models, 2003, vol. 38, no 7, pp. 171–82.
[11]
B. Arnold, R. Corbett-Detig, D. Hartl, K. Bomblies.
RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling, in: Mol. Ecol., 2013, vol. 22, no 11, pp. 3179–90.
[12]
R. Assar, A. V. Leisewitz, A. Garcia, N. C. Inestrosa, M. A. Montecino, D. J. Sherman.
Reusing and composing models of cell fate regulation of human bone precursor cells, in: BioSystems, April 2012, vol. 108, no 1-3, pp. 63-72. [ DOI : 10.1016/j.biosystems.2012.01.008 ]
https://hal.inria.fr/hal-00681022
[13]
R. Assar, D. J. Sherman.
Implementing biological hybrid systems: Allowing composition and avoiding stiffness, in: Applied Mathematics and Computation, August 2013, vol. 223, pp. 167–79.
https://hal.inria.fr/hal-00853997
[14]
R. Assar, F. Vargas, D. J. Sherman.
Reconciling competing models: a case study of wine fermentation kinetics, in: Algebraic and Numeric Biology 2010, Hagenberg, Austria, K. Horimoto, M. Nakatsui, N. Popov (editors), Springer, July 2010, vol. 6479, pp. 68–83. [ DOI : 10.1007/978-3-642-28067-2_6 ]
https://hal.inria.fr/inria-00541215
[15]
M. Bakonyi, C. R. Johnson.
The Euclidean Distance Matrix Completion Problem, in: SIAM J. Matrix Anal. App., 1995, vol. 16, no 2, pp. 646-654.
[16]
P. Blanchard, P. Chaumeil, J.-M. Frigerio, F. RIMET, F. Salin, S. Thérond, O. Coulaud, A. Franc.
A geometric view of Biodiversity: scaling to metagenomics, Inria ; INRA, January 2018, no RR-9144, pp. 1-16, https://arxiv.org/abs/1803.02272.
https://hal.inria.fr/hal-01685711
[17]
E. J. Candès, B. Recht.
Exact Matrix Completion via Convex Optimization, in: Found. Comput. Math., 2009, vol. 9, pp. 717-772.
[18]
A. Carlsson, J. Yilmaz, A. Green, S. Stymne, P. Hofvander.
Replacing fossil oil with fresh oil - with what and for what?, in: Eur J Lipid Sci Technol, 2011, vol. 113, no 7, pp. 812-831.
[19]
C. Combes.
Parasitism: The Ecology and Evolution of Intimate Interactions, University of Chicago Press, 2001.
[20]
P. Gayral, J. Melo-Ferreira, S. Glemin.
Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap, in: PLoS Genetic, 2013, vol. 9, no 4, e1003457.
[21]
M. Hasimoto, S. Hossain, A. Al Mamun, K. Matsuzaki, H. Arai.
Docosahexaenoic acid: one molecule diverse functions, in: Crit Rev Biotechnol., Aug 2017, vol. 37, no 5, pp. 579-597.
http://dx.doi.org/10.1080/07388551.2016.1207153
[22]
L. Liberti, C. Lavor, N. Maculan, A. Mucherino.
Euclidean Distance Geometry and Applications, in: SIAM review, 2014, vol. 56(1), pp. 3-69.
[23]
M. Lynch.
Estimation of Nucleotide Diversity, Disequilibrium Coefficients, and Mutation Rates from High-Coverage Genome-Sequencing Projects, in: Mol. Biol. Evol., 2008, vol. 25, no 11, pp. 2409–19.
[24]
F. Morcillo, D. Cros, N. Billotte, G. Ngando-Ebongue, H. Domonhédo, M. Pizot, T. Cuéllar, S. Espéout, R. Dhouib, F. Bourgis, S. Claverol, T. Tranbarger, B. Nouy, V. Arondel.
Improving palm oil quality through identification and mapping of the lipase gene causing oil deterioration, in: Nat Commun, 2013, vol. 4, 2160 p.
http://dx.doi.org/10.1038/ncomms3160
[25]
R. E. Ricklefs.
A comprehensive framework for global patterns in biodiversity, in: Ecology Letters, 2004, vol. 7, no 1, pp. 1–15.
http://dx.doi.org/10.1046/j.1461-0248.2003.00554.x
[26]
F. Rimet, P. Chaumeil, F. Keck, L. Kermarrec, V. Vasselon, M. Kahlert, A. Franc, A. Bouchez.
R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring, in: Database - The journal of Biological Databases and Curation, February 2016, vol. 2016. [ DOI : 10.1093/database/baw016 ]
https://hal.inria.fr/hal-01426772
[27]
S. T. Roweis, Z. Ghahramani.
A unifying review of linear Gaussian Models, in: Neural Computation, 1999, vol. 11, no 2, pp. 305–45.
[28]
L. K. Saul, S. T. Roweis.
Think globally, fit locally: unsupervised learning of low dimensional manifolds, in: Journal of Machine Learning Research, 2003, vol. 4, pp. 119–55.
[29]
D. W. Thompson.
On Growth and Form, Cambridge University Press, 1917.
[30]
J. Wang.
Geometric structure of high-dimensional data and dimensionality reduction, Springer & Higher Education Press, 2012.