Personnel
Overall Objectives
Research Program
Application Domains
New Software and Platforms
New Results
Partnerships and Cooperations
Dissemination
Bibliography
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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]
A. B. Canelas, N. Harrison, A. Fazio, J. Zhang, J.-P. Pitkänen, J. Van Den Brink, B. M. Bakker, L. Bogner, J. Bouwman, J. I. Castrillo, A. Cankorur, P. Chumnanpuen, P. Daran-Lapujade, D. Dikicioglu, K. Van Eunen, J. C. Ewald, J. J. Heijnen, B. Kirdar, I. Mattila, F. I. C. Mensonides, A. Niebel, M. Penttilä, J. T. Pronk, M. Reuss, L. Salusjärvi, U. Sauer, D. J. Sherman, M. Siemann-Herzberg, H. Westerhoff, J. De Winde, D. Petranovic, S. G. Oliver, C. T. Workman, N. Zamboni, J. Nielsen.
Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference y east strains, in: Nature Communications, December 2010, vol. 1, no 9, 145 p. [ DOI : 10.1038/ncomms1150 ]
https://hal.inria.fr/inria-00562005
[4]
L. Kermarrec, A. Franc, F. Rimet, P. Chaumeil, J.-M. Frigerio, J.-F. Humbert, A. Bouchez.
A next-generation sequencing approach to river biomonitoring using benthic diatoms, in: Freshwater Science, 2014, vol. 33, no 1, pp. 349-363.
http://www.jstor.org/stable/10.1086/675079
[5]
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
[6]
J.-L. Souciet, B. Dujon, C. Gaillardin, M. Johnston, P. V. Baret, P. Cliften, D. J. Sherman, J. Weissenbach, E. Westhof, P. Wincker, C. Jubin, J. Poulain, V. Barbe, B. Ségurens, F. Artiguenave, V. Anthouard, B. Vacherie, M.-E. Val, R. S. Fulton, P. Minx, R. Wilson, P. Durrens, G. Jean, C. Marck, T. Martin, M. Nikolski, T. Rolland, M.-L. Seret, S. Casaregola, L. Despons, C. Fairhead, G. Fischer, I. Lafontaine, V. Leh, M. Lemaire, J. De Montigny, C. Neuveglise, A. Thierry, I. Blanc-Lenfle, C. Bleykasten, J. Diffels, E. Fritsch, L. Frangeul, A. Goeffon, N. Jauniaux, R. Kachouri-Lafond, C. Payen, S. Potier, L. Pribylova, C. Ozanne, G.-F. Richard, C. Sacerdot, M.-L. Straub, E. Talla.
Comparative genomics of protoploid Saccharomycetaceae, in: Genome Research, 2009, vol. 19, pp. 1696-1709. [ DOI : 10.1101/gr.091546.109 ]
https://hal.inria.fr/inria-00407511
Publications of the year

Articles in International Peer-Reviewed Journals

[7]
W. Albertin, M. Chernova, P. Durrens, E. Guichoux, D. J. Sherman, I. Masneuf-Pomarede, P. Marullo.
Many interspecific chromosomal introgressions are highly prevalent in Holarctic Saccharomyces uvarum strains found in human-related fermentations, in: Yeast, August 2017, pp. 1-20. [ DOI : 10.1002/yea.3248 ]
https://hal.inria.fr/hal-01585808
[8]
A. Bretagnolle, A. Franc.
Emergence of an integrated city-system in France (XVIIth–XIXth centuries): Evidence from toolset in graph theory, in: Historical Methods: A Journal of Quantitative and Interdisciplinary History, 2017, vol. 50, no 1, pp. 49-65. [ DOI : 10.1080/01615440.2016.1237915 ]
https://hal.archives-ouvertes.fr/hal-01603847
[9]
J. Brusini, M. L. Wayne, A. Franc, C. Robin.
The impact of parasitism on resource allocation in a fungal host: the case of Cryphonectria parasitica and its mycovirus, Cryphonectria Hypovirus 1, in: Ecology and Evolution, 2017, vol. 7, no 15, pp. 5967–5976. [ DOI : 10.1002/ece3.3143 ]
https://hal.archives-ouvertes.fr/hal-01608310
[10]
H. Campbell-Sills, M. El Khoury, M. Gammacurta, C. Miot-Sertier, L. Dutilh, J. Vestner, V. Capozzi, D. J. Sherman, C. Hubert, O. Claisse, G. Spano, G. De Revel, P. Lucas.
Two different Oenococcus oeni lineages are associated to either red or white wines in Burgundy: genomics and metabolomics insights, in: OENO One, September 2017, vol. 51, no 3, pp. 309 - 322. [ DOI : 10.20870/oeno-one.2017.51.4.1861 ]
https://hal.inria.fr/hal-01666981
[11]
P. Durrens, C. Klopp, N. Biteau, V. Fitton-Ouhabi, K. Dementhon, I. Accoceberry, D. J. Sherman, T. Noël.
Genome Sequence of the Yeast Clavispora lusitaniae Type Strain CBS 6936, in: Genome Announcements, August 2017, vol. 5, no 31. [ DOI : 10.1128/genomeA.00724-17 ]
https://hal.inria.fr/hal-01583349
[12]
V. Lacoste, A. Salmier, S. Tirera, A. Franc, E. Darcissac, D. Donato, C. Bouchier, A. Lavergne, B. De Thoisy, N. Forrester.
Virome analysis of two sympatric bat species (Desmodus rotundus and Molossus molossus) in French Guiana, in: PLoS ONE, November 2017, vol. 12, no 11. [ DOI : 10.1371/journal.pone.0186943 ]
https://hal-riip.archives-ouvertes.fr/pasteur-01633803

Internal Reports

[13]
P. Blanchard, P. 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://hal.inria.fr/hal-01685711
References in notes
[14]
R. Alur.
SIGPLAN Notices, in: Generating Embedded Software from Hierarchical Hybrid Models, 2003, vol. 38, no 7, pp. 171–82.
[15]
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.
[16]
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
[17]
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
[18]
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
[19]
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.
[20]
E. J. Candès, B. Recht.
Exact Matrix Completion via Convex Optimization, in: Found. Comput. Math., 2009, vol. 9, pp. 717-772.
[21]
C. Combes.
Parasitism: The Ecology and Evolution of Intimate Interactions, University of Chicago Press, 2001.
[22]
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.
[23]
L. Liberti, C. Lavor, N. Maculan, A. Mucherino.
Euclidean Distance Geometry and Applications, in: SIAM review, 2014, vol. 56(1), pp. 3-69.
[24]
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.
[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]
S. T. Roweis, Z. Ghahramani.
A unifying review of linear Gaussian Models, in: Neural Computation, 1999, vol. 11, no 2, pp. 305–45.
[27]
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.
[28]
D. W. Thompson.
On Growth and Form, Cambridge University Press, 1917.
[29]
J. Wang.
Geometric structure of high-dimensional data and dimensionality reduction, Springer & Higher Education Press, 2012.