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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 Apr 1;36(4):691-708. doi: 10.1093/molbev/msz006.


Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data.

Moradigaravand D, Palm M, Farewell A, Mustonen V, Warringer J, Parts L.

PLoS Comput Biol. 2018 Dec 14;14(12):e1006258. doi: 10.1371/journal.pcbi.1006258. eCollection 2018 Dec.


Inhibiting conjugation as a tool in the fight against antibiotic resistance.

Graf FE, Palm M, Warringer J, Farewell A.

Drug Dev Res. 2019 Feb;80(1):19-23. doi: 10.1002/ddr.21457. Epub 2018 Oct 21. Review.


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 Oct 17;21(3):732-744. doi: 10.1016/j.celrep.2017.09.046.


Budding Yeast Strains and Genotype-Phenotype Mapping.

Liti G, Warringer J, Blomberg A.

Cold Spring Harb Protoc. 2017 Aug 1;2017(8):pdb.top077735. doi: 10.1101/pdb.top077735.


Yeast Reciprocal Hemizygosity to Confirm the Causality of a Quantitative Trait Loci-Associated Gene.

Warringer J, Liti G, Blomberg A.

Cold Spring Harb Protoc. 2017 Aug 1;2017(8):pdb.prot089078. doi: 10.1101/pdb.prot089078.


Mapping Quantitative Trait Loci in Yeast.

Liti G, Warringer J, Blomberg A.

Cold Spring Harb Protoc. 2017 Aug 1;2017(8):pdb.prot089060. doi: 10.1101/pdb.prot089060.


Isolation and Laboratory Domestication of Natural Yeast Strains.

Liti G, Warringer J, Blomberg A.

Cold Spring Harb Protoc. 2017 Aug 1;2017(8):pdb.prot089052. doi: 10.1101/pdb.prot089052.


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.


Disentangling genetic and epigenetic determinants of ultrafast adaptation.

Gjuvsland AB, Zörgö E, Samy JK, Stenberg S, Demirsoy IH, Roque F, Maciaszczyk-Dziubinska E, Migocka M, Alonso-Perez E, Zackrisson M, Wysocki R, Tamás MJ, Jonassen I, Omholt SW, Warringer J.

Mol Syst Biol. 2016 Dec 15;12(12):892. doi: 10.15252/msb.20166951.


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.


Scan-o-matic: High-Resolution Microbial Phenomics at a Massive Scale.

Zackrisson M, Hallin J, Ottosson LG, Dahl P, Fernandez-Parada E, Ländström E, Fernandez-Ricaud L, Kaferle P, Skyman A, Stenberg S, Omholt S, Petrovič U, Warringer J, Blomberg A.

G3 (Bethesda). 2016 Sep 8;6(9):3003-14. doi: 10.1534/g3.116.032342.


PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics.

Fernandez-Ricaud L, Kourtchenko O, Zackrisson M, Warringer J, Blomberg A.

BMC Bioinformatics. 2016 Jun 23;17:249. doi: 10.1186/s12859-016-1134-2.


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.


Replenishment and mobilization of intracellular nitrogen pools decouples wine yeast nitrogen uptake from growth.

Gutiérrez A, Sancho M, Beltran G, Guillamon JM, Warringer J.

Appl Microbiol Biotechnol. 2016 Apr;100(7):3255-65. doi: 10.1007/s00253-015-7273-y. Epub 2016 Jan 12.


The cellular growth rate controls overall mRNA turnover, and modulates either transcription or degradation rates of particular gene regulons.

García-Martínez J, Delgado-Ramos L, Ayala G, Pelechano V, Medina DA, Carrasco F, González R, Andrés-León E, Steinmetz L, Warringer J, Chávez S, Pérez-Ortín JE.

Nucleic Acids Res. 2016 May 5;44(8):3643-58. doi: 10.1093/nar/gkv1512. Epub 2015 Dec 29.


High-throughput biochemical fingerprinting of Saccharomyces cerevisiae by Fourier transform infrared spectroscopy.

Kohler A, Böcker U, Shapaval V, Forsmark A, Andersson M, Warringer J, Martens H, Omholt SW, Blomberg A.

PLoS One. 2015 Feb 23;10(2):e0118052. doi: 10.1371/journal.pone.0118052. eCollection 2015.


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. Epub 2014 Oct 27.


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. Epub 2014 Jan 21.


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. Epub 2014 Jan 14.


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. Epub 2013 Sep 13.


Genetic basis of variations in nitrogen source utilization in four wine commercial yeast strains.

Gutiérrez A, Beltran G, Warringer J, Guillamón JM.

PLoS One. 2013 Jun 24;8(6):e67166. doi: 10.1371/journal.pone.0067166. Print 2013.


A role for Myh1 in DNA repair after treatment with strand-breaking and crosslinking chemotherapeutic agents.

Jansson K, Alao JP, Viktorsson K, Warringer J, Lewensohn R, Sunnerhagen P.

Environ Mol Mutagen. 2013 Jun;54(5):327-37. doi: 10.1002/em.21784. Epub 2013 May 16.


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. Epub 2013 Mar 21.


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.


Improving stability and understandability of genotype-phenotype mapping in Saccharomyces using regularized variable selection in L-PLS regression.

Mehmood T, Warringer J, Snipen L, Sæbø S.

BMC Bioinformatics. 2012 Dec 8;13:327. doi: 10.1186/1471-2105-13-327.


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. Epub 2012 Nov 21.


Abundant gene-by-environment interactions in gene expression reaction norms to copper within Saccharomyces cerevisiae.

Hodgins-Davis A, Adomas AB, Warringer J, Townsend JP.

Genome Biol Evol. 2012;4(11):1061-79. doi: 10.1093/gbe/evs084. Erratum in: Genome Biol Evol. 2012;4(11):1188.


Exploration of multivariate analysis in microbial coding sequence modeling.

Mehmood T, Bohlin J, Kristoffersen AB, Sæbø S, Warringer J, Snipen L.

BMC Bioinformatics. 2012 May 14;13:97. doi: 10.1186/1471-2105-13-97.


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. Epub 2011 Dec 1.


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. Epub 2012 Jan 20.


A Partial Least Squares based algorithm for parsimonious variable selection.

Mehmood T, Martens H, Sæbø S, Warringer J, Snipen L.

Algorithms Mol Biol. 2011 Dec 5;6(1):27. doi: 10.1186/1748-7188-6-27.


The Ashbya gossypii EF-1α promoter of the ubiquitously used MX cassettes is toxic to Saccharomyces cerevisiae.

Babazadeh R, Jafari SM, Zackrisson M, Blomberg A, Hohmann S, Warringer J, Krantz M.

FEBS Lett. 2011 Dec 15;585(24):3907-13. doi: 10.1016/j.febslet.2011.10.029. Epub 2011 Oct 22.


Mining for genotype-phenotype relations in Saccharomyces using partial least squares.

Mehmood T, Martens H, Saebø S, Warringer J, Snipen L.

BMC Bioinformatics. 2011 Aug 3;12:318. doi: 10.1186/1471-2105-12-318.


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. Epub 2011 Jun 16.


Quantitative proteomics of yeast post-Golgi vesicles reveals a discriminating role for Sro7p in protein secretion.

Forsmark A, Rossi G, Wadskog I, Brennwald P, Warringer J, Adler L.

Traffic. 2011 Jun;12(6):740-53. doi: 10.1111/j.1600-0854.2011.01186.x. Epub 2011 Apr 8.


Systematic exploration of essential yeast gene function with temperature-sensitive mutants.

Li Z, Vizeacoumar FJ, Bahr S, Li J, Warringer J, Vizeacoumar FS, Min R, Vandersluis B, Bellay J, Devit M, Fleming JA, Stephens A, Haase J, Lin ZY, Baryshnikova A, Lu H, Yan Z, Jin K, Barker S, Datti A, Giaever G, Nislow C, Bulawa C, Myers CL, Costanzo M, Gingras AC, Zhang Z, Blomberg A, Bloom K, Andrews B, Boone C.

Nat Biotechnol. 2011 Apr;29(4):361-7. doi: 10.1038/nbt.1832. Epub 2011 Mar 27.


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. Epub 2011 Mar 21.


Depletion of eIF4G from yeast cells narrows the range of translational efficiencies genome-wide.

Park EH, Zhang F, Warringer J, Sunnerhagen P, Hinnebusch AG.

BMC Genomics. 2011 Jan 26;12:68. doi: 10.1186/1471-2164-12-68.


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. Epub 2011 Jan 25.


Sulfate assimilation mediates tellurite reduction and toxicity in Saccharomyces cerevisiae.

Ottosson LG, Logg K, Ibstedt S, Sunnerhagen P, Käll M, Blomberg A, Warringer J.

Eukaryot Cell. 2010 Oct;9(10):1635-47. doi: 10.1128/EC.00078-10. Epub 2010 Jul 30.


The HOG pathway dictates the short-term translational response after hyperosmotic shock.

Warringer J, Hult M, Regot S, Posas F, Sunnerhagen P.

Mol Biol Cell. 2010 Sep 1;21(17):3080-92. doi: 10.1091/mbc.E10-01-0006. Epub 2010 Jun 29.


A phenotypic study of TFS1 mutants differentially altered in the inhibition of Ira2p or CPY.

Gombault A, Warringer J, Caesar R, Godin F, Vallée B, Doudeau M, Chautard H, Blomberg A, Bénédetti H.

FEMS Yeast Res. 2009 Sep;9(6):867-74. doi: 10.1111/j.1567-1364.2009.00535.x. Epub 2009 May 30.


Robustness and fragility in the yeast high osmolarity glycerol (HOG) signal-transduction pathway.

Krantz M, Ahmadpour D, Ottosson LG, Warringer J, Waltermann C, Nordlander B, Klipp E, Blomberg A, Hohmann S, Kitano H.

Mol Syst Biol. 2009;5:281. doi: 10.1038/msb.2009.36. Epub 2009 Jun 16.


Reducing inter-replicate variation in fourier transform infrared spectroscopy by extended multiplicative signal correction.

Kohler A, Böcker U, Warringer J, Blomberg A, Omholt SW, Stark E, Martens H.

Appl Spectrosc. 2009 Mar;63(3):296-305.


mRNA stability changes precede changes in steady-state mRNA amounts during hyperosmotic stress.

Molin C, Jauhiainen A, Warringer J, Nerman O, Sunnerhagen P.

RNA. 2009 Apr;15(4):600-14. doi: 10.1261/rna.1403509. Epub 2009 Feb 17.


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. Epub 2009 Feb 11.


Chemogenetic fingerprinting by analysis of cellular growth dynamics.

Warringer J, Anevski D, Liu B, Blomberg A.

BMC Chem Biol. 2008 Aug 22;8:3. doi: 10.1186/1472-6769-8-3.


The tumor suppressor homolog in fission yeast, myh1(+), displays a strong interaction with the checkpoint gene rad1(+).

Jansson K, Warringer J, Farewell A, Park HO, Hoe KL, Kim DU, Hayles J, Sunnerhagen P.

Mutat Res. 2008 Sep 26;644(1-2):48-55. doi: 10.1016/j.mrfmmm.2008.07.001. Epub 2008 Jul 16.


The sodium pump Ena1p provides mechanistic insight into the salt sensitivity of vacuolar protein sorting mutants.

Logg K, Warringer J, Hashemi SH, Käll M, Blomberg A.

Biochim Biophys Acta. 2008 Jun;1783(6):974-84. doi: 10.1016/j.bbamcr.2008.02.022. Epub 2008 Mar 18.

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