The Hittinger Lab

Publications

(&equal contributions, @corresponding author)

98. de Lima AEP, Coplien J, Anthony LC, Sato TK, Zhang Y, Karlen SD, Hittinger CT, Maravelias CT. 2024. On the synthesis of biorefineries for high-yield isobutanol production: from biomass-to-alcohol experiments to system level analysis. RSC Sustain 2:2532-40.
97. Harrison MC, Ubbelohde EJ, LaBella AL, Opulente DA, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT@, Rokas@. 2024. Machine learning enables identification of an alternative yeast galactose utilization pathway. Proc Natl Acad Sci USA 121: e2315314121.
96. Opulente DA&, LaBella AL&, Harrison MC&&, Wolters JF&&, Liu C, Li Y, Kominek J, Steenwyk JL, Stoneman HR, VanDenAvond J, Miller CR, Langdon QK, Silva M, Gonçalves C, Ubbelohde EJ, Li Y, Buh KV, Jarzyna M, Haase MAB, Rosa CA, Čadež N, Libkind D, DeVirgilio JH, Hulfachor AB, Kurtzman CP, Sampaio JP, Gonçalves P, Zhou X, Shen XX, Groenewald M, Rokas A@, Hittinger CT@. 2024. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science. 384: eadj4503.
95. Sun L, David KT, Wolters JF, Karlen SD, Gonçalves C, Opulente DA, LaBella AL, Groenewald M, Zhou X, Shen XX, Rokas A, Hittinger CT@. 2024. Functional and evolutionary integration of a fungal gene with a bacterial operon. Mol Biol Evol 41: msae045.
94. David KT, Harrison MC, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Pennell M, Hittinger CT, Rokas A@. 2024. Saccharomycotina yeasts defy long-standing macroecological patterns. Proc Natl Acad Sci USA 121: e2316031121.
93. Pontes A, Paraíso F, Liu YC, Limtong S, Jindamorakot S, Jespersen L, Gonçalves C, Rosa CA, Tsai IJ, Rokas A, Hittinger CT, Gonçalves P, Sampaio JP. 2024. Tracking alternative versions of the galactose gene network in the genus Saccharomyces and their expansion after domestication. iScience 27: 108987.
92. Barros KO, Mader M, Krause DJ, Pangilinan J, Andreopoulos B, Lipzen A, Mondo SJ, Grigoriev IV, Rosa CA, Sato TK@, Hittinger CT@. 2024. Oxygenation influences xylose fermentation and gene expression in the yeast genera Spathaspora and Scheffersomyces. Biotechnol Biofuels Bioprod 17: 20.
91. Opulente DA@, Langdon QK, Jarzyna M, Buh KV, Haase MAB, Groenewald M, Hittinger CT@. 2023. Taxogenomic analysis of a novel yeast species isolated from soil, Pichia galeolata sp. nov. Yeast 40: 608-15.
90. Wolters JF, LaBella AL, Opulente DA, Rokas A, Hittinger CT@. 2023. Mitochondrial genome diversity across the subphylum Saccharomycotina. Front Microbiol 14: 1268944.
89. Crandall JG, Fisher KJ, Sato TK, Hittinger CT@. 2023. Ploidy evolution in a wild yeast is linked to an interaction between cell type and metabolism. PLoS Biol 21: e3001909.
88. Santos ARO, Barros KO, Batista TM, Souza GFL, Alvarenga FBM, Abegg MA, Sato TK, Hittinger CT, Lachance MA, Rosa CA. 2023. Saccharomycopsis praedatoria sp. nov., a predacious yeast isolated from soil and rotten wood in an Amazonian rainforest biome. Int J Syst Evol Microbiol 73: 006125.
87. de Lima AEP, Wrobel RL, Paul B, Anthony LC, Sato TK, Zhang Y, Hittinger CT, Maravelias CT. 2023. High yield co-production of isobutanol and ethanol from switchgrass: experiments, and process synthesis and analysis. Sustain Energy Fuels 7: 3266-3275.
86. Groenewald M@, Hittinger CT, Bensch K, Opulente DA, Shen XX, Li Y, Liu C, LaBella AL, Zhou X, Limtong S, Jindamorakot S, Gonçalves P, Robert V, Wolfe KH, Rosa CA, Boekhout T, Ĉadež N, Péter G, Sampaio JP, Lachance MA, Yurkov AM, Daniel HM, Takashima M, Boundy-Mills K, Libkind D, Aoki K, Sugita T, Rokas A. 2023. A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Stud Mycol 105: 1-22.
85. Nalabothu RL, Fisher KJ@, LaBella AL, Meyer TA, Opulente DA, Wolters JF, Rokas A, Hittinger CT@. 2023. Codon optimization improves the prediction of xylose metabolism from gene content in budding yeasts. Mol Biol Evol 40: msad111.
84. Parra M, Libkind D, Hittinger CT, Álvarez L, Bellora N. 2023. Assembly and comparative genome analysis of a Patagonian Aureobasidium pullulans isolate reveals unexpected intraspecific variation. Yeast 40: 197-213.
83. Schmitz JM, Wolters JF, Murray NH, Guerra RM, Bingman CA, Hittinger CT, Pagliarini DJ. 2023. Aim18p and Aim46p are chalcone isomerase domain-containing mitochondrial hemoproteins in Saccharomyces cerevisiae. J Biol Chem 299: 102981.
82. Peris D@, Ubbelohde EJ, Kuang MC, Kominek J, Langdon QK, Adams M, Koshalek JA, Hulfachor AB, Opulente DA, Hall DJ, Hyma K, Fay JC, Leducq JB, Charron G, Landry CR, Libkind D, Gonçalves C, Gonçalves P, Sampaio JP, Wang QM, Bai FY, Wrobel RL, Hittinger CT@. 2023. Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces. Nat Commun 14: 690.
81. Liu L, Ansari RU, Vang-Smith M, Hittinger CT@, Sato TK@. 2023. A role for ion homeostasis in yeast ionic liquid tolerance. microPubl Biol 2023: 10.17912/micropub.biology.000718.
80. Barros KO, Alvarenga FBM, Magni G, Souza GFL, Abegg MA, Palladino F, da Silva SS, Rodrigues RCLB, Sato TK, Hittinger CT, Rosa CA. 2023. The Brazilian Amazonian rainforest harbors a high diversity of yeasts associated with rotting wood, including many candidates for new yeast species. Yeast 40: 84-101.
79. Li Y, Liu H, Steenwyk JL, LaBella AL, Harrison MC, Groenewald M, Zhou X, Shen XX, Zhao T, Hittinger CT, Rokas A. 2022. Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum. Curr Biol 32: 5335-5343.e4.
78. Krause DJ, Hittinger CT@. 2022. Functional divergence in a multi-gene family is a key evolutionary innovation for anaerobic growth in Saccharomyces cerevisiae. Mol Biol Evol 39: msac202.
77. Vanacloig-Pedros E, Fisher KJ, Liu L, Debrauske DJ, Young MKM, Place M, Hittinger CT, Sato TK, Gasch AP. 2022. Comparative chemical genomic profiling across plant-based hydrolysate toxins reveals widespread antagonism in fitness contributions. FEMS Yeast Res 21: foac036.
76. Wadler CS, Wolters JF, Fortney NW, Throckmorton KO, Zhang Y, Miller CR, Schneider RM, Wendt-Pienkowski E, Currie CR, Donohue TJ, Noguera DR, Hittinger CT, Thomas MG. 2022. Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms. Biotechnol Biofuels Bioprod 15: 70.
75. Steenwyk JL, Phillips MA, Yang F, Date SS, Graham TR, Berman J, Hittinger CT, Rokas A. 2022. An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function. Sci Adv 8: eabn0105.
74. Gambacorta FV, Wagner ER, Jacobson TB, Tremaine M, Muehlbauer LK, McGee MA, Baerwald JJ, Wrobel RL, Wolters JF, Place M, Dietrich JJ, Xie D, Serate J, Gajbhiye S, Liu L, Vang-Smith M, Coon JJ, Zhang Y, Gasch AP, Amador-Noguez D, Hittinger CT, Sato TK, Pfleger BF. 2022. Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway. Synth Syst Biotechnol 7: 738-49.
73. Spurley WJ, Fisher KJ, Langdon QK, Buh KV, Jarzyna M, Haase MAB, Sylvester K, Moriarty RV, Rodriguez D, Sheddan A, Wright S, Sorlie L, Hulfachor AB, Opulente DA, Hittinger CT@. 2022. Substrate, temperature, and geographical patterns among nearly 2000 natural yeast isolates. Yeast 39: 55-68.
72. Lee SB, Tremaine M, Place M, Liu L, Pier A, Krause DJ, Xie D, Zhang Y, Landick R, Gasch AP, Hittinger CT@, Sato TK@. 2021. Crabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiae. Metab Eng 68: 119-130.
71. Čadež N, Bellora N, Ulloa R, Tome M, Petković H, Groenewald M, Hittinger CT, Libkind D. 2021. Hanseniaspora smithiae sp. nov., a novel apiculate yeast species from Patagonian forests that lacks the typical genomic domestication signatures for fermentative environments. Front Microbiol 12: 679894.
70. Li Y, Steenwyk JL, Chang Y, Wang Y, James TY, Stajich JE, Spatafora JW, Groenewald M, Dunn CW, Hittinger CT, Shen XX, Rokas A. 2021. A genome-scale phylogeny of the kingdom Fungi. Curr Biol 31: 1653-65.
69. LaBella AL, Opulente DA, Steenwyk JL, Hittinger CT, Rokas A. 2021. Signatures of optimal codon usage in metabolic genes inform budding yeast ecology. PLoS Biol 19: e3001185.
68. O'Brien CE, Oliveira-Pacheco J, Ó Cinnéide E, Haase MAB, Hittinger CT, Rogers TR, Zaragoza O, Bond U, Butler G. 2021. Population genomics of the pathogenic yeast Candida tropicalis identifies hybrid isolates in environmental samples. PLoS Pathog 17: e1009138.
67. Haase MAB, Kominek J, Opulente DA, Shen XX, LaBella AL, Zhou X, DeVirgilio J, Hulfachor AB, Kurtzman CP, Rokas A, Hittinger CT. 2021. Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo’s law of irreversible loss. Genetics 217: iyaa012.
66. Shen XX, Li Y, Hittinger CT, Chen XX, Rokas A. 2020. An investigation of irreproducibility in maximum likelihood phylogenetic inference. Nat Commun 11: 6096.
65. Shen XX, Steenwyk JL, LaBella AL, Opulente D, Zhou X, Kominek J, Li Y, Groenewald M, Hittinger CT, Rokas A. Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. Sci Adv. 2020 Nov 4: 6(45): eabd0079. doi: 10.1126/sciadv.abd0079.
64. Stoneman H, Wrobel R, Place M, Graham M, Krause D, De Chiara M, Liti G, Schacherer J, Landick R, Gasch A, Sato T, Hittinger CT. CRISpy-Pop: A Web Tool for Designing CRISPR/Cas9-Driven Genetic Modifications in Diverse Populations. G3. 10(11): 4287-4294.
63. Peris D, Alexander WG, Fisher KJ, Moriarty RV, Basuino MG, Ubbelohde EJ, Wrobel RL, Hittinger CT. Synthetic hybrids of six yeast species. Nat Commun. 11(1):2085.
62. Dharampal PS, Diaz-Garcia L, Haase MAB, Zalapa J, Currie CR, Hittinger CT, Steffan SA. 2020. Microbial diversity associated with the pollen stores of captive-bred bumble bee colonies. Insects 11: 250.
61. Langdon QK, Peris D, Eizaguirre JI, Opulente DA, Buh KV, Sylvester K, Jarzyna M, Rodríguez ME, Lopes CA, Libkind D@, Hittinger CT@. 2020. Postglacial migration shaped the genomic diversity and global distribution of the wild ancestor of lagerbrewing hybrids. PLoS Genet 16: e1008680.
60. Langdon QK, Peris D, Baker EP, Opulente DA, Nguyen HV, Bond U, Goncalves P, Sampaio JP, Libkind D, Hittinger CT. 2019. Fermentation innovation through complex hybridization of wild and domesticated yeasts. Nat Ecol Evol epub: https://doi: 10.1038/s41559-019-0998-8.
59. Labella AL, Opulente DA, Steenwyk JL, Hittinger CT, Rokas A. 2019. Variation and selection on codon usage bias across an entire subphylum. PLoS Genet epub: https://doi.org/10.1371/journal.pgen.1008304.
58. Krassowski T, Kominek J, Shen XX, Opulente DA, Zhou X, Rokas A, Hittinger CT, Wolfe KH. 2019. Multiple reinventions of mating-type switching during budding yeast evolution. Curr Biol 29: 2555-62.
57. 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@. 2019. Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts. PLoS Biol 17: e3000255.
56. Opulente DA, Langdon QK, Buh KV, Haase MAB, Sylvester K, Moriarty RV, Jarzyna M, Considine SL, Schneider RM, Hittinger CT@. 2019. Pathogenic budding yeasts isolated outside of clinical settings. FEMS Yeast Res 19: foz032.
55. Baker EP, Hittinger CT@. 2019. Evolution of a novel chimeric maltotriose transporter in Saccharomyces eubayanus from parent proteins unable to perform this function. PLoS Genetics. 15(4):e1007786
54. 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@. 2019. Eukaryotic acquisition of a bacterial operon. Cell epub: https://doi.org/10.1016/j.cell.2019.01.034.
53. Baker EP, Peris D, Moriarty RV, Li XC, Fay JC, Hittinger CT@. 2019. Mitochondrial DNA and temperature tolerance in lager yeasts. Sci Adv 5: eaav1869.
52. Li XC, Peris D, Hittinger CT, Sia EA, Fay JC. 2019. Mitochondria-encoded genes contribute to evolution of heat and cold tolerance in yeast. Sci Adv 5: eaav1848.
51. Čadež N, Bellora N, Ulloa R, Hittinger CT, Libkind D. 2019. 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. PLoS One 14: e0210792.
50. 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@. 2018. Tempo and mode of genome evolution in the budding yeast subphylum. Cell 175: 1533-45.
49. Krause DJ, Kominek J, Opulente DA, Shen XX, Zhou X, Langdon QK, DeVirgilio J, Hulfachor AB, Kurtzman CP, Rokas A, Hittinger CT@. Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts. Proc Natl Acad Sci USA 115: 11030-11035.
48. Langdon QK, Peris D, Kyle B, Hittinger CT@. sppIDer: a species identification tool to investigate hybrid genomes with high-throughput sequencing. Mol Biol Evol in press doi: https://doi.org/10.1101/333815.
47. Eizaguirre JI, Peris D, Rodríguez ME, Lopes CA, De Los Ríos P, Hittinger CT, Libkind D. Phylogeography of the wild Lager‐brewing ancestor (Saccharomyces eubayanus) in Patagonia. Environ Microbiol epub doi: 10.1111/1462-2920.14375.
46. Higgins DA, Young MK, 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. 2018. Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast. Genetics 210: 219-234.
45. Kuang MC, Kominek J, Alexander WG, Cheng JF, Wrobel RL, Hittinger CT. 2018. Repeated cis-regulatory tuning of a metabolic bottleneck gene during evolution. Mol Biol Evol epub.
44. 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. 2018. Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nat Commun 9: 1887.
43. 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. 2018. Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage. eLife 7: e33034.
42. Opulente DA, Rollinson EJ, Bernick-Roehr C, Hulfachor AB, Rokas A@, Kurtzman CP, Hittinger CT@. 2018. Factors driving metabolic diversity in the budding yeast subphylum. BMC Biol 16: 26.
41.Vakirlis N, Hebert AS, Opulente DA, Achaz G, Hittinger CT, Fischer G, Coon JJ, Lafontaine I. 2018. A molecular portrait of de novo genes in yeasts. Mol Biol Evol 35: 631-645.
40. Zhou X, Shen XX, Hittinger CT, Rokas A. 2018. Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets. Mol Biol Evol 35: 486-503.
39. Morais CG, Batista TM, Kominek J, Borelli BM, Furtado C, Moreira RG, Franco GR, Rosa LH, Fonseca C, Hittinger CT, Lachance MA, Rosa CA. 2017 Spathaspora boniae sp. nov., a D-xylose-fermenting species in the Candida albicans/Lodderomyces clade. Int J Syst Evol Microbiol 67: 3798–805.
38. Steffan SA, Dharampal PS, Diaz-Garcia L, Currie CR, Zalapa J, Hittinger CT. 2017. Empirical, metagenomic, and computational techniques illuminate the mechanisms by which fungicides compromise bee health. J Vis Exp 128: e54631.
37. Haase MAB, Kominek J, Langdon QK, Kurtzman CP, Hittinger CT@. 2017. Genome sequence and physiological analysis of Yamadazyma laniorum f.a. sp. nov. and a reevaluation of the apocryphal xylose fermentation of its sister species Candida tenuis. FEMS Yeast Res epub.
36. Shen XX, Hittinger CT, Rokas A. 2017. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nat Ecol Evol 1: 0126.
35. 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. 2017. Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production. Biotechnol Biofuels 10:78.
34. Shen XX, Zhou X, Kominek J, Kurtzman CP@, Hittinger CT@, Rokas A@. Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data. G3 6:3927-39.
33. Bellora N, Moliné M, David-Palma M, Coelho MA, Hittinger CT, Sampaio JP, Gonçalves P, Libkind D. 2016. Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma. BMC Genomics 17: 901.
32. Zhou X, Peris D, Kominek J, Kurtzman CP, Hittinger CT, Rokas A. 2015. in silico Whole Genome Sequencer & Analyzer (iWGS): a computational pipeline to guide the design and analysis of de novo genome sequencing studies. G3 6:3655-62.
31. 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. 2016. Directed evolution reveals unexected epistatic interactions that alter metabolic regulation and enable anaerobic xylose use by Saccharomyces cerevisiae. PLoS Genet 12: e1006372.
30. Kuang MC, Hutchins PD, Russell JD, Coon JJ, Hittinger CT. 2016. Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network. Elife. 2016 Sep 30; 5. e19027.
29. 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, MeierKolthoff 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. Comparative genomics of biotechnologically important yeasts. Proc Natl Acad Sci USA epub: 201603941.
28. Peris D, Langdon Q, Moriarty RV, Sylvester K, Bontrager M, Charron G, Leducq JB, Landry CR, Libkind D, Hittinger CT@. Complex ancestries of lager-brewing hybrids were shaped by standing variation in the wild yeast Saccharomyces eubayanus. PLoS Genet. 12(7): e1006155.
27. Wisecaver JH, Alexander WG, King SB, Hittinger CT, Rokas A. 2016. Dynamic evolution of nitric oxide detoxifying flavohemoglobins, a family of single-protein metabolic modules in bacteria and eukaryotes. Mol Biol Evol. 33(8):1979-87.
26. Lopes MR&, Morais CG& , Kominek J, Cadete RM, Soares MA, Uetanabaro APT, Fonseca C, Lachance MA, Hittinger CT, Rosa CA. 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. FEMS Yeast Res 16: fow044.
25. McIlwain SJ, Peris D, Sardi M, Moskvin OV, Zhan F, Myers K, Riley NM, Buzzell A, Parreiras L, Ong IM, Landick R, Coon JJ, Gasch AP, Sato TK, Hittinger CT@. 2016. Genome sequence and analysis of a stress-tolerant, wild-derived strain of Saccharomyces cerevisiae used in biofuels research. G3 6:(6) 1757-66.
24. Alexander WG, Wisecaver JH, Rokas A, Hittinger CT@. 2016. Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides. Proc Natl Acad Sci USA. 113(15):4116-21.
23. Alexander WG, Peris D, Pfannenstiel BT, Opulente DA, Kuang M, Hittinger CT(@). 2016. Efficient engineering of marker-free synthetic allotetraploids of Saccharomyces. Fungal Genet Biol. 89: 10-7.
22. Leducq JB, Nielly-Thibault L, Charron G, Eberlein C, Verta JP, Samani P, Sylvester K, Hittinger CT, Bell G, Landry CR. 2016. Speciation driven by hybridization and chromosomal plasticity in a wild yeast. Nat Microbiol 1: 15003.
21. Baker EC, Wang B, Bellora N, Peris D, Hulfachor A, Koshalek J, Adams M, Libkind D, Hittinger CT(@). 2015. The genome sequence of Saccharomyces eubayanus and the domestication of lager-brewing yeasts. Molecular Biology and Evolution. 32:2818-31.
20. Coelho MA, Almeida JMGCF, Hittinger CT, Gonçalves P. 2015. Draft genome sequence of Sporidiobolus salmonicolor CBS 6832, a red-pigmented basidiomycetous yeast. Genome Announc 3: e00444-15.
19. Sylvester K, Wang QM, James B, Mendez R, Hulfachor AB, Hittinger CT(@). 2015. Temperature and host preferences drive the diversification of Saccharomyces and other yeasts: a survey and the discovery of eight new yeast species. FEMS Yeast Res 15:fov002.
18. Alexander WG, Doering DT, Hittinger CT(@). 2014. High-efficiency genome editing and allele replacement in prototrophic and wild strains of Saccharomyces. Genetics 198(3):859-66.
17. Almeida P, Gonçalves C, Teixeira S, Libkind D, Bontrager M, Masneuf-Pomarede I, Albertin W, Durrens P, Sherman DJ, Marullo P, Hittinger CT, Gonçalves P, Sampaio JP. 2014. A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum. Nat Commun 2;5:4044.
16. Peris D, Sylvester K, Libkind D, Gonçalves P, Sampaio JP, Alexander WG, Hittinger CT(@). 2014. Population structure and reticulate evolution of Saccharomyces eubayanus and its lager-brewing hybrids. Molecular Ecology 23:2031-2045.
15. Leducq JB, Charron G, Samani P, Dubé AK, Sylvester K, James B, Almeida P, Sampaio JP, Hittinger CT, Bell G, Landry CR. 2014. Local climatic adaptation in a widespread microorganism. Proc Biol Sci 281: 20132472.
14. Libkind D (&), Hittinger CT (&), Valério E, Gonçalves C, Dover J, Johnston M, Gonçalves P, Sampaio JP. 2011. Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. Proceedings of the National Academy of Sciences of the USA 108:14539-44.
13. Scannell DR (&), Zill OA (&@), Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J, Johnston M, Hittinger CT (@). 2011. The awesome power of yeast evolutionary genetics: New genome sequences and strain resources for the Saccharomyces sensu stricto genus. G3: Genes | Genomes | Genetics 1: 11-25.
12. Hittinger CT, Gonçalves P, Sampaio JP, Dover J, Johnston M, Rokas A. 2010. Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature 464: 54-58.
11. Hittinger CT, Johnston M, Tossberg JT, Rokas A. 2010. Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life. Proceedings of the National Academy of Sciences of the USA 107 (4): 1476-1481.
10. Gibbons JG, Janson EM, Hittinger CT, Johnston M, Abbot P, Rokas A. 2009. Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Molecular Biology and Evolution 26 (12): 2731-2744.
9. Hittinger CT, Carroll SB. 2008. Evolution of an insect-specific GROUCHO interaction motif in the ENGRAILED selector protein. Evolution and Development 10 (5): 537-545.
8. Hittinger CT (@), Carroll SB (@). 2007. Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449 (7163): 677-681.
7. Tour E, Hittinger CT, McGinnis W. 2005. Evolutionarily conserved domains required for activation and repression functions of the Drosophila Ultrabithorax protein. Development 132 (23): 5271-5281.
6. Hittinger CT, Stern DL, Carroll SB. 2005. Pleiotropic functions of a conserved insect-specific Hox peptide motif. Development 132 (23): 5261-5270.
5. Hittinger CT, Rokas A, Carroll SB. 2004. Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. Proceedings of the National Academy of Sciences of the USA 101 (39): 14144-14149.
4. Palangat M, Hittinger CT, Landick R. 2004. Downstream DNA selectively affects a paused conformation of human RNA polymerase II. Journal of Molecular Biology 341 (2): 429-442.
3. King N, Hittinger CT, Carroll SB. 2003. Evolution of key cell signaling and adhesion protein families predates animal origins. Science 301 (5631): 361-363.
2. Guettler S, Jackson EN, Lucchese SA, Honaas L, Green A, Hittinger CT, Tian Y, Lilly WW, and Gathman AC. 2003. ESTs from the basidiomycete Schizophyllum commune grown on nitrogen-replete and nitrogen-limited media. Fungal Genetics and Biology 39 (2): 191-198.
1. Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L, Kresovich S, Matsuoka Y, Doebley J. 2002. Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proceedings of the National Academy of Sciences of the USA 99 (15): 9650-9655.

Reviews and Commentary

R20. Gonçalves C, Hittinger CT, Rokas A. 2024. Horizontal gene transfer in fungi and its ecological importance. In Fungal Associations: The Mycota vol 9, 3rd ed: 59-81. Springer: Cham, Switzerland.
R19. Chavez CM, Groenewald M, Hulfachor AB, Kpurubu G, Huerta R, Hittinger CT, Rokas A. 2024. The cell morphological diversity of Saccharomycotina yeasts. FEMS Yeast Res 24: foad055.
R18. Gabaldón T@, Hittinger CT@. 2022. Editorial: genomic insights on fungal hybrids. Front Fungal Biol 3: 1063609.
R17. Case NT, Berman J, Blehert DS, Cramer RA, Cuomo C, Currie CR, Ene IV, Fisher MC, Fritz-Laylin LK, Gerstein AC, Glass NL, Gow NAR, Gurr SJ, Hittinger CT, Hohl TM, Iliev ID, James TY, Jin H, Klein BS, Kronstad JW, Lorch JM, McGovern V, Mitchell AP, Segre JA, Shapiro RS, Sheppard DC, Sil A, Stajich JE, Stukenbrock EE, Taylor JW, Thompson D, Wright GD, Heitman J, Cowen LE. 2022. The future of fungi: threats and opportunities. G3 12: jkac224.
R16. Mozzachiodi S, Bai FY, Baldrian P, Bell G, Boundy-Mills K, Buzzini P, Čadež N, Cubillos FA, Dashko S, Dimitrov R, Fisher KJ, Gibson B, Gouliamova D, Greig D, Heistinger L, Hittinger CT, Jecmenica M, Koufopanou V, Landry CR, Mašínová T, Naumova ES, Opulente D, Peña JJ, Petrovič U, Tsai IJ, Turchetti B, Villarreal P, Yurkov A, Liti G, Boynton P. 2022. Yeasts from temperate forests. Yeast 39: 4-24.
R15. Harrison MC, LaBella AL, Hittinger CT@, Rokas A@. 2022. The evolution of the GALactose utilization pathway in budding yeasts. Trends Genet 38: 97-106.
R14. Yurkov A, Alves A, Bai FY, Boundy-Mills K, Buzzini P, Čadež N, Cardinali G, Casaregola S, Chaturvedi V, Collin V, Fell JW, Girard V, Groenewald M, Hagen F, Hittinger CT, Kachalkin AV, Kostrzewa M, Kouvelis V, Libkind D, Liu X, Maier T, Meyer W, Péter G, Piątek M, Robert V, Rosa CA, Sampaio JP, Sipiczki M, Stadler M, Sugita T, Sugiyama J, Takagi H, Takashima M, Turchetti B, Wang QM, Boekhout T. 2021. Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes. IMA Fungus 12: 18.
R13. Libkind D, Čadež N, Opulente DA, Langdon QK, Rosa CA, Sampaio JP, Gonçalves P, Hittinger CT, Lachance MA. 2020. Towards yeast taxogenomics: lessons from novel species descriptions based on complete genome sequences. FEMS Yeast Res epub: https://doi.org/10.1093/femsyr/foaa042.
R12. Timothy Y James, Jason E Stajich, Chris Todd Hittinger, Antonis Rokas. 2020. Toward a Fully Resolved Fungal Tree of Life. Annu Rev Microbiol.
R11. Libkind D, Peris D, Cubillos FA, Steenwyk JL, Opulente DA, Langdon QK, Rokas A, Hittinger CT. 2020. Into the wild: new yeast genomes from natural environments and new tools for their analysis. FEMS Yeast Res 20: foaa008.
R10. Hittinger CT@. 2020. Evaluation of Kuroda et al.: insight into yeast isobutanol tolerance with advances still needed. Cell Syst 10: 124.
R9. Lachance MA, Hittinger CT. 2018. Introducing 'ecoYeast': ecology and communities of yeasts. Yeast 35: 313.
R8. Hittinger CT, Steele JL, Ryder DS. Diverse yeasts for diverse fermented beverages and foods. Curr Opin Biotechnol epub: doi:10.1016/j.copbio.2017.10.004.
R7. Peris D, Pérez-Torrado R, Hittinger CT, Barrio E, Querol A. On the origins and industrial applications of Saccharomyces cerevisiae x Saccharomyces kudriavzevii hybrids. Yeast epub: doi:10.1002/yea.3283.
R6. Gibson B, Geertman JA, Hittinger CT, Krogerus K, Libkind D, Louis EJ, Magalhães F, Sampaio JP. New yeasts-new brews: modern approaches to brewing yeast design and development. 2017. FEMS Yeast Res 17: fox038.
R5. Hittinger CT@, Rokas A, Bai FY, Boekhout T, Gonçalves P, Jeffries TW, Kominek J, Lachance MA, Libkind D, Rosa CA, Sampaio JP, Kurtzman CP. Genomics and the making of yeast biodiversity. Curr Opin Genet Dev, 35:100-9.
R4. Hittinger CT (@), 2013. Saccharomyces diversity and evolution: a budding model genus. Trends in Genetics 29 (5): 309-317. Cover by CT Hittinger
R3. Hittinger CT (@), 2012. Endless rots most beautiful. Science 336 (6089): 1649-1650.
R2. Hittinger CT (@), Hesselberth JR. 2010. Nucleosome patterning evolution: steady aim despite moving targets. Molecular Systems Biology 6: 376.
R1. Rokas A, Hittinger CT. 2007. Transcriptional rewiring: the proof is in the eating.  Current Biology 17 (16): R626-R628.