-
Domestication reprogrammed the budding yeast life cycle
De Chiara M, Barré BP, Persson K, Irizar A, Vischioni C, Khaiwal S, Stenberg S, Amadi OC, Žun G, Doberšek K, Taccioli C, Schacherer J, Petrovič U, Warringer J, Liti G.
Nature Ecology & Evolution. doi: 10.1038/s41559-022-01671-9.
PMID: 35210580
-
Aborting meiosis allows recombination in sterile diploid yeast hybrids
Mozzachiodi S, Tattini L, Llored A, Irizar A, Škofljanc N, D'Angiolo M, De Chiara M, Barré BP, Yue JX, Lutazi A, Loeillet S, Laureau R, Marsit S, Stenberg S, Albaud B, Persson K, Legras JL, Dequin S, Warringer J, Nicolas A, Liti G.
Nature Communications. 2021 Nov 12;12(1):6564. doi: 10.1038/s41467-021-26883-8.
PMID: 34772931
-
A yeast living ancestor reveals the origin of genomic introgressions
D'Angiolo M, De Chiara M, Yue JX, Irizar A, Stenberg S, Persson K, Llored A, Barré B, Schacherer J, Marangoni R, Gilson E, Warringer J, Liti G@
Nature. 2020 Nov;587(7834):420-425.
PMID: 33177709 -
Discordant Evolution of Mitochondrial and Nuclear Yeast Genomes at Population Level
De Chiara M, Friedrich A, Barré B, Breitenbach M, Schacherer J@, Liti G@
BMC Biology. 2020; 18(1):49
PMID: 32393264
-
Intragenic Repeat Expansion in the Cell Wall Protein Gene HPF1 Controls Yeast Chronological Aging
Barré BP@, Hallin J, Yue JX, Persson K, Mikhalev E, Irizar A, Thompson D, Molin M, Warringer J, Liti G@
Genome Research. 2020; 30(5):697-710
PMID: 32277013
-
Accurate tracking of the mutational landscape of diploid hybrid genomes
Tattini L, Tellini N, Mozzachiodi S, D'Angiolo M, Loeillet S, Nicolas A, Liti G.
Mol Biol Evol. 2019. [Epub ahead of print]
- PMID: 31397846
-
simuG: a general-purpose genome simulator
Yue JX, Liti G.
Bioinformatics. 2019. [Epub ahead of print]
PMID: 31116378 -
Shared molecular targets confer resistance over short and long evolutionary timescales
Li J, Vázquez-García I, Persson K, González A, Yue JX, Barré B, Hall MN, Long A, Warringer J, Mustonen V, Liti G.
Mol Biol Evol. 2019
PMID: 30657986
-
Tetrad analysis in plants and fungi finds large differences in gene conversion rates but no GC bias
Liu H, Huang J, Sun X, Li J, Hu Y, Yu L, Liti G, Tian D, Hurst LD, Yang S.
Nat Ecol Evol. 2018 2:164-173.
PMID: 29158556
-
Genome evolution across 1,011 Saccharomyces cerevisiae isolates
Peter J*, De Chiara M*, Friedrich A, Yue JX, Pflieger D, Bergström A, Sigwalt A, Barre B, Freel K, Llored A, Cruaud C, Labadie K, Aury JM, Istace B, Lebrigand K, Barbry P, Engelen S, Lemainque A, Wincker P, Liti G@, Schacherer J@.
Nature. 2018 556:339-344.
PMID: 29643504*co-first authors, @co-senior authors
-
Long-read sequencing data analysis for yeasts
-
Yeast chromosome numbers minimized using genome editing
-
de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer
Istace B, Friedrich A, d'Agata L, Faye S, Payen E, Beluche O, Caradec C, Davidas S, Cruaud C, Liti G, Lemainque A, Engelen S, Wincker P, Schacherer J, Aury JM.
Gigascience. 2017 Feb 1;6(2):1-13. doi: 10.1093/gigascience/giw018.
PMID: 28369459 -
Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses
Cubillos FA, Brice C, Molinet J, Tisné S, Abarca V, Tapia SM, Oporto C, García V, Liti G, Martínez C.
G3 (Bethesda). 2017 Jun 7;7(6):1693-1705. doi: 10.1534/g3.117.042127.
PMID: 28592651
-
The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae
García-Ríos E, Morard M, Parts L, Liti G, Guillamón JM.
BMC Genomics. 2017 Feb 14;18(1):159. doi: 10.1186/s12864-017-3572-2.
PMID: 28196526
-
Mismatch Repair Incompatibilities in Diverse Yeast Populations
Bui DT, Friedrich A, Al-Sweel N, Liti G, Schacherer J, Aquadro CF, Alani E.
Genetics. 2017 Apr;205(4):1459-1471. doi: 10.1534/genetics.116.199513. Epub 2017 Feb 13.
PMID: 28193730
-
Contrasting evolutionary genome dynamics between domesticated and wild yeasts
Yue JX, Li J, Aigrain L, Hallin J, Persson K, Oliver K, Bergström A, Coupland P, Warringer J, Lagomarsino MC, Fischer G, Durbin R, Liti G.
Nat Genet. 2017 Jun;49(6):913-924. doi: 10.1038/ng.3847. Epub 2017 Apr 17.
PMID: 28416820
-
Clonal Heterogeneity Influences the Fate of New Adaptive Mutations
Vázquez-García I@, Salinas F, Li J, Fischer A, Barré B, Hallin J, Bergström A, Alonso-Perez E, Warringer J, Mustonen V@, Liti G@.
Cell Rep. 2017 ;21(3):732-744.
PMID: 29045840
@co-corresponding authors
-
Powerful decomposition of complex traits in a diploid model
Hallin J, Märtens K, Young AI, Zackrisson M, Salinas F, Parts L, Warringer J, Liti G.
Nat Commun. 2016 Nov 2;7:13311. doi: 10.1038/ncomms13311.
PMID: 27804950
-
ISSY32 Highlights
-
Ploidy influences the functional attributes of de novo lager yeast hybrids
Krogerus K, Arvas M, De Chiara M, Magalhães F, Mattinen L, Oja M, Vidgren V, Yue JX, Liti G, Gibson B.
Appl Microbiol Biotechnol. 2016 Aug;100(16):7203-22. doi: 10.1007/s00253-016-7588-3.
PMID: 27183995
-
Predicting quantitative traits from genome and phenome with near perfect accuracy
Märtens K, Hallin J, Warringer J, Liti G, Parts L.
Nat Commun. 2016 May 10;7:11512. doi: 10.1038/ncomms11512.
PMID: 27160605
-
Extensive Recombination of a Yeast Diploid Hybrid through Meiotic Reversion
Laureau R, Loeillet S, Salinas F, Bergström A, Legoix-Né P, Liti G, Nicolas A.
PLoS Genet. 2016 Feb 1;12(2):e1005781. doi: 10.1371/journal.pgen.1005781.
PMID: 26828862
-
Yeast 2.0: a new chapter
-
Concerted evolution of life stage performances signals recent selection on yeast nitrogen use
Ibstedt S, Stenberg S, Bagés S, Gjuvsland AB, Salinas F, Kourtchenko O, Samy JK, Blomberg A, Omholt SW, Liti G, Beltran G, Warringer J.
Mol Biol Evol. 2015 Jan;32(1):153-61. doi: 10.1093/molbev/msu285.
PMID: 25349282
-
Deletion of the Saccharomyces cerevisiae ARO8 gene, encoding an aromatic amino acid transaminase, enhances phenylethanol production from glucose
Romagnoli G, Knijnenburg TA, Liti G, Louis EJ, Pronk JT, Daran JM.
Yeast. 2015 Jan;32(1):29-45. doi: 10.1002/yea.3015.
PMID: 24733517
-
Elucidating the molecular architecture of adaptation via evolve and resequence experiments
Long A, Liti G, Luptak A, Tenaillon O.
Nat Rev Genet. 2015 Oct;16(10):567-82. doi: 10.1038/nrg3937.
PMID: 26347030
-
The fascinating and secret wild life of the budding yeast S. cerevisiae
-
ATG18 and FAB1 are involved in dehydration stress tolerance in Saccharomyces cerevisiae
López-Martínez G, Margalef-Català M, Salinas F, Liti G, Cordero-Otero R.
PLoS One. 2015 Mar 24;10(3):e0119606. doi: 10.1371/journal.pone.0119606.
PMID: 25803831
-
Saccharomyces pastorianus: genomic insights inspiring innovation for industry
-
A high-definition view of functional genetic variation from natural yeast genomes
Bergström A, Simpson JT, Salinas F, Barré B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R, Liti G.
Mol Biol Evol. 2014 Apr;31(4):872-88. doi: 10.1093/molbev/msu037
PMID: 24425782
-
Phenotypic characterisation of Saccharomyces spp. yeast for tolerance to stresses encountered during fermentation of lignocellulosic residues to produce bioethanol
Wimalasena TT, Greetham D, Marvin ME, Liti G, Chandelia Y, Hart A, Louis EJ, Phister TG, Tucker GA, Smart KA.
Microb Cell Fact. 2014 Mar 27;13(1):47. doi: 10.1186/1475-2859-13-47.
PMID: 24670111
-
Filling annotation gaps in yeast genomes using genome-wide contact maps
Marie-Nelly H, Marbouty M, Cournac A, Liti G, Fischer G, Zimmer C, Koszul R.
Bioinformatics. 2014 Aug 1;30(15):2105-13. doi: 10.1093/bioinformatics/btu162.
PMID: 24711652
-
A set of genetically diverged Saccharomyces cerevisiae strains with markerless deletions of multiple auxotrophic genes
Louvel H, Gillet-Markowska A, Liti G, Fischer G.
Yeast. 2014 Mar;31(3):91-101. doi: 10.1002/yea.2991.
PMID: 24288298
-
Standing genetic variation drives repeatable experimental evolution in outcrossing populations of Saccharomyces cerevisiae
Burke MK, Liti G, Long AD.
Mol Biol Evol. 2014 Dec;31(12):3228-39. doi: 10.1093/molbev/msu256.
PMID: 25172959
-
Mapping genetic variants underlying differences in the central nitrogen metabolism in fermenter yeasts
Jara M, Cubillos FA, García V, Salinas F, Aguilera O, Liti G, Martínez C.
PLoS One. 2014 Jan 21;9(1):e86533. doi: 10.1371/journal.pone.0086533.
PMID: 24466135
-
High-quality genome (re)assembly using chromosomal contact data
Marie-Nelly H, Marbouty M, Cournac A, Flot JF, Liti G, Parodi DP, Syan S, Guillén N, Margeot A, Zimmer C, Koszul R.
Nat Commun. 2014 Dec 17;5:5695. doi: 10.1038/ncomms6695.
PMID: 25517223
-
Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe
Brown WR, Thomas G, Lee NC, Blythe M, Liti G, Warringer J, Loose MW.
Proc Natl Acad Sci U S A. 2014 Feb 4;111(5):1903-8. doi: 10.1073/pnas.1216934111.
PMID: 2444988
-
High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome
Liti G, Nguyen Ba AN, Blythe M, Müller CA, Bergström A, Cubillos FA, Dafhnis-Calas F, Khoshraftar S, Malla S, Mehta N, Siow CC, Warringer J, Moses AM, Louis EJ, Nieduszynski CA.
BMC Genomics. 2013 Jan 31;14:69. doi: 10.1186/1471-2164-14-69.
PMID: 23368932
-
Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression
Dunn B, Paulish T, Stanbery A, Piotrowski J, Koniges G, Kroll E, Louis EJ, Liti G, Sherlock G, Rosenzweig F.
PLoS Genet. 2013 Mar;9(3):e1003366. doi: 10.1371/journal.pgen.1003366.
PMID: 23555283
-
Ancient evolutionary trade-offs between yeast ploidy states
Zörgö E, Chwialkowska K, Gjuvsland AB, Garré E, Sunnerhagen P, Liti G, Blomberg A, Omholt SW, Warringer J.
PLoS Genet. 2013 Mar;9(3):e1003388. doi: 10.1371/journal.pgen.1003388.
PMID: 23555297
-
Inferring genome-wide recombination landscapes from advanced intercross lines: application to yeast crosses
Illingworth CJ, Parts L, Bergström A, Liti G, Mustonen V.
PLoS One. 2013 May 2;8(5):e62266. doi: 10.1371/journal.pone.0062266.
PMID: 23658715
-
ICY 2012 highlights
-
High-resolution mapping of complex traits with a four-parent advanced intercross yeast population
Cubillos FA, Parts L, Salinas F, Bergström A, Scovacricchi E, Zia A, Illingworth CJ, Mustonen V, Ibstedt S, Warringer J, Louis EJ, Durbin R, Liti G.
Genetics. 2013 Nov;195(3):1141-55. doi: 10.1534/genetics.113.155515.
PMID: 24037264
-
'New' yeasts for a new Yeast
Armstrong J, Davis D, Liti G, Oliver S.
Yeast. 2012 Oct;29(10):407. doi: 10.1002/yea.2923.
PMID: 23065797
-
Advances in quantitative trait analysis in yeast
-
Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity
Wang QM, Liu WQ, Liti G, Wang SA, Bai FY.
Mol Ecol. 2012 Nov;21(22):5404-17. doi: 10.1111/j.1365-294X.2012.05732.x.
PMID: 22913817
-
Apparent ploidy effects on silencing are post-transcriptional at HML and telomeres in Saccharomyces cerevisiae
McLaughlan JM, Liti G, Sharp S, Maslowska A, Louis EJ.
PLoS One. 2012;7(7):e39044. doi: 10.1371/journal.pone.0039044.
PMID: 22792162
-
Life history shapes trait heredity by accumulation of loss-of-function alleles in yeast
Zörgö E, Gjuvsland A, Cubillos FA, Louis EJ, Liti G, Blomberg A, Omholt SW, Warringer J.
Mol Biol Evol. 2012 Jul;29(7):1781-9. doi: 10.1093/molbev/mss019.
PMID: 22319169
-
Quantifying selection acting on a complex trait using allele frequency time series data
Illingworth CJ, Parts L, Schiffels S, Liti G, Mustonen V.
Mol Biol Evol. 2012 Apr;29(4):1187-97. doi: 10.1093/molbev/msr289.
PMID: 22114362
-
The genetic basis of natural variation in oenological traits in Saccharomyces cerevisiae
Salinas F, Cubillos FA, Soto D, Garcia V, Bergström A, Warringer J, Ganga MA, Louis EJ, Liti G, Martinez C.
PLoS One. 2012;7(11):e49640. doi: 10.1371/journal.pone.0049640.
PMID: 23185390
-
Trait variation in yeast is defined by population history
Warringer J, Zörgö E, Cubillos FA, Zia A, Gjuvsland A, Simpson JT, Forsmark A, Durbin R, Omholt SW, Louis EJ, Liti G, Moses A, Blomberg A.
PLoS Genet. 2011 Jun;7(6):e1002111. doi: 10.1371/journal.pgen.1002111.
PMID: 21698134
-
A Geographically Diverse Collection of Schizosaccharomyces pombe Isolates Shows Limited Phenotypic Variation but Extensive Karyotypic Diversity
Brown WR, Liti G, Rosa C, James S, Roberts I, Robert V, Jolly N, Tang W, Baumann P, Green C, Schlegel K, Young J, Hirchaud F, Leek S, Thomas G, Blomberg A, Warringer J.
G3 (Bethesda). 2011 Dec;1(7):615-26. doi: 10.1534/g3.111.001123.
PMID: 22384373
-
The rise of yeast population genomics
Liti G, Schacherer J.
C R Biol. 2011 Aug-Sep;334(8-9):612-9. doi: 10.1016/j.crvi.2011.05.009.
PMID: 21819942
-
Revealing the genetic structure of a trait by sequencing a population under selection
Parts L, Cubillos FA, Warringer J, Jain K, Salinas F, Bumpstead SJ, Molin M, Zia A, Simpson JT, Quail MA, Moses A, Louis EJ, Durbin R, Liti G.
Genome Res. 2011 Jul;21(7):1131-8. doi: 10.1101/gr.116731.110.
PMID: 21422276
-
From sequence to function: Insights from natural variation in budding yeasts
Nieduszynski CA, Liti G.
Biochim Biophys Acta. 2011 Oct;1810(10):959-66. doi: 10.1016/j.bbagen.2011.02.004.
PMID: 21320572
-
Assessing the complex architecture of polygenic traits in diverged yeast populations
Cubillos FA, Billi E, Zörgö E, Parts L, Fargier P, Omholt S, Blomberg A, Warringer J, Louis EJ, Liti G.
Mol Ecol. 2011 Apr;20(7):1401-13. doi: 10.1111/j.1365-294X.2011.05005.x.
PMID: 21261765
-
Segregating YKU80 and TLC1 alleles underlying natural variation in telomere properties in wild yeast
Liti G, Haricharan S, Cubillos FA, Tierney AL, Sharp S, Bertuch AA, Parts L, Bailes E, Louis EJ.
PLoS Genet. 2009 Sep;5(9):e1000659. doi: 10.1371/journal.pgen.1000659.
PMID: 19763176
-
Population genomics of domestic and wild yeasts
Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, Barton DB, Bailes E, Nguyen AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R, Louis EJ.
Nature. 2009 Mar 19;458(7236):337-41. doi: 10.1038/nature07743.
PMID: 19212322
-
Generation of a large set of genetically tractable haploid and diploid Saccharomyces strains
Cubillos FA, Louis EJ, Liti G.
FEMS Yeast Res. 2009 Dec;9(8):1217-25. doi: 10.1111/j.1567-1364.2009.00583.x.
PMID: 19840116
-
Sequence diversity, reproductive isolation and species concepts in Saccharomyces
-
Inferences of evolutionary relationships from a population survey of LTR-retrotransposons and telomeric-associated sequences in the Saccharomyces sensu stricto complex
-
Yeast evolution and comparative genomics
-
Analysis of a Ty1-less variant of Saccharomyces paradoxus: the gain and loss of Ty1 elements
Moore SP, Liti G, Stefanisko KM, Nyswaner KM, Chang C, Louis EJ, Garfinkel DJ.
Yeast. 2004 Jun;21(8):649-60.
PMID: 15197730
-
NEJ1 prevents NHEJ-dependent telomere fusions in yeast without telomerase
