Saccharomyces Genome Database (YeastGenome.org), Department of Genetics at the School of Medicine, Stanford University, Center for Genomics and Personalized Medicine.
"The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms."
Saccharomyces Sensu Stricto, from the labs of Dunham, Eisen, Hittinger, Johnston, Rine, and Rokas.
"High-quality, well-annotated genome sequences and standardized laboratory strains fuel experimental and evolutionary research. We present improved genome sequences of three species of Saccharomyces sensu stricto yeasts: S. bayanus var. uvarum (CBS 7001), S. kudriavzevii (IFO 1802 T), S. kudriavzevii (ZP 591), and S. mikatae (IFO 1815 T), and describe their comparison to the genomes of S. cerevisiae and S. paradoxus ..."
UniPROBE, Bulyk Lab, Division of Genetics at Brigham and Women's Hospital, Boston.
"The UniPROBE Database is a repository for the experimental data from universal protein binding microarray (PBM) experiments (Berger et al., 2006) and their accompanying statistical analyses. This initial version of the site hosts the data from the publications listed in the references section of this site."
Yeast Gene Order Browser (YGOB), Dr. Kevin Byrne, Wolfe Laboratory, Trinity College Dublin
"YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes. There are detailed user guidelines. Alternatively you can start browsing immediately by typing the name of a yeast gene in the control console at the bottom of this page (e.g. ADH1). Standard bioinformatics tools are available through the browser interface and the icons for each are explained on the help page. "
16 December 2016
Peay KG, Kennedy PG, Talbot JM. Dimensions of biodiversity in the Earth mycobiome. Nat Rev Microbiol. 2016 Jul; 14(7):434-47.
2 December 2016
Hallin J, et al. Powerful decomposition of complex traits in a diploid model. Nat Comm. 2016; 7: 13311.
18 November 2016
Hosseini SR, Wagner A. The potential for non-adaptive origins of evolutionary innovations in central carbon metabolism. BMC Sys Bio. 2016 Oct 21; 10(1):97.
4 November 2016
Bastiaans E, Debets AJ, Aanen DK. Experimental evolution reveals that high relatedness protects multicellular cooperation from cheaters. Nat Commun. 2016 May 3; 7:11435.
26 October 2016
Lee ME, DeLoache WC, Cervantes B, Dueber JE. A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly. ACS Synth Biol. 2015 Sep 18; 4(9):975-86.
14 October 2016
Nagasawa M, et al. Social Evolution. Oxytocin-gaze positive loop and the coevolution of human-dog bonds. Science. 2015 Apr 17; 348(6232): 333-6.
7 October 2016
Pieczynska M. D., Wloch-Salamon D, Korona R, de Visser J. A. G. M. Rapid multiple-level coevolution in experimental populations of yeast killer and nonkiller strains. Evolution. 28 Apr 2016 70-6: 1342-1353
28 September 2016
Venkataram S, et al. Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast. Cell . 2016 Sep 8; 166(6): 1585-1596.
23 September 2016
Gallone B, et al. Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts. Cell. 2016 Sep 8; 166(6): 1397-1410.
16 September 2016
Baym M, Lieberman TD, Kelsi ED, Chait R, Gross R, Yelin I, Kishony R. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 2016 Sep: 353:6304.
12 August 2016
Pease JB, Haak DC, Hahn MW, Moyle LC. Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Evolution. PLoS Biol. 2016 Feb 12; 14(2): e1002379.
29 July 2016
Wolfe KH, Armisen D, Proux-Wera E, OhElgaertaigh SS, Azam H, Gordon JL, Byrne KP. Clade- and species-specific features of genome evolution in the Saccharomycetaceae. FEMS Yeast Res. 2015 Aug; 15(5): Epub 2015 Jun 10.
22 July 2016
Sarkisyan KS, et al. Local fitness landscape of the green flourescent protein. Nature 533. 397-401 (19 May 2016).
1 July 2016
Rich MS, Payen C, Rubin AF, Ong GT, Sanchez MR, Yachie N, Dunham MJ, Fields S. Comprehensive Analysis of the SUL1 Promoter of Saccharomyces cerevisiae. Genetics. 2016. May;2013(1):191-202.
17 June 2016
Semani P. Bell G. Experimental evolution of the grain of metabolic specialization in yeast. 2016. Ecol and Evolution; V6, I12, 3912-3922, (11 May 2016)
10 June 2016
Selmecki, et al. Polyploidy can drive rapid adaptation in yeast. 2015 March; Nature. 519, 349-352 (19March2015).
13 May 2016
Mills JA, et. al. Archiving Primary Data: Solutions for Long-Term Studies. 2015 Oct; Trends Ecol Evol. 30 (10):581-9
29 April 2016
Schwartz CM, Hussain MS, Blenner M, Wheeldeon I. Synthetic RNA Polymerase III Promoters Facilitate High-Efficiency CRISPR-Cas9-Mediated Genome Editing in Yarrowia lipolitica. 2016 Apr 16. ACS Synth Biol. 5(4):356-9.
22 April 2016
Tedersoo L, et al. Fungal biogeography. Global diversity and geography of soil fungi. 28 Nov 2014. Science. Vol. 346, Issue 6213.
15 April 2016
Hutchison C.A., et al. Design and synthesis of a minimal bacterial genome. 26 March 2016. Science. Vol. 351, Issue 6280.
8 April 2016
Lightening Journal Club!
18 March 2016
Gasch AP, Payseur BA, Pool JE. The Power of Natural Variation for Model Organism Biology. March 2016. Trends in Genetics; 32(3):147-154.
4 March 2016 - a double header!
Pittis A.A., Gabaldon T. Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry. 3 March 2016, Nature 531; 101-104.
McDonald M.J., Rice D.P., Desai M.M. Sex speeds adaptation by altering the dynamics of molecular evolution. 10 March 2016. Nature 531; 233-236.
26 Feb 2016
Salina F, de Boer C.G., Abarca V, Garcia V, Cuevas M, Araos S, Larrondo L.F., Martinez C, Cubillos F.A. Natural variation in non-coding regions underlying phenotypic diversity in budding yeast. Nature Scientific Reports. Feb 2016. 6:21849 | DOI: 10.1038/srep21849
19 Feb 2016
Blackburn EH, Greider CW, Szostak JW. Telomeres and telomerase: the path from maize, Tetrahymena and yeast to human cancer and aging. Nat Med. 2006 Oct;12(10);1133-8.
5 Feb 2016
Buckley L.B., Ehrenberger J.C., Angiletta M.J. Thermoregulatory behaviour limits local adaptation of thermal niches and confers sensitivity to climate change. Functional Ecology. 2015, 29, 1038-1047.
29 Jan 2016
Wei S, Williams Z. Rapid Short-Read Sequencing and Aneuploidy Detection Using MinION Nanopore Technology. Genetics. 2016. Jan;202(1):37-44.
22 Jan 2016
Rasmussen M, et al. The ancestry and affiliations of Kennewick Man. Nature. 2015 Jul 23. 523(7561):455-8.
4 Dec 2015
Gayevskiy V, Goddard MR. Saccharomyces eubayanus and Saccharomyces arboricola reside in North Island native New Zealand forests. Environ Microbiol. 2015 Nov 2. Epub ahead of print.
20 Nov 2015
Aakre C. D., Herrou J., Phung T.N., Perchuk B.S., Crosson S., Laub M.T. Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates. Cell 163, 594–606 (2015).
13 Nov 2015
Strope PK, Kozmin SG, Skelly DA, Magwene PM, Dietrich FS, McCusker JH. 2µ plasmid in Saccharomyces species and in Saccharomyces cerevisiae. FEMS Yeast Res. 2015 Dec; 15(8).
30 Oct 2015
Drinnenberg IA, Fink GR, Bartel DP. Compatibility with killer explains the rise of RNAi-deficient fungi. Science. 2011 Sep 16; 333(6049): 1592.
23 Oct 2015
Miller E, Greig D. Spore Germination Determines Yeast Inbreeding according to Fitness in the Local Environment. The American Society of Naturalists. V 185, No 2 (Feb 2015), pp. 291-301.
9 Oct 2015
Almeida P, et al. A population Genomics Insight into the Mediterranean Origins of Wine Yeast Domestication. Mol Ecol. 6 Aug 2015.
2 Oct 2015
Rockah-Shmuel L., Toth-Petroczy A., Tawfik D. S.. Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations. PLOS Computational Biology. 14 Aug 2015.
25 Sep 2015
Lightening Journal Club!
4 Sep 2015
Haak W, Lizaridis I, Patterson N, Rohland N, Mallick S, Llamas B, Brandt G, Nordenfelt S, et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature. 11 Jun 2015.
31 Aug 2015
Marcet-Houben M, Gabaldon T. Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage. PLOS Bio. 7 Aug 2015.
24 Aug 2015
Sorrells TR, Booth LN, Tuch BB, Johnson AD. Intersecting transcription networks constrain gene regulatory evolution. Nature. 2015 Jul 16; 523 (7560): 361-5.
3 Aug 2015
Sathe L, Bolinger C, Mannan M.A., Dever T, Dey M. Evidence that Base-pairing Interactions between Intron and mRNA Leader Sequences Inhibits Initiation of HAC1 mRNA Translation in Yeast*. J Biol Chem. 2015 Jul 14.
20 July 2015
Huerta-Sanchez E, Jin X, Asan, Bianba Z, Peter BM, Vinckenbosch N, Liang Y, Yi X, He M, Somel M, Ni P, Wang B, Ou X, Huasang, Luosang J, Cuo ZX, Li K, Gao G, Yin Y, Wang W, Zhang X, Xu X, Yang H, Li Y, Wang J, Wang J, Nielsen R. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature. 2014. 14; 512(7513): 194-7.
6 July 2015
Storz J.F., Runck A.M., Sabatino S.J., Kelly J.K., Ferrand N, Moriyama H, Weber R.E., Fago A. Evolutionary and functional insights into the mechanism underlying high-altitude adaptation of deer mouse hemoglobin. PNAS. 2009. 106(34):14450-5.
29 June 2015
Strope PK, Skelly DA, Kozmin SG, Mahadevan G, Stone EA, Magwene PM, Dietrich SF, McCusker JH. The 100-genomes strains, an S. cerevisiae resource that illuminstes its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen. Genome Res. 2015 May;25(5):762-74.
22 June 2015
Hou J, Friedrich A, Gounot J-S, Schacherer J. Comprehensive survey of condition-specific reproductive isolation reveals genetic incompatibility in yeast. Nature Communications. May 2015. 6:7214
15 May 2015
Paliwal S, Fiumera AC, Fiumera HL. Mitochondrial-nuclear epistasis contributes to phenotypic variation and coadaptation in natural isolates of Saccharomyces cerevisiae. Genetics. 2014. Nov;198(3):1251-65.
8 May 2015
Bluher D, Reinhardt-Tews A, Hey M, Lilie H, Golbik R, Breunig KD, Anders A. An ancient oxidoreductase making differential use of its cofactors. Biol Chem. 2014. Jul;395(7-8):855-69.
1 May 2015
Eckert-Boulet N, Pedersen ML, Krogh BO, Lisby M. Optimization of ordered plasmid assembly by gap repair in Saccharomyces cerevisiae. Yeast. 2012. 29: 323-334.
10 April 2015
Lightening Journal Club!
13 Mar 2015
Khanal A, McLoughlin S Y, Kershner J P, Copley S D. Differential Effects of a Mutation on the Normal and Promiscuous Activities of Orthologs: Implications for Natural and Directed Evolution. Mol. Biol. Evol. 2014. 32(1):100-108.
27 Feb 2015
Hanson S, Byrne K P, Wolfe K H. Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system. PNAS. 2014 Nov 11; 111(45): E4851-8.
20 Feb 2015
Monerawela C, James T C, Wolfe K H, Bond U. Loss of lager specific genes and subtelomeric regions define two different Saccharomyces cerevisiae lineages for Saccharomyces pastorianus GroupI and II strains. FEMS Yeast Research. 15, 2015, 1-11.
6 Feb 2015
Seehausen O, Butlin R K, Keller I, Wagner C E, Boughman J W, Hohenlohe P A, Peichel C L, Saetre G-P, et al. Genomics and the origin of species. Nat Rev Genet. (2014 Mar; 15(3): 176-92.
30 Jan 2015
Lynch M. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci USA. (2007) 104.
19 Dec 2014
Lachance M-A, Lawrie D, Dobson J, Piggott J. Biogeography and population structure of the Neotropical endemic yeast species Metschnikowia lochheadii. Springer. (2008)94;3:403-414.
21 Nov 2014
Lightening Journal Club!
14 Nov 2014
Coolon JD, McManus CJ, Stevenson KR, Graveley BR, Wittkopp PJ. Tempo and mode of regulatory evolution in Drosophila. Genome Res. (2014) May; 24(5):797-808.
7 Nov 2014
Perez-Traves L, Lopes CA, Querol A, Barrio E. On the Complexity of the Saccharomyces bayanus Taxon: Hybridization and Potential Hybrid Speciation. PLOS One. (2014) 4;9(4):e93729.
31 October 2014
Paget CM, Schwartz J-M, and Delneri D. Environmental systems biology of cold-tolerant phenotype in Saccharomyces species adapted to grow at different temperatures. Molecular Ecology. (2014) 23, 5241–5257.
25 October 2014
Ramsey SA, Smith JJ, Orrell D, Marelli M, Petersen TW, de Atauri P, Bolouri H, Aitchison JD. Dual feedback loops in the GAL regulation suppress cellular heterogeneity in yeast. Nat Genet. 2006 Sep; 38(9): 1082-7.
17 October 2014
Blount B, Weenink T, Ellis To. Construction of synthetic regulatory networks in yeast. 2012. FEBS Letters. 586(2012) 2112-2121.
3 October 2014
Bergstrom A, Simpson JT, Salinas F, Barre B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warrington J, Durbin R, Liti G. A high-definition view of functional genetic variation from natural yeast genomes. 2014. Mol Biol Evol. 31(4):872-88.
26 September 2014
Morin I, Gudin S, Mintz E, Cuillel M. Dissecting the role of the N-termina metal-binding domains in activating the yeast copper ATPase in vivo. 2009. FEBS J. Aug; 276(16):4483-95.
19 September 2014
Zanders SE, Eickbush MT, Yu JS, Kang J-W, Fowler KR, Smith GR, Malik HS. Genome rearrangements and pervasive meiotic drive cause hybrid infertility in fission yeast. 2014. eLife. 24 June 2014.
5 September 2014
Artieri C, Fraser H. Evolution at two levels of gene expression in yeast. 2014. Genome Res. 24: 411-421.
22 August 2014
Hong KK, Vongsangnak W, Vemuri GN, Nielsen J. Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis. 2011. PNAS. 19: 108(29): 12179-84.
12 August 2014
Teo WS, Hee KS, Chang MW. Bacterial FadR and synthetic promoters function as modular fatty acid sensor-regulators in Saccaromyces cerevisia. 2013. Eng. Life. Sci. 13, 456-463.
15 July 2014
Harrison E, MacLean RC, Koufopanou V, Burt A. Sex drives intracellular conflict in yeast. 2014. J Evol Biol. (Epub)
8 July 2014
Ferrer-Admetila A, Liang M, Korneliussen T, Nielsen R. On detecting incomplete soft or hard selective sweeps using haplotype structure. 2014. Mol Biol Evol. 31(5):1275-91.
1 July 2014
Francesca N, Canale D, Settanni L, Moschetti G. Dissemination of wine-related yeasts by migratory birds. 2012. Environmental Microbiology Reports. 4(1), 105-112.
24 June 2014
Afroz T, Biliouris K, Boykin K, Kaznessis Y, Beisel C. Trade-offs in Engineering Sugar Utilization Pathways for Titratable Control. 2014. ACS Synthetic Biology. EPub.
10 June 2014
Walther A, Hesselbart A, Wendland J. Genome Sequence of Saccharomyces carlsbergensis, the World's First Pure Culture Lager Yeast. 2014. G3. 4:783.
3 June 2014
Plucain J, et al. Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Eschericia coli. 2014. Science. 343, 1366.
27 May 2014
Payne J, Wagner A. The Robustness and Evolvability of Transcription Factor Binding Sites. 2014. Science. 343, 875.
13 May 2014
Kolaczkowski B, Kern A, Holloway A, Begun D. Genomic Differentiation Between Termperate and Tropical Australian Populations of Drosophila melanogaster. 2011. Genetics. 187: 245-260.
16 April 2014
Farzadfard F, Perli S, Lu T. Tunable and Multifunctional Eukaryotic Transcription Factors based on CRISPR/Cas. 2013. ACS Synth Bio. 2: 604-613.
2 April 2014
S Minear, A. F. O'Donnell, A. Ballew, G. Giaever, C. Nislow, T. Stearns, M. S. Cyert. Curcumin Inhibits Growth of Saccharoyces cerevisiae through Iron Chelation. 2011. Eurkaryotic Cell. 10(110:1574.
26 March 2014
DH Wohlbach, A Kuo, TK Sato, et al. Comparative genomics of xylose-fermenting fungi for enhanced biofuel production. 2011. PNAS (2011 Aug 9; 108(32): 13212-7
19 March 2014
E Rintala, MG Wiebe, A Tamminen, L Ruohonen, M Penttiia. Transcription of hexose transporters of Saccharomyces cerevisiae is affected by change in oxygen provision. 2008. BMC Microbiol (2008 Marr 28; 8:53)
5 March 2014
A Hagman, T Sall, C Compagno, J Piskur. Yeast "make-accumulate-consume" life strategy evolved as a multi-step process that predates the whole genome duplication. 2013. PLoS One 8 (7):e68734
26 February 2014
New AM, Cerulus B, Govers SK, Perez-Samper G, Zhu B, et al. Different Levels of Catabolite Repression Optimize Growth in Stable and Variable Environments. 2014. PLoS Biol 1 (1): e1001764. doi:10.1371/journal.pbio.1001764
12 February 2014
HC Martin, JI Roop, JG Schraiber, TY Hsu, RB Brem. Evolution of a membane protein regulon in Saccharomyces. 2012. Mol Biol Evol. 1747-1756.
5 February 2014
N Wei, J Quarterman, SR Kim, JHD Cate, YS Jin. Enhanced biofuel production through coupled acetic acid and xylose consumption by engineered yeast. 2013. Nature Communications. 4:2580.
29 January 2014
AA Caudy, MJ Dunham, et al. A new system for comparative functional genomics of Saccharomyces yeasts. 2013. Genetics. 195(1):275-287.
22 January 2014
MJ Dunham and DM Fowler. Contemporary, yeast-based approaches to understanding human genetic variation. 2013. Current Opinion in Genetics & Development. 23:658-664.
15 January 2014
EM Young, A Tong, H Bui, C Spofford, H Alper. Rewiring yeast sugar transporter preference through modifying a conserved protein motif. 2013. PNAS.
8 January 2014
SL Maguire, SS OhEigeartaigh, KP Byrne, MS Schroder, P O’Gaora, KH Wolfe, and G Butler. Comparative Genome Analysis and Gene Finding in Candida
Species Using CGOB. 2013. Mol. Biol. Evol. 30(6):1281–1291
18 December 2013
TK Sato, T Liu, LS Parreiras, DL Williams, DJ Wohlbach, BD Bice, IS Ong, RJ Breuer, L Qin, D Busalacchi , S Deshpande, C Daum, AP Gasch, and DB Hodge. Harnessing Genetic Diversity in Saccharomyces cerevisiae for Improved Fermentation of
Xylose in Hydrolysates of Alkaline Hydrogen Peroxide Pretreated Biomass. 2013. Appl. Environ. Microbiol.
5 December 2013
Baker, C. R., Hanson-Smith, V., & Johnson, A. D. (2013). Following gene duplication, paralog interference constrains transcriptional circuit evolution.Science, 342(6154), 104-108.
14 November 2013
Connelly C. F. and J. M. Akey. 2012. On the prospects of whole-genome association mapping in Saccharomyces cerevisiae. Genetics 191:1345–53.
24 October 2013
Skelly DA, Merrihew GE, Riffle M, Connelly CF, Kerr EO, Johansson M, Jaschob D, Graczyk B, Shulman NJ, Wakefield J, Cooper SJ, Fields S, Noble WS, Muller EGD, Davis TN, Dunham MJ, MacCoss MJ, Akey JM (2013) Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast. Genome Res 23: 1496-1504.
8 October 2013
NGA Kuijpers, S Chroumpi, T Vos, D Solis-Escalante, L Bosman, JT Pronk, JM Daran, & P Daran-Lapujade. One-step assembly and targeted integration of multigene
constructs assisted by the I-SceI meganuclease in Saccharomyces cerevisiae. 2013. FEMS Yeast Research.
16 August 2013
C Bermejo, F Haerizadeh, MSC Sadoine, D Chermak and WB Frommer. Differential regulation of glucose transport activity in yeast by specific cAMP signatures. 2013. Biochem Journal.
26 July 2013
DA Thompson, S Roy, M Chan, MP Styczynsky, J Pfiffner, C French, A Socha, A Thielke, S Napolitano, P Muller, M Kellis, JH Konieczka, I Wapinski, A Regev. Evolutionary principles of modular gene regulation in yeasts. 2013. eLife.
19 July 2013
C Li, Z Wang, and J Zhang. Toward Genome-Wide Identification of
Bateson–Dobzhansky–Muller Incompatibilities in Yeast: A Simulation Study. 2013. Genome Biology and Evolution.
7 June 2013
Uri Alon. Network motifs: theory and experimental approaches. 2007. Nature.
13 May 2013
JJ Lohmueller, TZ Armel, PA Silver. A tunable zinc finger-based framework for Boolean logic computation in mammalian cells. 2012. Nucleic Acids Journal.
28 April 2013
DJ Kvitek, G Sherlock. Reciprocal Sign Epistasis between Frequently Experimentally Evolved Adaptive Mutations Causes a Rugged Fitness Landscape. 2011. PLOS Genetics. V7: I4.
23 April 2013
R Wieczorke, S Krampe, T Weierstall, K Freidel, CP Hollenberg, E Boles. Concurrent knock-out of at least 20 transporter genes is required to block uptake of hexoses in Saccharomyces cerevisiae. 1999. FEBS Letters. Volume 464 Issue 3, 123-128.
1 April 2013
Baker, C. R., Booth, L. N., Sorrells, T. R., & Johnson, A. D. (2012). Protein modularity, cooperative binding, and hybrid regulatory states underlie transcriptional network diversification. Cell, 151(1), 80-95.
17 October 2012
Youk, H., & van Oudenaarden, A. (2009). Growth landscape formed by perception and import of glucose in yeast. Nature, 462(7275), 875-879.
Chris Todd Hittinger
Laboratory of Genetics
425-G Henry Mall
4340-4360 Genetics/Biotechnology Center
Madison, Wisconsin 53706-1580
Contact the Lab: HittingerLab at genetics(dot) wisc(dot)edu UW Directory Link