Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts
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Abstract
Cell-cycle checkpoints and DNA repair processes protect organisms from potentially lethal mutational damage. Compared to other budding yeasts in the subphylum Saccharomycotina, we noticed that a lineage in the genus Hanseniaspora exhibited very high evolutionary rates, low Guanine-Cytosine (GC) content, small genome sizes, and lower gene numbers. To better understand Hanseniaspora evolution, we analyzed 25 genomes, including 11 newly sequenced, representing 18/21 known species in the genus. Our phylogenomic analyses identify two Hanseniaspora lineages, a faster-evolving lineage (FEL), which began diversifying approximately 87 million years ago (mya), and a slower-evolving lineage (SEL), which began diversifying approximately 54 mya. Remarkably, both lineages lost genes associated with the cell cycle and genome integrity, but these losses were greater in the FEL. E.g., all species lost the cell-cycle regulator WHIskey 5 (WHI5), and the FEL lost components of the spindle checkpoint pathway (e.g., Mitotic Arrest-Deficient 1 [MAD1], Mitotic Arrest-Deficient 2 [MAD2]) and DNA-damage-checkpoint pathway (e.g., Mitosis Entry Checkpoint 3 [MEC3], RADiation sensitive 9 [RAD9]). Similarly, both lineages lost genes involved in DNA repair pathways, including the DNA glycosylase gene 3-MethylAdenine DNA Glycosylase 1 (MAG1), which is part of the base-excision repair pathway, and the DNA photolyase gene PHotoreactivation Repair deficient 1 (PHR1), which is involved in pyrimidine dimer repair. Strikingly, the FEL lost 33 additional genes, including polymerases (i.e., POLymerase 4 [POL4] and POL32) and telomere-associated genes (e.g., Repressor/activator site binding protein-Interacting Factor 1 [RIF1], Replication Factor A 3 [RFA3], Cell Division Cycle 13 [CDC13], Pbp1p Binding Protein [PBP2]). Echoing these losses, molecular evolutionary analyses reveal that, compared to the SEL, the FEL stem lineage underwent a burst of accelerated evolution, which resulted in greater mutational loads, homopolymer instabilities, and higher fractions of mutations associated with the common endogenously damaged base, 8-oxoguanine. We conclude that Hanseniaspora is an ancient lineage that has diversified and thrived, despite lacking many otherwise highly conserved cell-cycle and genome integrity genes and pathways, and may represent a novel, to our knowledge, system for studying cellular life without them.
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PEX11 was clearly lost in 25 species belonging to the fast-evolving lineage of Hanseniaspora sp. Saccharomycodales, known for multiple gene losses.
“It was, however, clearly lost in 25 species belonging to the fast-evolving lineage of Hanseniaspora sp. Saccharomycodales, known for multiple gene losses (Steenwyk et al. 2019).”
From Mitochondrial retrograde control of transcription evolves with respiratory stress, metabolic adaptation, and virulence in budding yeasts (2026) · cites this paper as Steenwyk et al. 2019
The Introduction (page unavailable) describes a faster-evolving Hanseniaspora lineage with extensive gene losses, supporting that background description. It says the study analyzed 25 genomes from 18 species across two lineages—not 25 species in the faster-evolving lineage. A search for PEX11 found no passage in our copy establishing its loss. (LLM, conf=0.87)
Experimental — accuracy not yet measuredIn 12 genomes, four or more Cit homologs were found, and the only genome where no citrate synthase gene could be identified belongs to Hanseniaspora jakobsenii, a member of a clade known for multiple gene losses and high divergence.
“In 12 genomes, we found four or more Cit homologs, and the only genome where no citrate synthase gene could be identified belongs to Hanseniaspora jakobsenii—a member of a clade known for multiple gene losses and high divergence (Steenwyk et al. 2019; Gonçalves et al. 2025).”
From Mitochondrial retrograde control of transcription evolves with respiratory stress, metabolic adaptation, and virulence in budding yeasts (2026) · cites this paper as Steenwyk et al. 2019
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Cites
Trimmomatic: a flexible trimmer for Illumina sequence data
Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548 · see citing works
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209 · see citing works
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291 · see citing works
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M. V., Kulikov, A. S., Lesin, V. M., Nikolenko, S., Pham, S., Prjibelski, A. D., et al. (2012) · Journal of Computational Biology · doi:10.1089/cmb.2012.0021 · Cited by 25,691 · see citing works
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074 · see citing works
A Simple Sequentially Rejective Multiple Test Procedure
(1979) · Scandinavian Journal of Statistics · doi:10.2307/4615733 · Cited by 21,526 · see citing works
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894 · see citing works
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571 · see citing works
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879 · see citing works
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Capella-Gutiérrez, S., Silla-Martinez, J., & Gabaldón, T. (2009) · Bioinform. · doi:10.1093/bioinformatics/btp348 · Cited by 12,052 · see citing works
QUAST: quality assessment tool for genome assemblies
Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt086 · Cited by 11,172 · see citing works
The NumPy Array: A Structure for Efficient Numerical Computation
van der Walt, S., Colbert, S. C., & Varoquaux, G. P. (2011) · Computing in Science & Engineering · doi:10.1109/mcse.2011.37 · Cited by 10,445 · see citing works
Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection
Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., & Mori, H. (2006) · Molecular Systems Biology · doi:10.1038/msb4100050 · Cited by 7,858 · see citing works
KEGG as a reference resource for gene and protein annotation
Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., & Tanabe, M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1070 · Cited by 7,387 · see citing works
A Rapid Bootstrap Algorithm for the RAxML Web Servers
Stamatakis, A., Hoover, P., & Rougemont, J. (2008) · Systematic Biology · doi:10.1080/10635150802429642 · Cited by 7,028 · see citing works
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975 · see citing works
Biopython: freely available python tools for computational molecular biology and bioinformatics
Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., et al. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp163 · Cited by 6,080 · see citing works
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, L., Stoeckert, C. J., & Roos, D. S. (2003) · Genome Research · doi:10.1101/gr.1224503 · Cited by 5,707 · see citing works
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., et al. (2012) · GigaScience · doi:10.1186/2047-217x-1-18 · Cited by 5,274 · see citing works
The Gene Ontology (GO) database and informatics resource
Gene Ontology Consortium (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh036 · Cited by 4,533 · see citing works
Functional profiling of the Saccharomyces cerevisiae genome
Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., et al. (2002) · Nature · doi:10.1038/nature00935 · Cited by 4,316 · see citing works
Winzeler, E. A., Shoemaker, D. D., Astromoff, A., Liang, H., Anderson, K., Andre, B., Bangham, R., Benito, R., Boeke, J. D., Bussey, H., et al. (1999) · Science · doi:10.1126/science.285.5429.901 · Cited by 3,953 · see citing works
ABySS: A parallel assembler for short read sequence dataPreprint
Simpson, J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones, S. J. M., & Birol, İ. (2009) · Genome Research · doi:10.1101/gr.089532.108 · Cited by 3,583 · see citing works
Kurtzman, C. P., & Lodder, J. (1972) · Mycologia · doi:10.2307/3758036 · Cited by 3,441 · see citing works
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
Suyama, M., Torrents, D., & Bork, P. (2006) · Nucleic Acids Res. · doi:10.1093/nar/gkl315 · Cited by 3,238 · see citing works
The DNA damage response: putting checkpoints in perspective
Zhou, B.-B. S., & Elledge, S. J. (2000) · Nature · doi:10.1038/35044005 · Cited by 3,213 · see citing works
Korf, I. F. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-59 · Cited by 3,160 · see citing works
An Improved General Amino Acid Replacement Matrix
Le, S. Q., & Gascuel, O. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn067 · Cited by 3,127 · see citing works
BUSCO applications from quality assessments to gene prediction and phylogenomics
Waterhouse, R. M., Seppey, M., Simão, F. A., Manni, M., Ioannidis, P., Klioutchnikov, G., Kriventseva, E. V., & Zdobnov, E. M. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msx319 · Cited by 2,214 · see citing works
Holt, C., & Yandell, M. D. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-491 · Cited by 2,042 · see citing works
Saccharomyces Genome Database: the genomics resource of budding yeast
Cherry, J., Hong, E., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., Christie, K., Costanzo, M., Dwight, S., Engel, S., et al. (2011) · Nucleic Acids Res. · doi:10.1093/nar/gkr1029 · Cited by 1,886 · see citing works
Schaeffer, S. E. (2007) · Computer Science Review · doi:10.1016/j.cosrev.2007.05.001 · Cited by 1,679 · see citing works
Gene prediction with a hidden Markov model and a new intron submodel
Stanke, M., & Waack, S. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg1080 · Cited by 1,643 · see citing works
Genome-scale approaches to resolving incongruence in molecular phylogenies.
Rokas, A., Williams, B. L., King, N., & Carroll, S. B. (2003) · Nature · doi:10.1038/nature02053 · Cited by 1,512 · see citing works
Self-citationEvolution of the angiosperms: calibrating the family tree
Wikström, N., Savolainen, V., & Chase, M. W. (2001) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2001.1782 · Cited by 1,508 · see citing works
MycoCosm portal: gearing up for 1000 fungal genomes
Grigoriev, I. V., Nikitin, R., Haridas, S., Kuo, A., Ohm, R., Otillar, R., Riley, R., Salamov, A., Zhao, X., Korzeniewski, F., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1183 · Cited by 1,498 · see citing works
Lindahl, T. L., & Wood, R. D. (1999) · Science · doi:10.1126/science.286.5446.1897 · Cited by 1,489 · see citing works
High Frequency of Hypermutable Pseudomonas aeruginosa in Cystic Fibrosis Lung Infection
Oliver, A., Cantón, R., Campo, P., Baquero, F., & Blázquez, J. (2000) · Science · doi:10.1126/science.288.5469.1251 · Cited by 1,466 · see citing works
Zimin, A. V., Marçais, G., Puiu, D., Roberts, M., Salzberg, S. L., & Yorke, J. A. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt476 · Cited by 1,421 · see citing works
GOATOOLS: A Python library for Gene Ontology analyses
Klopfenstein, D. V., Zhang, L., Pedersen, B. S., Ramírez, F., Vesztrocy, A. W., Naldi, A., Mungall, C., Yunes, J. M., Botvinnik, O. B., Weigel, M., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-28948-z · Cited by 1,307 · see citing works
The Origins of Genome Architecture
Abdel‐Haleem, H. (2007) · Journal of Heredity · doi:10.1093/jhered/esm073 · Cited by 1,140 · see citing works
Endogenous DNA damage in humans: a review of quantitative data
Bont, R. D. (2004) · Mutagenesis · doi:10.1093/mutage/geh025 · Cited by 1,065 · see citing works
Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi
Katinka, M., Duprat, S., Cornillot, E., Méténier, G., Thomarat, F., Prensier, G., Barbe, V., Peyretaillade, E., Brottier, P., Wincker, P., et al. (2001) · Nature · doi:10.1038/35106579 · Cited by 1,051 · see citing works
A review on SNP and other types of molecular markers and their use in animal genetics
Alain Vignal, A., Denis Milan, A., SanCristobal, M., & Eggen, A. A. (2002) · Genetics Selection Evolution · doi:10.1186/1297-9686-34-3-275 · Cited by 1,043 · see citing works
Is a new and general theory of molecular systematics emerging?
Edwards, S. V. (2009) · Evolution · doi:10.1111/j.1558-5646.2008.00549.x · Cited by 1,040 · see citing works
Boeva, V., Popova, T. G., Kevin Bleakley, A., Chiche, P., Cappo, J., Schleiermacher, G., Janoueix‐Lerosey, I., Delattre, O., & Barillot, E. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr670 · Cited by 1,012 · see citing works
The origins of genome architecture
(2007) · Choice Reviews Online · doi:10.5860/choice.45-0862 · Cited by 953 · see citing works
Mirarab, S., & Warnow, T. J. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv234 · Cited by 948 · see citing works
An Introduction to Sequence Similarity (“Homology”) Searching
Pearson, W. R. (2013) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0301s42 · Cited by 946 · see citing works
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training.Preprint
Ter-Hovhannisyan, V., Lomsadze, A., Chernoff, Y., & Borodovsky, M. (2008) · Genome Research · doi:10.1101/gr.081612.108 · Cited by 919 · see citing works
Evolution of high mutation rates in experimental populations of E. coli
Sniegowski, P. D., Gerrish, P. J., & Lenski, R. E. (1997) · Nature · doi:10.1038/42701 · Cited by 879 · see citing works
The Newick utilities: high-throughput phylogenetic tree processing in the U nix shell
Junier, T., & Zdobnov, E. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq243 · Cited by 802 · see citing works
Rate, molecular spectrum, and consequences of human mutation
Lynch, M. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0912629107 · Cited by 792 · see citing works
Albalat, R., & Cañestro, C. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.39 · Cited by 775 · see citing works
Defects in a cell cycle checkpoint may be responsible for the genomic instability of cancer cells
Hartwell, L. H. (1992) · Cell · doi:10.1016/0092-8674(92)90586-2 · Cited by 770 · see citing works
Efficient de novo assembly of large genomes using compressed data structuresPreprint
Simpson, J. T., & Durbin, R. M. (2011) · Genome Research · doi:10.1101/gr.126953.111 · Cited by 767 · see citing works
Comprehensive Analysis of Hypermutation in Human Cancer
Campbell, B. B., Light, N. D., Fabrizio, D. A., Zatzman, M., Fuligni, F., de Borja, R., Davidson, S., Edwards, M., Elvin, J. A., Hodel, K. P., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.048 · Cited by 759 · see citing works
Systematic Identification of Pathways That Couple Cell Growth and Division in Yeast
Jorgensen, P., Nishikawa, J. L., Breitkreutz, B., & Tyers, M. (2002) · Science · doi:10.1126/science.1070850 · Cited by 753 · see citing works
Weinert, T. A., Kiser, G. L., & Hartwell, L. H. (1994) · Genes & Development · doi:10.1101/gad.8.6.652 · Cited by 750 · see citing works
Informed and automated k -mer size selection for genome assembly
Chikhi, R., & Medvedev, P. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt310 · Cited by 725 · see citing works
A genome-wide view of the spectrum of spontaneous mutations in yeast.
Lynch, M., Sung, W., Morris, K., Coffey, N., Landry, C. R., Dopman, E. B., Dickinson, W. J., Okamoto, K., Kulkarni, S., Hartl, D. L., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803466105 · Cited by 708 · see citing works
Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts
Gallone, B., Steensels, J., Prahl, T., Soriaga, L., Saels, V., Herrera-Malaver, B., Merlevede, A., Roncoroni, M., Voordeckers, K., Miraglia, L., et al. (2016) · Cell · doi:10.1016/j.cell.2016.08.020 · Cited by 679 · see citing works
Role of mutator alleles in adaptive evolution
Taddéi, F., Radman, M., Smith, J. M., Toupance, B., Gouyon, P. H., & Godelle, B. (1997) · Nature · doi:10.1038/42696 · Cited by 678 · see citing works
A beginner's guide to eukaryotic genome annotation
Yandell, M. D., & Ence, D. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3174 · Cited by 626 · see citing works
Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
Shen, X.-X., Opulente, D. A., Kominek, J., Zhou, X., Steenwyk, J. L., Buh, K. V., Haase, M. A. B., Wisecaver, J. H., Wang, M., Doering, D. T., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.023 · Cited by 619 · see citing works
Self-citationCell Cycle Regulation by Checkpoints
Barnum, K. J., & O’Connell, M. J. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0888-2_2 · Cited by 609 · see citing works
DNA‐damage repair; the good, the bad, and the ugly
Hakem, R. (2008) · The EMBO Journal · doi:10.1038/emboj.2008.15 · Cited by 547 · see citing works
The base excision repair pathway
Seeberg, E., Eide, L., & Bjørås, M. (1995) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)89086-6 · Cited by 542 · see citing works
The BLAST Sequence Analysis Tool
Madden, T. (2013) · Cited by 535 · see citing works
The Mechanisms of UV Mutagenesis
Ikehata, H., & Ono, T. (2011) · Journal of Radiation Research · doi:10.1269/jrr.10175 · Cited by 515 · see citing works
Costs and Benefits of High Mutation Rates: Adaptive Evolution of Bacteria in the Mouse Gut
Giraud, A., Matić, I., Tenaillon, O., Clara, A., Radman, M., Fons, M., & Taddéi, F. (2001) · Science · doi:10.1126/science.1056421 · Cited by 482 · see citing works
Evidence That Mutation Is Universally Biased towards AT in Bacteria
Hershberg, R., & Petrov, D. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001115 · Cited by 467 · see citing works
Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times
dos Reis, M., & Yang, Z. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr045 · Cited by 431 · see citing works
CDK Activity Antagonizes Whi5, an Inhibitor of G1/S Transcription in Yeast
Costanzo, M., Nishikawa, J. L., Tang, X., Millman, J. S., Schub, O., Breitkreuz, K. E., Dewar, D., Rupeš, I., Andrews, B., & Tyers, M. (2004) · Cell · doi:10.1016/j.cell.2004.05.024 · Cited by 428 · see citing works
Precise estimates of mutation rate and spectrum in yeast
Zhu, Y. O., Siegal, M. L., Hall, D. W., & Petrov, D. A. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1323011111 · Cited by 421 · see citing works
The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine
Yoshida, K., Schuenemann, V. J., Cano, L. M., Pais, M., Mishra, B., Sharma, R., Lanz, C., Martin, F. N., Kamoun, S., Krause, J., et al. (2013) · eLife · doi:10.7554/elife.00731 · Cited by 407 · see citing works
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs
Waterhouse, R. M., Tegenfeldt, F., Li, J., Zdobnov, E. M., & Kriventseva, E. V. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1116 · Cited by 387 · see citing works
Comparative genomics of biotechnologically important yeasts
Riley, R. W., Haridas, S., Wolfe, K. H., Lopes, M., Hittinger, C. T., Göker, M., Salamov, A., Wisecaver, J. H., Long, T. M., Calvey, C. H., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1603941113 · Cited by 362 · see citing works
Keightley, P. D., Trivedi, U. H., Thomson, M. L., Oliver, F., Kumar, S., & Blaxter, M. (2009) · Genome Research · doi:10.1101/gr.091231.109 · Cited by 359 · see citing works
Yeast Cbk1 and Mob2 Activate Daughter-Specific Genetic Programs to Induce Asymmetric Cell Fates
Colman‐Lerner, A., Chin, T., & Brent, R. (2001) · Cell · doi:10.1016/s0092-8674(01)00596-7 · Cited by 351 · see citing works
Bayesian molecular clock dating of species divergences in the genomics era
dos Reis, M., Donoghue, P. C. J., & Yang, Z. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2015.8 · Cited by 339 · see citing works
Coevolution with viruses drives the evolution of bacterial mutation rates
Pál, C., Macia, M. D., Oliver, A., Schachar, I. H., & Buckling, A. G. J. (2007) · Nature · doi:10.1038/nature06350 · Cited by 324 · see citing works
Myung, K., Datta, A., & Kolodner, R. D. (2001) · Cell · doi:10.1016/s0092-8674(01)00227-6 · Cited by 322 · see citing works
Philippe, H., Delsuc, F., Brinkmann, H., & Lartillot, N. (2005) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev.ecolsys.35.112202.130205 · Cited by 306 · see citing works
IME1, a positive regulator gene of meiosis in S. cerevisiae
Kassir, Y., Granot, D., & Simchen, G. (1988) · Cell · doi:10.1016/0092-8674(88)90427-8 · Cited by 298 · see citing works
Relations between chemical structure and biological activity in peptides
Sneath, P. H. A. (1966) · Journal of Theoretical Biology · doi:10.1016/0022-5193(66)90112-3 · Cited by 291 · see citing works
The anaphase-promoting complex: a key factor in the regulation of cell cycle
Castro, A., Bernis, C., Vigneron, S., Labbé, J., & Lorca, T. (2005) · Oncogene · doi:10.1038/sj.onc.1207973 · Cited by 287 · see citing works
DNA Damage Response Genes and the Development of Cancer Metastasis
Broustas, C. G., & Lieberman, H. B. (2014) · Radiation Research · doi:10.1667/rr13515.1 · Cited by 276 · see citing works
Healey, K. R., Zhao, Y., Perez, W. B., Lockhart, S. R., Sobel, J. D., Farmakiotis, D., Kontoyiannis, D. P., Sanglard, D., Taj-Aldeen, S. J., Alexander, B. D., et al. (2016) · Nature Communications · doi:10.1038/ncomms11128 · Cited by 276 · see citing works
Genomic insights into the evolutionary origin of Myxozoa within Cnidaria
Chang, E. S., Neuhof, M., Rubinstein, N. D., Diamant, A., Philippe, H., Huchon, D., & Cartwright, P. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1511468112 · Cited by 262 · see citing works
Lighter: fast and memory-efficient sequencing error correction without counting
Song, L., Florea, L. D., & Langmead, B. (2014) · Genome Biology · doi:10.1186/s13059-014-0509-9 · Cited by 260 · see citing works
Sucrose Utilization in Budding Yeast as a Model for the Origin of Undifferentiated Multicellularity
Koschwanez, J. H., Foster, K. R., & Murray, A. W. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001122 · Cited by 243 · see citing works
Selection-Driven Gene Loss in Bacteria
Koskiniemi, S., Sun, S., Berg, O. G., & Andersson, D. I. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002787 · Cited by 232 · see citing works
Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data
Shen, X., Zhou, X., Kominek, J., Kurtzman, C. P., Hittinger, C. T., & Rokas, A. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.034744 · Cited by 211 · see citing works
Heenan, E. J., & Sancar, A. (2008) · Wiley Encyclopedia of Chemical Biology · doi:10.1002/9780470048672.wecb131 · Cited by 209 · see citing works
A review on SNP and other types of molecular markers and their use in animal genetics
Alain Vignal, A., Denis Milan, A., SanCristobal, M., & Eggen, A. (2002) · Genetics Selection Evolution · doi:10.1051/gse:2002009 · Cited by 209 · see citing works
Comprehensive variation discovery in single human genomes
Weisenfeld, N., Yin, S., Sharpe, T., Lau, B., Hegarty, R., Holmes, L., Sogoloff, B., Tabbaa, D., Williams, L., Russ, C., et al. (2014) · Nature Genetics · doi:10.1038/ng.3121 · Cited by 196 · see citing works
nQuire: a statistical framework for ploidy estimation using next generation sequencing
Weiß, C. L., Pais, M., Cano, L. M., Kamoun, S., & Burbano, H. A. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2128-z · Cited by 192 · see citing works
The functional spectrum of low-frequency coding variation
Marth, G., Yu, F., Indap, A. R., Garimella, K. V., Gravel, S., Leong, W. F., Tyler‐Smith, C., Bainbridge, M. N., Blackwell, T. W., Zheng-Bradley, X., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-9-r84 · Cited by 190 · see citing works
Automatic Lip-Contour Extraction and Mouth-Structure Segmentation in Images
Gómez-Mendoza, J.-B., Prieto, F., & Redarce, T. (2010) · Computing in Science & Engineering · doi:10.1109/mcse.2010.145 · Cited by 187 · see citing works
Oenological Impact of the Hanseniaspora/Kloeckera Yeast Genus on Wines—A Review
Martín, V., Valera, M. J., Medina, K., Boido, E., & Carrau, F. (2018) · Fermentation · doi:10.3390/fermentation4030076 · Cited by 183 · see citing works
Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts
Hittinger, C. T., Rokas, A., & Carroll, S. B. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404319101 · Cited by 178 · see citing works
Genome measures used for quality control are dependent on gene function and ancestry
Wang, J., Raskin, L., Samuels, D. C., Shyr, Y., & Guo, Y. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu668 · Cited by 173 · see citing works
Kocot, K. M., Citarella, M. R., Moroz, L. L., & Halanych, K. M. (2013) · Evolutionary Bioinformatics · doi:10.4137/ebo.s12813 · Cited by 166 · see citing works
Zhou, X., Shen, X.-X., Hittinger, C. T., & Rokas, A. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msx302 · Cited by 164 · see citing works
Tyrosyl-DNA phosphodiesterase (Tdp1) participates in the repair of Top2-mediated DNA damage
Nitiss, K. C., Malik, M., He, X., White, S. W., & Nitiss, J. L. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603455103 · Cited by 157 · see citing works
Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary
Liu, L., Zhang, J., Rheindt, F. E., Lei, F., Qu, Y., Wang, Y., Zhang, Y., Sullivan, C., Nie, W., Wang, J., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1616744114 · Cited by 150 · see citing works
Segal, E. S., Gritsenko, V., Levitan, A., Yadav, B., Dror, N., Steenwyk, J. L., Silberberg, Y., Mielich, K., Rokas, A., Gow, N. A. R., et al. (2018) · mBio · doi:10.1128/mbio.02048-18 · Cited by 150 · see citing works
Self-citationMolecular evolution of the telomere-associated MAL loci of Saccharomyces.
Charron, M. J., Read, E., Haut, S., & Michels, C. A. (1989) · Genetics · doi:10.1093/genetics/122.2.307 · Cited by 149 · see citing works
Zhu, Y. O., Sherlock, G. J., & Petrov, D. A. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.029397 · Cited by 145 · see citing works
Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi
Slot, J. C., & Rokas, A. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914418107 · Cited by 144 · see citing works
Evolution of networks and sequences in eukaryotic cell cycle control
Cross, F. R., Buchler, N. E. G., & Skotheim, J. M. (2011) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2011.0078 · Cited by 144 · see citing works
Remarkably ancient balanced polymorphisms in a multi-locus gene network
Hittinger, C. T., Gonçalves, P. M., Sampaio, J. P., Dover, J., Johnston, M., & Rokas, A. (2010) · Nature · doi:10.1038/nature08791 · Cited by 135 · see citing works
From Sugar of Grape to Alcohol of Wine: Sensorial Impact of Alcohol in Wine
Jordão, A. M., Vilela, A., & Cosme, F. (2015) · Beverages · doi:10.3390/beverages1040292 · Cited by 128 · see citing works
Mutational landscape of yeast mutator strains
Serero, A., Jubin, C., Loeillet, S., Legoix-Né, P., & Nicolas, A. G. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1314423111 · Cited by 126 · see citing works
Hanseniaspora uvarum from Winemaking Environments Show Spatial and Temporal Genetic Clustering
Albertin, W., Setati, M. E., Miot-Sertier, C., Mostert, T. T., Colonna-Ceccaldi, B., Coulon, J., Girard, P., Moine, V., Pillet, M., Salin, F., et al. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.01569 · Cited by 124 · see citing works
Structure of the MIND Complex Defines a Regulatory Focus for Yeast Kinetochore Assembly
Dimitrova, Y. N., Jenni, S., Valverde, R., Khin, Y., & Harrison, S. C. (2016) · Cell · doi:10.1016/j.cell.2016.10.011 · Cited by 121 · see citing works
Non-randomness of Ammo-acid Changes in the Evolution of Homologous Proteins
Epstein, C. J. (1967) · Nature · doi:10.1038/215355a0 · Cited by 116 · see citing works
Analysis of Low Molecular Weight Carbohydrates in Food and Beverages: A Review
Montero, C. M., Dodero, M. C. R., Guillén-Sánchez, D. A., & Barroso, C. G. (2004) · Chromatographia · doi:10.1365/s10337-003-0134-3 · Cited by 112 · see citing works
Genome-scale mutational signatures of aflatoxin in cells, mice, and human tumorsPreprint
Huang, M.-N., Yu, W., Teoh, W. W., Ardin, M., Jusakul, A., Ng, A., Boot, A., Abedi-Ardekani, B., Villar, S., Myint, S. S., et al. (2017) · bioRxiv · doi:10.1101/gr.220038.116 · Cited by 111 · see citing works
The Role of Altered Nucleotide Excision Repair and UVB-Induced DNA Damage in Melanomagenesis
Budden, T., & Bowden, N. A. (2013) · International Journal of Molecular Sciences · doi:10.3390/ijms14011132 · Cited by 110 · see citing works
Checkpoint Adaptation Precedes Spontaneous and Damage-Induced Genomic Instability in Yeast
Galgoczy, D. J., & Toczyski, D. P. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.5.1710-1718.2001 · Cited by 109 · see citing works
Huang, M., de Calignon, A., Nicolas, A. G., & Galibert, F. (2000) · Current Genetics · doi:10.1007/s002940000149 · Cited by 107 · see citing works
Boyce, K. J., Wang, Y., Verma, S., Shakya, V. P. S., Xue, C., & Idnurm, A. (2017) · mBio · doi:10.1128/mbio.00595-17 · Cited by 101 · see citing works
Rhodes, J., Beale, M. A., Vanhove, M., Jarvis, J. N., Kannambath, S., Simpson, J. A., Ryan, A., Meintjes, G., Harrison, T. S., Fisher, M. C., et al. (2017) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.116.037499 · Cited by 100 · see citing works
A Gip1p–Glc7p phosphatase complex regulates septin organization and spore wall formation
Tachikawa, H., Bloecher, A., Tatchell, K., & Neiman, A. M. (2001) · The Journal of Cell Biology · doi:10.1083/jcb.200107008 · Cited by 97 · see citing works
THE EVOLUTION OF STRESS-INDUCED HYPERMUTATION IN ASEXUAL POPULATIONS
Ram, Y., & Hadany, L. (2012) · Evolution · doi:10.1111/j.1558-5646.2012.01576.x · Cited by 92 · see citing works
Natural yeast flora of different varieties of grapes used for wine making in India
Chavan, P. S., Mane, S. S., Kulkarni, G., Shaikh, S., Ghormade, V., Nerkar, D. P., Shouche, Y. S., & Deshpande, M. V. (2009) · Food Microbiology · doi:10.1016/j.fm.2009.05.005 · Cited by 88 · see citing works
Billmyre, R. B., Clancey, S. A., & Heitman, J. (2017) · eLife · doi:10.7554/elife.28802 · Cited by 79 · see citing works
ploidyNGS: visually exploring ploidy with Next Generation Sequencing data
dos Santos, R. A. C., Goldman, G. H., & Riaño‐Pachón, D. M. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx204 · Cited by 78 · see citing works
Expression of the yeast PHR1 gene is induced by DNA-damaging agents.
Sebastian, J., Kraus, B. L., & Sancar, G. B. (1990) · Molecular and Cellular Biology · doi:10.1128/mcb.10.9.4630 · Cited by 76 · see citing works
CARTWRIGHT, J. L., Gasmi, L., Spiller, D. G., & McLennan, A. G. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m005015200 · Cited by 74 · see citing works
Structure of the DASH/Dam1 complex shows its role at the yeast kinetochore-microtubule interface
Jenni, S., & Harrison, S. C. (2018) · Science · doi:10.1126/science.aar6436 · Cited by 72 · see citing works
Simplicity and Complexity of Microsporidian Genomes
Keeling, P. J., & Slamovits, C. H. (2004) · Eukaryotic Cell · doi:10.1128/ec.3.6.1363-1369.2004 · Cited by 69 · see citing works
Xiao, W., & Chow, B. L. (1998) · Current Genetics · doi:10.1007/s002940050313 · Cited by 65 · see citing works
Clade- and species-specific features of genome evolution in the Saccharomycetaceae
Wolfe, K. H., Armisén, D., Proux‐Wéra, E., hÉigeartaigh, S. Ó., Azam, H., Gordon, J., & Byrne, K. P. (2015) · FEMS Yeast Research · doi:10.1093/femsyr/fov035 · Cited by 64 · see citing works
Using BLOSUM in Sequence AlignmentsPreprint
Mount, D. W. (2008) · Cold Spring Harbor Protocols · doi:10.1101/pdb.top39 · Cited by 63 · see citing works
The Evolution of Low Mutation Rates in Experimental Mutator Populations of Saccharomyces cerevisiae
McDonald, M. J., Hsieh, Y.-Y., Yu, Y.-H., Chang, S., & Leu, J. (2012) · Current Biology · doi:10.1016/j.cub.2012.04.056 · Cited by 62 · see citing works
Steenwyk, J. L., & Rokas, A. (2017) · G3 Genes Genomes Genetics · doi:10.1534/g3.117.040105 · Cited by 60 · see citing works
Factors driving metabolic diversity in the budding yeast subphylum
Opulente, D. A., Rollinson, E. J., Bernick-Roehr, C., Hulfachor, A. B., Rokas, A., Kurtzman, C. P., & Hittinger, C. T. (2018) · BMC Biology · doi:10.1186/s12915-018-0498-3 · Cited by 58 · see citing works
Heinrich, S., Sewart, K., Windecker, H., Langegger, M., Schmidt, N., Hustedt, N., & Hauf, S. (2014) · EMBO Reports · doi:10.1002/embr.201338114 · Cited by 57 · see citing works
Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi
Medina, E. M., Turner, J. J., Gordân, R., Skotheim, J. M., & Buchler, N. E. G. (2016) · eLife · doi:10.7554/elife.09492 · Cited by 57 · see citing works
Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation
Steenwyk, J. L., & Rokas, A. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00288 · Cited by 53 · see citing works
Cdc13 subcomplexes regulate multiple telomere functions.
Lustig, A. J. (2001) · Nature Structural Biology · doi:10.1038/86157 · Cited by 52 · see citing works
Lubelsky, Y., Reuven, N. B., & Shaul, Y. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.23.10665-10673.2005 · Cited by 48 · see citing works
Xiao, W., Chow, B. L., Hanna, M. D., & Doetsch, P. W. (2001) · Mutation Research/DNA Repair · doi:10.1016/s0921-8777(01)00113-6 · Cited by 45 · see citing works
Ngo, H.-P., & Lydall, D. A. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001072 · Cited by 42 · see citing works
Čadež, N., Bellora, N., Ulloa, R. J., Hittinger, C. T., & Libkind, D. (2019) · PLoS ONE · doi:10.1371/journal.pone.0210792 · Cited by 42 · see citing works
Nunoshiba, T. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh868 · Cited by 39 · see citing works
A damage-responsive DNA binding protein regulates transcription of the yeast DNA repair gene PHR1.
Sebastian, J., & Sancar, G. B. (1991) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.88.24.11251 · Cited by 37 · see citing works
Jindamorakot, S., Ninomiya, S., Limtong, S., Yongmanitchai, W., Tuntirungkij, M., Potacharoen, W., Tanaka, K., Kawasaki, H., & Nakase, T. (2009) · FEMS Yeast Research · doi:10.1111/j.1567-1364.2009.00568.x · Cited by 37 · see citing works
Langenberg, A.-K., Bink, F. J., Wolff, L., Walter, S., von Wallbrunn, C., Grossmann, M., Heinisch, J. J., & Schmitz, H. (2017) · Applied and Environmental Microbiology · doi:10.1128/aem.01580-17 · Cited by 36 · see citing works
Zhou, X., Peris, D., Kominek, J., Kurtzman, C. P., Hittinger, C. T., & Rokas, A. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.034249 · Cited by 35 · see citing works
Genome Sequence of the Native Apiculate Wine Yeast Hanseniaspora vineae T02/19AF
Giorello, F., Berná, L., Greif, G., Camesasca, L., Salzman, V., Medina, K., Robello, C., Gaggero, C., Aguilar, P. S., & Carrau, F. (2014) · Genome Announcements · doi:10.1128/genomea.00530-14 · Cited by 34 · see citing works
Genome Sequences of Three Species of Hanseniaspora Isolated from Spontaneous Wine Fermentations
Sternes, P. R., Lee, D., Kutyna, D. R., & Borneman, A. R. (2016) · Genome Announcements · doi:10.1128/genomea.01287-16 · Cited by 32 · see citing works
Čadež, N., Raspor, P., & Smith, M. T. (2006) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.64052-0 · Cited by 31 · see citing works
Ouoba, L. I. I., Nielsen, D. S., Anyogu, A., Kando, C. K., Diawara, B., Jespersen, L., & Sutherland, J. P. (2015) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.000461 · Cited by 29 · see citing works
Expression of the Yeast PHR1 Gene Is Induced by DNA-Damaging Agents
Sebastian, J., Kraus, B. L., & Sancar, G. B. (1990) · Molecular and Cellular Biology · doi:10.1128/mcb.10.9.4630-4637.1990 · Cited by 28 · see citing works
Nag, D. K., Koonce, M. P., & Axelrod, J. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.12.7029 · Cited by 15 · see citing works
Chang, C., Huang, L.-Y., Chen, S.-F., & Lee, C.-F. (2011) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.034231-0 · Cited by 12 · see citing works
Hendler, A., Medina, E. M., Kishkevich, A., Abu‐Qarn, M., Klier, S., Buchler, N. E. G., de Bruin, R. A. M., & Aharoni, A. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006778 · Cited by 11 · see citing works
Anaphase-Promoting Complex 7 is a Prognostic Factor in Human Colorectal Cancer
Kim, I. Y., Kwon, H. Y., Park, K. H., & Kim, D. S. (2017) · Annals of Coloproctology · doi:10.3393/ac.2017.33.4.139 · Cited by 11 · see citing works
Sterling, C. H., & Sweasy, J. B. (2005) · Genetics · doi:10.1534/genetics.105.049254 · Cited by 10 · see citing works
Genome Sequence of the Nonconventional Wine Yeast Hanseniaspora guilliermondii UTAD222
Seixas, I., Barbosa, C. R., Salazar, S. B., Mendes‐Faia, A., Wang, Y., Güldener, U., Mendes‐Ferreira, A., & Mira, N. P. (2017) · Genome Announcements · doi:10.1128/genomea.01515-16 · Cited by 8 · see citing works
Genome Sequence of the Wine Yeast Saccharomycodes ludwigii UTAD17
Tavares, M. J., Güldener, U., Esteves, M., Mendes‐Faia, A., Mendes‐Ferreira, A., & Mira, N. P. (2018) · Microbiology Resource Announcements · doi:10.1128/mra.01195-18 · Cited by 6 · see citing works
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Treatment strategies for cryptococcal infection: challenges, advances and future outlook
Iyer, K. R., Revie, N. M., Fu, C., Robbins, N., & Cowen, L. E. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00511-0 · Cited by 363 · see citing works
Tran, T., Grandvalet, C., Verdier, F., Martin, A., Alexandre, H., & Tourdot‐Maréchal, R. (2020) · Foods · doi:10.3390/foods9070963 · Cited by 175 · see citing works
Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota
Shen, X., Steenwyk, J. L., LaBella, A. L., Opulente, D. A., Zhou, X., Kominek, J., Li, Y., Groenewald, M., Hittinger, C. T., & Rokas, A. (2020) · Science Advances · doi:10.1126/sciadv.abd0079 · Cited by 157 · see citing works
Liu, F., Hu, Z.-D., Zhao, X.-M., Zhao, W.-N., Feng, Z.-X., Yurkov, A., Alwasel, S., Boekhout, T., Bensch, K., Hui, F.-L., et al. (2024) · Persoonia - Molecular Phylogeny and Evolution of Fungi · doi:10.3767/persoonia.2024.52.02 · Cited by 143 · see citing works
Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts
Opulente, D. A., LaBella, A. L., Harrison, M.-C., Wolters, J. F., Liu, C., Li, Y., Kominek, J., Steenwyk, J. L., Stoneman, H. R., VanDenAvond, J., et al. (2024) · Science · doi:10.1126/science.adj4503 · Cited by 121 · see citing works
Self-citationBillmyre, R. B., Applen Clancey, S., Li, L. X., Doering, T. L., & Heitman, J. (2020) · Nature Communications · doi:10.1038/s41467-019-13890-z · Cited by 102 · see citing works
Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota
Galindo, L. J., López‐García, P., Torruella, G., Karpov, S. A., & Moreira, D. (2021) · Nature Communications · doi:10.1038/s41467-021-25308-w · Cited by 91 · see citing works
UV Radiation in DNA Damage and Repair Involving DNA-Photolyases and Cryptochromes
Vechtomova, Y. L., Telegina, T. A., Buglak, A. A., & Kritsky, M. (2021) · Biomedicines · doi:10.3390/biomedicines9111564 · Cited by 92 · see citing works
An investigation of irreproducibility in maximum likelihood phylogenetic inference
Shen, X., Li, Y., Hittinger, C. T., Chen, X., & Rokas, A. (2020) · Nature Communications · doi:10.1038/s41467-020-20005-6 · Cited by 84 · see citing works
Evolutionary Dynamics of the Spindle Assembly Checkpoint in Eukaryotes
Kops, G. J. P. L., Snel, ., & Tromer, E. C. (2020) · Current Biology · doi:10.1016/j.cub.2020.02.021 · Cited by 73 · see citing works
A computational screen for alternative genetic codes in over 250,000 genomes
Shulgina, Y., & Eddy, S. R. (2021) · eLife · doi:10.7554/elife.71402 · Cited by 69 · see citing works
Dissecting Incongruence between Concatenation- and Quartet-Based Approaches in Phylogenomic Data
Shen, X., Steenwyk, J. L., & Rokas, A. (2021) · Systematic Biology · doi:10.1093/sysbio/syab011 · Cited by 64 · see citing works
Gonçalves, P. M., Gonçalves, C., Brito, P. H., & Sampaio, J. P. (2020) · Yeast · doi:10.1002/yea.3463 · Cited by 62 · see citing works
Advances in understanding the evolution of fungal genome architecture
Priest, S. J., Yadav, V., & Heitman, J. (2020) · F1000Research · doi:10.12688/f1000research.25424.1 · Cited by 60 · see citing works
What are the 100 most cited fungal genera?
Bhunjun, C. S., Chen, Y. J., Phukhamsakda, C., Boekhout, T., Groenewald, J. Z., McKenzi, E. H. C., Francisco, E. C., Frisvad, J. C., Groenewald, M., Hurdeal, V. G., et al. (2024) · Studies in Mycology · doi:10.3114/sim.2024.108.01 · Cited by 57 · see citing works
Exploring future applications of the apiculate yeast Hanseniaspora
van Wyk, N., Badura, J., von Wallbrunn, C., & Pretorius, I. S. (2023) · Critical Reviews in Biotechnology · doi:10.1080/07388551.2022.2136565 · Cited by 53 · see citing works
The contribution of DNA repair pathways to genome editing and evolution in filamentous pathogens
Huang, J. T., & Cook, D. E. (2022) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuac035 · Cited by 52 · see citing works
Into the wild: new yeast genomes from natural environments and new tools for their analysis
Libkind, D., Peris, D., Cubillos, F. A., Steenwyk, J. L., Opulente, D. A., Langdon, Q. K., Rokas, A., & Hittinger, C. T. (2020) · FEMS Yeast Research · doi:10.1093/femsyr/foaa008 · Cited by 48 · see citing works
Priest, S. J., Yadav, V., Roth, C., Dahlmann, T. A., Kück, U., Magwene, P. M., & Heitman, J. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01183-z · Cited by 47 · see citing works
The promise and pitfalls of synteny in phylogenomics
Steenwyk, J. L., & King, N. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002632 · Cited by 48 · see citing works
Evolutionary Repair Experiments as a Window to the Molecular Diversity of Life
LaBar, T., Hsieh, Y.-Y. P., Fumasoni, M., & Murray, A. W. (2020) · Current Biology · doi:10.1016/j.cub.2020.03.046 · Cited by 44 · see citing works
Salas-Leiva, D. E., Tromer, E. C., Curtis, B. A., Jerlström-Hultqvist, J., Kolísko, M., Yi, Z., Salas‐Leiva, J. S., Gallot-Lavallée, L., Williams, S. K., Kops, G. J. P. L., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26077-2 · Cited by 45 · see citing works
Non-Saccharomyces as Biotools to Control the Production of Off-Flavors in Wines
Morata, A., Loira, I., González, C., & Escott, C. (2021) · Molecules · doi:10.3390/molecules26154571 · Cited by 44 · see citing works
Jiang, P., Ollodart, A. R., Sudhesh, V., Herr, A. J., Dunham, M. J., & Harris, K. (2021) · eLife · doi:10.7554/elife.68285 · Cited by 43 · see citing works
orthofisher: a broadly applicable tool for automated gene identification and retrieval
Steenwyk, J. L., & Rokas, A. (2021) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkab250 · Cited by 40 · see citing works
Evolution of Proteins of the DNA Photolyase/Cryptochrome Family
Vechtomova, Y. L., Telegina, T. A., & Kritsky, M. S. (2020) · Biochemistry (Moscow) · doi:10.1134/s0006297920140072 · Cited by 41 · see citing works
Can gene-inactivating mutations lead to evolutionary novelty?
Murray, A. W. (2020) · Current Biology · doi:10.1016/j.cub.2020.03.072 · Cited by 39 · see citing works
Saubin, M., Devillers, H., Proust, L., Brier, C., Grondin, C., Pradal, M., Legras, J., & Neuvéglise, C. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02960 · Cited by 38 · see citing works
Fumasoni, M., & Murray, A. W. (2020) · eLife · doi:10.7554/elife.51963 · Cited by 36 · see citing works
Variable Spontaneous Mutation and Loss of Heterozygosity among Heterozygous Genomes in Yeast
Nguyen, D. T., Wu, B., Long, H., Zhang, N., Patterson, C. E., Simpson, S., Morris, K., Thomas, W. K., Lynch, M., & Hao, W. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa150 · Cited by 37 · see citing works
Chen, X., Fang, D., Xu, Y., Duan, K., Yoshida, S., Yang, S., Sahu, S. K., Fu, H., Guang, X., Liu, M., et al. (2023) · Nature Plants · doi:10.1038/s41477-023-01517-7 · Cited by 34 · see citing works
Valera, M. J., Olivera, V., Boido, E., Dellacassa, E. S., & Carrau, F. (2021) · Fermentation · doi:10.3390/fermentation7030162 · Cited by 37 · see citing works
Levin, M. (2025) · BioEssays · doi:10.1002/bies.202400196 · Cited by 34 · see citing works
Mutators Enhance Adaptive Micro-Evolution in Pathogenic Microbes
Boyce, K. J. (2022) · Microorganisms · doi:10.3390/microorganisms10020442 · Cited by 34 · see citing works
Farkas, Z. J., Kovács, K., Sarkadi, Z., Kalapis, D., Fekete, G., Birtyik, F., Ayaydin, F., Molnár, C., Horváth, P., Pál, C., et al. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01730-1 · Cited by 33 · see citing works
Steenwyk, J. L., Goltz, D., Buida, T. J., Li, Y., Shen, X., & Rokas, A. (2022) · PLoS Biology · doi:10.1371/journal.pbio.3001827 · Cited by 34 · see citing works
Genomic Instability in Fungal Plant Pathogens
Covo, S. (2020) · Genes · doi:10.3390/genes11040421 · Cited by 32 · see citing works
Reticulate evolution: Detection and utility in the phylogenomics era
Bjornson, S., Verbruggen, H., Upham, N. S., & Steenwyk, J. L. (2024) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2024.108197 · Cited by 34 · see citing works
Valera, M. J., Boido, E., Ramos, J. C., Manta, E., Radí, R., Dellacassa, E. S., & Carrau, F. (2020) · Applied and Environmental Microbiology · doi:10.1128/aem.00701-20 · Cited by 31 · see citing works
The cell morphological diversity of Saccharomycotina yeasts
Chavez, C. M., Groenewald, M., Hulfachor, A. B., Kpurubu, G., Huerta, R., Hittinger, C. T., & Rokas, A. (2023) · FEMS Yeast Research · doi:10.1093/femsyr/foad055 · Cited by 32 · see citing works
Development of Genetic Modification Tools for Hanseniasporauvarum
Badura, J., van Wyk, N., Brezina, S., Pretorius, I. S., Rauhut, D., Wendland, J., & von Wallbrunn, C. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22041943 · Cited by 29 · see citing works
How Many Is Enough? - Challenges of Multinucleated Cell Division in Malaria Parasites
Simon, C. S., Stürmer, V. S., & Guizetti, J. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.658616 · Cited by 27 · see citing works
Carrau, F., Dellacassa, E. S., Boido, E., Medina, K., Valera, M. J., Fariña, L., Perez, G., Martín, V., Álvarez-Valín, F., & Balestrazzi, L. (2023) · FEMS Yeast Research · doi:10.1093/femsyr/foad010 · Cited by 26 · see citing works
de Voorde, D. V., Díaz-Muñoz, C., Hernandez, C. E., Weckx, S., & Vuyst, L. D. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1232323 · Cited by 28 · see citing works
Valera, M. J., Boido, E., Dellacassa, E. S., & Carrau, F. (2020) · Fermentation · doi:10.3390/fermentation6030078 · Cited by 27 · see citing works
Steenwyk, J. L., Phillips, M. A., Yang, F. J., Date, S. S., Graham, T. R., Berman, J. G., Hittinger, C. T., & Rokas, A. (2022) · Science Advances · doi:10.1126/sciadv.abn0105 · Cited by 23 · see citing works
Haase, M. A. B., Kominek, J., Opulente, D. A., Shen, X., LaBella, A. L., Zhou, X., DeVirgilio, J. H., Hulfachor, A. B., Kurtzman, C. P., Rokas, A., et al. (2020) · Genetics · doi:10.1093/genetics/iyaa012 · Cited by 23 · see citing works
Is Natural Population of Candida tropicalis Sexual, Parasexual, and/or Asexual?
Xu, J. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.751676 · Cited by 25 · see citing works
Guaragnella, N., Chiara, M., Capece, A., Romano, P., Pietrafesa, R., Siesto, G., Manzari, C., & Pesole, G. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.03133 · Cited by 23 · see citing works
Pirrone, A., Prestianni, R., Naselli, V., Todaro, A., Farina, V., Tinebra, I., Guzzon, R., Badalamenti, N., Maggio, A., Gaglio, R., et al. (2022) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2022.109868 · Cited by 24 · see citing works
A Noncanonical DNA Damage Checkpoint Response in a Major Fungal Pathogen
Shor, E., Garcia‐Rubio, R., DeGregorio, L., & Perlin, D. S. (2020) · mBio · doi:10.1128/mbio.03044-20 · Cited by 23 · see citing works
Phillips, M. A., Steenwyk, J. L., Shen, X., & Rokas, A. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab219 · Cited by 21 · see citing works
Microbial Interactions in Kombucha through the Lens of Metabolomics
Tran, T., Roullier‐Gall, C., Verdier, F., Martin, A., Schmitt‐Kopplin, P., Alexandre, H., Grandvalet, C., & Tourdot‐Maréchal, R. (2022) · Metabolites · doi:10.3390/metabo12030235 · Cited by 23 · see citing works
Mead, M. E., Steenwyk, J. L., Silva, L. P., de Castro, P. A., Saeed, N., Hillmann, F., Goldman, G. H., & Rokas, A. (2021) · Genetics · doi:10.1093/genetics/iyab066 · Cited by 23 · see citing works
Badura, J., Kiene, F. E., Brezina, S., Fritsch, S., Semmler, H., Rauhut, D., Pretorius, I. S., von Wallbrunn, C., & van Wyk, N. (2023) · Fermentation · doi:10.3390/fermentation9020109 · Cited by 22 · see citing works
Temporal and spatial dynamics within the fungal microbiome of grape fermentation
Onetto, C. A., Ward, C. M., Heuvel, S. V. D., Hale, L. J., Cuijvers, K. M., & Borneman, A. R. (2024) · Environmental Microbiology · doi:10.1111/1462-2920.16660 · Cited by 21 · see citing works
Limited DNA repair gene repertoire in Ascomycete yeast revealed by comparative genomics
Milo, S., Misgav, R. H., Hazkani‐Covo, E., & Covo, S. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz242 · Cited by 20 · see citing works
Čadež, N., Bellora, N., Ulloa, R. J., Tome, M., Petković, H., Groenewald, M., Hittinger, C. T., & Libkind, D. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.679894 · Cited by 20 · see citing works
Human Follicular Mites: Ectoparasites Becoming Symbionts
Smith, G., Manzano-Marı́n, A., Reyes‐Prieto, M., Antunes, C. S. R., Ashworth, V., Goselle, O. N., Jan, A., Moya, A., Latorre, A., Perotti, M. A., et al. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac125 · Cited by 20 · see citing works
Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum
Li, Y., Liu, H., Steenwyk, J. L., LaBella, A. L., Harrison, M., Groenewald, M., Zhou, X., Shen, X., Zhao, T., Hittinger, C. T., et al. (2022) · Current Biology · doi:10.1016/j.cub.2022.10.025 · Cited by 18 · see citing works
Novakomyces olei sp. nov., the First Member of a Novel Taphrinomycotina Lineage
Čadež, N., Dlauchy, D., Tome, M., & Péter, G. (2021) · Microorganisms · doi:10.3390/microorganisms9020301 · Cited by 18 · see citing works
Application of Hanseniaspora vineae to improve white wine quality
Martín, V., Valera, M. J., Medina, K., Dellacassa, E. S., Schneider, R., Boido, E., & Carrau, F. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-823497-6.00004-1 · Cited by 18 · see citing works
Genetic and phenotypic diversity of wine-associated Hanseniaspora species
Onetto, C. A., Ward, C. M., Varela, C., Hale, L. J., Schmidt, S. A., Borneman, A. R., & Borneman (2025) · FEMS Yeast Research · doi:10.1093/femsyr/foaf031 · Cited by 17 · see citing works
Linder, T. (2019) · Microorganisms · doi:10.3390/microorganisms7080247 · Cited by 17 · see citing works
Mitochondrial genome diversity across the subphylum Saccharomycotina
Wolters, J. F., LaBella, A. L., Opulente, D. A., Rokas, A., & Hittinger, C. T. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1268944 · Cited by 17 · see citing works
van Wyk, N., Scansani, S., Beisert, B., Brezina, S., Fritsch, S., Semmler, H., Pretorius, I. S., Rauhut, D., & von Wallbrunn, C. (2022) · Applied Sciences · doi:10.3390/app12146919 · Cited by 16 · see citing works
Onetto, C. A., McCarthy, J., & Schmidt, S. A. (2025) · Yeast · doi:10.1002/yea.4000 · Cited by 15 · see citing works
Badura, J., Medić, M., van Wyk, N., Krause, B., Semmler, H., Brezina, S., Pretorius, I. S., Rauhut, D., & von Wallbrunn, C. (2022) · Microorganisms · doi:10.3390/microorganisms11010014 · Cited by 15 · see citing works
The Influence of the Number of Tree Searches on Maximum Likelihood Inference in Phylogenomics
Liu, C., Zhou, X., Li, Y., Hittinger, C. T., Pan, R., Huang, J., Chen, X., Rokas, A., Chen, Y., & Shen, X. (2024) · Systematic Biology · doi:10.1093/sysbio/syae031 · Cited by 15 · see citing works
Abrams, M. B., Chuong, J. N., AlZaben, F., Dubin, C. A., Skerker, J. M., & Brem, R. B. (2021) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkab412 · Cited by 13 · see citing works
Evolutionary Divergence in DNA Damage Responses among Fungi
Steenwyk, J. L. (2021) · mBio · doi:10.1128/mbio.03348-20 · Cited by 14 · see citing works
Fumasoni, M., & Murray, A. W. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009875 · Cited by 13 · see citing works
Cissé, O. H., Ma, L., & Kovacs, J. A. (2024) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00202-22 · Cited by 11 · see citing works
Hiltunen, M., Brännström, I. O., Alfjorden, A., Pecková, H., Swords, F., Hooper, C., Holzer, A. S., Bass, D., & Burki, F. (2024) · BMC Biology · doi:10.1186/s12915-024-01898-x · Cited by 9 · see citing works
Feng, B., Li, Y., Xu, B., Liu, H., Steenwyk, J. L., David, K. T., Tian, X., Gonçalves, C., Opulente, D. A., LaBella, A. L., et al. (2025) · Molecular Systems Biology · doi:10.1038/s44320-025-00118-0 · Cited by 9 · see citing works
Haase, M. A. B., Steenwyk, J. L., & Boeke, J. D. (2024) · Genetics · doi:10.1093/genetics/iyae008 · Cited by 10 · see citing works
Valera, M. J., Boido, E., Fariña, L., Dellacassa, E. S., & Carrau, F. (2025) · FEMS Yeast Research · doi:10.1093/femsyr/foaf049 · Cited by 10 · see citing works
Pantothenate Auxotrophy in a Naturally Occurring Biocontrol Yeast
Rueda-Mejia, M. P., Bühlmann, A., Ortiz‐Merino, R. A., Lutz, S., Ahrens, C. H., Künzler, M., & Freimoser, F. M. (2023) · Applied and Environmental Microbiology · doi:10.1128/aem.00884-23 · Cited by 10 · see citing works
Snails as Taxis for a Large Yeast Biodiversity
Akan, M., Michling, F., Matti, K., Krause, S., Muno-Bender, J., & Wendland, J. (2020) · Fermentation · doi:10.3390/fermentation6030090 · Cited by 10 · see citing works
Exploring the role of production and release of proteins for microbial interactions in kombucha
Rey, J. R., Tran, T., Aumeunier, A., Rieu, A., Verdier, F., Martin, A., Alexandre, H., Tourdot‐Maréchal, R., & Grandvalet, C. (2024) · LWT · doi:10.1016/j.lwt.2024.116016 · Cited by 9 · see citing works
Tavares, M. J., Güldener, U., Mendes‐Ferreira, A., & Mira, N. P. (2021) · BMC Genomics · doi:10.1186/s12864-021-07438-z · Cited by 9 · see citing works
O’Meara, M. J., Rapala, J. R., Nichols, C. B., Alexandre, C., Billmyre, R. B., Steenwyk, J. L., Alspaugh, J. A., & O’Meara, T. R. (2024) · PLoS Genetics · doi:10.1371/journal.pgen.1011158 · Cited by 8 · see citing works
Pontes, A., Paraíso, F., Silva, M. R., Lagoas, C., Aires, A., Brito, P. H., Rosa, C. A., Lachance, M., Sampaio, J. P., Gonçalves, C., et al. (2024) · BMC Biology · doi:10.1186/s12915-024-01929-7 · Cited by 8 · see citing works
Seixas, I., Santos, D. M. F., Vasconcelos, I., Mira, N. P., & Mendes‐Ferreira, A. (2023) · FEMS Yeast Research · doi:10.1093/femsyr/foad021 · Cited by 8 · see citing works
Genome Analysis of a Newly Discovered Yeast Species, Hanseniaspora menglaensis
Ryan, A. P., Groenewald, M., Smith, M. T., Holohan, C., Boekhout, T., Wolfe, K. H., & Butler, G. (2024) · Journal of Fungi · doi:10.3390/jof10030180 · Cited by 8 · see citing works
Hanseniaspora terricola sp. nov., an ascomycetous yeast isolated from Tibet
Liu, Z., Wang, M., Wang, G., Li, A., Wangmu, & Wang, Q. (2019) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.004741 · Cited by 8 · see citing works
Sex without crossing over in the yeast Saccharomycodes ludwigii
Papaioannou, I. A., Dutreux, F., Peltier, F. A., Maekawa, H., Delhomme, N., Bardhan, A., Friedrich, A., Schacherer, J., & Knop, M. (2021) · Genome biology · doi:10.1186/s13059-021-02521-w · Cited by 8 · see citing works
Zheng, M., Qi, X., Chang, Y., Zhao, H., & Hu, K. (2025) · Journal of Food Composition and Analysis · doi:10.1016/j.jfca.2025.107461 · Cited by 7 · see citing works
Genomic factors shaping codon usage across the Saccharomycotina subphylum
Zavala, B., Dineen, L., Fisher, K. J., Opulente, D. A., Harrison, M., Wolters, J. F., Shen, X., Zhou, X., Groenewald, M., Hittinger, C. T., et al. (2024) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkae207 · Cited by 6 · see citing works
Schwarz, L. V., Valera, M. J., Delamare, A. P. L., Carrau, F., & Echeverrigaray, S. (2022) · Current Research in Microbial Sciences · doi:10.1016/j.crmicr.2022.100129 · Cited by 6 · see citing works
PCR-based gene targeting in Hanseniaspora uvarum
Badura, J., van Wyk, N., Zimmer, K., Pretorius, I. S., von Wallbrunn, C., & Wendland, J. (2023) · FEMS Yeast Research · doi:10.1093/femsyr/foad034 · Cited by 6 · see citing works
Genome Sequence of the Wine Yeast Saccharomycodes ludwigii UTAD17
Tavares, M. J., Güldener, U., Esteves, M., Mendes‐Faia, A., Mendes‐Ferreira, A., & Mira, N. P. (2018) · Microbiology Resource Announcements · doi:10.1128/mra.01195-18 · Cited by 6 · see citing works
Franco‐Duarte, R., Čadež, N., Rito, T., Drumonde‐Neves, J., Reyes-Domínguez, Y., Pais, C., Sousa, M. J., & Soares, P. (2022) · RepositoriUM · doi:10.3390/jof8010052
Ancient co-option of LTR retrotransposons as yeast centromeres
Haase, M. A. B., Lazar‐Stefanita, L., Baudry, L., Wudzinska, A. M., Zhou, X., Rokas, A., Hittinger, C. T., Pfander, B., Musacchio, A., & Boeke, J. D. (2026) · Nature · doi:10.1038/s41586-025-10092-0 · Cited by 5 · see citing works
Specific origin selection and excess functional MCM2–7 loading in ORC-deficient cells
Shibata, Y., Peycheva, M., Shibata, E., Malzl, D., Pavri, R., & Dutta, A. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf518 · Cited by 2 · see citing works
Levin, M. G. (2024) · doi:10.31219/osf.io/yq9xe · Cited by 5 · see citing works
Gonçalves, C., Steenwyk, J. L., Rinker, D. C., Opulente, D. A., LaBella, A. L., Harrison, M.-C., Wolters, J. F., Zhou, X., Shen, X.-X., Covo, S., et al. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf285 · Cited by 4 · see citing works
Huang, L., Yang, C., Ge, Q., & Peng, B. (2025) · Food Microbiology · doi:10.1016/j.fm.2025.105007 · Cited by 4 · see citing works
Fan, Y., Du, M., Zhang, W., Deng, W., Yang, E., Wang, S., Yan, L., Zhang, L., Kang, S., Steenwyk, J. L., et al. (2025) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2025.108423 · Cited by 4 · see citing works
Natural trait variation across Saccharomycotina species
Wang, J.-T. J., Steenwyk, J. L., & Brem, R. B. (2024) · FEMS Yeast Research · doi:10.1093/femsyr/foae002 · Cited by 4 · see citing works
- Authors
- Steenwyk, J. L., Opulente, D. A., Kominek, J., Shen, X.-X., Zhou, X., Labella, A. L., Bradley, N. P., Eichman, B. F., Čadež, N., Libkind, D., DeVirgilio, J., Hulfachor, A. B., Kurtzman, C. P., Hittinger, C. T., & Rokas, A.
- Affiliations
- Vanderbilt University (US)
- University of Wisconsin–Madison (US)
- South China Agricultural University (CN)
- University of Ljubljana (SI)
- Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
- Agricultural Research Service (US)
- Corresponding author
- Hittinger, Chris Todd
- Rokas, Antonis
- ORCID
- Venue
- PLoS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2019-05-21
- Volume
- 17
- Issue
- 5
- Pages
- e3000255
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- PMC
- PMC6528967
- OpenAlex
- W2911336472
- Cited by
- 162
- References
- 169
- Citations by year
- 2026: 14 · 2025: 18 · 2024: 34 · 2023: 13 · 2022: 17 · 2021: 38 · 2020: 22 · 2019: 5 · 2018: 1
- FWCI
- 6.78
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- creativecommons.org/publicdomain/zero/1.0/ (vor)
- Locations
- PLoS Biology (publishedVersion, public-domain)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, cc-by)
- Figshare (cc-by)
- Funders
- National Science Foundation (DEB-1442113, DEB-1442148, DGE-1445197)
- DOE Office of Science (BER DE-FC02-07ER64494 and DE-SC0018409)
- Pew Charitable Trusts (Pew Scholar in the Biomedical Sciences)
- Vilas Trust Estate (Vilas Faculty Early Career Investigator)
- John Simon Guggenheim Memorial Foundation (2018 Guggenheim Fellowship)
- National Key Project for Basic Research of China (973 Program, No. 2015CB150600)
- Slovenian Research Agency (P4-0116)
- CONICET (PIP 392)
- FONCyT (PICT 2542)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Yeasts and Rust Fungi Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Keywords
- PorA, gene loss, cell cycle checkpoint genes, DNA repair genes, spindle assembly checkpoint, DNA damage checkpoint, base excision repair, pyrimidine dimer repair, mutational load, 8-oxoguanine, genome size reduction, genome stability, Saccharomycotina, yeast evolution, phylogenomics
- MeSH terms
- Base Sequence, Cell Cycle, DNA Damage, DNA Repair, Saccharomycetales, Genes, Fungal, Phenotype, Phylogeny, Evolution, Molecular
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