TY - JOUR AU - Vasconcelos, B. AU - Teixeira, J. C. AU - Dragone, G. AU - Teixeira, J. A. PY - 2019 DA - 2019// TI - Oleaginous yeasts for sustainable lipid production–from biodiesel to surf boards, a wide range of “green” applications JO - Appl Microbiol Biotechnol VL - 103 UR - https://doi.org/10.1007/s00253-019-09742-x DO - 10.1007/s00253-019-09742-x ID - Vasconcelos2019 ER - TY - JOUR AU - Shi, S. AU - Zhao, H. PY - 2017 DA - 2017// TI - Metabolic engineering of oleaginous yeasts for production of fuels and chemicals JO - Front Microbiol VL - 8 UR - https://doi.org/10.3389/fmicb.2017.02185 DO - 10.3389/fmicb.2017.02185 ID - Shi2017 ER - TY - BOOK AU - Ratledge, C. PY - 2002 DA - 2002// TI - Regulation of lipid accumulation in oleaginous micro-organisms PB - Portland Press Limited CY - London UR - https://doi.org/10.1042/bst0301047 DO - 10.1042/bst0301047 ID - Ratledge2002 ER - TY - JOUR AU - Beopoulos, A. AU - Nicaud, J. -. M. AU - Gaillardin, C. PY - 2011 DA - 2011// TI - An overview of lipid metabolism in yeasts and its impact on biotechnological processes JO - Appl Microbiol Biotechnol VL - 90 UR - https://doi.org/10.1007/s00253-011-3212-8 DO - 10.1007/s00253-011-3212-8 ID - Beopoulos2011 ER - TY - JOUR AU - Ratledge, C. AU - Wynn, J. P. PY - 2002 DA - 2002// TI - The biochemistry and molecular biology of lipid accumulation in oleaginous microorganisms JO - Adv Appl Microbiol VL - 51 UR - https://doi.org/10.1016/S0065-2164(02)51000-5 DO - 10.1016/S0065-2164(02)51000-5 ID - Ratledge2002 ER - TY - JOUR AU - Ageitos, J. M. AU - Vallejo, J. A. AU - Veiga-Crespo, P. AU - Villa, T. G. PY - 2011 DA - 2011// TI - Oily yeasts as oleaginous cell factories JO - Appl Microbiol Biotechnol VL - 90 UR - https://doi.org/10.1007/s00253-011-3200-z DO - 10.1007/s00253-011-3200-z ID - Ageitos2011 ER - TY - JOUR AU - Chi, Z. AU - Zheng, Y. AU - Ma, J. AU - Chen, S. PY - 2011 DA - 2011// TI - Oleaginous yeast cryptococcus curvatus culture with dark fermentation hydrogen production effluent as feedstock for microbial lipid production JO - Int J Hydrogen Energy VL - 36 UR - https://doi.org/10.1016/j.ijhydene.2011.04.124 DO - 10.1016/j.ijhydene.2011.04.124 ID - Chi2011 ER - TY - JOUR AU - Ykema, A. AU - Verbree, E. C. AU - Kater, M. M. AU - Smit, H. PY - 1988 DA - 1988// TI - Optimization of lipid production in the oleaginous yeast apiotrichum curvatum in wheypermeate JO - Appl Microbiol Biotechnol VL - 29 ID - Ykema1988 ER - TY - JOUR AU - Zhou, W. AU - Gong, Z. AU - Zhang, L. AU - Liu, Y. AU - Yan, J. AU - Zhao, M. PY - 2017 DA - 2017// TI - Feasibility of lipid production from waste paper by the oleaginous yeast cryptococcus curvatus JO - BioResources VL - 12 UR - https://doi.org/10.15376/biores.12.3.5249-5263 DO - 10.15376/biores.12.3.5249-5263 ID - Zhou2017 ER - TY - JOUR AU - Annamalai, N. AU - Sivakumar, N. AU - Oleskowicz-Popiel, P. PY - 2018 DA - 2018// TI - Enhanced production of microbial lipids from waste office paper by the oleaginous yeast cryptococcus curvatus JO - Fuel VL - 217 UR - https://doi.org/10.1016/j.fuel.2017.12.108 DO - 10.1016/j.fuel.2017.12.108 ID - Annamalai2018 ER - TY - JOUR AU - Bracharz, F. AU - Beukhout, T. AU - Mehlmer, N. AU - Bru¨ck, T. PY - 2017 DA - 2017// TI - Opportunities and challenges in the development of cutaneotrichosporon oleaginosus atcc 20509 as a new cell factory for custom tailored microbial oils JO - Microbial Cell Factor VL - 16 UR - https://doi.org/10.1186/s12934-017-0791-9 DO - 10.1186/s12934-017-0791-9 ID - Bracharz2017 ER - TY - JOUR AU - Yaguchi, A. AU - Rives, D. AU - Blenner, M. PY - 2017 DA - 2017// TI - New kids on the block: emerging oleaginous yeast of biotechnological importance JO - AIMS Microbiol VL - 3 UR - https://doi.org/10.3934/microbiol.2017.2.227 DO - 10.3934/microbiol.2017.2.227 ID - Yaguchi2017 ER - TY - JOUR AU - Meesters, P. A. AU - Eggink, G. PY - 1996 DA - 1996// TI - Isolation and characterization of a δ-9 fatty acid desaturase gene from the oleaginous yeast cryptococcus curvatus cbs 570 JO - Yeast VL - 12 UR - https://doi.org/3.0.CO;2-O DO - 3.0.CO;2-O ID - Meesters1996 ER - TY - JOUR AU - Li, Y. AU - Zhao, Z. K. AU - Bai, F. PY - 2007 DA - 2007// TI - High-density cultivation of oleaginous yeast rhodosporidium toruloides y4 in fed-batch culture JO - Enzyme Microbial technology VL - 41 UR - https://doi.org/10.1016/j.enzmictec.2007.02.008 DO - 10.1016/j.enzmictec.2007.02.008 ID - Li2007 ER - TY - JOUR AU - Meng, X. AU - Yang, J. AU - Xu, X. AU - Zhang, L. AU - Nie, Q. AU - Xian, M. PY - 2009 DA - 2009// TI - Biodiesel production from oleaginous microorganisms JO - Renewable Energy VL - 34 UR - https://doi.org/10.1016/j.renene.2008.04.014 DO - 10.1016/j.renene.2008.04.014 ID - Meng2009 ER - TY - JOUR AU - Wu, S. AU - Zhao, X. AU - Shen, H. AU - Wang, Q. AU - Zhao, Z. K. PY - 2011 DA - 2011// TI - Microbial lipid production by rhodosporidium toruloides under sulfate-limited conditions JO - Biores Technol VL - 102 UR - https://doi.org/10.1016/j.biortech.2010.09.033 DO - 10.1016/j.biortech.2010.09.033 ID - Wu2011 ER - TY - JOUR AU - Liu, J. AU - Huang, X. AU - Chen, R. AU - Yuan, M. AU - Liu, J. PY - 2017 DA - 2017// TI - Efficient bioconversion of high-content volatile fatty acids into microbial lipids by cryptococcus curvatus atcc 20509 JO - Biores Technol VL - 239 UR - https://doi.org/10.1016/j.biortech.2017.04.070 DO - 10.1016/j.biortech.2017.04.070 ID - Liu2017 ER - TY - JOUR AU - Liang, Y. AU - Cui, Y. AU - Trushenski, J. AU - Blackburn, J. W. PY - 2010 DA - 2010// TI - Converting crude glycerol derived from yellow grease to lipids through yeast fermentation JO - Biores Technol VL - 101 UR - https://doi.org/10.1016/j.biortech.2010.04.061 DO - 10.1016/j.biortech.2010.04.061 ID - Liang2010 ER - TY - JOUR AU - Liu, X. -. Z. AU - Wang, Q. -. M. AU - G¨oker, M. AU - Groenewald, M. AU - Kachalkin, A. AU - Lumbsch, H. T. AU - Millanes, A. AU - Wedin, M. AU - Yurkov, A. AU - Boekhout, T. PY - 2015 DA - 2015// TI - Towards an integrated phylogenetic classification of the tremellomycetes JO - Stud Mycol VL - 81 UR - https://doi.org/10.1016/j.simyco.2015.12.001 DO - 10.1016/j.simyco.2015.12.001 ID - Liu2015 ER - TY - JOUR AU - Fell, J. W. AU - Boekhout, T. AU - Fonseca, A. AU - Scorzetti, G. AU - Statzell-Tallman, A. PY - 2000 DA - 2000// TI - Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rdna d1/d2 domain sequence analysis JO - Int J Syst Evol Microbiol VL - 50 UR - https://doi.org/10.1099/00207713-50-3-1351 DO - 10.1099/00207713-50-3-1351 ID - Fell2000 ER - TY - JOUR AU - Gujjari, P. AU - Suh, S. -. O. AU - Coumes, K. AU - Zhou, J. J. PY - 2011 DA - 2011// TI - Characterization of oleaginous yeasts revealed two novel species: Trichosporon cacaoliposimilis sp. nov. and trichosporon oleaginosus sp. nov. JO - Mycologia VL - 103 UR - https://doi.org/10.3852/10-403 DO - 10.3852/10-403 ID - Gujjari2011 ER - TY - JOUR AU - Evans, C. T. AU - Ratledge, C. PY - 1983 DA - 1983// TI - A comparison of the oleaginous yeast, candida curvata, grown on different carbon sources in continuous and batch culture JO - Lipids VL - 18 UR - https://doi.org/10.1007/BF02534673 DO - 10.1007/BF02534673 ID - Evans1983 ER - TY - JOUR AU - Evans, C. T. AU - Ratledge, C. PY - 1984 DA - 1984// TI - Induction of xylulose-5-phosphate phosphoketolase in a variety of yeasts grown on d-xylose: the key to efficient xylose metabolism JO - Arch Microbiol VL - 139 UR - https://doi.org/10.1007/BF00692711 DO - 10.1007/BF00692711 ID - Evans1984 ER - TY - JOUR AU - Huang, X. -. F. AU - Wang, Y. -. H. AU - Shen, Y. AU - Peng, K. -. M. AU - Lu, L. -. J. AU - Liu, J. PY - 2019 DA - 2019// TI - Using non-ionic surfactant as an accelerator to increase extracellular lipid production by oleaginous yeast cryptococcus curvatus mucl 29819 JO - Biores Technol VL - 274 UR - https://doi.org/10.1016/j.biortech.2018.11.100 DO - 10.1016/j.biortech.2018.11.100 ID - Huang2019 ER - TY - JOUR AU - Awad, D. AU - Bohnen, F. AU - Mehlmer, N. AU - Brueck, T. PY - 2019 DA - 2019// TI - Multi-factorial-guided media optimization for enhanced biomass and lipid formation by the oleaginous yeast cutaneotrichosporon oleaginosus JO - Front Bioeng Biotechnol VL - 7 UR - https://doi.org/10.3389/fbioe.2019.00054 DO - 10.3389/fbioe.2019.00054 ID - Awad2019 ER - TY - JOUR AU - G¨orner, C. AU - Redai, V. AU - Bracharz, F. AU - Schrepfer, P. AU - Garbe, D. AU - Bru¨ck, T. PY - 2016 DA - 2016// TI - Genetic engineering and production of modified fatty acids by the non-conventional oleaginous yeast trichosporon oleaginosus atcc 20509 JO - Green Chem VL - 18 UR - https://doi.org/10.1039/C5GC01767J DO - 10.1039/C5GC01767J ID - G¨orner2016 ER - TY - JOUR AU - Reed, J. L. AU - Vo, T. D. AU - Schilling, C. H. AU - Palsson, B. O. PY - 2003 DA - 2003// TI - An expanded genome-scale model of escherichia coli k-12 (i jr904 gsm/gpr) JO - Genome Biol VL - 4 UR - https://doi.org/10.1186/gb-2003-4-9-r54 DO - 10.1186/gb-2003-4-9-r54 ID - Reed2003 ER - TY - JOUR AU - Close, D. AU - Ojumu, J. PY - 2016 DA - 2016// TI - Draft genome sequence of the oleaginous yeast Cryptococcus curvatus atcc 20509 JO - Genome Announc VL - 4 ID - Close2016 ER - TY - JOUR AU - Hoff, K. J. AU - Lange, S. AU - Lomsadze, A. AU - Borodovsky, M. AU - Stanke, M. PY - 2015 DA - 2015// TI - Braker1: unsupervised rna-seq-based genome annotation with genemark-et and augustus JO - Bioinformatics VL - 32 UR - https://doi.org/10.1093/bioinformatics/btv661 DO - 10.1093/bioinformatics/btv661 ID - Hoff2015 ER - TY - JOUR AU - Tehlivets, O. AU - Scheuringer, K. AU - Kohlwein, S. D. PY - 2007 DA - 2007// TI - Fatty acid synthesis and elongation in yeast JO - Biochimica et Biophy Acta Mol Cell Biol Lipids VL - 1771 ID - Tehlivets2007 ER - TY - JOUR AU - Klug, L. AU - Daum, G. PY - 2014 DA - 2014// TI - Yeast lipid metabolism at a glance JO - FEMS Yeast Res VL - 14 UR - https://doi.org/10.1111/1567-1364.12141 DO - 10.1111/1567-1364.12141 ID - Klug2014 ER - TY - JOUR AU - Fakas, S. PY - 2017 DA - 2017// TI - Lipid biosynthesis in yeasts: A comparison of the lipid biosynthetic pathway between the model nonoleaginous yeast saccharomyces cerevisiae and the model oleaginous yeast yarrowia lipolytica JO - Eng Life Sci VL - 17 UR - https://doi.org/10.1002/elsc.201600040 DO - 10.1002/elsc.201600040 ID - Fakas2017 ER - TY - JOUR AU - Garba, L. AU - Shukuri Mo, M. AU - Nurbaya Os, S. AU - Noor Zalih, R. PY - 2017 DA - 2017// TI - Review on fatty acid desaturases and their roles in temperature acclimatisation JO - J Appl Sci VL - 17 UR - https://doi.org/10.3923/jas.2017.282.295 DO - 10.3923/jas.2017.282.295 ID - Garba2017 ER - TY - JOUR AU - Rismani-Yazdi, H. AU - Haznedaroglu, B. Z. AU - Bibby, K. AU - Peccia, J. PY - 2011 DA - 2011// TI - Transcriptome sequencing and annotation of the microalgae dunaliella tertiolecta: pathway description and gene discovery for production of next-generation biofuels JO - BMC Genom VL - 12 UR - https://doi.org/10.1186/1471-2164-12-148 DO - 10.1186/1471-2164-12-148 ID - Rismani-Yazdi2011 ER - TY - JOUR AU - Capusoni, C. AU - Rodighiero, V. AU - Cucchetti, D. AU - Galafassi, S. AU - Bianchi, D. AU - Franzosi, G. AU - Compagno, C. PY - 2017 DA - 2017// TI - Characterization of lipid accumulation and lipidome analysis in the oleaginous yeasts rhodosporidium azoricum and trichosporon oleaginosus JO - Biores Technol VL - 238 UR - https://doi.org/10.1016/j.biortech.2017.03.188 DO - 10.1016/j.biortech.2017.03.188 ID - Capusoni2017 ER - TY - JOUR AU - Carman, G. M. AU - Kersting, M. C. PY - 2004 DA - 2004// TI - Phospholipid synthesis in yeast: regulation by phosphorylation JO - Biochem Cell Biol VL - 82 UR - https://doi.org/10.1139/o03-064 DO - 10.1139/o03-064 ID - Carman2004 ER - TY - JOUR AU - Loira, N. AU - Dulermo, T. AU - Nicaud, J. -. M. AU - Sherman, D. J. PY - 2012 DA - 2012// TI - A genome-scale metabolic model of the lipid-accumulating yeast yarrowia lipolytica JO - BMC Syst Biol VL - 6 UR - https://doi.org/10.1186/1752-0509-6-35 DO - 10.1186/1752-0509-6-35 ID - Loira2012 ER - TY - JOUR AU - Berg, M. A. AU - Jong-Gubbels, P. AU - Kortland, C. J. AU - Dijken, J. P. AU - Pronk, J. T. AU - Steensma, H. Y. PY - 1996 DA - 1996// TI - The two acetyl-coenzyme a synthetases of saccharomyces cerevisiae differ with respect to kinetic properties and transcriptional regulation JO - J Biol Chem VL - 271 UR - https://doi.org/10.1074/jbc.271.46.28953 DO - 10.1074/jbc.271.46.28953 ID - Berg1996 ER - TY - JOUR AU - Chan, S. H. AU - Cai, J. AU - Wang, L. AU - Simons-Senftle, M. N. AU - Maranas, C. D. PY - 2017 DA - 2017// TI - Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models JO - Bioinformatics VL - 33 UR - https://doi.org/10.1093/bioinformatics/btx453 DO - 10.1093/bioinformatics/btx453 ID - Chan2017 ER - TY - JOUR AU - Dikicioglu, D. AU - Kırdar, B. AU - Oliver, S. G. PY - 2015 DA - 2015// TI - Biomass composition: the “elephant in the room” of metabolic modelling JO - Metabolomics VL - 11 UR - https://doi.org/10.1007/s11306-015-0819-2 DO - 10.1007/s11306-015-0819-2 ID - Dikicioglu2015 ER - TY - JOUR AU - Tchakouteu, S. S. AU - Chatzifragkou, A. AU - Kalantzi, O. AU - Koutinas, A. A. AU - Aggelis, G. AU - Papanikolaou, S. PY - 2015 DA - 2015// TI - Oleaginous yeast cryptococcus curvatus exhibits interplay between biosynthesis of intracellular sugars and lipids JO - Eur J Lipid Sci Technol VL - 117 UR - https://doi.org/10.1002/ejlt.201400347 DO - 10.1002/ejlt.201400347 ID - Tchakouteu2015 ER - TY - STD TI - Meeuwse P. Production of Fungal Lipids: Kinetic Modeling and Process Design. 2011 ID - ref42 ER - TY - STD TI - Yang Y, Sha M. A beginner’s guide to bioprocess modes–batch, fed-batch, and continuous fermentation. Technical report, Eppendorf Application Note. 2019 ID - ref43 ER - TY - JOUR AU - Meesters, P. AU - Huijberts, G. AU - Eggink, G. PY - 1996 DA - 1996// TI - High-cell-density cultivation of the lipid accumulating yeast cryptococcus curvatus using glycerol as a carbon source JO - Appl Microbiol Biotechnol VL - 45 UR - https://doi.org/10.1007/s002530050731 DO - 10.1007/s002530050731 ID - Meesters1996 ER - TY - JOUR AU - Yu, X. AU - Zheng, Y. AU - Xiong, X. AU - Chen, S. PY - 2014 DA - 2014// TI - Co-utilization of glucose, xylose and cellobiose by the oleaginous yeast cryptococcus curvatus JO - Biomass Bioenerg VL - 71 UR - https://doi.org/10.1016/j.biombioe.2014.09.023 DO - 10.1016/j.biombioe.2014.09.023 ID - Yu2014 ER - TY - JOUR AU - Ykema, A. AU - Verbree, E. AU - Verseveld, H. AU - Smit, H. PY - 1986 DA - 1986// TI - Mathematical modelling of lipid production by oleaginous yeasts in continuous cultures JO - Antonie Van Leeuwenhoek VL - 52 UR - https://doi.org/10.1007/BF00423410 DO - 10.1007/BF00423410 ID - Ykema1986 ER - TY - JOUR AU - Botham, P. A. AU - Ratledge, C. PY - 1979 DA - 1979// TI - A biochemical explanation for lipid accumulation in candida 107 and other oleaginous micro-organisms JO - Microbiology VL - 114 ID - Botham1979 ER - TY - JOUR AU - Evans, C. T. AU - Scragg, A. H. AU - Ratledge, C. PY - 1983 DA - 1983// TI - Regulation of citrate efflux from mitochondria oleaginous and non-oleaginous yeasts by adenine nucleotides JO - Eur J Biochem VL - 132 UR - https://doi.org/10.1111/j.1432-1033.1983.tb07407.x DO - 10.1111/j.1432-1033.1983.tb07407.x ID - Evans1983 ER - TY - JOUR AU - Zhang, H. AU - Zhang, L. AU - Chen, H. AU - Chen, Y. Q. AU - Chen, W. AU - Song, Y. AU - Ratledge, C. PY - 2014 DA - 2014// TI - Enhanced lipid accumulation in the yeast yarrowia lipolytica by over-expression of atp: citrate lyase from mus musculus JO - J Biotechnol VL - 192 UR - https://doi.org/10.1016/j.jbiotec.2014.10.004 DO - 10.1016/j.jbiotec.2014.10.004 ID - Zhang2014 ER - TY - JOUR AU - Kerkhoven, E. J. AU - Pomraning, K. R. AU - Baker, S. E. AU - Nielsen, J. PY - 2016 DA - 2016// TI - Regulation of amino-acid metabolism controls flux to lipid accumulation in yarrowia lipolytica JO - NPJ Syst Biol Appl VL - 2 UR - https://doi.org/10.1038/npjsba.2016.5 DO - 10.1038/npjsba.2016.5 ID - Kerkhoven2016 ER - TY - JOUR AU - Huerlimann, R. AU - Steinig, E. J. AU - Loxton, H. AU - Zenger, K. R. AU - Jerry, D. R. AU - Heimann, K. PY - 2014 DA - 2014// TI - The effect of nitrogen limitation on acetyl-coa carboxylase expression and fatty acid content in chromera velia and isochrysis aff. galbana (tiso) JO - Gene VL - 543 UR - https://doi.org/10.1016/j.gene.2014.04.022 DO - 10.1016/j.gene.2014.04.022 ID - Huerlimann2014 ER - TY - JOUR AU - Kourist, R. AU - Bracharz, F. AU - Lorenzen, J. AU - Kracht, O. N. AU - Chovatia, M. AU - Daum, C. AU - Deshpande, S. AU - Lipzen, A. AU - Nolan, M. AU - Ohm, R. A. PY - 2015 DA - 2015// TI - Genomics and transcriptomics analyses of the oil-accumulating basidiomycete yeast trichosporon oleaginosus: insights into substrate utilization and alternative evolutionary trajectories of fungal mating systems JO - MBio VL - 6 UR - https://doi.org/10.1128/mBio.00918-15 DO - 10.1128/mBio.00918-15 ID - Kourist2015 ER - TY - JOUR AU - Fell, D. A. AU - Thomas, S. PY - 1995 DA - 1995// TI - Physiological control of metabolic flux: the requirement for multisite modulation JO - Biochem J VL - 311 UR - https://doi.org/10.1042/bj3110035 DO - 10.1042/bj3110035 ID - Fell1995 ER - TY - JOUR AU - Pfitzner, A. AU - Kubicek, C. AU - R¨ohr, M. PY - 1987 DA - 1987// TI - Presence and regulation of atp: citrate lyase from the citric acid producing fungus aspergillus niger JO - Archive Microbiol VL - 147 UR - https://doi.org/10.1007/BF00492910 DO - 10.1007/BF00492910 ID - Pfitzner1987 ER - TY - JOUR AU - Potapova, I. A. AU - El-Maghrabi, M. R. AU - Doronin, S. V. AU - Benjamin, W. B. PY - 2000 DA - 2000// TI - Phosphorylation of recombinant human atp: citrate lyase by camp-dependent protein kinase abolishes homotropic allosteric regulation of the enzyme by citrate and increases the enzyme activity. allosteric activation of atp: citrate lyase by phosphorylated sugars JO - Biochemistry VL - 39 UR - https://doi.org/10.1021/bi992159y DO - 10.1021/bi992159y ID - Potapova2000 ER - TY - JOUR AU - Moon, N. J. AU - Hammond, E. AU - Glatz, B. A. PY - 1978 DA - 1978// TI - Conversion of cheese whey and whey permeate to oil and single-cell protein1 JO - J Dairy Sci VL - 61 UR - https://doi.org/10.3168/jds.S0022-0302(78)83762-X DO - 10.3168/jds.S0022-0302(78)83762-X ID - Moon1978 ER - TY - JOUR AU - Dobin, A. AU - Davis, C. A. AU - Schlesinger, F. AU - Drenkow, J. AU - Zaleski, C. AU - Jha, S. AU - Batut, P. AU - Chaisson, M. AU - Gingeras, T. R. PY - 2013 DA - 2013// TI - Star: ultrafast universal rna-seq aligner JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts635 DO - 10.1093/bioinformatics/bts635 ID - Dobin2013 ER - TY - JOUR AU - Love, M. I. AU - Huber, W. AU - Anders, S. PY - 2014 DA - 2014// TI - Moderated estimation of fold change and dispersion for rna-seq data with deseq2 JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0550-8 DO - 10.1186/s13059-014-0550-8 ID - Love2014 ER - TY - JOUR AU - Kim, D. AU - Langmead, B. AU - Salzberg, S. L. PY - 2015 DA - 2015// TI - Hisat: a fast spliced aligner with low memory requirements JO - Nat Methods VL - 12 UR - https://doi.org/10.1038/nmeth.3317 DO - 10.1038/nmeth.3317 ID - Kim2015 ER - TY - JOUR AU - Koehorst, J. J. AU - Dam, J. C. AU - Saccenti, E. AU - Martins Santos, V. A. AU - Suarez-Diez, M. AU - Schaap, P. J. PY - 2017 DA - 2017// TI - Sapp: functional genome annotation and analysis through a semantic framework using fair principles JO - Bioinformatics VL - 34 UR - https://doi.org/10.1093/bioinformatics/btx767 DO - 10.1093/bioinformatics/btx767 ID - Koehorst2017 ER - TY - JOUR AU - Dam, J. C. AU - Koehorst, J. J. AU - Vik, J. O. AU - Santos, V. A. M. AU - Schaap, P. J. AU - Suarez-Diez, M. PY - 2019 DA - 2019// TI - The empusa code generator and its application to gbol, an extendable ontology for genome annotation JO - Scientific data VL - 6 ID - Dam2019 ER - TY - JOUR AU - Zdobnov, E. M. AU - Apweiler, R. PY - 2001 DA - 2001// TI - Interproscan–an integration platform for the signature-recognition methods in interpro JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.9.847 DO - 10.1093/bioinformatics/17.9.847 ID - Zdobnov2001 ER - TY - JOUR AU - Nguyen, N. -. N. AU - Srihari, S. AU - Leong, H. W. AU - Chong, K. -. F. PY - 2015 DA - 2015// TI - Enzdp: Improved enzyme annotation for metabolic network reconstruction based on domain composition profiles JO - J Bioinformat Comput Biol VL - 13 UR - https://doi.org/10.1142/S0219720015430039 DO - 10.1142/S0219720015430039 ID - Nguyen2015 ER - TY - STD TI - Matlab. Version R2015b. The MathWorks Inc., Natick, Massachusetts. 2015 ID - ref64 ER - TY - JOUR AU - Heirendt, L. AU - Arreckx, S. AU - Pfau, T. AU - Mendoza, S. N. AU - Richelle, A. AU - Heinken, A. AU - Haraldsdottir, H. S. AU - Wachowiak, J. AU - Keating, S. M. AU - Vlasov, V. PY - 2019 DA - 2019// TI - Creation and analysis of biochemical constraint-based models using the cobra toolbox v. 3.0 JO - Nat Protoc VL - 14 UR - https://doi.org/10.1038/s41596-018-0098-2 DO - 10.1038/s41596-018-0098-2 ID - Heirendt2019 ER - TY - STD TI - GLPK (GNU Linear Programming Kit). 2009. https://www.gnu.org/software/glpk/ UR - https://www.gnu.org/software/glpk/ ID - ref66 ER - TY - JOUR AU - Pan, P. AU - Hua, Q. PY - 2012 DA - 2012// TI - Reconstruction and in silico analysis of metabolic network for an oleaginous yeast, yarrowia lipolytica JO - PLoS ONE VL - 7 UR - https://doi.org/10.1371/journal.pone.0051535 DO - 10.1371/journal.pone.0051535 ID - Pan2012 ER - TY - JOUR AU - Kavˇsˇcek, M. AU - Bhutada, G. AU - Madl, T. AU - Natter, K. PY - 2015 DA - 2015// TI - Optimization of lipid production with a genome-scale model of yarrowia lipolytica JO - BMC Syst Biol VL - 9 UR - https://doi.org/10.1186/s12918-015-0217-4 DO - 10.1186/s12918-015-0217-4 ID - Kavˇsˇcek2015 ER - TY - JOUR AU - Mishra, P. AU - Lee, N. -. R. AU - Lakshmanan, M. AU - Kim, M. AU - Kim, B. -. G. AU - Lee, D. -. Y. PY - 2018 DA - 2018// TI - Genome-scale model-driven strain design for dicarboxylic acid production in yarrowia lipolytica JO - BMC Syst Biol VL - 12 UR - https://doi.org/10.1186/s12918-018-0542-5 DO - 10.1186/s12918-018-0542-5 ID - Mishra2018 ER - TY - JOUR AU - Nookaew, I. AU - Jewett, M. C. AU - Meechai, A. AU - Thammarongtham, C. AU - Laoteng, K. AU - Cheevadhanarak, S. AU - Nielsen, J. AU - Bhumiratana, S. PY - 2008 DA - 2008// TI - The genome-scale metabolic model iin800 of saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism JO - BMC Syst Biol VL - 2 UR - https://doi.org/10.1186/1752-0509-2-71 DO - 10.1186/1752-0509-2-71 ID - Nookaew2008 ER - TY - JOUR AU - Kanehisa, M. AU - Goto, S. PY - 2000 DA - 2000// TI - Kegg: kyoto encyclopedia of genes and genomes JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.27 DO - 10.1093/nar/28.1.27 ID - Kanehisa2000 ER - TY - JOUR AU - Teusink, B. AU - Passarge, J. AU - Reijenga, C. A. AU - Esgalhado, E. AU - Weijden, C. C. AU - Schepper, M. AU - Walsh, M. C. AU - Bakker, B. M. AU - Dam, K. AU - Westerhoff, H. V. PY - 2000 DA - 2000// TI - Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? testing biochemistry JO - Eur J Biochem VL - 267 UR - https://doi.org/10.1046/j.1432-1327.2000.01527.x DO - 10.1046/j.1432-1327.2000.01527.x ID - Teusink2000 ER - TY - JOUR AU - Raimundo, N. AU - Baysal, B. E. AU - Shadel, G. S. PY - 2011 DA - 2011// TI - Revisiting the tca cycle: signaling to tumor formation JO - Trends Mol Med VL - 17 UR - https://doi.org/10.1016/j.molmed.2011.06.001 DO - 10.1016/j.molmed.2011.06.001 ID - Raimundo2011 ER - TY - JOUR AU - Fritzemeier, C. J. AU - Hartleb, D. AU - Szappanos, B. AU - Papp, B. AU - Lercher, M. J. PY - 2017 DA - 2017// TI - Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal JO - PLoS Comput Biol VL - 13 UR - https://doi.org/10.1371/journal.pcbi.1005494 DO - 10.1371/journal.pcbi.1005494 ID - Fritzemeier2017 ER - TY - STD TI - Cooper GM, Hausman RE. The Cell: A Molecular Approach. 4th Edition. 2004 ID - ref75 ER - TY - JOUR AU - Schellenberger, J. AU - Que, R. AU - Fleming, R. M. AU - Thiele, I. AU - Orth, J. D. AU - Feist, A. M. AU - Zielinski, D. C. AU - Bordbar, A. AU - Lewis, N. E. AU - Rahmanian, S. PY - 2011 DA - 2011// TI - Quantitative prediction of cellular metabolism with constraint-based models: the cobra toolbox v2. 0 JO - Nat Prot VL - 6 UR - https://doi.org/10.1038/nprot.2011.308 DO - 10.1038/nprot.2011.308 ID - Schellenberger2011 ER - TY - JOUR AU - Schellenberger, J. AU - Palsson, B. Ø. PY - 2009 DA - 2009// TI - Use of randomized sampling for analysis of metabolic networks JO - J Biol Chem VL - 284 UR - https://doi.org/10.1074/jbc.R800048200 DO - 10.1074/jbc.R800048200 ID - Schellenberger2009 ER - TY - JOUR AU - Bordel, S. AU - Agren, R. AU - Nielsen, J. PY - 2010 DA - 2010// TI - Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes JO - PLoS Comput Biol VL - 6 UR - https://doi.org/10.1371/journal.pcbi.1000859 DO - 10.1371/journal.pcbi.1000859 ID - Bordel2010 ER - TY - JOUR AU - Chelliah, V. AU - Juty, N. AU - Ajmera, I. AU - Ali, R. AU - Dumousseau, M. AU - Glont, M. AU - Hucka, M. AU - Jalowicki, G. AU - Keating, S. AU - Knight-Schrijver, V. PY - 2015 DA - 2015// TI - Biomodels: ten-year anniversary JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1181 DO - 10.1093/nar/gku1181 ID - Chelliah2015 ER - TY - JOUR AU - Qiao, K. AU - Wasylenko, T. M. AU - Zhou, K. AU - Xu, P. AU - Stephanopoulos, G. PY - 2017 DA - 2017// TI - Lipid production in yarrowia lipolytica is maximized by engineering cytosolic redox metabolism JO - Nat Biotechnol VL - 35 UR - https://doi.org/10.1038/nbt.3763 DO - 10.1038/nbt.3763 ID - Qiao2017 ER - TY - JOUR AU - Papanikolaou, S. AU - Aggelis, G. PY - 2002 DA - 2002// TI - Lipid production by yarrowia lipolytica growing on industrial glycerol in a single-stage continuous culture JO - Biores Technol VL - 82 UR - https://doi.org/10.1016/S0960-8524(01)00149-3 DO - 10.1016/S0960-8524(01)00149-3 ID - Papanikolaou2002 ER - TY - JOUR AU - Fei, Q. AU - O’Brien, M. AU - Nelson, R. AU - Chen, X. AU - Lowell, A. AU - Dowe, N. PY - 2016 DA - 2016// TI - Enhanced lipid production by rhodosporidium toruloides using different fed-batch feeding strategies with lignocellulosic hydrolysate as the sole carbon source JO - Biotechnol Biofuels VL - 9 UR - https://doi.org/10.1186/s13068-016-0542-x DO - 10.1186/s13068-016-0542-x ID - Fei2016 ER - TY - JOUR AU - Johnson, V. W. AU - Singh, M. AU - Saini, V. S. AU - Adhikari, D. K. AU - Sista, V. AU - Yadav, N. K. PY - 1995 DA - 1995// TI - Utilization of molasses for the production of fat by an oleaginous yeast, rhodotorula glutinis iip-30 JO - J Ind Microbiol VL - 14 UR - https://doi.org/10.1007/BF01570057 DO - 10.1007/BF01570057 ID - Johnson1995 ER - TY - JOUR AU - Anschau, A. AU - Xavier, M. C. AU - Hernalsteens, S. AU - Franco, T. T. PY - 2014 DA - 2014// TI - Effect of feeding strategies on lipid production by lipomyces starkeyi JO - Biores Technol VL - 157 UR - https://doi.org/10.1016/j.biortech.2014.01.104 DO - 10.1016/j.biortech.2014.01.104 ID - Anschau2014 ER - TY - JOUR AU - Hassan, M. AU - Blanc, P. J. AU - Granger, L. -. M. AU - Pareilleux, A. AU - Goma, G. PY - 1993 DA - 1993// TI - Lipid production by an unsaturated fatty acid auxotroph of the oleaginous yeast apiotrichum curvatum grown in single-stage continuous culture JO - Appl Microbiol Biotechnol VL - 40 UR - https://doi.org/10.1007/BF00175735 DO - 10.1007/BF00175735 ID - Hassan1993 ER -