Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts
暂无分享,去创建一个
Guy Baele | Loren Miraglia | Steven Maere | Ariel S. Schwartz | Jan Steensels | Veerle Saels | Kevin J. Verstrepen | Adriaan Merlevede | Maryann M. Taylor | Brigida Gallone | L. Miraglia | K. Verstrepen | Jan Steensels | Steven Maere | G. Baele | T. Richardson | K. Voordeckers | B. Herrera-Malaver | C. Teiling | L. Soriaga | Miguel Roncoroni | Brigida Gallone | Troels Prahl | Veerle Saels | Adriaan Merlevede | B. Steffy | Christopher White | Ariel Schwartz | Toby Richardson | Leah B. Soriaga | Troels Prahl | Leah Soriaga | Beatriz Herrera-Malaver | Miguel Roncoroni | Karin Voordeckers | Clotilde Teiling | Brian Steffy | Maryann Taylor | Christopher White | Beatriz Herrera-Malaver | Miguel Roncoroni
[1] M. Kawamukai,et al. PAD1 and FDC1 are essential for the decarboxylation of phenylacrylic acids in Saccharomyces cerevisiae. , 2010, Journal of bioscience and bioengineering.
[2] John C. Dittmar,et al. ScreenMill: A freely available software suite for growth measurement, analysis and visualization of high-throughput screen data , 2010, BMC Bioinformatics.
[3] David van Dijk,et al. Slow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage , 2015, Nature Communications.
[4] A Ellinger,et al. Isolation of two developmentally regulated genes involved in spore wall maturation in Saccharomyces cerevisiae. , 1990, Genes & development.
[5] R. Lanfear,et al. Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. , 2012, Molecular biology and evolution.
[6] I. Dunham,et al. Rapid assessment of S. cerevisiae mating type by PCR. , 1990, Trends in genetics : TIG.
[7] Frédéric Delsuc,et al. MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons , 2011, PloS one.
[8] Leonid Kruglyak,et al. Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae , 2009, Nature.
[9] A. Couloux,et al. A population genomics insight into the Mediterranean origins of wine yeast domestication , 2015, Molecular ecology.
[10] Alexey M. Kozlov,et al. ExaML version 3: a tool for phylogenomic analyses on supercomputers , 2015, Bioinform..
[11] Burkhard Morgenstern,et al. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints , 2005, Nucleic Acids Res..
[12] K. Verstrepen,et al. Large-Scale Selection and Breeding To Generate Industrial Yeasts with Superior Aroma Production , 2014, Applied and Environmental Microbiology.
[13] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[14] J. Berman,et al. Acquisition of Aneuploidy Provides Increased Fitness during the Evolution of Antifungal Drug Resistance , 2009, PLoS genetics.
[15] Anders Blomberg,et al. Trait Variation in Yeast Is Defined by Population History , 2011, PLoS genetics.
[16] Daniel J. Kvitek,et al. Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments , 2012, Genome research.
[17] Jason M. Sheltzer,et al. Aneuploidy Drives Genomic Instability in Yeast , 2011, Science.
[18] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[19] Björn Usadel,et al. Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..
[20] Alexei J. Drummond,et al. Bayesian Phylogeography Finds Its Roots , 2009, PLoS Comput. Biol..
[21] G. Liti,et al. Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity , 2012, Molecular ecology.
[22] David Levine,et al. A high-performance computing toolset for relatedness and principal component analysis of SNP data , 2012, Bioinform..
[23] Alexandros Stamatakis,et al. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..
[24] K. Katoh,et al. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.
[25] W. J. Dickinson,et al. A genome-wide view of the spectrum of spontaneous mutations in yeast , 2008, Proceedings of the National Academy of Sciences.
[26] Mark D. White,et al. UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis , 2015, Nature.
[27] Manuel A. R. Ferreira,et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.
[28] Daniel A. Skelly,et al. The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen , 2015, Genome research.
[29] Michael M. Desai,et al. Sex Speeds Adaptation by Altering the Dynamics of Molecular Evolution , 2016, Nature.
[30] Peer Bork,et al. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments , 2006, Nucleic Acids Res..
[31] L. Loewe,et al. High Deleterious Genomic Mutation Rate in Stationary Phase of Escherichia coli , 2003, Science.
[32] M. DePristo,et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.
[33] D. Cavalieri,et al. Social wasps are a Saccharomyces mating nest , 2016, Proceedings of the National Academy of Sciences.
[34] Zhengwei Zhu,et al. CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..
[35] Christopher R. Jones,et al. Sex increases the efficacy of natural selection in experimental yeast populations , 2005, Nature.
[36] F. Karst,et al. Optimisation of interdelta analysis for Saccharomyces cerevisiae strain characterisation. , 2003, FEMS microbiology letters.
[37] M. Lercher,et al. PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R , 2014, Molecular biology and evolution.
[38] M. Suchard,et al. Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. , 2012, Molecular biology and evolution.
[39] K. Verstrepen,et al. Taming wild yeast: potential of conventional and nonconventional yeasts in industrial fermentations. , 2014, Annual review of microbiology.
[40] Nicholas A. Bokulich,et al. Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate , 2013, Proceedings of the National Academy of Sciences.
[41] Toni Gabaldón,et al. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..
[42] Norman Pavelka,et al. Aneuploidy Underlies Rapid Adaptive Evolution of Yeast Cells Deprived of a Conserved Cytokinesis Motor , 2008, Cell.
[43] Pablo Cingolani,et al. © 2012 Landes Bioscience. Do not distribute. , 2022 .
[44] Robert P. Davey,et al. Population genomics of domestic and wild yeasts , 2008, Nature.
[45] Siu-Ming Yiu,et al. IDBA - A Practical Iterative de Bruijn Graph De Novo Assembler , 2010, RECOMB.
[46] M. Matsuoka,et al. Genetic approaches to crop improvement: responding to environmental and population changes , 2008, Nature Reviews Genetics.
[47] K. Verstrepen,et al. Adaptation to High Ethanol Reveals Complex Evolutionary Pathways , 2015, PLoS genetics.
[48] N. Friedman,et al. Natural history and evolutionary principles of gene duplication in fungi , 2007, Nature.
[49] M. Suchard,et al. Bayesian random local clocks, or one rate to rule them all , 2010, BMC Biology.
[50] Isabelle Gagnon-Arsenault,et al. Evolutionary rescue by compensatory mutations is constrained by genomic and environmental backgrounds , 2015, Molecular systems biology.
[51] Alexandros Stamatakis,et al. How Many Bootstrap Replicates Are Necessary? , 2009, RECOMB.
[52] Alexandros Stamatakis,et al. How Many Bootstrap Replicates Are Necessary? , 2009, RECOMB.
[53] R. H.J.MULLE. THE RELATION OF RECOMBINATION TO MUTATIONAL ADVANCE , 2002 .
[54] Guy Baele,et al. Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency , 2013, Bioinform..
[55] I. Hornsey. A history of beer and brewing , 2003 .
[56] Virginia R. Badler,et al. Chemical evidence for ancient beer , 1992, Nature.
[57] Stephen J O'Brien,et al. From wild animals to domestic pets, an evolutionary view of domestication , 2009, Proceedings of the National Academy of Sciences.
[58] Anthony R. Borneman,et al. Whole-Genome Comparison Reveals Novel Genetic Elements That Characterize the Genome of Industrial Strains of Saccharomyces cerevisiae , 2011, PLoS genetics.
[59] K. Meusemann,et al. FASconCAT: Convenient handling of data matrices. , 2010, Molecular phylogenetics and evolution.
[60] David Botstein,et al. Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[61] Leopold Parts,et al. Population genomics of domestic and wild yeasts , 2008 .
[62] M. Suchard,et al. Bayesian Phylogenetics with BEAUti and the BEAST 1.7 , 2012, Molecular biology and evolution.
[63] Paul M. Magwene,et al. Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae , 2011, Proceedings of the National Academy of Sciences.
[64] Anita Saraf,et al. Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast , 2010, Nature.
[65] Amparo Querol,et al. Molecular characterization of a chromosomal rearrangement involved in the adaptive evolution of yeast strains. , 2002, Genome research.
[66] D. Greig,et al. Saccharomyces cerevisiae: a nomadic yeast with no niche? , 2015, FEMS yeast research.
[67] Yongchao Liu,et al. Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data , 2013, Bioinform..
[68] Anthony R. Borneman,et al. Whole Genome Comparison Reveals High Levels of Inbreeding and Strain Redundancy Across the Spectrum of Commercial Wine Strains of Saccharomyces cerevisiae , 2016, G3: Genes, Genomes, Genetics.
[69] David Haussler,et al. The UCSC genome browser database: update 2007 , 2006, Nucleic Acids Res..
[70] Albert J. Vilella,et al. Genome-wide DNA polymorphism analyses using VariScan , 2006, BMC Bioinformatics.
[71] Israel Steinfeld,et al. BMC Bioinformatics BioMed Central , 2008 .
[72] Leopold Parts,et al. A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes , 2014, Molecular biology and evolution.
[73] M. Stephens,et al. fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets , 2014, Genetics.
[74] L. Hosoya,et al. The nature of selection during plant domestication , 2009 .
[75] Gonçalo R. Abecasis,et al. The variant call format and VCFtools , 2011, Bioinform..
[76] Andrew W. Murray,et al. Rapid Expansion and Functional Divergence of Subtelomeric Gene Families in Yeasts , 2010, Current Biology.
[77] Joaquin F. Christiaens,et al. The fungal aroma gene ATF1 promotes dispersal of yeast cells through insect vectors. , 2014, Cell reports.