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Fermentation innovation through complex hybridization of wild and domesticated yeasts.

Langdon QK, Peris D, Baker EP, Opulente DA, Nguyen HV, Bond U, Gonçalves P, Sampaio JP, Libkind D, Hittinger CT.

Nat Ecol Evol. 2019 Oct 21. doi: 10.1038/s41559-019-0998-8. [Epub ahead of print]


Variation and selection on codon usage bias across an entire subphylum.

LaBella AL, Opulente DA, Steenwyk JL, Hittinger CT, Rokas A.

PLoS Genet. 2019 Jul 31;15(7):e1008304. doi: 10.1371/journal.pgen.1008304. eCollection 2019 Jul.


Multiple Reinventions of Mating-type Switching during Budding Yeast Evolution.

Krassowski T, Kominek J, Shen XX, Opulente DA, Zhou X, Rokas A, Hittinger CT, Wolfe KH.

Curr Biol. 2019 Aug 5;29(15):2555-2562.e8. doi: 10.1016/j.cub.2019.06.056. Epub 2019 Jul 25.


Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts.

Steenwyk JL, Opulente DA, Kominek J, Shen XX, Zhou X, Labella AL, Bradley NP, Eichman BF, Čadež N, Libkind D, DeVirgilio J, Hulfachor AB, Kurtzman CP, Hittinger CT, Rokas A.

PLoS Biol. 2019 May 21;17(5):e3000255. doi: 10.1371/journal.pbio.3000255. eCollection 2019 May.


Pathogenic budding yeasts isolated outside of clinical settings.

Opulente DA, Langdon QK, Buh KV, Haase MAB, Sylvester K, Moriarty RV, Jarzyna M, Considine SL, Schneider RM, Hittinger CT.

FEMS Yeast Res. 2019 May 1;19(3). pii: foz032. doi: 10.1093/femsyr/foz032.


Evolution of a novel chimeric maltotriose transporter in Saccharomyces eubayanus from parent proteins unable to perform this function.

Baker EP, Hittinger CT.

PLoS Genet. 2019 Apr 4;15(4):e1007786. doi: 10.1371/journal.pgen.1007786. eCollection 2019 Apr.


Eukaryotic Acquisition of a Bacterial Operon.

Kominek J, Doering DT, Opulente DA, Shen XX, Zhou X, DeVirgilio J, Hulfachor AB, Groenewald M, Mcgee MA, Karlen SD, Kurtzman CP, Rokas A, Hittinger CT.

Cell. 2019 Mar 7;176(6):1356-1366.e10. doi: 10.1016/j.cell.2019.01.034. Epub 2019 Feb 21.


Mitochondrial DNA and temperature tolerance in lager yeasts.

Baker EP, Peris D, Moriarty RV, Li XC, Fay JC, Hittinger CT.

Sci Adv. 2019 Jan 30;5(1):eaav1869. doi: 10.1126/sciadv.aav1869. eCollection 2019 Jan.


Mitochondria-encoded genes contribute to evolution of heat and cold tolerance in yeast.

Li XC, Peris D, Hittinger CT, Sia EA, Fay JC.

Sci Adv. 2019 Jan 30;5(1):eaav1848. doi: 10.1126/sciadv.aav1848. eCollection 2019 Jan.


Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina.

Čadež N, Bellora N, Ulloa R, Hittinger CT, Libkind D.

PLoS One. 2019 Jan 30;14(1):e0210792. doi: 10.1371/journal.pone.0210792. eCollection 2019.


Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum.

Shen XX, Opulente DA, Kominek J, Zhou X, Steenwyk JL, Buh KV, Haase MAB, Wisecaver JH, Wang M, Doering DT, Boudouris JT, Schneider RM, Langdon QK, Ohkuma M, Endoh R, Takashima M, Manabe RI, Čadež N, Libkind D, Rosa CA, DeVirgilio J, Hulfachor AB, Groenewald M, Kurtzman CP, Hittinger CT, Rokas A.

Cell. 2018 Nov 29;175(6):1533-1545.e20. doi: 10.1016/j.cell.2018.10.023. Epub 2018 Nov 8.


Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts.

Krause DJ, Kominek J, Opulente DA, Shen XX, Zhou X, Langdon QK, DeVirgilio J, Hulfachor AB, Kurtzman CP, Rokas A, Hittinger CT.

Proc Natl Acad Sci U S A. 2018 Oct 23;115(43):11030-11035. doi: 10.1073/pnas.1806268115. Epub 2018 Oct 8.


sppIDer: A Species Identification Tool to Investigate Hybrid Genomes with High-Throughput Sequencing.

Langdon QK, Peris D, Kyle B, Hittinger CT.

Mol Biol Evol. 2018 Nov 1;35(11):2835-2849. doi: 10.1093/molbev/msy166.


Phylogeography of the wild Lager-brewing ancestor (Saccharomyces eubayanus) in Patagonia.

Eizaguirre JI, Peris D, Rodríguez ME, Lopes CA, De Los Ríos P, Hittinger CT, Libkind D.

Environ Microbiol. 2018 Oct;20(10):3732-3743. doi: 10.1111/1462-2920.14375. Epub 2018 Oct 2.


Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast.

Higgins DA, Young MKM, Tremaine M, Sardi M, Fletcher JM, Agnew M, Liu L, Dickinson Q, Peris D, Wrobel RL, Hittinger CT, Gasch AP, Singer SW, Simmons BA, Landick R, Thelen MP, Sato TK.

Genetics. 2018 Sep;210(1):219-234. doi: 10.1534/genetics.118.301161. Epub 2018 Jul 25.


Repeated Cis-Regulatory Tuning of a Metabolic Bottleneck Gene during Evolution.

Kuang MC, Kominek J, Alexander WG, Cheng JF, Wrobel RL, Hittinger CT.

Mol Biol Evol. 2018 Aug 1;35(8):1968-1981. doi: 10.1093/molbev/msy102.


Evolutionary instability of CUG-Leu in the genetic code of budding yeasts.

Krassowski T, Coughlan AY, Shen XX, Zhou X, Kominek J, Opulente DA, Riley R, Grigoriev IV, Maheshwari N, Shields DC, Kurtzman CP, Hittinger CT, Rokas A, Wolfe KH.

Nat Commun. 2018 May 14;9(1):1887. doi: 10.1038/s41467-018-04374-7.


Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage.

Gonçalves C, Wisecaver JH, Kominek J, Oom MS, Leandro MJ, Shen XX, Opulente DA, Zhou X, Peris D, Kurtzman CP, Hittinger CT, Rokas A, Gonçalves P.

Elife. 2018 Apr 12;7. pii: e33034. doi: 10.7554/eLife.33034.


Introducing 'ecoYeast': ecology and communities of yeasts.

Lachance MA, Hittinger CT.

Yeast. 2018 Apr;35(4):313. doi: 10.1002/yea.3307. No abstract available.


Factors driving metabolic diversity in the budding yeast subphylum.

Opulente DA, Rollinson EJ, Bernick-Roehr C, Hulfachor AB, Rokas A, Kurtzman CP, Hittinger CT.

BMC Biol. 2018 Mar 2;16(1):26. doi: 10.1186/s12915-018-0498-3.


A Molecular Portrait of De Novo Genes in Yeasts.

Vakirlis N, Hebert AS, Opulente DA, Achaz G, Hittinger CT, Fischer G, Coon JJ, Lafontaine I.

Mol Biol Evol. 2018 Mar 1;35(3):631-645. doi: 10.1093/molbev/msx315.


Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets.

Zhou X, Shen XX, Hittinger CT, Rokas A.

Mol Biol Evol. 2018 Feb 1;35(2):486-503. doi: 10.1093/molbev/msx302.


Diverse yeasts for diverse fermented beverages and foods.

Hittinger CT, Steele JL, Ryder DS.

Curr Opin Biotechnol. 2018 Feb;49:199-206. doi: 10.1016/j.copbio.2017.10.004. Epub 2017 Nov 2. Review.


Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health.

Steffan SA, Dharampal PS, Diaz-Garcia L, Currie CR, Zalapa J, Hittinger CT.

J Vis Exp. 2017 Oct 9;(128). doi: 10.3791/54631.


On the origins and industrial applications of Saccharomyces cerevisiae × Saccharomyces kudriavzevii hybrids.

Peris D, Pérez-Torrado R, Hittinger CT, Barrio E, Querol A.

Yeast. 2018 Jan;35(1):51-69. doi: 10.1002/yea.3283. Epub 2017 Dec 6. Review.


Spathaspora boniae sp. nov., a D-xylose-fermenting species in the Candida albicans/Lodderomyces clade.

Morais CG, Batista TM, Kominek J, Borelli BM, Furtado C, Moreira RG, Franco GR, Rosa LH, Fonseca C, Hittinger CT, Lachance MA, Rosa CA.

Int J Syst Evol Microbiol. 2017 Oct;67(10):3798-3805. doi: 10.1099/ijsem.0.002186. Epub 2017 Sep 8.


Contentious relationships in phylogenomic studies can be driven by a handful of genes.

Shen XX, Hittinger CT, Rokas A.

Nat Ecol Evol. 2017 Apr 10;1(5):126. doi: 10.1038/s41559-017-0126.


New yeasts-new brews: modern approaches to brewing yeast design and development.

Gibson B, Geertman JA, Hittinger CT, Krogerus K, Libkind D, Louis EJ, Magalhães F, Sampaio JP.

FEMS Yeast Res. 2017 Jun 1;17(4). doi: 10.1093/femsyr/fox038. Review.


Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production.

Peris D, Moriarty RV, Alexander WG, Baker E, Sylvester K, Sardi M, Langdon QK, Libkind D, Wang QM, Bai FY, Leducq JB, Charron G, Landry CR, Sampaio JP, Gonçalves P, Hyma KE, Fay JC, Sato TK, Hittinger CT.

Biotechnol Biofuels. 2017 Mar 27;10:78. doi: 10.1186/s13068-017-0763-7. eCollection 2017.


Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma.

Bellora N, Moliné M, David-Palma M, Coelho MA, Hittinger CT, Sampaio JP, Gonçalves P, Libkind D.

BMC Genomics. 2016 Nov 9;17(1):901.


Correction: Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae.

Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, Sardi M, McIlwain SJ, Ong IM, Breuer RJ, Narasimhan RA, McGee MA, Dickinson Q, La Reau A, Xie D, Tian M, Piotrowski JS, Reed JL, Zhang Y, Coon JJ, Hittinger CT, Gasch AP, Landick R.

PLoS Genet. 2016 Nov 9;12(11):e1006447. doi: 10.1371/journal.pgen.1006447. eCollection 2016 Nov.


Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network.

Kuang MC, Hutchins PD, Russell JD, Coon JJ, Hittinger CT.

Elife. 2016 Sep 30;5. pii: e19027. doi: 10.7554/eLife.19027.


Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae.

Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, Sardi M, McIlwain SJ, Ong IM, Breuer RJ, Avanasi Narasimhan R, McGee MA, Dickinson Q, La Reau A, Xie D, Tian M, Reed JL, Zhang Y, Coon JJ, Hittinger CT, Gasch AP, Landick R.

PLoS Genet. 2016 Oct 14;12(10):e1006372. doi: 10.1371/journal.pgen.1006372. eCollection 2016 Oct. Erratum in: PLoS Genet. 2016 Nov 9;12 (11):e1006447.


Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data.

Shen XX, Zhou X, Kominek J, Kurtzman CP, Hittinger CT, Rokas A.

G3 (Bethesda). 2016 Dec 7;6(12):3927-3939. doi: 10.1534/g3.116.034744.


In Silico Whole Genome Sequencer and Analyzer (iWGS): a Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies.

Zhou X, Peris D, Kominek J, Kurtzman CP, Hittinger CT, Rokas A.

G3 (Bethesda). 2016 Nov 8;6(11):3655-3662. doi: 10.1534/g3.116.034249.


Speciation driven by hybridization and chromosomal plasticity in a wild yeast.

Leducq JB, Nielly-Thibault L, Charron G, Eberlein C, Verta JP, Samani P, Sylvester K, Hittinger CT, Bell G, Landry CR.

Nat Microbiol. 2016 Jan 11;1:15003. doi: 10.1038/nmicrobiol.2015.3.


Comparative genomics of biotechnologically important yeasts.

Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW.

Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9882-7. doi: 10.1073/pnas.1603941113. Epub 2016 Aug 17.


Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus.

Peris D, Langdon QK, Moriarty RV, Sylvester K, Bontrager M, Charron G, Leducq JB, Landry CR, Libkind D, Hittinger CT.

PLoS Genet. 2016 Jul 6;12(7):e1006155. doi: 10.1371/journal.pgen.1006155. eCollection 2016 Jul.


Dynamic Evolution of Nitric Oxide Detoxifying Flavohemoglobins, a Family of Single-Protein Metabolic Modules in Bacteria and Eukaryotes.

Wisecaver JH, Alexander WG, King SB, Hittinger CT, Rokas A.

Mol Biol Evol. 2016 Aug;33(8):1979-87. doi: 10.1093/molbev/msw073. Epub 2016 Apr 12.


Genomic analysis and D-xylose fermentation of three novel Spathaspora species: Spathaspora girioi sp. nov., Spathaspora hagerdaliae f. a., sp. nov. and Spathaspora gorwiae f. a., sp. nov.

Lopes MR, Morais CG, Kominek J, Cadete RM, Soares MA, Uetanabaro AP, Fonseca C, Lachance MA, Hittinger CT, Rosa CA.

FEMS Yeast Res. 2016 Jun;16(4). pii: fow044. doi: 10.1093/femsyr/fow044. Epub 2016 May 1.


Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research.

McIlwain SJ, Peris D, Sardi M, Moskvin OV, Zhan F, Myers KS, Riley NM, Buzzell A, Parreiras LS, Ong IM, Landick R, Coon JJ, Gasch AP, Sato TK, Hittinger CT.

G3 (Bethesda). 2016 Jun 1;6(6):1757-66. doi: 10.1534/g3.116.029389.


Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides.

Alexander WG, Wisecaver JH, Rokas A, Hittinger CT.

Proc Natl Acad Sci U S A. 2016 Apr 12;113(15):4116-21. doi: 10.1073/pnas.1517242113. Epub 2016 Mar 29.


Genomics and the making of yeast biodiversity.

Hittinger CT, Rokas A, Bai FY, Boekhout T, Gonçalves P, Jeffries TW, Kominek J, Lachance MA, Libkind D, Rosa CA, Sampaio JP, Kurtzman CP.

Curr Opin Genet Dev. 2015 Dec;35:100-9. doi: 10.1016/j.gde.2015.10.008. Epub 2015 Nov 30. Review.


Efficient engineering of marker-free synthetic allotetraploids of Saccharomyces.

Alexander WG, Peris D, Pfannenstiel BT, Opulente DA, Kuang M, Hittinger CT.

Fungal Genet Biol. 2016 Apr;89:10-17. doi: 10.1016/j.fgb.2015.11.002. Epub 2015 Nov 7.


The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts.

Baker E, Wang B, Bellora N, Peris D, Hulfachor AB, Koshalek JA, Adams M, Libkind D, Hittinger CT.

Mol Biol Evol. 2015 Nov;32(11):2818-31. doi: 10.1093/molbev/msv168. Epub 2015 Aug 11.


Draft Genome Sequence of Sporidiobolus salmonicolor CBS 6832, a Red-Pigmented Basidiomycetous Yeast.

Coelho MA, Almeida JM, Hittinger CT, Gonçalves P.

Genome Announc. 2015 May 21;3(3). pii: e00444-15. doi: 10.1128/genomeA.00444-15.


Temperature and host preferences drive the diversification of Saccharomyces and other yeasts: a survey and the discovery of eight new yeast species.

Sylvester K, Wang QM, James B, Mendez R, Hulfachor AB, Hittinger CT.

FEMS Yeast Res. 2015 May;15(3). pii: fov002. doi: 10.1093/femsyr/fov002. Epub 2015 Mar 4.


High-efficiency genome editing and allele replacement in prototrophic and wild strains of Saccharomyces.

Alexander WG, Doering DT, Hittinger CT.

Genetics. 2014 Nov;198(3):859-66. doi: 10.1534/genetics.114.170118. Epub 2014 Sep 9.


A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum.

Almeida P, Gonçalves C, Teixeira S, Libkind D, Bontrager M, Masneuf-Pomarède I, Albertin W, Durrens P, Sherman DJ, Marullo P, Hittinger CT, Gonçalves P, Sampaio JP.

Nat Commun. 2014 Jun 2;5:4044. doi: 10.1038/ncomms5044.

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