Publications

Selected publications

Li J, Vázquez-García I, Persson K, González A, Yue J-X, Barré B, Hall MN, Long AD, Warringer J, Mustonen V, Liti G. (2017) Patterns of selection reveal shared molecular targets over short and long evolutionary timescales. (submitted) [preprint]

Yue J-X, Liti G. (2018) Long-read sequencing data analysis for yeasts. Nature Protocols, 13:1213–1231. [software]

Peter J^, De Chiara M^, Friedrich A, Yue J-X, Pflieger D, Bergström A, Sigwalt A, Barré B, Freel K, Llored A, Cruaud C, Labadie K, Aury JM, Istace B, Lebrigand K, Barbry P, Engelen S, Lemainque A, Liti G*, Schacherer J*. (2018) Genome evolution across 1,011 Saccharomyces cerevisiae isolates. Nature, 556:339–344.

Vázquez-García I, Salinas F, Li J, Fischer A, Barré B, Hallin J, Bergström A, Alonso-Perez E, Warringer J, Mustonen V, Liti G. (2017) Clonal heterogeneity influences the fate of new adaptive mutations. Cell Reports, 21(3): 732-744.

Yue J-X, Li J, Aigrain L, Hallin J, Persson K, Oliver K, Bergström A, Coupland P, Warringer J, Cosentino Lagomarsino M, Fischer G, Durbin R, Liti G. (2017) Contrasting evolutionary genome dynamics between domesticated and wild yeasts. Nature Genetics, 49:913–924. [YPRP resources]

Hallin J, Märtens K, Young AI, Zackrisson M, Salinas F, Parts L, Warringer J, Liti G. (2016) Powerful decomposition of complex traits in a diploid model. Nature Communications, 7:13311.

Märtens K, Hallin J, Warringer J, Liti G, Parts L. (2016) Predicting quantitative traits from genome and phenome with near perfect accuracy. Nature Communications, 7:11512.

Laureau R, Loeillet S, Salinas F, Bergström A, Legoix-Né P, Liti G, Nicolas A. (2016) Extensive recombination of a yeast diploid hybrid through meiotic reversion. PLoS Genetics, 12(2):e1005781.

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. (2014) A high-definition view of functional genetic variation from natural yeast genomes. Molecular Biology and Evolution, 31(4):872-888.

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. (2013) High resolution mapping of complex traits with a four-parent advanced intercross yeast population. Genetics, 195(3):1141-1155.

Parts L, Cubillos FA, Warringer J, Jain K, Salinas F, Bumpstead SJ, Molin M, Zia A, Simpson JT, Quail MA, Moses AM, Louis EJ, Durbin R, Liti G. Revealing the genetic structure of a trait by sequencing a population under selection. Genome Research, 21(7):1131-1138.

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 MJT, van Oudenaarden A, Barton DBH, Bailes E, Nguyen Ba AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R and Louis EJ. (2009) Population genomics of domestic and wild yeasts. Nature, 458(7236):337-341.

Full publications

2018

Li J, Vázquez-García I, Persson K, González A, Yue J-X, Barré B, Hall MN, Long AD, Warringer J, Mustonen V, Liti G. (2017) Patterns of selection reveal shared molecular targets over short and long evolutionary timescales. (submitted) [preprint]

Yue JX, Liti G. (2018) Long-read sequencing data analysis for yeasts. Nature Protocols (in press) [preprint] [software]

Jackson Peter^, Matteo De Chiara^, Anne Friedrich, Jia-Xing Yue, David Pflieger, Anders Bergström, Anastasie Sigwalt, Benjamin Barré, Kelle Freel, Agnès Llored, Corinne Cruaud, Karine Labadie, Jean Marc Aury, Benjamin Istace, Kevin Lebrigand, Pascal Barbry, Stefan Engelen, Arnaud Lemainque, Gianni Liti*, Joseph Schacherer*. (2018) Genome evolution across 1,011 Saccharomyces cerevisiae isolates. Nature, advance online. (doi:10.1038/s41586-018-0030-5)

2017

Liu H, Huang J, Sun X, Li J, Yu L, Hu Y, Liti G, Tian D, Hurst LD, Yang S. (2017) Tetrad analysis in plants and fungi finds large differences in gene conversion rates but no GC bias. Nature Ecology and Evolution, 2:164-173.

Vázquez-García I, Salinas F, Li J, Fischer A, Barré B, Hallin J, Bergström A, Alonso-Perez E, Warringer J, Mustonen V, Liti G. (2017) Clonal heterogeneity influences the fate of new adaptive mutations. Cell Reports, 21(3): 732-744.

Giordano F, Aigrain L, Quail MA, Coupland P, Bonfield JK, Davies RM, Tischler G, Jackson DK, Keane TM, Li J, Yue J-X, Liti G, Durbin R, Ning Z. (2017) De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms. Scientific Reports, 7(1):3935.

Yue J-X, Li J, Aigrain L, Hallin J, Persson K, Oliver K, Bergström A, Coupland P, Warringer J, Cosentino Lagomarsino M, Fischer G, Durbin R, Liti G. (2017) Contrasting evolutionary genome dynamics between domesticated and wild yeasts. Nature Genetics, 49:913–924. [YPRP resources]

García-Ríos E, Morard M, Parts L, Liti G, Guillamón JM. (2017) The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae. BMC Genomics, 18(1):159.

Bui DT, Friedrich A, Al-Sweel N, Liti G, Schacherer J, Aquadro CF, Alani E. (2017) Mismatch repair incompatibilities in diverse yeast populations. Genetics, 205(4):1459-1471.

2016

Hallin J, Märtens K, Young AI, Zackrisson M, Salinas F, Parts L, Warringer J, Liti G. (2016) Powerful decomposition of complex traits in a diploid model. Nature Communications, 7:13311.

Liti G, Buzzini P. (2016) ISSY32 Highlights. Yeast. 33(7):241-242.

Krogerus K, Arvas M, De Chiara M, Magalhães F, Mattinen L, Oja M, Vidgren V, Yue J-X, Liti G, Gibson B. (2016) Ploidy influences the functional attributes of de novo lager yeast hybrids. Applied Microbiology Biotechnology, 100(16):7203-7222.

Märtens K, Hallin J, Warringer J, Liti G, Parts L. (2016) Predicting quantitative traits from genome and phenome with near perfect accuracy. Nature Communications, 7:11512.

Laureau R, Loeillet S, Salinas F, Bergström A, Legoix-Né P, Liti G, Nicolas A. (2016) Extensive recombination of a yeast diploid hybrid through meiotic reversion. PLoS Genetics, 12(2):e1005781.

Liti G. (2016) Yeast 2.0: a new chapter. Yeast, 33(1):3-4.

2015

Ibstedt S, Stenberg S, Bagés S, Gjuvsland AB, Salinas F, Kourtchenko O, Samy JK, Blomberg A, Omholt SW, Liti G, Beltran G, Warringer J. (2015) Concerted evolution of life stage performances signals recent selection on yeast nitrogen use. Molecular Biology and Evolution, 32(1):153-161.

Long A, Liti G, Luptak A, Tenaillon O. (2015) Elucidating the molecular architecture of adaptation via evolve and resequence experiments. Nature Reviews Genetics, 16(10):567-582.

Liti G. (2015) The fascinating and secret wild life of the budding yeast S. cerevisiae. eLife, 25:4.

López-Martínez G, Margalef-Català M, Salinas F, Liti G, Cordero-Otero R. (2015) ATG18 and FAB1 are involved in dehydration stress tolerance in Saccharomyces cerevisiae. PLoS One, 10(3):e0119606.

Gibson B, Liti G. Saccharomyces pastorianus: genomic insights inspiring innovation for industry. Yeast, 32(1):17-27.

Romagnoli G, Knijnenburg TA, Liti G, Louis EJ, Pronk JT, Daran JM. (2015) Deletion of the Saccharomyces cerevisiae ARO8 gene, encoding an aromatic amino acid transaminase, enhances phenylethanol production from glucose. Yeast, 32(1):29-45.

2014

Marie-Nelly H, Marbouty M, Cournac A, Flot JF, Liti G, Parodi DP, Syan S, Guillén N, Margeot A, Zimmer C, Koszul R. (2014) High-quality genome (re)assembly using chromosomal contact data. Nature Communications, 17(5):5695.

Burke MK, Liti G, Long AD. (2014) Standing genetic variation drives repeatable experimental evolution in outcrossing populations of Saccharomyces cerevisiae. Molecular Biology and Evolution, 31(12):3228-3239.

Marie-Nelly H, Marbouty M, Cournac A, Liti G, Fischer G, Zimmer C, Koszul R. (2014) Filling annotation gaps in yeast genomes using genome-wide contact maps. Bioinformatics, 30(15):2105-2113.

Wimalasena TT, Greetham D, Marvin ME, Liti G, Chandelia Y, Hart A, Louis EJ, Phister TG, Tucker GA, Smart KA. (2014) Phenotypic characterisation of Saccharomyces spp.yeast for tolerance to stresses encountered during fermentation of lignocellulosic residues to produce bioethanol. Microbial Cell Factories, 13(1):47.

Jara M, Cubillos FA, García V, Salinas F, Aguilera O, Liti G, Martínez C. (2014) Mapping genetic variants underlying differences in the central nitrogen metabolism in fermenter yeasts. PLoS One, 9(1):e86533.

Brown WR, Thomas G, Lee NC, Blythe M, Liti G, Warringer J, Loose MW. (2014) Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe. PNAS, 111(5):1903-1908.

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. (2014) A high-definition view of functional genetic variation from natural yeast genomes. Molecular Biology and Evolution, 31(4):872-888.

Louvel H, Gillet-Markowska A, Liti G, Fischer G. (2014) A set of genetically diverged Saccharomyces cerevisiae strains with markerless deletions of multiple auxotrophic genes. Yeast, 31(3):91-101.

2013

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. (2013) High resolution mapping of complex traits with a four-parent advanced intercross yeast population. Genetics, 195(3):1141-1155.

Illingworth CJ, Parts L, Bergström A, Liti G, Mustonen V. (2013) Inferring genome-wide recombination landscapes from advanced intercross lines: application to yeast crosses. PLoS One, 8(5):e62266.

Zörgö E, Chwialkowska K, Gjuvsland A, Garre E, Sunnerhagen P, Liti G, Blomberg A, Omholt SW, Warringer J. (2013) Ancient evolutionary trade-offs between yeast ploidy states. PLoS Genetics, 9(3):e1003388.

Dunn B, Paulish T, Stanbery A, Piotrowski J, Koniges G, Kroll E, Louis EJ, Liti G, Sherlock G, Rosenzweig F. Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression. (2013) PLoS Genetics, 9(3):e1003366.

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. (2013) High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome. BMC Genomics, 14(1):69.

Abbas C, Kurtzman C, Liti G. ICY 2012 highlights. (2013) Yeast, 30(8):293-294.

2012

Salinas F, Cubillos FA, Soto D, Garcia V, Bergström A, Warringer J, Ganga MA, Louis EJ, Liti G, Martinez C. (2012) The genetic basis of natural variation in oenological traits in Saccharomyces cerevisiae. PLoS One, 7(11):e49640.

Armstrong J, Davis D, Liti G, Oliver S. (2012) ‘New’ yeasts for a new Yeast. Yeast, 29(10):407.

Liti G, Louis EJ. Advances in quantitative trait analysis in yeast. (2012) PLoS Genetics, 8(8):e1002912.

Wang Q-M, Liu W-Q, Liti G, Wang SA, Bai F-Y. (2012) Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity. Molecular Ecology, 21(22):5404-5417.

McLaughlan MJ, Liti G, Sharp S, Maslowska A, Louis EJ. (2012) Apparent ploidy effects on silencing are post-transcriptional at HML and telomeres in Saccharomyces cerevisiae. PLoS One, 7(7):e39044.

Zörgö E, Gjuvsland A, Cubillos FA, Louis EJ, Liti G, Blomberg A, Omholt SW, Warringer J. (2012) Life history shapes trait heredity by promoting accumulation of loss-of-function alleles in yeast. Molecular Biology and Evolution, 29(7):1781-1789.

Illingworth CJ, Parts L, Schiffels S, Liti G, Mustonen V. (2012) Quantifying selection acting on a complex trait using allele frequency time-series data. Molecular Biology and Evolution, 29(4):1187-1197.

2011

Brown WRA, 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. (2011) A geographically diverse collection of Schizosaccharomyces pombe isolates shows limited phenotypic variation but extensive karyotypic diversity. G3: Genes, Genomes, Genetics, 1(7):615-26.

Liti G, Schacherer J. (2011) The rise of yeast population genomics. Comptes Rendus Biologies, 334(8-9):612-619.

Warringer J, Zörgö E, Cubillos FA, Zia A, Gjuvsland A, Simpson JT, Forsmark A, Durbin R, Omholt SW, Louis EJ, Liti G, Moses AM, Blomberg A. (2011) Trait variation in yeast is defined by population history. PLoS Genetics, 7(6):e1002111.

Parts L, Cubillos FA, Warringer J, Jain K, Salinas F, Bumpstead SJ, Molin M, Zia A, Simpson JT, Quail MA, Moses AM, Louis EJ, Durbin R, Liti G. Revealing the genetic structure of a trait by sequencing a population under selection. Genome Research, 21(7):1131-1138.

Nieduszynski CA, Liti G. (2011) From sequence to function: insights from natural variation in budding yeasts. Biochemical Biophysical Acta, 1810 (10):959-966.

Cubillos FA, Billi E, Zörgö E, Parts L, Fargier P, Omholt S, Blomberg A, Warringer J, Louis EJ, Liti G. (2011) Assessing the complex architecture of polygenic traits in yeast. Molecular Ecology, 20(7):1401-1413.

2009

Cubillos FA, Louis EJ, Liti G. (2009) Generation of a large set of genetically tractable haploid and diploid Saccharomyces strains. FEMS Yeast Research, 9:1217-1225.

Liti G, Haricharan S, Cubillos FA, Tierney AL, Sharp S, Bertuch AA, Parts L, Bailes E, Louis EJ. (2009) Segregating YKU80 and TLC1 alleles underlying natural variation in telomere properties in wild yeast. PLoS Genetics, 5(9):e1000659.

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 MJT, van Oudenaarden A, Barton DBH, Bailes E, Nguyen Ba AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R and Louis EJ. (2009) Population genomics of domestic and wild yeasts. Nature, 458(7236):337-341.

2006

Liti G, Barton DBH, Louis EJ. (2006) Sequence diversity, reproductive isolation and species concepts in Saccharomyces. Genetics, 174(2):839-850.

2005

Liti G, Louis EJ. (2005) Yeast evolution and comparative genomics. Annual Review of Microbiology, 59:135-153.

Liti G, Peruffo A, James SA, Roberts IN, Louis EJ. (2005) Inferences of evolutionary relationships from a population survey of LTR‐retrotransposons and telomeric‐associated sequences in the Saccharomyces sensu stricto. Yeast, 22(3):177-192.

2004

Moore SP, Liti G, Stefanisko KM, Nyswaner KM, Chang C, Louis EJ, Garfinkel DJ. (2004) Analysis of a Ty1‐less variant of Saccharomyces paradoxus: the gain and loss of Ty1 elements. Yeast, 21(8):649-660.

2003

Liti G, Louis EJ. (2003) NEJ1 prevents NHEJ-dependent telomere fusions in yeast without telomerase. Molecular Cell, 11(5):1373-1378.

 

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