Phylogenomics of a Saccharomyces cerevisiae cocoa strain reveals adaptation to a West African fermented food population

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · see citing works

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

MUSCLE: multiple sequence alignment with high accuracy and high throughput

Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662 · see citing works

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895 · 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

Minimap2: Pairwise alignment for nucleotide sequences

Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807 · see citing works

Fast and sensitive protein alignment using DIAMOND

Buchfink, B., Xie, C., & Huson, D. H. (2015) · Nature Methods · doi:10.1038/nmeth.3176 · Cited by 14,201 · see citing works

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv351 · Cited by 13,344 · see citing works

Second-generation PLINK: rising to the challenge of larger and richer datasets

Chang, C. C., Chow, C. C., Tellier, L. C., Vattikuti, S., Purcell, S. M., & Lee, J. J. (2015) · Gigascience · doi:10.1186/s13742-015-0047-8 · Cited by 12,709 · 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

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J. R., Young, S., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0112963 · Cited by 8,994 · see citing works

adegenet: a R package for the multivariate analysis of genetic markers

Jombart, T. (2008) · Bioinform. · doi:10.1093/bioinformatics/btn129 · Cited by 7,788 · see citing works

OrthoFinder: phylogenetic orthology inference for comparative genomics

Emms, D. M., & Kelly, S. (2019) · Genome Biology · doi:10.1186/s13059-019-1832-y · Cited by 7,676 · see citing works

Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separationPreprint

Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017) · Genome Research · doi:10.1101/gr.215087.116 · Cited by 7,340 · see citing works

UniProt: the universal protein knowledgebase in 2021

The UniProt Consortium, Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Agivetova, R., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1100 · Cited by 6,372 · see citing works

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

Gouy, M., Guindon, S., & Gascuel, O. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp259 · Cited by 5,820 · see citing works

Versatile and open software for comparing large genomes

Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254 · see citing works

Food microbiology : fundamentals and frontiers

Doyle, M. P., Beuchat, L. R., & Montville, T. J. (2013) · doi:10.1128/9781555819972 · Cited by 3,589 · see citing works

NanoPack: visualizing and processing long-read sequencing data

De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M., & Van Broeckhoven, C. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty149 · Cited by 3,168 · see citing works

Fast and accurate de novo genome assembly from long uncorrected readsPreprint

Vaser, R., Sović, I., Nagarajan, N., & Šikić, M. (2017) · Genome Research · doi:10.1101/gr.214270.116 · Cited by 3,059 · see citing works

CDD/SPARCLE: the conserved domain database in 2020

Lu, S., Wang, J., Chitsaz, F., Derbyshire, M. K., Geer, R. C., Gonzales, N. R., Gwadz, M., Hurwitz, D. I., Marchler, G. H., Song, J. S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz991 · Cited by 3,049 · see citing works

InterProScan – an integration platform for the signature-recognition methods in InterPro

Zdobnov, E. M., & Apweiler, R. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.9.847 · Cited by 2,915 · see citing works

NOVOPlasty: de novo assembly of organelle genomes from whole genome data

Dierckxsens, N., Mardulyn, P., & Smits, G. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw955 · Cited by 2,848 · see citing works

pegas: an R package for population genetics with an integrated–modular approach

Paradis, E. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp696 · Cited by 2,601 · see citing works

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

Zimmermann, L., Stephens, A., Nam, S.-Z., Rau, D., Kübler, J., Lozajic, M., Gabler, F., Söding, J., Lupas, A. N., & Alva, V. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.12.007 · Cited by 2,522 · see citing works

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

Holt, C., & Yandell, M. D. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-491 · Cited by 2,042 · see citing works

Lactic acid bacteria as functional starter cultures for the food fermentation industry

Leroy, F., & De Vuyst, L. (2004) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2003.09.004 · Cited by 1,852 · see citing works

Anvi’o: an advanced analysis and visualization platform for ‘omics data

Eren, A. M., Esen, Ö. C., Quince, C., Vineis, J. H., Morrison, H. G., Sogin, M. L., & Delmont, T. O. (2015) · PeerJ · doi:10.7717/peerj.1319 · Cited by 1,823 · see citing works

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

Raj, A., Stephens, M., & Pritchard, J. K. (2014) · Genetics · doi:10.1534/genetics.114.164350 · Cited by 1,666 · see citing works

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

Pritchard, L., Glover, R. H., Humphris, S. N., Elphinstone, J. G., & Toth, I. K. (2015) · Analytical Methods · doi:10.1039/c5ay02550h · Cited by 1,597 · see citing works

Population genomics of domestic and wild yeasts

Liti, G., Carter, D. M., Moses, A. M., Warringer, J., Parts, L., James, S. A., Davey, R., Roberts, I. N., Burt, A., Koufopanou, V., et al. (2008) · Nature · doi:10.1038/nature07743 · Cited by 1,391 · see citing works

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources

Stanke, M., Schöffmann, O., Morgenstern, B., & Waack, S. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-62 · Cited by 1,304 · see citing works

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

Roach, M. J., Schmidt, S. A., & Borneman, A. R. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2485-7 · Cited by 1,152 · see citing works

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

Peter, J., De Chiara, M., Friedrich, A., Yue, J.-X., Pflieger, D., Bergström, A., Sigwalt, A., Barre, B., Freel, K., Llored, A., et al. (2018) · Nature · doi:10.1038/s41586-018-0030-5 · Cited by 1,117 · 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

The international scientific association for probiotics and prebiotics (ISAPP) consensus statement on fermented foods

Marco, M. L., Sanders, M. E., Gänzle, M., Arrieta, M. C., Cotter, P. D., De Vuyst, L., Hill, C., Holzapfel, W., Lebeer, S., Merenstein, D., et al. (2021) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-020-00390-5 · Cited by 937 · 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

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) · doi:10.1038/ncomms14061 · Cited by 815 · see citing works

The Microbiology of Cocoa Fermentation and its Role in Chocolate Quality

Schwan, R. F., & Wheals, A. E. (2004) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408690490464104 · Cited by 743 · 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

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

Evidence for Domesticated and Wild Populations of Saccharomyces cerevisiae

Fay, J. C., & Benavides, J. A. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010005 · Cited by 447 · see citing works

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome

Delmont, T. O., & Eren, A. M. (2018) · PeerJ · doi:10.7717/peerj.4320 · Cited by 433 · see citing works

STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface

Ramasamy, R. K., Ramasamy, S., Bindroo, B. B., & Naik, V. G. (2014) · SpringerPlus · doi:10.1186/2193-1801-3-431 · Cited by 397 · see citing works

The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogenPreprint

Strope, P. K., Skelly, D. A., Kozmin, S. G., Mahadevan, G., Stone, E. A., Magwene, P. M., Dietrich, F. S., & McCusker, J. H. (2015) · Genome Research · doi:10.1101/gr.185538.114 · Cited by 337 · see citing works

Point mutations identify the conserved, intron-contained TACTAAC box as an essential splicing signal sequence in yeast

Langford, C. J., Klinz, F., Donath, C., & Gallwitz, D. (1984) · Cell · doi:10.1016/0092-8674(84)90344-1 · Cited by 330 · see citing works

Dynamics and Biodiversity of Populations of Lactic Acid Bacteria andAcetic Acid Bacteria Involved in Spontaneous Heap Fermentation of Cocoa Beans inGhana

Camu, N., Winter, T. D., Verbrugghe, K., Cleenwerck, I., Vandamme, P. A. R., Takrama, J. S., Vancanneyt, M., & Vuyst, L. D. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.02189-06 · Cited by 323 · see citing works

The cocoa bean fermentation process: from ecosystem analysis to starter culture development

Vuyst, L. D., & Weckx, S. (2016) · Journal of Applied Microbiology · doi:10.1111/jam.13045 · Cited by 322 · see citing works

Functional role of yeasts, lactic acid bacteria and acetic acid bacteria in cocoa fermentation processes

Vuyst, L. D., & Leroy, F. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa014 · Cited by 286 · see citing works

Bread, beer and wine: Yeast domestication in the Saccharomyces sensu stricto complex

Sicard, D., & Legras, J. (2011) · Comptes Rendus Biologies · doi:10.1016/j.crvi.2010.12.016 · Cited by 283 · see citing works

Taming Wild Yeast: Potential of Conventional and Nonconventional Yeasts in Industrial Fermentations

Steensels, J., & Verstrepen, K. J. (2014) · Annual Review of Microbiology · doi:10.1146/annurev-micro-091213-113025 · Cited by 282 · see citing works

Dynamics of volatile and non-volatile compounds in cocoa (Theobroma cacao L.) during fermentation and drying processes using principal components analysis

Rodríguez-Campos, J., Escalona‐Buendía, H. B., Orozco‐Avila, I., Lugo‐Cervantes, E., & Jaramillo‐Flores, M. E. (2010) · Food Research International · doi:10.1016/j.foodres.2010.10.028 · Cited by 278 · see citing works

Yeasts are essential for cocoa bean fermentation

Ho, V. T. T., Zhao, J. J., & Fleet, G. H. (2014) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2013.12.014 · Cited by 266 · see citing works

The origin and adaptive evolution of domesticated populations of yeast from Far East Asia

Duan, S.-F., Han, P.-J., Wang, Q.-M., Liu, W.-Q., Shi, J.-Y., Li, K., Zhang, X.-L., & Bai, F.-Y. (2018) · Nature Communications · doi:10.1038/s41467-018-05106-7 · Cited by 244 · see citing works

Sourdough production: fermentation strategies, microbial ecology, and use of non-flour ingredients

Vuyst, L. D., Comasio, A., & Kerrebroeck, S. V. (2021) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2021.1976100 · Cited by 242 · see citing works

Occurrence and diversity of yeasts involved in fermentation of West African cocoa beans

Jespersen, L., Nielsen, D. S., Hønholt, S., & Jakobsen, M. (2004) · FEMS Yeast Research · doi:10.1016/j.femsyr.2004.11.002 · Cited by 232 · see citing works

Rapid, Transcript-Specific Changes in Splicing in Response to Environmental Stress

Pleiss, J. A., Whitworth, G. B., Bergkessel, M., & Guthrie, C. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.07.018 · Cited by 226 · see citing works

Distinct Domestication Trajectories in Top-Fermenting Beer Yeasts and Wine Yeasts

Gonçalves, M., Pontes, A., Almeida, P., Barbosa, R. G., Serra, M. L., Libkind, D., Hutzler, M., Gonçalves, P. M., & Sampaio, J. P. (2016) · Current Biology · doi:10.1016/j.cub.2016.08.040 · Cited by 224 · see citing works

Optimizing chocolate production through traceability: A review of the influence of farming practices on cocoa bean quality

Saltini, R., Akkerman, R., & Frosch, S. (2012) · Food Control · doi:10.1016/j.foodcont.2012.05.054 · Cited by 211 · see citing works

The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver

Pandurangan, A., Stahlhacke, J., Oates, M., Smithers, B., & Gough, J. (2018) · Nucleic Acids Res. · doi:10.1093/nar/gky1130 · Cited by 203 · see citing works

The Reliability of Metagenome-Assembled Genomes (MAGs) in Representing Natural Populations: Insights from Comparing MAGs against Isolate Genomes Derived from the Same Fecal Sample

Meziti, A., Rodriguez‐R, L. M., Hatt, J. K., Peña, Á., Lévy, K., & Konstantinidis, K. T. (2021) · Applied and Environmental Microbiology · doi:10.1128/aem.02593-20 · Cited by 193 · see citing works

Transport of carboxylic acids in yeasts.

Casal, M., Paiva, S., Queirós, O., & Soares-Silva, I. (2008) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2008.00128.x · Cited by 185 · see citing works

An overview of the physical and biochemical transformation of cocoa seeds to beans and to chocolate: Flavor formation

Santander, M., Rodríguez, J., Vaillant, F. E., & Escobar, S. (2019) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2019.1581726 · Cited by 185 · see citing works

Yeast diversity of Ghanaian cocoa bean heap fermentations

Daniel, H., Vrancken, G., Takrama, J. F., Camu, N., Vos, P. D., & Vuyst, L. D. (2009) · FEMS Yeast Research · doi:10.1111/j.1567-1364.2009.00520.x · Cited by 182 · see citing works

A population genomics insight into the Mediterranean origins of wine yeast domestication

Almeida, P., Barbosa, R. G., Zalar, P., Imanishi, Y., Shimizu, K., Turchetti, B., Legras, J., Serra, M. L., Dequin, S., Couloux, A., et al. (2015) · Molecular Ecology · doi:10.1111/mec.13341 · Cited by 174 · see citing works

The fascinating and secret wild life of the budding yeast S. cerevisiae

Liti, G. (2015) · eLife · doi:10.7554/elife.05835 · Cited by 165 · see citing works

Spontaneous organic cocoa bean box fermentations in Brazil are characterized by a restricted species diversity of lactic acid bacteria and acetic acid bacteria

Papalexandratou, Z., Vrancken, G., Bruyne, K. D., Vandamme, P. A. R., & Vuyst, L. D. (2011) · Food Microbiology · doi:10.1016/j.fm.2011.06.003 · Cited by 155 · see citing works

On-farm implementation of a starter culture for improved cocoa bean fermentation and its influence on the flavour of chocolates produced thereof

Lefeber, T., Papalexandratou, Z., Gobert, W., Camu, N., & Vuyst, L. D. (2011) · Food Microbiology · doi:10.1016/j.fm.2011.12.021 · Cited by 144 · see citing works

Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus predominate during well-performed Malaysian cocoa bean box fermentations, underlining the importance of these microbial species for a successful cocoa bean fermentation process

Papalexandratou, Z., Lefeber, T., Bahrim, B., Lee, O. S., Daniel, H., & Vuyst, L. D. (2013) · Food Microbiology · doi:10.1016/j.fm.2013.02.015 · Cited by 142 · see citing works

Whole Genome Comparison Reveals High Levels of Inbreeding and Strain Redundancy Across the Spectrum of Commercial Wine Strains of Saccharomyces cerevisiae

Borneman, A. R., Forgan, A. H., Kolouchova, R., Fraser, J. A., & Schmidt, S. A. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.115.025692 · Cited by 135 · see citing works

Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq

Cromie, G. A., Hyma, K. E., Ludlow, C. L., Garmendia‐Torres, C., Gilbert, T., May, P., Huang, A. A., Dudley, A. M., & Fay, J. C. (2013) · G3 Genes Genomes Genetics · doi:10.1534/g3.113.007492 · Cited by 134 · see citing works

Shotgun Metagenomics of a Water Kefir Fermentation Ecosystem Reveals a Novel Oenococcus Species

Verce, M., De Vuyst, L., & Weckx, S. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00479 · Cited by 121 · see citing works

History and Domestication of Saccharomyces cerevisiae in Bread Baking

Lahue, C., Madden, A. A., Dunn, R. R., & Heil, C. S. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.584718 · Cited by 121 · see citing works

Beginnings of microbiology and biochemistry: the contribution of yeast research

Barnett, J. A. (2003) · Microbiology · doi:10.1099/mic.0.26089-0 · Cited by 120 · see citing works

Dynamic behavior of Saccharomyces cerevisiae, Pichia kluyveri and Hanseniaspora uvarum during spontaneous and inoculated cocoa fermentations and their effect on sensory characteristics of chocolate

Batista, N. N., Ramos, C. L., Dias, D. R., Pinheiro, A. C. M., & Schwan, R. F. (2015) · LWT · doi:10.1016/j.lwt.2015.03.051 · Cited by 114 · see citing works

Detailed Analysis of the Microbial Population in Malaysian Spontaneous Cocoa Pulp Fermentations Reveals a Core and Variable Microbiota

Meersman, E., Steensels, J., Mathawan, M., Wittocx, P.-J., Saels, V., Struyf, N., Bernaert, H., Vrancken, G., & Verstrepen, K. J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0081559 · Cited by 104 · see citing works

Incipient Balancing Selection through Adaptive Loss of Aquaporins in Natural Saccharomyces cerevisiae Populations

Will, J., Kim, H. S., Clarke, J., Painter, J. C., Fay, J. C., & Gasch, A. P. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000893 · Cited by 99 · see citing works

Unravelling the contribution of lactic acid bacteria and acetic acid bacteria to cocoa fermentation using inoculated organisms

Ho, V. T. T., Fleet, G. H., & Zhao, J. J. (2018) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2018.04.040 · Cited by 89 · see citing works

Independent Origins of Yeast Associated with Coffee and Cacao Fermentation

Ludlow, C. L., Cromie, G. A., Garmendia‐Torres, C., Sirr, A., Hays, M., Field, C., Jeffery, E. W., Fay, J. C., & Dudley, A. M. (2016) · Current Biology · doi:10.1016/j.cub.2016.02.012 · Cited by 84 · see citing works

Evidence for Two Main Domestication Trajectories in Saccharomyces cerevisiae Linked to Distinct Bread-Making Processes

Bigey, F., Segond, D., Friedrich, A., Guézenec, S., Bourgais, A., Huyghe, L., Agier, N., Nidelet, T., & Sicard, D. (2020) · Current Biology · doi:10.1016/j.cub.2020.11.016 · Cited by 84 · see citing works

Assessment of the yeast species composition of cocoa bean fermentations in different cocoa-producing regions using denaturing gradient gel electrophoresis

Papalexandratou, Z., & Vuyst, L. D. (2011) · FEMS Yeast Research · doi:10.1111/j.1567-1364.2011.00747.x · Cited by 83 · see citing works

Alternative Splicing of PTC7 inSaccharomyces cerevisiaeDetermines Protein Localization

Juneau, K., Nislow, C., & Davis, R. W. (2009) · Genetics · doi:10.1534/genetics.109.105155 · Cited by 82 · see citing works

A polyploid admixed origin of beer yeasts derived from European and Asian wine populations

Fay, J. C., Liu, P., Ong, G. T., Dunham, M. J., Cromie, G. A., Jeffery, E. W., Ludlow, C. L., & Dudley, A. M. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000147 · Cited by 81 · see citing works

Curing of Cocoa Beans: Fine-Scale Monitoring of the Starter Cultures Applied and Metabolomics of the Fermentation and Drying Steps

Díaz-Muñoz, C., de Voorde, D. V., Comasio, A., Verce, M., Hernandez, C. E., Weckx, S., & Vuyst, L. D. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.616875 · Cited by 76 · see citing works

Evidence of Natural Hybridization in Brazilian Wild Lineages of Saccharomyces cerevisiae

Barbosa, R. G., Almeida, P., Safar, S. V. B., Santos, R. O., Morais, P. B., Nielly‐Thibault, L., Leducq, J., Landry, C. R., Gonçalves, P. M., Rosa, C. A., et al. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evv263 · Cited by 74 · see citing works

Impact of a Microbial Cocktail Used as a Starter Culture on Cocoa Fermentation and Chocolate Flavor

Moreira, I. M. D. V., Vilela, L. D. F., Miguel, M. G. D. C. P., Santos, C. R., Lima, N., & Schwan, R. F. (2017) · Molecules · doi:10.3390/molecules22050766 · Cited by 73 · see citing works

Food Evolution: The Impact of Society and Science on the Fermentation of Cocoa Beans

Öztürk, G., & Young, G. M. (2017) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.12264 · Cited by 71 · see citing works

Tuning Chocolate Flavor through Development of Thermotolerant Saccharomyces cerevisiae Starter Cultures with Increased Acetate Ester Production

Meersman, E., Steensels, J., Struyf, N., Paulus, T., Saels, V., Mathawan, M., Allegaert, L., Vrancken, G., & Verstrepen, K. J. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.02556-15 · Cited by 65 · see citing works

The genomes of fermentative Saccharomyces

Dequin, S., & Casarégola, S. (2011) · Comptes Rendus Biologies · doi:10.1016/j.crvi.2011.05.019 · Cited by 63 · see citing works

A Combined Metagenomics and Metatranscriptomics Approach to Unravel Costa Rican Cocoa Box Fermentation Processes Reveals Yet Unreported Microbial Species and Functionalities

Verce, M., Schoonejans, J., Aguirre, C. H., Bravo, R. M., Vuyst, L. D., & Weckx, S. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.641185 · Cited by 63 · see citing works

Functional yeast starter cultures for cocoa fermentation

Díaz-Muñoz, C., & Vuyst, L. D. (2021) · Journal of Applied Microbiology · doi:10.1111/jam.15312 · Cited by 60 · see citing works

Revisiting the Taxonomic Synonyms and Populations of Saccharomyces cerevisiae-Phylogeny, Phenotypes, Ecology and Domestication

Pontes, A., Hutzler, M., Brito, P. H., & Sampaio, J. P. (2020) · Microorganisms · doi:10.3390/microorganisms8060903 · Cited by 54 · see citing works

The environmental and intrinsic yeast diversity of Cuban cocoa bean heap fermentations

Maura, Y. F., Balzarini, T., Borges, P. C., Evrard, P. A., Vuyst, L. D., & Daniel, H. (2016) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2016.06.012 · Cited by 50 · see citing works

Key features of the two-intron Saccharomyces cerevisiae gene SUS1 contribute to its alternative splicing

Hossain, M. A., Rodriguez, C. M., & Johnson, T. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr497 · Cited by 49 · see citing works

Microbiology and technology of fermented foods

Ibrahim, S. A. (2020) · Journal of Dairy Research · doi:10.1017/s0022029920000059 · Cited by 49 · 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

Genetic analysis ofSaccharomyces cerevisiaestrains isolated from palm wine in eastern Nigeria. Comparison with other African strains

Ezeronye, O. U., & Legras, J. (2009) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2008.04118.x · Cited by 44 · see citing works

The Pangenome: Diversity, Dynamics and Evolution of Genomes

Tettelin, H., & Medini, D. (2020) · Springer eBooks · doi:10.1007/978-3-030-38281-0 · Cited by 43 · see citing works

Multiple Rounds of Artificial Selection Promote Microbe Secondary Domestication—The Case of Cachaça Yeasts

Barbosa, R. G., Pontes, A., Santos, R. O., Montandon, G. G., Ponzzes-Gomes, C. M. P. B. S., Morais, P. B., Gonçalves, P. M., Rosa, C. A., & Sampaio, J. P. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy132 · Cited by 41 · see citing works

Adaptive Gene Content and Allele Distribution Variations in the Wild and Domesticated Populations of Saccharomyces cerevisiae

Han, D., Han, P., Rumbold, K., Dabassa, A., Duan, S., Song, L., Shi, J., Li, K., Wang, Q., & Bai, F. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.631250 · Cited by 39 · see citing works

Investigation of Genetic Relationships Between Hanseniaspora Species Found in Grape Musts Revealed Interspecific Hybrids With Dynamic Genome Structures

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

The Saccharomyces Genome Database: A Tool for DiscoveryPreprint

Cherry, J. M. (2015) · Cold Spring Harbor Protocols · doi:10.1101/pdb.top083840 · Cited by 34 · see citing works

Characterization and Degradation of Pectic Polysaccharides in Cocoa Pulp

Meersman, E., Struyf, N., Kyomugasho, C., Kermani, Z. J., Santiago, J. S., Baert, E., Hemdane, S., Vrancken, G., Verstrepen, K. J., Courtin, C. M., et al. (2017) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.7b03854 · Cited by 34 · see citing works

Population genomics reveals evolution and variation of Saccharomyces cerevisiae in the human and insects gut

Ramazzotti, M., Stefanini, I., Paola, M. D., Filippo, C. D., Rizzetto, L., Berná, L., Dapporto, L., Rivero, D., Tocci, N., Weil, T., et al. (2018) · Environmental Microbiology · doi:10.1111/1462-2920.14422 · Cited by 33 · see citing works

Aspergillus niger citrate exporter revealed by comparison of two alternative citrate producing conditions

Odoni, D. I., Laothanachareon, T., Vázquez‐Vilar, M., van Gaal, M. P., Schonewille, T., Bruinsma, L., dos Santos, V. A. P. M., Tamayo‐Ramos, J. A., Diez, M. S., & Schaap, P. J. (2019) · FEMS Microbiology Letters · doi:10.1093/femsle/fnz071 · Cited by 32 · see citing works

Diversity of Saccharomyces cerevisiae strains isolated from Borassus akeassii palm wines from Burkina Faso in comparison to other African beverages

Tapsoba, F., Legras, J., Savadogo, A., Dequin, S., & Traore, A. S. (2015) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2015.07.010 · Cited by 27 · see citing works

Influence of S. cerevisiae and P. kluyveri as starters on chocolate flavour

Moreira, I. M. D. V., Costa, J., Vilela, L. D. F., Lima, N., Santos, C. R., & Schwan, R. F. (2021) · Journal of the Science of Food and Agriculture · doi:10.1002/jsfa.11082 · Cited by 20 · see citing works

Population Genomics of Intron Splicing in 38 Saccharomyces cerevisiae Genome Sequences

Skelly, D. A., Ronald, J., Connelly, C. F., & Akey, J. M. (2009) · Genome Biology and Evolution · doi:10.1093/gbe/evp046 · Cited by 19 · see citing works

Eukaryotic Pangenomes

Richard, G. (2020) · Springer eBooks · doi:10.1007/978-3-030-38281-0_12 · Cited by 12 · see citing works

Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.

Carlino, N., Blanco-Míguez, A., Punčochář, M., Mengoni, C., Pinto, F., Tatti, A., Manghi, P., Armanini, F., Avagliano, M., Barcenilla, C., et al. (2024) · Cell · doi:10.1016/j.cell.2024.07.039 · Cited by 146 · see citing works

Yeast strains do have an impact on the production of cured cocoa beans, as assessed with Costa Rican Trinitario cocoa fermentation processes and chocolates thereof

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

Long-read metagenomics gives a more accurate insight into the microbiota of long-ripened gouda cheeses

Decadt, H., Díaz-Muñoz, C., Vermote, L., Pradal, I., Vuyst, L. D., & Weckx, S. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1543079 · Cited by 11 · see citing works

Yeast adapts to diverse ecological niches driven by genomics and metabolic reprogramming

Wang, H., Nielsen, J., Zhou, Y. J., & Lu, H. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2502044122 · Cited by 10 · see citing works

Prediction of change in suitable habitats of Senna obtusifolia and Senna tora under climate change

Chen, Y., Luo, C., Huang, X. S., Li, W., Han, Y., Ji, H., Zhou, J., & Liao, H. (2024) · Scientific Reports · doi:10.1038/s41598-024-81883-0 · Cited by 4 · see citing works

Genetic conflicts in budding yeast: The 2μ plasmid as a model selfish element

Hays, M. (2024) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2024.04.002 · Cited by 2 · see citing works

Environmental contributors to bacterially dominated fermenting consortia of artisanal Mezcal

Becerra-Lucio, P. A., Pérez‐Rueda, E., Dias, G. M., Labrín-Sotomayor, N. Y., Mendoza‐Mendoza, A., Partida‐Martínez, L. P., Zarza, E., & Peña-Ramírez, Y. J. (2026) · BMC Microbiology · doi:10.1186/s12866-026-05199-x · Cited by 1 · see citing works

Saccharomyces cerevisiae - Fermented Garlic Attenuates Gamma-irradiation Induced Brain and Liver Toxicity Via Regulation of the NF-κB and STAT3 Signaling Pathway

El-Sonbaty, S. M., Elhameed, H. F. A., & Ismail, A. F. M. (2023) · Egyptian Journal of Radiation Sciences and Applications · doi:10.21608/ejrsa.2023.236135.1161

Species-wide survey of transcript and protein abundance variation in yeast

Teyssonnière, É. (2023) · theses.fr (ABES) · doi:10.70675/9c5f617cz3bcfz4064z9e8eza0b9f5bca082

Molecular and Physiological Analysis of Saccharomyces cerevisiae Strains Associated with Taberna, an Alcoholic Beverage from the Sap of Coyol Palm (Acrocomia aculeata Jacq. Lodd. Ex Mart.)

Tawas-Penagos, M., Narváez-Zapata, J. A., Lappe-Oliveras, P., & Verdugo-Valdez, A. G. (2026) · Beverages · doi:10.3390/beverages12050057

Unravelling the genome of a Saccharomyces cerevisiae strain involved in cocoa fermentation through a hybrid sequencing approach

Munoz, C. D. (2020) · VUBIR (Vrije Universiteit Brussel)

The genetic polymorphism in Saccharomyces cerevisiae wild strains is correlated to their isolation area: the case of Nero d'Avola

Capece, A., Romaniello, R., ROMANO, P., & Serafino, V. (2006) · CINECA IRIS Institutional Research Information System (University of Basilicata)

Taxogenetics of the saccharomyces sensu stricto yeasts from western and south Africa

Naumov, G. I., Naumova, E. S., Sancho, E. D., & Korhola, M. (1993) · Cryptogamie Mycologie · doi:10.5962/p.354392 · Cited by 9 · see citing works

Characterization and evaluation of indigenous Saccharomyces cerevisiae strains isolated from South African vineyards

der Westhuizen, V., & Johannes, T. (1999)

Genetic pre-adaptations in Saccharomyces cerevisiae Andean chicha isolates facilitate industrial brewery application

Flores, J., König, S., Hutzler, M., Kunz, O., Krogerus, K., Lehnhardt, F., Magalhães, F., Svedlund, N., Grijalva‐Vallejos, N., & Gibson, B. R. (2025) · Food Microbiology · doi:10.1016/j.fm.2025.104815 · Cited by 5 · see citing works