TY - JOUR AU - Oud, B. AU - Maris, A. J. AU - Daran, J. M. AU - Pronk, J. T. PY - 2012 DA - 2012// TI - Genome-wide analytical approaches for reverse metabolic engineering of industrially relevant phenotypes in yeast JO - FEMS Yeast Res VL - 12 UR - https://doi.org/10.1111/j.1567-1364.2011.00776.x DO - 10.1111/j.1567-1364.2011.00776.x ID - Oud2012 ER - TY - JOUR AU - Smith, D. R. AU - Quinlan, A. R. AU - Peckham, H. E. AU - Makowsky, K. AU - Tao, W. AU - Woolf, B. PY - 2008 DA - 2008// TI - Rapid whole-genome mutational profiling using next-generation sequencing technologies JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.077776.108 DO - 10.1101/gr.077776.108 ID - Smith2008 ER - TY - JOUR AU - Crom, S. AU - Schackwitz, W. AU - Pennacchio, L. AU - Magnuson, J. K. AU - Culley, D. E. AU - Collett, J. R. PY - 2009 DA - 2009// TI - Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing JO - Proc Natl Acad Sci U S A VL - 106 UR - https://doi.org/10.1073/pnas.0905848106 DO - 10.1073/pnas.0905848106 ID - Crom2009 ER - TY - JOUR AU - Sarin, S. AU - Bertrand, V. AU - Bigelow, H. AU - Boyanov, A. AU - Doitsidou, M. AU - Poole, R. J. PY - 2010 DA - 2010// TI - Analysis of multiple ethyl methanesulfonate-mutagenized Caenorhabditis elegans strains by whole-genome sequencing JO - Genetics VL - 185 UR - https://doi.org/10.1534/genetics.110.116319 DO - 10.1534/genetics.110.116319 ID - Sarin2010 ER - TY - JOUR AU - Harper, M. A. AU - Chen, Z. AU - Toy, T. AU - Machado, I. M. AU - Nelson, S. F. AU - Liao, J. C. PY - 2011 DA - 2011// TI - Phenotype sequencing: identifying the genes that cause a phenotype directly from pooled sequencing of independent mutants JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0016517 DO - 10.1371/journal.pone.0016517 ID - Harper2011 ER - TY - JOUR AU - Parts, L. AU - Cubillos, F. A. AU - Warringer, J. AU - Jain, K. AU - Salinas, F. AU - Bumpstead, S. J. PY - 2011 DA - 2011// TI - Revealing the genetic structure of a trait by sequencing a population under selection JO - Genome Res VL - 21 UR - https://doi.org/10.1101/gr.116731.110 DO - 10.1101/gr.116731.110 ID - Parts2011 ER - TY - JOUR AU - Zhang, Y. X. AU - Perry, K. AU - Vinci, V. A. AU - Powell, K. AU - Stemmer, W. P. C. AU - Cardayre, S. B. PY - 2002 DA - 2002// TI - Genome shuffling leads to rapid phenotypic improvement in bacteria JO - Nature VL - 415 UR - https://doi.org/10.1038/415644a DO - 10.1038/415644a ID - Zhang2002 ER - TY - JOUR AU - Pinel, D. AU - D’Aoust, F. AU - Cardayre, S. B. AU - Bajwa, P. K. AU - Lee, H. AU - Martin, V. J. J. PY - 2011 DA - 2011// TI - Saccharomyces cerevisiae genome shuffling through recursive population mating leads to improved tolerance to spent sulfite liquor JO - Appl Environ Microbiol VL - 77 UR - https://doi.org/10.1128/AEM.02769-10 DO - 10.1128/AEM.02769-10 ID - Pinel2011 ER - TY - JOUR AU - Patnaik, R. AU - Louie, S. AU - Gavrilovic, V. AU - Perry, K. AU - Stemmer, W. P. C. AU - Ryan, C. M. PY - 2002 DA - 2002// TI - Genome shuffling of Lactobacillus for improved acid tolerance JO - Nat Biotechnol VL - 20 UR - https://doi.org/10.1038/nbt0702-707 DO - 10.1038/nbt0702-707 ID - Patnaik2002 ER - TY - JOUR AU - Dai, M. H. AU - Copley, S. D. PY - 2004 DA - 2004// TI - Genome shuffling improves degradation of the anthropogenic pesticide pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723 JO - Appl Environ Microbiol VL - 70 UR - https://doi.org/10.1128/AEM.70.4.2391-2397.2004 DO - 10.1128/AEM.70.4.2391-2397.2004 ID - Dai2004 ER - TY - JOUR AU - Biot-Pelletier, D. AU - Martin, V. J. J. PY - 2014 DA - 2014// TI - Evolutionary engineering by genome shuffling JO - Appl Microbiol Biotechnol VL - 98 UR - https://doi.org/10.1007/s00253-014-5616-8 DO - 10.1007/s00253-014-5616-8 ID - Biot-Pelletier2014 ER - TY - JOUR AU - Almeida, J. R. M. AU - Modig, T. AU - Petersson, A. AU - Hahn-Hägerdal, B. AU - Lidén, G. AU - Gorwa-Grauslund, M. F. PY - 2007 DA - 2007// TI - Increased tolerance and conversion of inhibitors in lignocellulosic hydrolysates by Saccharomyces cerevisiae JO - J Chem Technol Biotechnol VL - 82 UR - https://doi.org/10.1002/jctb.1676 DO - 10.1002/jctb.1676 ID - Almeida2007 ER - TY - JOUR AU - Liu, Z. L. PY - 2011 DA - 2011// TI - Molecular mechanisms of yeast tolerance and in situ detoxification of lignocellulose hydrolysates JO - Appl Microbiol Biotechnol VL - 90 UR - https://doi.org/10.1007/s00253-011-3167-9 DO - 10.1007/s00253-011-3167-9 ID - Liu2011 ER - TY - CHAP AU - Liu, Z. L. AU - Blaschek, H. P. ED - Vertes, A. ED - Qureshi, N. ED - Yukawa, H. ED - Blaschek, H. PY - 2010 DA - 2010// TI - Lignocellulosic biomass conversion to ethanol by Saccharomyces BT - Biomass to biofuels: strategies for global industries PB - Sons, Ltd CY - West Sussex, U. K ID - Liu2010 ER - TY - JOUR AU - Palmqvist, E. AU - Hahn-Hägerdal, B. PY - 2000 DA - 2000// TI - Fermentation of lignocellulosic hydrolysates. I: Inhibition and detoxification JO - Biores Technol VL - 74 UR - https://doi.org/10.1016/S0960-8524(99)00160-1 DO - 10.1016/S0960-8524(99)00160-1 ID - Palmqvist2000 ER - TY - JOUR AU - Richardson, T. L. AU - Harner, N. K. AU - Bajwa, P. K. AU - Trevors, J. T. AU - Lee, H. PY - 2011 DA - 2011// TI - Approaches to deal with toxic inhibitors during fermentation of lignocellulosic substrates JO - Acs Sym Ser VL - 1067 UR - https://doi.org/10.1021/bk-2011-1067.ch007 DO - 10.1021/bk-2011-1067.ch007 ID - Richardson2011 ER - TY - JOUR AU - Pinel, D. AU - Gawand, P. AU - Mahadevan, R. AU - Martin, V. J. J. PY - 2011 DA - 2011// TI - ‘Omics’ technologies and systems biology for engineering Saccharomyces cerevisiae strains for lignocellulosic bioethanol production JO - Biofuels VL - 2 UR - https://doi.org/10.4155/bfs.11.120 DO - 10.4155/bfs.11.120 ID - Pinel2011 ER - TY - JOUR AU - Gorsich, S. W. AU - Slininger, P. J. AU - Liu, Z. L. PY - 2005 DA - 2005// TI - Physiological responses to furfural and HMF and the link to other stress pathways JO - J Biotechnol VL - 118 ID - Gorsich2005 ER - TY - JOUR AU - Petersson, A. AU - Almeida, J. R. M. AU - Modig, T. AU - Karhumaa, K. AU - Hahn-Hägerdal, B. AU - Gorwa-Grauslund, M. F. PY - 2006 DA - 2006// TI - A 5-hydroxymethyl furfural reducing enzyme encoded by the Saccharomyces cerevisiae ADH6 gene conveys HMF tolerance JO - Yeast VL - 23 UR - https://doi.org/10.1002/yea.1370 DO - 10.1002/yea.1370 ID - Petersson2006 ER - TY - JOUR AU - Keating, J. D. AU - Panganiban, C. AU - Mansfield, S. D. PY - 2006 DA - 2006// TI - Tolerance and adaptation of ethanologenic yeasts to lignocellulosic inhibitory compounds JO - Biotechnol Bioeng VL - 93 UR - https://doi.org/10.1002/bit.20838 DO - 10.1002/bit.20838 ID - Keating2006 ER - TY - CHAP AU - Pinel, D. AU - Martin, V. J. J. ED - Patnaik, R. PY - 2012 DA - 2012// TI - Meiotic recombination-based genome shuffling of Saccharomyces cerevisiae and Schefferomyces stiptis for increased inhibitor tolerance to lignocellulosic substrate toxicity BT - Engineering complex phenotypes in industrial strains PB - Sons, Inc CY - Hoboken, New Jersey UR - https://doi.org/10.1002/9781118433034.ch9 DO - 10.1002/9781118433034.ch9 ID - Pinel2012 ER - TY - JOUR AU - Helle, S. S. AU - Murray, A. AU - Lam, J. AU - Cameron, D. R. AU - Duff, S. J. PY - 2004 DA - 2004// TI - Xylose fermentation by genetically modified Saccharomyces cerevisiae 259ST in spent sulfite liquor JO - Bioresour Technol VL - 92 UR - https://doi.org/10.1016/j.biortech.2003.08.011 DO - 10.1016/j.biortech.2003.08.011 ID - Helle2004 ER - TY - JOUR AU - Olsson, L. AU - HahnHagerdal, B. PY - 1996 DA - 1996// TI - Fermentation of lignocellulosic hydrolysates for ethanol production JO - Enzyme Microb Tech VL - 18 UR - https://doi.org/10.1016/0141-0229(95)00157-3 DO - 10.1016/0141-0229(95)00157-3 ID - Olsson1996 ER - TY - JOUR AU - Parajó, J. C. AU - Domíngues, H. AU - Domínguez, J. M. PY - 1998 DA - 1998// TI - Biotechnological production of xylitol. Part 3: operation in culture media made from lignocellulose hydrolysates JO - Bioresour Technol VL - 66 UR - https://doi.org/10.1016/S0960-8524(98)00037-6 DO - 10.1016/S0960-8524(98)00037-6 ID - Parajó1998 ER - TY - STD TI - Helle S, Duff S. Supplementing spent sulfite liquor with a lignocellulosic hydrolysate to increase pentose/hexose co-fermentation efficiency and ethanol yield. Final report-Natural Resources Canada-Tembec Industries; 2004. http://www.lifesciencesbc.ca/files/dufffinal_report.pdf. UR - http://www.lifesciencesbc.ca/files/dufffinal_report.pdf ID - ref25 ER - TY - JOUR AU - Yassour, M. AU - Kaplan, T. AU - Fraser, H. B. AU - Levin, J. Z. AU - Pfiffner, J. AU - Adiconis, X. PY - 2009 DA - 2009// TI - Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing JO - Proc Natl Acad Sci U S A VL - 106 UR - https://doi.org/10.1073/pnas.0812841106 DO - 10.1073/pnas.0812841106 ID - Yassour2009 ER - TY - JOUR AU - Nagalakshmi, U. AU - Wang, Z. AU - Waern, K. AU - Shou, C. AU - Raha, D. AU - Gerstein, M. PY - 2008 DA - 2008// TI - The transcriptional landscape of the yeast genome defined by RNA sequencing JO - Science VL - 320 UR - https://doi.org/10.1126/science.1158441 DO - 10.1126/science.1158441 ID - Nagalakshmi2008 ER - TY - JOUR AU - Kumar, P. AU - Henikoff, S. AU - Ng, P. C. PY - 2009 DA - 2009// TI - Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm JO - Nat Protoc VL - 4 UR - https://doi.org/10.1038/nprot.2009.86 DO - 10.1038/nprot.2009.86 ID - Kumar2009 ER - TY - JOUR AU - Ng, P. C. AU - Henikoff, S. PY - 2003 DA - 2003// TI - SIFT: predicting amino acid changes that affect protein function JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg509 DO - 10.1093/nar/gkg509 ID - Ng2003 ER - TY - JOUR AU - Sim, N. L. AU - Kumar, P. AU - Hu, J. AU - Henikoff, S. AU - Schneider, G. AU - Ng, P. C. PY - 2012 DA - 2012// TI - SIFT web server: predicting effects of amino acid substitutions on proteins JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gks539 DO - 10.1093/nar/gks539 ID - Sim2012 ER - TY - JOUR AU - Ozkaynak, E. AU - Finley, D. AU - Solomon, M. J. AU - Varshavsky, A. PY - 1987 DA - 1987// TI - The yeast ubiquitin genes: a family of natural gene fusions JO - EMBO J VL - 6 ID - Ozkaynak1987 ER - TY - JOUR AU - Modig, T. AU - Lidén, G. AU - Taherzadeh, M. J. PY - 2002 DA - 2002// TI - Inhibition effects of furfural on alcohol dehydrogenase, aldehyde dehydrogenase and pyruvate dehydrogenase JO - Biochem J VL - 363 UR - https://doi.org/10.1042/0264-6021:3630769 DO - 10.1042/0264-6021:3630769 ID - Modig2002 ER - TY - JOUR AU - Goldberg, A. L. PY - 2003 DA - 2003// TI - Protein degradation and protection against misfolded or damaged proteins JO - Nature VL - 426 UR - https://doi.org/10.1038/nature02263 DO - 10.1038/nature02263 ID - Goldberg2003 ER - TY - JOUR AU - Hochstrasser, M. PY - 1996 DA - 1996// TI - Ubiquitin-dependent protein degradation JO - Annu Rev Genet VL - 30 UR - https://doi.org/10.1146/annurev.genet.30.1.405 DO - 10.1146/annurev.genet.30.1.405 ID - Hochstrasser1996 ER - TY - JOUR AU - Kimura, Y. AU - Tanaka, K. PY - 2010 DA - 2010// TI - Regulatory mechanisms involved in the control of ubiquitin homeostasis JO - J Biochem VL - 147 UR - https://doi.org/10.1093/jb/mvq044 DO - 10.1093/jb/mvq044 ID - Kimura2010 ER - TY - JOUR AU - Hershko, A. AU - Ciechanover, A. PY - 1998 DA - 1998// TI - The ubiquitin system JO - Annu Rev Biochem VL - 67 UR - https://doi.org/10.1146/annurev.biochem.67.1.425 DO - 10.1146/annurev.biochem.67.1.425 ID - Hershko1998 ER - TY - JOUR AU - Mukhopadhyay, D. AU - Riezman, H. PY - 2007 DA - 2007// TI - Proteasome-independent functions of ubiquitin in endocytosis and signaling JO - Science VL - 315 UR - https://doi.org/10.1126/science.1127085 DO - 10.1126/science.1127085 ID - Mukhopadhyay2007 ER - TY - JOUR AU - Finley, D. AU - Ozkaynak, E. AU - Varshavsky, A. PY - 1987 DA - 1987// TI - The yeast polyubiquitin gene is essential for resistance to high temperatures, starvation, and other stresses JO - Cell VL - 48 UR - https://doi.org/10.1016/0092-8674(87)90711-2 DO - 10.1016/0092-8674(87)90711-2 ID - Finley1987 ER - TY - JOUR AU - Hanna, J. AU - Meides, A. AU - Zhang, D. P. AU - Finley, D. PY - 2007 DA - 2007// TI - A ubiquitin stress response induces altered proteasome composition JO - Cell VL - 129 UR - https://doi.org/10.1016/j.cell.2007.03.042 DO - 10.1016/j.cell.2007.03.042 ID - Hanna2007 ER - TY - JOUR AU - Leggett, D. S. AU - Hanna, J. AU - Borodovsky, A. AU - Crosas, B. AU - Schmidt, M. AU - Baker, R. T. PY - 2002 DA - 2002// TI - Multiple associated proteins regulate proteasome structure and function JO - Mol Cell VL - 10 UR - https://doi.org/10.1016/S1097-2765(02)00638-X DO - 10.1016/S1097-2765(02)00638-X ID - Leggett2002 ER - TY - JOUR AU - Hanna, J. AU - Leggett, D. S. AU - Finley, D. PY - 2003 DA - 2003// TI - Ubiquitin depletion as a key mediator of toxicity by translational inhibitors JO - Mol Cell Biol VL - 23 UR - https://doi.org/10.1128/MCB.23.24.9251-9261.2003 DO - 10.1128/MCB.23.24.9251-9261.2003 ID - Hanna2003 ER - TY - JOUR AU - Chernova, T. A. AU - Allen, K. D. AU - Wesoloski, L. M. AU - Shanks, J. R. AU - Chernoff, Y. O. AU - Wilkinson, K. D. PY - 2003 DA - 2003// TI - Pleiotropic effects of Ubp6 loss on drug sensitivities and yeast prion are due to depletion of the free ubiquitin pool JO - J Biol Chem VL - 278 UR - https://doi.org/10.1074/jbc.M310283200 DO - 10.1074/jbc.M310283200 ID - Chernova2003 ER - TY - JOUR AU - Hernández-López, M. J. AU - Garcia-Marqués, S. AU - Randez-Gil, F. AU - Prieto, J. A. PY - 2011 DA - 2011// TI - Multicopy suppression screening of Saccharomyces cerevisiae identifies the ubiquitination machinery as a main target for improving growth at low temperatures JO - Appl Environ Microbiol VL - 77 UR - https://doi.org/10.1128/AEM.00404-11 DO - 10.1128/AEM.00404-11 ID - Hernández-López2011 ER - TY - JOUR AU - Kolling, R. AU - Hollenberg, C. P. PY - 1994 DA - 1994// TI - The ABC-transporter Ste6 accumulates in the plasma membrane in a ubiquitinated form in endocytosis mutants JO - EMBO J VL - 13 ID - Kolling1994 ER - TY - JOUR AU - Hein, C. AU - Springael, J. Y. AU - Volland, C. AU - Haguenauer-Tsapis, R. AU - Andre, B. PY - 1995 DA - 1995// TI - NPl1, an essential yeast gene involved in induced degradation of Gap1 and Fur4 permeases, encodes the Rsp5 ubiquitin-protein ligase JO - Mol Microbiol VL - 18 UR - https://doi.org/10.1111/j.1365-2958.1995.mmi_18010077.x DO - 10.1111/j.1365-2958.1995.mmi_18010077.x ID - Hein1995 ER - TY - JOUR AU - Hicke, L. AU - Riezman, H. PY - 1996 DA - 1996// TI - Ubiquitination of a yeast plasma membrane receptor signals its ligand-stimulated endocytosis JO - Cell VL - 84 UR - https://doi.org/10.1016/S0092-8674(00)80982-4 DO - 10.1016/S0092-8674(00)80982-4 ID - Hicke1996 ER - TY - JOUR AU - Lin, C. H. AU - MacGurn, J. A. AU - Chu, T. AU - Stefan, C. J. AU - Emr, S. D. PY - 2008 DA - 2008// TI - Arrestin-related ubiquitin-ligase adaptors regulate endocytosis and protein turnover at the cell surface JO - Cell VL - 135 UR - https://doi.org/10.1016/j.cell.2008.09.025 DO - 10.1016/j.cell.2008.09.025 ID - Lin2008 ER - TY - JOUR AU - Goh, W. S. AU - Orlov, Y. AU - Li, J. AU - Clarke, N. D. PY - 2010 DA - 2010// TI - Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local JO - PLoS Comput Biol VL - 6 UR - https://doi.org/10.1371/journal.pcbi.1000649 DO - 10.1371/journal.pcbi.1000649 ID - Goh2010 ER - TY - JOUR AU - Harbison, C. T. AU - Gordon, D. B. AU - Lee, T. I. AU - Rinaldi, N. J. AU - Macisaac, K. D. AU - Danford, T. W. PY - 2004 DA - 2004// TI - Transcriptional regulatory code of a eukaryotic genome JO - Nature VL - 431 UR - https://doi.org/10.1038/nature02800 DO - 10.1038/nature02800 ID - Harbison2004 ER - TY - JOUR AU - Lee, T. I. AU - Rinaldi, N. J. AU - Robert, F. AU - Odom, D. T. AU - Bar-Joseph, Z. AU - Gerber, G. K. PY - 2002 DA - 2002// TI - Transcriptional regulatory networks in Saccharomyces cerevisiae JO - Science VL - 298 UR - https://doi.org/10.1126/science.1075090 DO - 10.1126/science.1075090 ID - Lee2002 ER - TY - JOUR AU - Workman, C. T. AU - Mak, H. C. AU - McCuine, S. AU - Tagne, J. B. AU - Agarwal, M. AU - Ozier, O. PY - 2006 DA - 2006// TI - A systems approach to mapping DNA damage response pathways JO - Science VL - 312 UR - https://doi.org/10.1126/science.1122088 DO - 10.1126/science.1122088 ID - Workman2006 ER - TY - JOUR AU - Zhu, C. AU - Byers, K. J. AU - McCord, R. P. AU - Shi, Z. AU - Berger, M. F. AU - Newburger, D. E. PY - 2009 DA - 2009// TI - High-resolution DNA-binding specificity analysis of yeast transcription factors JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.090233.108 DO - 10.1101/gr.090233.108 ID - Zhu2009 ER - TY - JOUR AU - Vyas, V. K. AU - Berkey, C. D. AU - Miyao, T. AU - Carlson, M. PY - 2005 DA - 2005// TI - Repressors Nrg1 and Nrg2 regulate a set of stress-responsive genes in Saccharomyces cerevisiae JO - Eukaryot Cell VL - 4 UR - https://doi.org/10.1128/EC.4.11.1882-1891.2005 DO - 10.1128/EC.4.11.1882-1891.2005 ID - Vyas2005 ER - TY - JOUR AU - Kuchin, S. AU - Vyas, V. K. AU - Carlson, M. PY - 2002 DA - 2002// TI - Snf1 protein kinase and the repressors Nrg1 and Nrg2 regulate FLO11, haploid invasive growth, and diploid pseudohyphal differentiation JO - Mol Cell Biol VL - 22 UR - https://doi.org/10.1128/MCB.22.12.3994-4000.2002 DO - 10.1128/MCB.22.12.3994-4000.2002 ID - Kuchin2002 ER - TY - JOUR AU - Mayordomo, I. AU - Estruch, F. AU - Sanz, P. PY - 2002 DA - 2002// TI - Convergence of the target of rapamycin and the Snf1 protein kinase pathways in the regulation of the subcellular localization of Msn2, a transcriptional activator of STRE (Stress Response Element)-regulated genes JO - J Biol Chem VL - 277 UR - https://doi.org/10.1074/jbc.M204198200 DO - 10.1074/jbc.M204198200 ID - Mayordomo2002 ER - TY - JOUR AU - Mira, N. P. AU - Becker, J. D. AU - Sá-Correia, I. PY - 2010 DA - 2010// TI - Genomic expression program involving the Haa1p-regulon in Saccharomyces cerevisiae response to acetic acid JO - OMICS VL - 14 UR - https://doi.org/10.1089/omi.2010.0048 DO - 10.1089/omi.2010.0048 ID - Mira2010 ER - TY - JOUR AU - Fernandes, A. R. AU - Mira, N. P. AU - Vargas, R. C. AU - Canelhas, I. AU - Sá-Correia, I. PY - 2005 DA - 2005// TI - Saccharomyces cerevisiae adaptation to weak acids involves the transcription factor Haa1p and Haa1p-regulated genes JO - Biochem Biophys Res Commun VL - 337 UR - https://doi.org/10.1016/j.bbrc.2005.09.010 DO - 10.1016/j.bbrc.2005.09.010 ID - Fernandes2005 ER - TY - JOUR AU - Magasanik, B. PY - 2003 DA - 2003// TI - Ammonia assimilation by Saccharomyces cerevisiae JO - Eukaryot Cell VL - 2 UR - https://doi.org/10.1128/EC.2.5.827-829.2003 DO - 10.1128/EC.2.5.827-829.2003 ID - Magasanik2003 ER - TY - JOUR AU - Ding, M. Z. AU - Wang, X. AU - Liu, W. AU - Cheng, J. S. AU - Yang, Y. AU - Yuan, Y. J. PY - 2012 DA - 2012// TI - Proteomic research reveals the stress response and detoxification of yeast to combined inhibitors JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0043474 DO - 10.1371/journal.pone.0043474 ID - Ding2012 ER - TY - JOUR AU - Mira, N. P. AU - Palma, M. AU - Guerreiro, J. F. AU - Sá-Correia, I. PY - 2010 DA - 2010// TI - Genome-wide identification of Saccharomyces cerevisiae genes required for tolerance to acetic acid JO - Microb Cell Fact VL - 9 UR - https://doi.org/10.1186/1475-2859-9-79 DO - 10.1186/1475-2859-9-79 ID - Mira2010 ER - TY - JOUR AU - Hess, D. C. AU - Lu, W. AU - Rabinowitz, J. D. AU - Botstein, D. PY - 2006 DA - 2006// TI - Ammonium toxicity and potassium limitation in yeast JO - PLoS Biol VL - 4 UR - https://doi.org/10.1371/journal.pbio.0040351 DO - 10.1371/journal.pbio.0040351 ID - Hess2006 ER - TY - JOUR AU - Bayer, T. S. AU - Hoff, K. G. AU - Beisel, C. L. AU - Lee, J. J. AU - Smolke, C. D. PY - 2009 DA - 2009// TI - Synthetic control of a fitness tradeoff in yeast nitrogen metabolism JO - J Biol Eng VL - 3 UR - https://doi.org/10.1186/1754-1611-3-1 DO - 10.1186/1754-1611-3-1 ID - Bayer2009 ER - TY - JOUR AU - Wegele, H. AU - Müller, L. AU - Buchner, J. PY - 2004 DA - 2004// TI - Hsp70 and Hsp90–a relay team for protein folding JO - Rev Physiol Biochem Pharmacol VL - 151 UR - https://doi.org/10.1007/s10254-003-0021-1 DO - 10.1007/s10254-003-0021-1 ID - Wegele2004 ER - TY - JOUR AU - Verghese, J. AU - Abrams, J. AU - Wang, Y. AU - Morano, K. A. PY - 2012 DA - 2012// TI - Biology of the heat shock response and protein chaperones: budding yeast (Saccharomyces cerevisiae) as a model system JO - Microbiol Mol Biol Rev VL - 76 UR - https://doi.org/10.1128/MMBR.05018-11 DO - 10.1128/MMBR.05018-11 ID - Verghese2012 ER - TY - JOUR AU - Jones, G. W. AU - Masison, D. C. PY - 2003 DA - 2003// TI - Saccharomyces cerevisiae Hsp70 mutations affect [PSI+] prion propagation and cell growth differently and implicate Hsp40 and tetratricopeptide repeat cochaperones in impairment of [PSI+] JO - Genetics VL - 163 ID - Jones2003 ER - TY - JOUR AU - Loovers, H. M. AU - Guinan, E. AU - Jones, G. W. PY - 2007 DA - 2007// TI - Importance of the Hsp70 ATPase domain in yeast prion propagation JO - Genetics VL - 175 UR - https://doi.org/10.1534/genetics.106.066019 DO - 10.1534/genetics.106.066019 ID - Loovers2007 ER - TY - JOUR AU - Duncan, K. AU - Edwards, R. M. AU - Coggins, J. R. PY - 1987 DA - 1987// TI - The pentafunctional arom enzyme of Saccharomyces cerevisiae is a mosaic of monofunctional domains JO - Biochem J VL - 246 ID - Duncan1987 ER - TY - JOUR AU - Bauer, B. E. AU - Rossington, D. AU - Mollapour, M. AU - Mamnun, Y. AU - Kuchler, K. AU - Piper, P. W. PY - 2003 DA - 2003// TI - Weak organic acid stress inhibits aromatic amino acid uptake by yeast, causing a strong influence of amino acid auxotrophies on the phenotypes of membrane transporter mutants JO - Eur J Biochem VL - 270 UR - https://doi.org/10.1046/j.1432-1033.2003.03701.x DO - 10.1046/j.1432-1033.2003.03701.x ID - Bauer2003 ER - TY - JOUR AU - Yoshikawa, K. AU - Tanaka, T. AU - Furusawa, C. AU - Nagahisa, K. AU - Hirasawa, T. AU - Shimizu, H. PY - 2009 DA - 2009// TI - Comprehensive phenotypic analysis for identification of genes affecting growth under ethanol stress in Saccharomyces cerevisiae JO - Fems Yeast Research VL - 9 UR - https://doi.org/10.1111/j.1567-1364.2008.00456.x DO - 10.1111/j.1567-1364.2008.00456.x ID - Yoshikawa2009 ER - TY - JOUR AU - Stambuk, B. U. AU - Panek, A. D. AU - Crowe, J. H. AU - Crowe, L. M. AU - Araujo, P. S. PY - 1998 DA - 1998// TI - Expression of high-affinity trehalose-H+ symport in Saccharomyces cerevisiae JO - Biochim Biophys Acta VL - 1379 UR - https://doi.org/10.1016/S0304-4165(97)00087-1 DO - 10.1016/S0304-4165(97)00087-1 ID - Stambuk1998 ER - TY - JOUR AU - Jules, M. AU - Guillou, V. AU - Francois, J. AU - Parrou, J. L. PY - 2004 DA - 2004// TI - Two distinct pathways for trehalose assimilation in the yeast Saccharomyces cerevisiae JO - Appl Environ Microbiol VL - 70 UR - https://doi.org/10.1128/AEM.70.5.2771-2778.2004 DO - 10.1128/AEM.70.5.2771-2778.2004 ID - Jules2004 ER - TY - JOUR AU - Babrzadeh, F. AU - Jalili, R. AU - Wang, C. AU - Shokralla, S. AU - Pierce, S. AU - Robinson-Mosher, A. PY - 2012 DA - 2012// TI - Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1 JO - Mol Genet Genomics VL - 287 UR - https://doi.org/10.1007/s00438-012-0695-7 DO - 10.1007/s00438-012-0695-7 ID - Babrzadeh2012 ER - TY - JOUR AU - Carreto, L. AU - Eiriz, M. F. AU - Gomes, A. C. AU - Pereira, P. M. AU - Schuller, D. AU - Santos, M. A. PY - 2008 DA - 2008// TI - Comparative genomics of wild type yeast strains unveils important genome diversity JO - BMC Genomics VL - 9 UR - https://doi.org/10.1186/1471-2164-9-524 DO - 10.1186/1471-2164-9-524 ID - Carreto2008 ER - TY - JOUR AU - Dunn, B. AU - Levine, R. P. AU - Sherlock, G. PY - 2005 DA - 2005// TI - Microarray karyotyping of commercial wine yeast strains reveals shared, as well as unique, genomic signatures JO - BMC Genomics VL - 6 UR - https://doi.org/10.1186/1471-2164-6-53 DO - 10.1186/1471-2164-6-53 ID - Dunn2005 ER - TY - JOUR AU - Ask, M. AU - Mapelli, V. AU - Hock, H. AU - Olsson, L. AU - Bettiga, M. PY - 2013 DA - 2013// TI - Engineering glutathione biosynthesis of Saccharomyces cerevisiae increases robustness to inhibitors in pretreated lignocellulosic materials JO - Microb Cell Fact VL - 12 UR - https://doi.org/10.1186/1475-2859-12-87 DO - 10.1186/1475-2859-12-87 ID - Ask2013 ER - TY - JOUR AU - Stephen, D. W. AU - Jamieson, D. J. PY - 1997 DA - 1997// TI - Amino acid-dependent regulation of the Saccharomyces cerevisiae GSH1 gene by hydrogen peroxide JO - Mol Microbiol VL - 23 UR - https://doi.org/10.1046/j.1365-2958.1997.2081572.x DO - 10.1046/j.1365-2958.1997.2081572.x ID - Stephen1997 ER - TY - JOUR AU - Nijkamp, J. F. AU - Broek, M. AU - Datema, E. AU - Kok, S. AU - Bosman, L. AU - Luttik, M. A. PY - 2012 DA - 2012// TI - De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology JO - Microb Cell Fact VL - 11 UR - https://doi.org/10.1186/1475-2859-11-36 DO - 10.1186/1475-2859-11-36 ID - Nijkamp2012 ER - TY - JOUR AU - Langmead, B. AU - Trapnell, C. AU - Pop, M. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - Ultrafast and memory-efficient alignment of short DNA sequences to the human genome JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-3-r25 DO - 10.1186/gb-2009-10-3-r25 ID - Langmead2009 ER - TY - JOUR AU - Li, H. AU - Ruan, J. AU - Durbin, R. PY - 2008 DA - 2008// TI - Mapping short DNA sequencing reads and calling variants using mapping quality scores JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.078212.108 DO - 10.1101/gr.078212.108 ID - Li2008 ER - TY - JOUR AU - Nakamura, K. AU - Oshima, T. AU - Morimoto, T. AU - Ikeda, S. AU - Yoshikawa, H. AU - Shiwa, Y. PY - 2011 DA - 2011// TI - Sequence-specific error profile of Illumina sequencers JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkr344 DO - 10.1093/nar/gkr344 ID - Nakamura2011 ER - TY - JOUR AU - Oyola, S. O. AU - Otto, T. D. AU - Gu, Y. AU - Maslen, G. AU - Manske, M. AU - Campino, S. PY - 2012 DA - 2012// TI - Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes JO - BMC Genomics VL - 13 UR - https://doi.org/10.1186/1471-2164-13-1 DO - 10.1186/1471-2164-13-1 ID - Oyola2012 ER - TY - JOUR AU - Xie, C. AU - Tammi, M. T. PY - 2009 DA - 2009// TI - CNV-seq, a new method to detect copy number variation using high-throughput sequencing JO - Bmc Bioinformatics VL - 10 UR - https://doi.org/10.1186/1471-2105-10-80 DO - 10.1186/1471-2105-10-80 ID - Xie2009 ER - TY - JOUR AU - Artimo, P. AU - Jonnalagedda, M. AU - Arnold, K. AU - Baratin, D. AU - Csardi, G. AU - Castro, E. PY - 2012 DA - 2012// TI - ExPASy: SIB bioinformatics resource portal JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gks400 DO - 10.1093/nar/gks400 ID - Artimo2012 ER - TY - JOUR AU - Baggerly, K. A. AU - Deng, L. AU - Morris, J. S. AU - Aldaz, C. M. PY - 2003 DA - 2003// TI - Differential expression in SAGE: accounting for normal between-library variation JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg173 DO - 10.1093/bioinformatics/btg173 ID - Baggerly2003 ER - TY - JOUR AU - Huang, W. AU - Sherman, B. T. AU - Lempicki, R. A. PY - 2009 DA - 2009// TI - Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources JO - Nat Protoc VL - 4 UR - https://doi.org/10.1038/nprot.2008.211 DO - 10.1038/nprot.2008.211 ID - Huang2009 ER - TY - JOUR AU - Merico, D. AU - Isserlin, R. AU - Bader, G. D. PY - 2011 DA - 2011// TI - Visualizing gene-set enrichment results using the Cytoscape plug-in enrichment map JO - Methods Mol Biol VL - 781 UR - https://doi.org/10.1007/978-1-61779-276-2_12 DO - 10.1007/978-1-61779-276-2_12 ID - Merico2011 ER - TY - JOUR AU - Merico, D. AU - Isserlin, R. AU - Stueker, O. AU - Emili, A. AU - Bader, G. D. PY - 2010 DA - 2010// TI - Enrichment map: a network-based method for gene-set enrichment visualization and interpretation JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0013984 DO - 10.1371/journal.pone.0013984 ID - Merico2010 ER - TY - JOUR AU - Cherry, J. M. AU - Hong, E. L. AU - Amundsen, C. AU - Balakrishnan, R. AU - Binkley, G. AU - Chan, E. T. PY - 2012 DA - 2012// TI - Saccharomyces Genome Database: the genomics resource of budding yeast JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr1029 DO - 10.1093/nar/gkr1029 ID - Cherry2012 ER - TY - JOUR AU - Abdulrehman, D. AU - Monteiro, P. T. AU - Teixeira, M. C. AU - Mira, N. P. AU - Lourenco, A. B. AU - Santos, S. C. PY - 2011 DA - 2011// TI - YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkq964 DO - 10.1093/nar/gkq964 ID - Abdulrehman2011 ER - TY - JOUR AU - Monteiro, P. T. AU - Mendes, N. D. AU - Teixeira, M. C. AU - d’Orey, S. AU - Tenreiro, S. AU - Mira, N. P. PY - 2008 DA - 2008// TI - YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkm976 DO - 10.1093/nar/gkm976 ID - Monteiro2008 ER - TY - JOUR AU - Teixeira, M. C. AU - Monteiro, P. AU - Jain, P. AU - Tenreiro, S. AU - Fernandes, A. R. AU - Mira, N. P. PY - 2006 DA - 2006// TI - The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj013 DO - 10.1093/nar/gkj013 ID - Teixeira2006 ER - TY - JOUR AU - Russell, D. W. AU - Jensen, R. AU - Zoller, M. J. AU - Burke, J. AU - Errede, B. AU - Smith, M. PY - 1986 DA - 1986// TI - Structure of the Saccharomyces cerevisiae HO gene and analysis of its upstream regulatory region JO - Mol Cell Biol VL - 6 ID - Russell1986 ER -