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Biology of Genomes


Our research projects aim at understanding the biology of prokaryotic and eukaryotic genomes. We are combining experimental approaches based on molecular genetics and functional genomics to quantitative explorations of genome sequences requiring bio-informatic skills and the development of new tools. We are interested by the relationships between replication/recombination, the gene organization along chromosomes and their effect on gene expression in both yeast and bacteria. In yeast, we study the evolution of gene content and all mutational mechanisms leading to chromosomal rearrangements, variations of nucleotide composition and sequence polymorphisms at different scales, from cells to populations, and from strains to species. In bacteria, we are studying how chromosome structure can affect gene expression regulation as a function of the DNA replication cycle using single cell measurements.

Selected Publications
Yousuf M, Iuliani I, Veetil RT, Seshasayee A S N, Sclavi B, Cosentino Lagomarsino M.
Early fate of exogenous promoters in E. coli.
Nucleic Acids Research. (2020).
O'Donnell S, Fischer G.
MUM&Co: Accurate detection of all SV types through whole genome alignment.
Bioinformatics (Oxford, England). 36(10), pp.3242-3243 (2020).
Drillon G, Champeimont R, Oteri F, Fischer G, Carbone A.
Phylogenetic reconstruction based on synteny block and gene adjacencies.
Molecular Biology and Evolution. 37(9), pp.2747–2762 (2020).
Fleiss A, O'Donnell S, Fournier T, Lu W, Agier N, Delmas S, Schacherer J, Fischer G.
Reshuffling yeast chromosomes with CRISPR/Cas9.
PLOS Genetics. 15, pp.1-26 (2019).
Agier N, Delmas S, Zhang Q, Fleiss A, Jaszczyszyn Y, van Dijk E, Thermes C, Weigt M, Cosentino Lagomarsino M, Fischer G.
The evolution of the temporal program of genome replication.
Nat Commun. 9(1), pp.2199 (2018).
Vakirilis N, Hebert AS, Opulente DA, Achaz G, Hittinger CTodd, Fischer G, Coon JJ, Lafontaine I.
A molecular portrait of de novo genes in yeasts.
Mol Biol Evol. 35(3), pp.631-645 (2018).
Yue J-X, Li J, Aigrain L, Hallin J, Persson K, Oliver K, Bergstrom A, Coupland P, Warringer J, Cosentino Lagomarsino M, Fischer G, Durbin R, Liti G.
Contrasting evolutionary genome dynamics between domesticated and wild yeasts.
Nat Genet. 49(6), pp.913-924 (2017).
Vakirilis N, Sarilar V, Drillon G, Fleiss A, Agier N, Meyniel J-P, Blanpain L, Carbone A, Devillers H, Dubois K, Gillet-Markowska A, Graziani S, Huu-Vang N, Poirel M, Reisser C, Schott J, Schacherer J, Lafontaine I, Llorente B, Neuvéglise C, Fischer G.
Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus.
Genome Res. (2016).
Gillet-Markowska A, Richard H, Fischer G, Lafontaine I.
Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries.
Bioinformatics. 31(6), pp.801-8 (2015).
Gillet-Markowska A, Louvel G, Fischer G.
bz-rates: A Web Tool to Estimate Mutation Rates from Fluctuation Analysis.
G3: Genes|Genomes|Genetics. (2015).
Friedrich A, Jung P, Reisser C, Fischer G, Schacherer J.
Population genomics reveals chromosome-scale heterogeneous evolution in a protoploid yeast.
Molecular Biology and Evolution. 32(1), (2015).
Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, Richardson SM, Dymond JS, Kuang Z, Scheifele LZ, Cooper EM, Cai Y, Zeller K, Agmon N, Han JS, Hadjithomas M, Tullman J, Caravelli K, Cirelli K, Guo Z, London V, Yeluru A, Murugan S, Kandavelou K, Agier N, Fischer G, Yang K, J Martin A, Bilgel M, Bohutski P, Boulier KM, Capaldo BJ, Chang J, Charoen K, Choi WJin, Deng P, DiCarlo JE, Doong J, Dunn J, Feinberg JI, Fernandez C, Floria CE, Gladowski D, Hadidi P, Ishizuka I, Jabbari J, Lau CYL, Lee PA, Li S, Lin D, Linder ME, Ling J, Liu J, Liu J, London M, Ma H, Mao J, McDade JE, McMillan A, Moore AM, Oh WChan, Ouyang Y, Patel R, Paul M, Paulsen LC, Qiu J, Rhee A, Rubashkin MG, Soh IY, Sotuyo NE, Srinivas V, Suarez A, Wong A, Wong R, Xie WRose, Xu Y, Yu AT, Koszul R, Bader JS, Boeke JD, Chandrasegaran S.
Total synthesis of a functional designer eukaryotic chromosome.
Science. 344(6179), pp.55-8 (2014).

Open Positions