TY - JOUR AU - Zyl, W. H. AU - Lynd, L. R. AU - Haan, R. AU - McBride, J. E. PY - 2007 DA - 2007// TI - Consolidated bioprocessing for bioethanol productionusing Saccharomyces cerevisiae JO - Adv Biochem Eng Biotechnol VL - 108 ID - Zyl2007 ER - TY - JOUR AU - Jung, Y. H. AU - Kim, I. J. AU - Kim, H. K. AU - Kim, K. H. PY - 2013 DA - 2013// TI - Dilute acid pretreatment of lignocellulose for wholeslurry ethanol fermentation JO - Bioresour Technol VL - 132 UR - https://doi.org/10.1016/j.biortech.2012.12.151 DO - 10.1016/j.biortech.2012.12.151 ID - Jung2013 ER - TY - JOUR AU - Schrickx, J. M. AU - Raedts, M. J. AU - Stouthamer, H. AU - Verseveld, H. W. PY - 1995 DA - 1995// TI - Organic acid production by Aspergillus niger in recycling culture analyzed by capillaryelectrophoresis JO - Anal Biochem VL - 231 UR - https://doi.org/10.1006/abio.1995.1518 DO - 10.1006/abio.1995.1518 ID - Schrickx1995 ER - TY - JOUR AU - Zhou, Y. J. AU - Buijs, N. AU - Siewers, V. AU - Nielsen, J. PY - 2014 DA - 2014// TI - Fatty acid-derived biofuels and chemicals productionin Saccharomyces cerevisiae JO - Front Bioeng Biotechnol VL - 2 ID - Zhou2014 ER - TY - JOUR AU - Tanaka, K. AU - Ishii, Y. AU - Ogawa, J. AU - Shima, J. PY - 2012 DA - 2012// TI - Enhancement of acetic acid tolerance in Saccharomyces cerevisiae by overexpression ofthe Haa1 gene, encoding a transcriptional activator JO - Appl Environ Microbiol VL - 78 UR - https://doi.org/10.1128/AEM.02356-12 DO - 10.1128/AEM.02356-12 ID - Tanaka2012 ER - TY - JOUR AU - Walker, G. M. PY - 2011 DA - 2011// TI - Pichia anomala: cell physiology andbiotechnology relative to other yeasts JO - Antonie van Leeuwenhoek Int J Gen Mol Microbiol VL - 99 UR - https://doi.org/10.1007/s10482-010-9491-8 DO - 10.1007/s10482-010-9491-8 ID - Walker2011 ER - TY - STD TI - Kostas ET, White D, Du C, Cook DJ. Selection of yeast strains forbioethanol production from UK seaweeds. J Appl Phycol 2015. ID - ref7 ER - TY - JOUR AU - Fredlund, E. AU - Druvefors, U. AU - Boysen, M. AU - Lingsten, K. AU - Schnurer, J. PY - 2002 DA - 2002// TI - Physiological characteristics of the biocontrolyeast J121 JO - FEMS Yeast Res VL - 2 ID - Fredlund2002 ER - TY - JOUR AU - Brandao, R. L. AU - Rosa, J. C. C. AU - Nicoli, J. R. AU - Almeida, M. V. S. AU - do Carmo, A. P. AU - Queiros, H. T. AU - Castro, I. M. PY - 2014 DA - 2014// TI - Investigating acid stress response in differentSaccharomyces strains JO - J Mycol VL - 2014 ID - Brandao2014 ER - TY - JOUR AU - Kawahata, M. AU - Masaki, K. AU - Fujii, T. AU - Iefuji, H. PY - 2006 DA - 2006// TI - Yeast genes involved in response to lactic acid andacetic acid: acidic conditions caused by the organic acids in Saccharomyces cerevisiae cultures induceexpression of intracellular metal metabolism genes regulated byAft1p JO - FEMS Yeast Res VL - 6 UR - https://doi.org/10.1111/j.1567-1364.2006.00089.x DO - 10.1111/j.1567-1364.2006.00089.x ID - Kawahata2006 ER - TY - JOUR AU - Schneider, J. AU - Rupp, O. AU - Trost, E. AU - Jaenicke, S. AU - Passoth, V. AU - Goesmann, A. AU - Tauch, A. AU - Brinkrolf, K. PY - 2012 DA - 2012// TI - Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis ofbiotechnologically important antimicrobial activities JO - FEMS Yeast Res VL - 12 UR - https://doi.org/10.1111/j.1567-1364.2012.00791.x DO - 10.1111/j.1567-1364.2012.00791.x ID - Schneider2012 ER - TY - JOUR AU - Zha, Y. AU - Hossain, A. H. AU - Tobola, F. AU - Sedee, N. AU - Havekes, M. AU - Punt, P. J. PY - 2013 DA - 2013// TI - Pichia anomala 29X: a resistant strainfor lignocellulosic biomass hydrolysate fermentation JO - FEMS Yeast Res VL - 13 UR - https://doi.org/10.1111/1567-1364.12062 DO - 10.1111/1567-1364.12062 ID - Zha2013 ER - TY - JOUR AU - Fredlund, E. AU - Blank, L. M. AU - Schnürer, J. AU - Sauer, U. AU - Passoth, V. PY - 2004 DA - 2004// TI - Oxygen- and glucose-dependent regulation of centralcarbon metabolism in Pichia anomala JO - Appl Environ Microbiol VL - 70 UR - https://doi.org/10.1128/AEM.70.10.5905-5911.2004 DO - 10.1128/AEM.70.10.5905-5911.2004 ID - Fredlund2004 ER - TY - JOUR AU - Simpson, J. T. AU - Wong, K. AU - Jackman, S. D. AU - Schein, J. E. AU - Jones, S. J. M. AU - Birol, I. PY - 2009 DA - 2009// TI - ABySS : a parallel assembler for short read sequencedata JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.089532.108 DO - 10.1101/gr.089532.108 ID - Simpson2009 ER - TY - JOUR AU - Bankevich, A. AU - Nurk, S. AU - Antipov, D. AU - Gurevich, A. AU - Dvorkin, M. AU - Kulikov, A. S. AU - Lesin, V. M. AU - Nikolenko, S. I. AU - Pham, S. AU - Prjibelski, A. D. AU - Pyshkin, A. AU - Sirotkin, A. AU - Vyahhi, N. AU - Tesler, G. AU - Alekseyev, M. AU - Pevzner, P. PY - 2012 DA - 2012// TI - SPAdes: a new genome assembly algorithm and itsapplications to single-cell sequencing JO - J Comput Biol VL - 19 UR - https://doi.org/10.1089/cmb.2012.0021 DO - 10.1089/cmb.2012.0021 ID - Bankevich2012 ER - TY - JOUR AU - Zerbino, D. R. AU - Birney, E. PY - 2008 DA - 2008// TI - Velvet: algorithms for de novo short read assemblyusing de Bruijn graphs JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.074492.107 DO - 10.1101/gr.074492.107 ID - Zerbino2008 ER - TY - JOUR AU - Gurevich, A. AU - Saveliev, V. AU - Vyahhi, N. AU - Tesler, G. PY - 2013 DA - 2013// TI - QUAST: quality assessment tool for genomeassemblies JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt086 DO - 10.1093/bioinformatics/btt086 ID - Gurevich2013 ER - TY - JOUR AU - Trapnell, C. AU - Roberts, A. AU - Goff, L. AU - Pertea, G. AU - Kim, D. AU - Kelley, D. R. AU - Pimentel, H. AU - Salzberg, S. L. AU - Rinn, J. L. AU - Pachter, L. PY - 2012 DA - 2012// TI - Differential gene and transcript expression analysisof RNA-seq experiments with TopHat and Cufflinks JO - Nat Protoc VL - 7 UR - https://doi.org/10.1038/nprot.2012.016 DO - 10.1038/nprot.2012.016 ID - Trapnell2012 ER - TY - JOUR AU - Supek, F. AU - Bošnjak, M. AU - Škunca, N. AU - Šmuc, T. PY - 2011 DA - 2011// TI - Revigo summarizes and visualizes long lists of geneontology terms JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0021800 DO - 10.1371/journal.pone.0021800 ID - Supek2011 ER - TY - JOUR AU - Fernandes, A. R. AU - Sá-Correia, I. PY - 2001 DA - 2001// TI - The activity of plasma membraneH+-ATPase is strongly stimulated duringSaccharomyces cerevisiae adaptationto growth under high copper stress, accompanying intracellularacidification JO - Yeast VL - 18 UR - https://doi.org/10.1002/yea.702 DO - 10.1002/yea.702 ID - Fernandes2001 ER - TY - JOUR AU - Viegas, C. AU - Almeida, P. F. AU - Cavaco, M. AU - Sá-Correia, I. PY - 1998 DA - 1998// TI - The H+-ATPase in theplasma membrane of Saccharomycescerevisiae is activated during growth latency in octanoicacid-supplemented medium accompanying the decrease in intracellular pH andcell viability JO - Appl Environ Microbiol VL - 64 ID - Viegas1998 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: multiple sequence alignment with highaccuracy and high throughput JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh340 DO - 10.1093/nar/gkh340 ID - Edgar2004 ER - TY - JOUR AU - Waterhouse, A. M. AU - Procter, J. B. AU - Martin, D. M. AU - Clamp, M. AU - Barton, G. J. PY - 2009 DA - 2009// TI - Jalview Version 2-A multiple sequence alignmenteditor and analysis workbench JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp033 DO - 10.1093/bioinformatics/btp033 ID - Waterhouse2009 ER - TY - JOUR AU - Portillo, F. AU - Eraso, P. AU - Serrano, R. PY - 1991 DA - 1991// TI - Analysis of the regulatory domain of yeast plasmamembrane H+-ATPase by directed mutagenesis andintragenic suppression JO - FEBS Lett VL - 287 UR - https://doi.org/10.1016/0014-5793(91)80018-X DO - 10.1016/0014-5793(91)80018-X ID - Portillo1991 ER - TY - JOUR AU - Goossens, A. AU - Fuente, N. AU - Forment, J. AU - Serrano, R. AU - Portillo, F. PY - 2000 DA - 2000// TI - Regulation of yeast H(+)-ATPase by protein kinasesbelonging to a family dedicated to activation of plasma membranetransporters JO - Mol Cell Biol VL - 20 UR - https://doi.org/10.1128/MCB.20.20.7654-7661.2000 DO - 10.1128/MCB.20.20.7654-7661.2000 ID - Goossens2000 ER - TY - JOUR AU - Okuda, S. AU - Yamada, T. AU - Hamajima, M. AU - Itoh, M. AU - Katayama, T. AU - Bork, P. AU - Goto, S. AU - Kanehisa, M. PY - 2008 DA - 2008// TI - KEGG Atlas mapping for global analysis of metabolicpathways JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkn282 DO - 10.1093/nar/gkn282 ID - Okuda2008 ER - TY - JOUR AU - Yamashita, T. AU - Nakamaru-Ogiso, E. AU - Miyoshi, H. AU - Matsuno-Yagi, A. AU - Yagi, T. PY - 2007 DA - 2007// TI - Roles of bound quinone in the single subunitNADH-quinone oxidoreductase (Ndi1) from Saccharomyces cerevisiae JO - J Biol Chem VL - 282 UR - https://doi.org/10.1074/jbc.M610646200 DO - 10.1074/jbc.M610646200 ID - Yamashita2007 ER - TY - JOUR AU - Ruyters, S. AU - Mukherjee, V. AU - Verstrepen, K. J. AU - Thevelein, J. M. AU - Willems, K. A. AU - Lievens, B. PY - 2014 DA - 2014// TI - Assessing the potential of wild yeasts forbioethanol production JO - J Ind Microbiol Biotechnol VL - 42 UR - https://doi.org/10.1007/s10295-014-1544-y DO - 10.1007/s10295-014-1544-y ID - Ruyters2014 ER - TY - JOUR AU - Piper, P. AU - Calderon, C. O. AU - Hatzixanthis, K. AU - Mollapour, M. PY - 2001 DA - 2001// TI - Weak acid adaptation: the stress response thatconfers yeasts with resistance to organic acid foodpreservatives JO - Microbiology VL - 147 UR - https://doi.org/10.1099/00221287-147-10-2635 DO - 10.1099/00221287-147-10-2635 ID - Piper2001 ER - TY - JOUR AU - Morth, J. P. AU - Pedersen, B. P. AU - Buch-Pedersen, M. J. AU - Andersen, J. P. AU - Vilsen, B. AU - Palmgren, M. G. AU - Nissen, P. PY - 2011 DA - 2011// TI - A structural overview of the plasma membraneNa+, K+-ATPase andH+-ATPase ion pumps JO - Nat Rev Mol Cell Biol VL - 12 UR - https://doi.org/10.1038/nrm3031 DO - 10.1038/nrm3031 ID - Morth2011 ER - TY - JOUR AU - Eraso, P. AU - Gancedo, C. PY - 1987 DA - 1987// TI - Activation of yeast plasma membrane ATPase by acidpH during growth JO - FEBS Lett VL - 224 UR - https://doi.org/10.1016/0014-5793(87)80445-3 DO - 10.1016/0014-5793(87)80445-3 ID - Eraso1987 ER - TY - JOUR AU - Martínez-Muñoz, G. A. AU - Kane, P. PY - 2008 DA - 2008// TI - Vacuolar and plasma membrane proton pumpscollaborate to achieve cytosolic pH homeostasis in yeast JO - J Biol Chem VL - 283 UR - https://doi.org/10.1074/jbc.M710470200 DO - 10.1074/jbc.M710470200 ID - Martínez-Muñoz2008 ER - TY - JOUR AU - Ullah, A. AU - Chandrasekaran, G. AU - Brul, S. AU - Smits, G. J. PY - 2013 DA - 2013// TI - Yeast adaptation to weak acids prevents futileenergy expenditure JO - Front Microbiol VL - 4 UR - https://doi.org/10.3389/fmicb.2013.00142 DO - 10.3389/fmicb.2013.00142 ID - Ullah2013 ER - TY - CHAP AU - Alberts, B. AU - Johnson, A. AU - Lewis, J. AU - Raff, M. AU - Roberts, K. AU - Walter, P. ED - Alberts, B. ED - Johnson, A. ED - Lewis, J. ED - Raff, M. ED - Roberts, K. ED - Walter, P. PY - 2002 DA - 2002// TI - Electron-transport chains and their protonpumps BT - Molecular biology of the cell PB - Garland Science CY - New York ID - Alberts2002 ER - TY - JOUR AU - Zhou, J. AU - Liu, L. AU - Chen, J. PY - 2011 DA - 2011// TI - Improved ATP supply enhances acid tolerance ofCandida glabrata during pyruvic acidproduction JO - J Appl Microbiol VL - 110 UR - https://doi.org/10.1111/j.1365-2672.2010.04865.x DO - 10.1111/j.1365-2672.2010.04865.x ID - Zhou2011 ER - TY - JOUR AU - Kok, S. AU - Yilmaz, D. AU - Daran, J. M. AU - Pronk, J. T. AU - Maris, A. J. A. PY - 2012 DA - 2012// TI - In vivo analysis of Saccharomyces cerevisiae plasma membrane ATPase Pma1pisoforms with increased in vitro H+/ATP stoichiometry JO - Int J Gen Mol Microbiol VL - 102 ID - Kok2012 ER - TY - JOUR AU - Marcet-Houben, M. AU - Marceddu, G. AU - Gabaldón, T. PY - 2009 DA - 2009// TI - Phylogenomics of the oxidative phosphorylation infungi reveals extensive gene duplication followed by functionaldivergence JO - BMC Evol Biol VL - 9 UR - https://doi.org/10.1186/1471-2148-9-295 DO - 10.1186/1471-2148-9-295 ID - Marcet-Houben2009 ER - TY - CHAP AU - Papa, S. AU - Petruzzella, V. AU - Scacco, S. ED - Lajtha, A. ED - Dienel, G. ED - Gibson, G. PY - 2007 DA - 2007// TI - Electron transport, structure, redox-coupledprotonmotive activity and pathological disorders of respiratory chaincomplexes BT - Handbook of neurochemistry and molecular neurobiology PB - Springer CY - Berlin Heidelberg UR - https://doi.org/10.1007/978-0-387-30411-3_5 DO - 10.1007/978-0-387-30411-3_5 ID - Papa2007 ER - TY - JOUR AU - Chen, A. K. L. AU - Gelling, C. AU - Rogers, P. L. AU - Dawes, I. W. AU - Rosche, B. PY - 2009 DA - 2009// TI - Response of Saccharomycescerevisiae to stress-free acidification JO - J Microbiol VL - 47 UR - https://doi.org/10.1007/s12275-008-0167-2 DO - 10.1007/s12275-008-0167-2 ID - Chen2009 ER - TY - JOUR AU - Claret, S. AU - Gatti, X. AU - Thoraval, D. AU - Crouzet, M. PY - 2005 DA - 2005// TI - The Rgd1p Rho GTPase-activating protein and theMid2p cell wall sensor are required at low pH for protein kinase C pathwayactivation and cell survival in Saccharomycescerevisiae JO - Eukaryot Cell VL - 4 UR - https://doi.org/10.1128/EC.4.8.1375-1386.2005 DO - 10.1128/EC.4.8.1375-1386.2005 ID - Claret2005 ER - TY - JOUR AU - Aguilera, F. AU - Peinado, R. AU - Millán, C. AU - Ortega, J. M. AU - Mauricio, J. C. PY - 2006 DA - 2006// TI - Relationship between ethanol tolerance,H+-ATPase activity and the lipid compositionof the plasma membrane in different wine yeast strains JO - Int J Food Microbiol VL - 110 UR - https://doi.org/10.1016/j.ijfoodmicro.2006.02.002 DO - 10.1016/j.ijfoodmicro.2006.02.002 ID - Aguilera2006 ER - TY - JOUR AU - Fujita, S. AU - Senda, Y. AU - Nakaguchi, S. AU - Hashimoto, T. PY - 2001 DA - 2001// TI - Multiplex PCR using internal transcribed spacer 1and 2 regions for rapid detection and identification of yeaststrains JO - J Clin Microbiol VL - 39 UR - https://doi.org/10.1128/JCM.39.10.3617-3622.2001 DO - 10.1128/JCM.39.10.3617-3622.2001 ID - Fujita2001 ER - TY - JOUR AU - Löoke, M. AU - Kristjuahan, K. AU - Kristjuhan, A. PY - 2011 DA - 2011// TI - Extraction of genomic DNA from yeasts for PCR-basedapplications JO - Biotechniques VL - 50 ID - Löoke2011 ER - TY - JOUR AU - Bolger, A. M. AU - Lohse, M. AU - Usadel, B. PY - 2014 DA - 2014// TI - Trimmomatic: a flexible trimmer for Illuminasequence data JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu170 DO - 10.1093/bioinformatics/btu170 ID - Bolger2014 ER - TY - JOUR AU - Haridas, S. AU - Breuill, C. AU - Bohlmann, J. AU - Hsiang, T. PY - 2011 DA - 2011// TI - A biologist’s guide to de novo genome assembly usingnext-generation sequence data: a test with fungal genomes JO - J Microbiol Methods VL - 86 UR - https://doi.org/10.1016/j.mimet.2011.06.019 DO - 10.1016/j.mimet.2011.06.019 ID - Haridas2011 ER - TY - JOUR AU - Falcon, S. AU - Gentleman, R. PY - 2007 DA - 2007// TI - Using GOstats to test gene lists for GO termassociation JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btl567 DO - 10.1093/bioinformatics/btl567 ID - Falcon2007 ER - TY - JOUR AU - Altschup, S. F. AU - Science, C. AU - Pennsylvania, T. AU - University, S. AU - Park, U. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - J Mol Biol VL - 215 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschup1990 ER - TY - JOUR AU - Cole, C. AU - Barber, J. D. AU - Barton, G. J. PY - 2008 DA - 2008// TI - The Jpred 3 secondary structure predictionserver JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkn238 DO - 10.1093/nar/gkn238 ID - Cole2008 ER - TY - JOUR AU - Cuff, J. AU - Barton, G. J. PY - 2000 DA - 2000// TI - Application of multiple sequence alignment profilesto improve protein secondary structure prediction JO - Proteins VL - 40 UR - https://doi.org/3.0.CO;2-Q DO - 3.0.CO;2-Q ID - Cuff2000 ER - TY - JOUR AU - Peng, J. AU - Xu, J. PY - 2011 DA - 2011// TI - RaptorX: exploiting structure information forprotein alignment by statistical inference JO - Proteins VL - 79 UR - https://doi.org/10.1002/prot.23175 DO - 10.1002/prot.23175 ID - Peng2011 ER -