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GQF publications since 2008

August 2017

2017

Edel K. H., Marchadier E., Brownlee C., Kudla J., Hetherington A. M. (2017) The Evolution of Calcium-Based Signalling in Plants. Curr Biol, 27 (13) R667-R679. Review.

2016

Henry A., Martin O. C. (2016) Short relaxation times but long transient times in both simple and complex reaction networks. J R Soc Interface, 13 (120)

Marchadier E., Oates M. E., Fang H., Donoghue P. C., Hetherington A. M., Gough J. (2016) Evolution of the Calcium-Based Intracellular Signaling System. Genome Biol Evol, 8 (7) 2118-32.

Martin O. C., Krzywicki A., Zagorski M. (2016) Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. Phys Life Rev, 17 124-58.

Mori M., Hwa T., Martin O. C., De Martino A., Marinari E. (2016) Constrained Allocation Flux Balance Analysis. PLoS Comput Biol, 12 (6) e1004913.

Legrand J., Bolotin-Fukuhara M., Bourgais A., Fairhead C., Sicard D. (2016) Life-history strategies and carbon metabolism gene dosage in the Nakaseomyces yeasts. FEMS Yeast Res, 16 (2).

Lhomme E., Urien C., Legrand J., Dousset X., Onno B., Sicard D. (2016) Sourdough microbial community dynamics: An analysis during French organic bread-making processes. Food Microbiol, 53 (Pt A) 41-50.

Sabarly V., Aubron C., Glodt J., Balliau T., Langella O., Chevret D., Rigal O., Bourgais A., Picard B., de Vienne D., Denamur E., Bouvet O., Dillmann C. (2016) Interactions between genotype and environment drive the metabolic phenotype within Escherichia coli isolates. Environ Microbiol, 18 (1) 100-17.

2015

Blein-Nicolas M., Albertin W., da Silva T., Valot B., Balliau T., Masneuf-Pomarede I., Bely M., Marullo P., Sicard D., Dillmann C., de Vienne D., Zivy M. (2015) A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast. Mol Cell Proteomics, 14 (8) 2056-71.

da Silva T., Albertin W., Dillmann C., Bely M., la Guerche S., Giraud C., Huet S., Sicard D., Masneuf-Pomarede I., de Vienne D., Marullo P. (2015) Hybridization within Saccharomyces Genus Results in Homoeostasis and Phenotypic Novelty in Winemaking Conditions. PLoS One, 10 (5) e0123834.

Durand E., Tenaillon M. I., Raffoux X., Thepot S., Falque M., Jamin P., Bourgais A., Ressayre A., Dillmann C. (2015) Dearth of polymorphism associated with a sustained response to selection for flowering time in maize. BMC Evol Biol, 15 103.

Grigolon S., Sollich P., Martin O. C. (2015) Modelling the emergence of polarity patterns for the intercellular transport of auxin in plants. J R Soc Interface, 12 (106)

 

Legrand J., Temime L., Lawrence C., Herrmann J. L., Boelle P. Y., Guillemot D., Group o. b. o. t. i. S. (2015) Occupational Determinants of Methicillin-Resistant Staphylococcus aureus Colonization Among Healthcare Workers: A Longitudinal Study in a Rehabilitation Center. Infection Control and Hospital Epidemiology, 36 (07) 767-776.

 

Obadia T., Silhol R., Opatowski L., Temime L., Legrand J., Thiebaut A. C., Herrmann J. L., Fleury E., Guillemot D., Boelle P. Y. (2015) Detailed Contact Data and the Dissemination of Staphylococcus aureus in Hospitals. PLoS Comput Biol, 11 (3) e1004170.

Ressayre A., Glemin S., Montalent P., Serre-Giardi L., Dillmann C., Joets J. (2015) Introns Structure Patterns of Variation in Nucleotide Composition in Arabidopsis thaliana and Rice Protein-Coding Genes. Genome Biol Evol, 7 (10) 2913-28.

 

Samal A., Martin O. C. (2015) Statistical Physics Methods Provide the Exact Solution to a Long-Standing Problem of Genetics. Phys Rev Lett, 114 (23)

Zivy M., Wienkoop S., Renaut J., Pinheiro C., Goulas E., Carpentier S. (2015) The quest for tolerant varieties: the importance of integrating "omics" techniques to phenotyping. Front Plant Sci, 6 448.

2014

Anderson L. K., Lohmiller L. D., Tang X., Hammond D. B., Javernick L., Shearer L., Basu-Roy S., Martin O. C., Falque M. (2014) Combined fluorescent and electron microscopic imaging unveils the specific properties of two classes of meiotic crossovers. Proc Natl Acad Sci U S A, 111 (37) 13415-20.

Barve A., Hosseini S. R., Martin O. C., Wagner A. (2014) Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms. BMC Syst Biol, 8 (1) 48.

Glémin S., Clement Y., David J., Ressayre A. (2014) GC content evolution in coding regions of angiosperm genomes: a unifying hypothesis. Trends Genet, 30 (7) 263-270.

Jahns M. T., Vezon D., Chambon A., Pereira L., Falque M., Martin O. C., Chelysheva L., Grelon M. (2014) Crossover localisation is regulated by the neddylation posttranslational regulatory pathway. PLoS Biol, 12 (8) e1001930.

Spor A., Kvitek D. J., Nidelet T., Martin J., Legrand J., Dillmann C., Bourgais A., de Vienne D., Sherlock G., Sicard D. (2014) Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeast. Evolution, 68 (3) 772-90.

Suay L., Zhang D. S., Eber F., Jouy H., Lode M., Huteau V., Coriton O., Szadkowski E., Leflon M., Martin O. C., Falque M., Jenczewski E., Paillard S., Chevre A. M. (2014) Crossover rate between homologous chromosomes and interference are regulated by the addition of specific unpaired chromosomes in Brassica. New Phytol, 201 (2) 645-656.

2013

Albertin W., da Silva T., Rigoulet M., Salin B., Masneuf-Pomarede I., de Vienne D., Sicard D., Bely M., Marullo P. (2013) The mitochondrial genome impacts respiration but not fermentation in interspecific Saccharomyces hybrids. PLoS One, 8 (9) e75121.

Albertin W., Marullo P., Bely M., Aigle M., Bourgais A., Langella O., Balliau T., Chevret D., Valot B., da Silva T., Dillmann C., de Vienne D., Sicard D. (2013) Linking post-translational modifications and variation of phenotypic traits. Mol Cell Proteomics, 12 (3) 720-35.

Basu-Roy S., Gauthier F., Giraut L., Mezard C., Falque M., Martin O. C. (2013) Hot Regions of Noninterfering Crossovers Coexist with a Nonuniformly Interfering Pathway in Arabidopsis thaliana. Genetics, 195 (3) 769-79.

Bauer E., Falque M., Walter H., Bauland C., Camisan C., Campo L., Meyer N., Ranc N., Rincent R., Schipprack W., Altmann T., Flament P., Melchinger A. E., Menz M., Moreno-Gonzalez J., Ouzunova M., Revilla P., Charcosset A., Martin O. C., Schon C. C. (2013) Intraspecific variation of recombination rate in maize. Genome Biol, 14 (9) R103.

Blein-Nicolas M., Albertin W., Valot B., Marullo P., Sicard D., Giraud C., Huet S., Bourgais A., Dillmann C., de Vienne D., Zivy M. (2013) Yeast proteome variations reveal different adaptive responses to grape must fermentation. Mol Biol Evol, 30 (6) 1368-83.

Henry A., Moneger F., Samal A., Martin O. C. (2013) Network function shapes network structure: the case of the Arabidopsis flower organ specification genetic network. Mol Biosyst, 9 (7) 1726-35.

Zagorski M., Krzywicki A., Martin O. C. (2013) Edge usage, motifs, and regulatory logic for cell cycling genetic networks. Phys Rev E Stat Nonlin Soft Matter Phys, 87 (1) 012727.

2012

Blein-Nicolas M., Xu H., de Vienne D., Giraud C., Huet S., Zivy M. (2012) Including shared peptides for estimating protein abundances: a significant improvement for quantitative proteomics. Proteomics, 12 (18) 2797-801.

Durand E., Bouchet S., Bertin P., Ressayre A., Jamin P., Charcosset A., Dillmann C., Tenaillon M. I. (2012) Flowering time in maize: linkage and epistasis at a major effect locus. Genetics, 190 (4) 1547-62.

Till-Bottraud I., Gouyon P. H., Ressayre A., Godelle B. (2012) Gametophytic vs. sporophytic control of pollen aperture number: a generational conflict. Theor Popul Biol, 82 (3) 147-57.

2011

Albert B., Raquin C., Prigent M., Nadot S., Brisset F., Yang M., Ressayre A. (2011) Successive microsporogenesis affects pollen aperture pattern in the tam mutant of Arabidopsis thaliana. Ann Bot, 107 (8) 1421-6.

Albert B., Ressayre A., Nadot S. (2011) Correlation between pollen aperture pattern and callose deposition in late tetrad stage in three species producing atypical pollen grains. Am J Bot, 98 (2) 189-96.

Albertin W., Marullo P., Aigle M., Dillmann C., de Vienne D., Bely M., Sicard D. (2011) Population size drives industrial Saccharomyces cerevisiae alcoholic fermentation and is under genetic control. Appl Environ Microbiol, 77 (8) 2772-84.

Burda Z., Krzywicki A., Martin O. C., Zagorski M. (2011) Motifs emerge from function in model gene regulatory networks. Proc Natl Acad Sci U S A, 108 (42) 17263-8.

Espinosa-Soto C., Martin O. C., Wagner A. (2011) Phenotypic plasticity can facilitate adaptive evolution in gene regulatory circuits. BMC Evol Biol, 11 5.

Espinosa-Soto C., Martin O. C., Wagner A. (2011) Phenotypic robustness can increase phenotypic variability after nongenetic perturbations in gene regulatory circuits. J Evol Biol, 24 (6) 1284-97.

Ganal M. W., Durstewitz G., Polley A., Berard A., Buckler E. S., Charcosset A., Clarke J. D., Graner E. M., Hansen M., Joets J., Le Paslier M. C., McMullen M. D., Montalent P., Rose M., Schon C. C., Sun Q., Walter H., Martin O. C., Falque M. (2011) A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS One, 6 (12) e28334.

Gauthier F., Martin O. C., Falque M. (2011) CODA (crossover distribution analyzer): quantitative characterization of crossover position patterns along chromosomes. BMC Bioinformatics, 12 27.

Gervais C. E., Castric V., Ressayre A., Billiard S. (2011) Origin and diversification dynamics of self-incompatibility haplotypes. Genetics, 188 (3) 625-36.

Giraut L., Falque M., Drouaud J., Pereira L., Martin O. C., Mezard C. (2011) Genome-wide crossover distribution in Arabidopsis thaliana meiosis reveals sex-specific patterns along chromosomes. PLoS Genet, 7 (11) e1002354.

Martin O. C., Hospital F. (2011) Distribution of parental genome blocks in recombinant inbred lines. Genetics, 189 (2) 645-54.

Muyle A., Serres-Giardi L., Ressayre A., Escobar J., Glemin S. (2011) GC-biased gene conversion and selection affect GC content in the Oryza genus (rice). Mol Biol Evol, 28 (9) 2695-706.

Sabarly V., Bouvet O., Glodt J., Clermont O., Skurnik D., Diancourt L., de Vienne D., Denamur E., Dillmann C. (2011) The decoupling between genetic structure and metabolic phenotypes in Escherichia coli leads to continuous phenotypic diversity. J Evol Biol, 24 (7) 1559-71.

Samal A., Martin O. C. (2011) Randomizing genome-scale metabolic networks. PLoS One, 6 (7) e22295.

Samal A., Wagner A., Martin O. C. (2011) Environmental versatility promotes modularity in genome-scale metabolic networks. BMC Syst Biol, 5 135.

Sicard D., Legras J. L. (2011) Bread, beer and wine: yeast domestication in the Saccharomyces sensu stricto complex. C R Biol, 334 (3) 229-36.

Wang S., Spor A., Nidelet T., Montalent P., Dillmann C., de Vienne D., Sicard D. (2011) Switch between life history strategies due to changes in glycolytic enzyme gene dosage in Saccharomyces cerevisiae. Appl Environ Microbiol, 77 (2) 452-9.

2010

Albert B., Nadot S., Dreyer L., Ressayre A. (2010) The influence of tetrad shape and intersporal callose wall formation on pollen aperture pattern ontogeny in two eudicot species. Ann Bot, 106 (4) 557-64.

Bourguignon P. Y., Samal A., Kepes F., Jost J., Martin O. C. (2010) Challenges in experimental data integration within genome-scale metabolic models. Algorithms Mol Biol, 5 20.

*Burda Z., Krzywicki A., Martin O. C., Zagorski M. (2010) Distribution of essential interactions in model gene regulatory networks under mutation-selection balance. Phys Rev E Stat Nonlin Soft Matter Phys, 82 (1 Pt 1) 011908.

Durand E., Tenaillon M. I., Ridel C., Coubriche D., Jamin P., Jouanne S., Ressayre A., Charcosset A., Dillmann C. (2010) Standing variation and new mutations both contribute to a fast response to selection for flowering time in maize inbreds. BMC Evol Biol, 10 2.

Fievet J. B., Dillmann C., de Vienne D. (2010) Systemic properties of metabolic networks lead to an epistasis-based model for heterosis. Theor Appl Genet, 120 (2) 463-73.

Junier I., Martin O. C., Kepes F. (2010) Spatial and topological organization of DNA chains induced by gene co-localization. PLoS Comput Biol, 6 (2) e1000678.

Samal A., Matias Rodrigues J. F., Jost J., Martin O. C., Wagner A. (2010) Genotype networks in metabolic reaction spaces. BMC Syst Biol, 4 30.

Santure A. W., Ewen J. G., Sicard D., Roff D. A., Moller A. P. (2010) Population structure in the barn swallow, Hirundo rustica: a comparison between neutral DNA markers and quantitative traits. Biol J Linn Soc, 99 (2) 306-314.

Spor A., Dillmann C., Wang S., de Vienne D., Sicard D., Parent E. (2010) Hierarchical Bayesian Modelling for Saccharomyces cerevisiae population dynamics. Int J Food Microbiol, 142 (1-2) 25-35.

2009

Albert B., Gouyon P. H., Ressayre A. (2009) Microsporogenesis variation in Codiaeum producing inaperturate pollen grain. C R Biol, 332 (6) 507-16.

Albertin W., Marullo P., Aigle M., Bourgais A., Bely M., Dillmann C., de Vienne D., Sicard D. (2009) Evidence for autotetraploidy associated with reproductive isolation in Saccharomyces cerevisiae: towards a new domesticated species. J Evol Biol, 22 (11) 2157-70.

Edelist C., Raffoux X., Falque M., Dillmann C., Sicard D., Rieseberg L. H., Karrenberg S. (2009) Differential expression of candidate salt-tolerance genes in the halophyte Helianthus paradoxus and its glycophyte progenitors H. annuus and H. petiolaris (Asteraceae). Am J Bot, 96 (10) 1830-8.

Falque M., Anderson L. K., Stack S. M., Gauthier F., Martin O. C. (2009) Two types of meiotic crossovers coexist in maize. Plant Cell, 21 (12) 3915-25.

Johannes F., Porcher E., Teixeira F. K., Saliba-Colombani V., Simon M., Agier N., Bulski A., Albuisson J., Heredia F., Audigier P., Bouchez D., Dillmann C., Guerche P., Hospital F., Colot V. (2009) Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet, 5 (6) e1000530.

Martin O. C., Wagner A. (2009) Effects of recombination on complex regulatory circuits. Genetics, 183 (2) 673-84, 1SI-8SI.

Marullo P., Mansour C., Dufour M., Albertin W., Sicard D., Bely M., Dubourdieu D. (2009) Genetic improvement of thermo-tolerance in wine Saccharomyces cerevisiae strains by a backcross approach. FEMS Yeast Res, 9 (8) 1148-60.

Saintenac C., Falque M., Martin O. C., Paux E., Feuillet C., Sourdille P. (2009) Detailed recombination studies along chromosome 3B provide new insights on crossover distribution in wheat (Triticum aestivum L.). Genetics, 181 (2) 393-403.

Spor A., Nidelet T., Simon J., Bourgais A., de Vienne D., Sicard D. (2009) Niche-driven evolution of metabolic and life-history strategies in natural and domesticated populations of Saccharomyces cerevisiae. BMC Evol Biol, 9 296.

2008

Jorg T., Martin O. C., Wagner A. (2008) Neutral network sizes of biological RNA molecules can be computed and are not atypically small. BMC Bioinformatics, 9 464.

Kuang H., van Eck H. J., Sicard D., Michelmore R., Nevo E. (2008) Evolution and genetic population structure of prickly lettuce (Lactuca serriola) and its RGC2 resistance gene cluster. Genetics, 178 (3) 1547-58.

Martin O. C., Wagner A. (2008) Multifunctionality and robustness trade-offs in model genetic circuits. Biophys J, 94 (8) 2927-37.

Nadot S., Furness C. A., Sannier J., Penet L., Triki-Teurtroy S., Albert B., Ressayre A. (2008) Phylogenetic comparative analysis of microsporogenesis in angiosperms with a focus on monocots. Am J Bot, 95 (11) 1426-36.

Spor A., Wang S., Dillmann C., de Vienne D., Sicard D. (2008) "Ant" and "grasshopper" life-history strategies in Saccharomyces cerevisiae. PLoS One, 3 (2) e1579.