TY - STD TI - Sandmann G. Carotenoids of Biotechnological Importance. In: Biotechnology of Isoprenoids. Edited by Schrader J, Bohlmann J, vol. 148: New York: Springer International Publishing; 2015. p 449–67. ID - ref1 ER - TY - JOUR AU - Schmidt, I. AU - Schewe, H. AU - Gassel, S. AU - Jin, C. AU - Buckingham, J. AU - Hümbelin, M. AU - Sandmann, G. AU - Schrader, J. PY - 2011 DA - 2011// TI - Biotechnological production of astaxanthin with Phaffia rhodozyma/Xanthophyllomyces dendrorhous JO - Appl Microbiol Biotechnol VL - 89 UR - https://doi.org/10.1007/s00253-010-2976-6 DO - 10.1007/s00253-010-2976-6 ID - Schmidt2011 ER - TY - STD TI - Fell JW, Johnson EA. Phaffia M.W. Miller, Yoneyama & Soneda (1976). In: The yeasts: a taxonomic study. Kurtzman C, Fell JW, Boekhout T, editors. Amsterdam: Elsevier; 2011. p 1853–4. ID - ref3 ER - TY - JOUR AU - Ambati, R. R. AU - Phang, S. -. M. AU - Ravi, S. AU - Aswathanarayana, R. G. PY - 2014 DA - 2014// TI - Astaxanthin: sources, extraction, stability, biological activities and its commercial applications—a review JO - Mar Drugs VL - 12 UR - https://doi.org/10.3390/md12010128 DO - 10.3390/md12010128 ID - Ambati2014 ER - TY - JOUR AU - Schroeder, W. A. AU - Johnson, E. A. PY - 1995 DA - 1995// TI - Singlet oxygen and peroxyl radicals regulate carotenoid biosynthesis in Phaffia rhodozyma JO - J Biol Chem VL - 270 UR - https://doi.org/10.1074/jbc.270.31.18374 DO - 10.1074/jbc.270.31.18374 ID - Schroeder1995 ER - TY - JOUR AU - David‐Palma, M. AU - Libkind, D. AU - Sampaio, J. P. PY - 2014 DA - 2014// TI - Global distribution, diversity hot spots and niche transitions of an astaxanthin‐producing eukaryotic microbe JO - Mol Ecol VL - 23 UR - https://doi.org/10.1111/mec.12642 DO - 10.1111/mec.12642 ID - David‐Palma2014 ER - TY - JOUR AU - Libkind, D. AU - Tognetti, C. AU - Ruffini, A. AU - Sampaio, J. P. AU - Broock, M. PY - 2011 DA - 2011// TI - Xanthophyllomyces dendrorhous (Phaffia rhodozyma) on stromata of Cyttaria hariotii in northwestern Patagonian Nothofagus forests JO - Rev Argent Microbiol VL - 43 ID - Libkind2011 ER - TY - JOUR AU - Jinno, S. AU - Hata, K. AU - Shimidzu, N. AU - Okita, T. PY - 1998 DA - 1998// TI - Phaffiaol, a new antioxidant isolated from a yeast Phaffia rhodozym JO - J Antibiot VL - 51 UR - https://doi.org/10.7164/antibiotics.51.508 DO - 10.7164/antibiotics.51.508 ID - Jinno1998 ER - TY - JOUR AU - Libkind, D. AU - Moline, M. AU - Broock, M. PY - 2011 DA - 2011// TI - Production of the UVB‐absorbing compound mycosporine–glutaminol–glucoside by Xanthophyllomyces dendrorhous (Phaffia rhodozyma) JO - FEMS Yeast Res VL - 11 UR - https://doi.org/10.1111/j.1567-1364.2010.00688.x DO - 10.1111/j.1567-1364.2010.00688.x ID - Libkind2011 ER - TY - JOUR AU - Moliné, M. AU - Arbeloa, E. M. AU - Flores, M. R. AU - Libkind, D. AU - Farías, M. E. AU - Bertolotti, S. G. AU - Churio, M. S. AU - Broock, M. R. PY - 2011 DA - 2011// TI - UVB photoprotective role of mycosporines in yeast: photostability and antioxidant activity of mycosporine-glutaminol-glucoside JO - Radiat Res VL - 175 UR - https://doi.org/10.1667/RR2245.1 DO - 10.1667/RR2245.1 ID - Moliné2011 ER - TY - CHAP AU - Phaff, H. AU - Miller, M. AU - Yoneyama, M. AU - Soneda, M. PY - 1972 DA - 1972// TI - A comparative study of the yeast florae associated with trees on the Japanese islands and on the west coast of North America BT - Proceedings of the 4th IFS: Fermentation Technology Today Meeting Society of Fermentation Technology, Osaka, Japan ID - Phaff1972 ER - TY - JOUR AU - Golubev, V. AU - Bab’eva, I. AU - Blagodatskaya, V. AU - Reshetova, I. PY - 1977 DA - 1977// TI - Taxonomic study of yeasts isolated from spring sap flows of birch (Betula verrucosa Ehrh.) JO - Microbiology VL - 46 ID - Golubev1977 ER - TY - JOUR AU - Weber, R. W. AU - Davoli, P. AU - Anke, H. PY - 2006 DA - 2006// TI - A microbial consortium involving the astaxanthin producer Xanthophyllomyces dendrorhous on freshly cut birch stumps in Germany JO - Mycologist VL - 20 UR - https://doi.org/10.1016/j.mycol.2006.03.010 DO - 10.1016/j.mycol.2006.03.010 ID - Weber2006 ER - TY - JOUR AU - Libkind, D. AU - Moliné, M. AU - García, V. AU - Fontenla, S. AU - Broock, M. PY - 2008 DA - 2008// TI - Characterization of a novel South American population of the astaxanthin producing yeast Xanthophyllomyces dendrorhous (Phaffia rhodozyma) JO - Ind Microbiol Biotechnol VL - 35 UR - https://doi.org/10.1007/s10295-007-0275-8 DO - 10.1007/s10295-007-0275-8 ID - Libkind2008 ER - TY - STD TI - Kües U, James TY, Heitman J. 6 Mating Type in Basidiomycetes: Unipolar, Bipolar, and Tetrapolar Patterns of Sexuality. In: Evolution of fungi and fungal-like organisms. New York: Springer; 2011. p 97–160. ID - ref15 ER - TY - JOUR AU - Kucsera, J. AU - Pfeiffer, I. AU - Ferenczy, L. PY - 1998 DA - 1998// TI - Homothallic life cycle in the diploid red yeast Xanthophyllomyces dendrorhous (Phaffia rhodozyma) JO - Antonie Van Leeuwenhoek VL - 73 UR - https://doi.org/10.1023/A:1000699626367 DO - 10.1023/A:1000699626367 ID - Kucsera1998 ER - TY - JOUR AU - Golubev, W. I. PY - 1995 DA - 1995// TI - Perfect state of Rhodomyces dendrorhous (Phaffia rhodozyma) JO - Yeast VL - 11 UR - https://doi.org/10.1002/yea.320110202 DO - 10.1002/yea.320110202 ID - Golubev1995 ER - TY - JOUR AU - Fell, J. AU - Blatt, G. PY - 1999 DA - 1999// TI - Separation of strains of the yeasts Xanthophyllomyces dendrorhous and Phaffia rhodozyma based on rDNA IGS and ITS sequence analysis JO - J Ind Microbiol Biotechnol VL - 23 UR - https://doi.org/10.1038/sj.jim.2900681 DO - 10.1038/sj.jim.2900681 ID - Fell1999 ER - TY - JOUR AU - Libkind, D. AU - Ruffini, A. AU - Broock, M. AU - Alves, L. AU - Sampaio, J. P. PY - 2007 DA - 2007// TI - Biogeography, host specificity, and molecular phylogeny of the basidiomycetous yeast Phaffia rhodozyma and its sexual form, Xanthophyllomyces dendrorhous JO - Appl Environ Microbiol VL - 73 UR - https://doi.org/10.1128/AEM.01432-06 DO - 10.1128/AEM.01432-06 ID - Libkind2007 ER - TY - JOUR AU - Sharma, R. AU - Gassel, S. AU - Steiger, S. AU - Xia, X. AU - Bauer, R. AU - Sandmann, G. AU - Thines, M. PY - 2015 DA - 2015// TI - The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provides insights into the organization of its acetyl-CoA derived pathways and the evolution of Agaricomycotina JO - BMC Genomics VL - 16 UR - https://doi.org/10.1186/s12864-015-1380-0 DO - 10.1186/s12864-015-1380-0 ID - Sharma2015 ER - TY - JOUR AU - Tautz, D. AU - Domazet-Lošo, T. PY - 2011 DA - 2011// TI - The evolutionary origin of orphan genes JO - Nat Rev Genet VL - 12 UR - https://doi.org/10.1038/nrg3053 DO - 10.1038/nrg3053 ID - Tautz2011 ER - TY - STD TI - Csuros M, Rogozin IB, Koonin EV. A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes. PLoS Comput Biol. 2011; doi:10.1371/journal.pcbi.1002150. ID - ref22 ER - TY - JOUR AU - Parra, G. AU - Bradnam, K. AU - Ning, Z. AU - Keane, T. AU - Korf, I. PY - 2009 DA - 2009// TI - Assessing the gene space in draft genomes JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn916 DO - 10.1093/nar/gkn916 ID - Parra2009 ER - TY - JOUR AU - Gostinčar, C. AU - Ohm, R. A. AU - Kogej, T. AU - Sonjak, S. AU - Turk, M. AU - Zajc, J. AU - Zalar, P. AU - Grube, M. AU - Sun, H. AU - Han, J. PY - 2014 DA - 2014// TI - Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-549 DO - 10.1186/1471-2164-15-549 ID - Gostinčar2014 ER - TY - JOUR AU - Libkind, D. AU - Hittinger, C. T. AU - Valério, E. AU - Gonçalves, C. AU - Dover, J. AU - Johnston, M. AU - Gonçalves, P. AU - Sampaio, J. P. PY - 2011 DA - 2011// TI - Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast JO - Proc Natl Acad Sci VL - 108 UR - https://doi.org/10.1073/pnas.1105430108 DO - 10.1073/pnas.1105430108 ID - Libkind2011 ER - TY - STD TI - Almeida P, Gonçalves C, Teixeira S, Libkind D, Bontrager M, Masneuf-Pomarède I, Albertin W, Durrens P, Sherman DJ, Marullo P. A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum. Nat Commun. 2014; doi:10.1038/ncomms5044. ID - ref26 ER - TY - JOUR AU - Peris, D. AU - Sylvester, K. AU - Libkind, D. AU - Gonçalves, P. AU - Sampaio, J. P. AU - Alexander, W. G. AU - Hittinger, C. T. PY - 2014 DA - 2014// TI - Population structure and reticulate evolution of Saccharomyces eubayanus and its lager‐brewing hybrids JO - Mol Ecol VL - 23 UR - https://doi.org/10.1111/mec.12702 DO - 10.1111/mec.12702 ID - Peris2014 ER - TY - JOUR AU - Peris, D. AU - Langdon, Q. K. AU - Moriarty, R. V. AU - Sylvester, K. AU - Bontrager, M. AU - Charron, G. AU - Leducq, J. B. AU - Landry, C. R. AU - Libkind, D. AU - Hittinger, C. T. PY - 2016 DA - 2016// TI - Complex ancestries of lager-brewing hybrids were shaped by standing variation in the wild yeast saccharomyces eubayanus JO - PLoS Genet VL - 12 UR - https://doi.org/10.1371/journal.pgen.1006155 DO - 10.1371/journal.pgen.1006155 ID - Peris2016 ER - TY - JOUR AU - Schroeder, W. A. AU - Johnson, E. A. PY - 1995 DA - 1995// TI - Carotenoids protect Phaffia rhodozyma against singlet oxygen damage JO - J Ind Microbiol VL - 14 UR - https://doi.org/10.1007/BF01573965 DO - 10.1007/BF01573965 ID - Schroeder1995 ER - TY - JOUR AU - Johnson, E. A. PY - 2003 DA - 2003// TI - Phaffia rhodozyma: colorful odyssey JO - Int Microbiol VL - 6 UR - https://doi.org/10.1007/s10123-003-0130-3 DO - 10.1007/s10123-003-0130-3 ID - Johnson2003 ER - TY - JOUR AU - Marcoleta, A. AU - Niklitschek, M. AU - Wozniak, A. AU - Lozano, C. AU - Alcaíno, J. AU - Baeza, M. AU - Cifuentes, V. PY - 2011 DA - 2011// TI - Glucose and ethanol-dependent transcriptional regulation of the astaxanthin biosynthesis pathway in Xanthophyllomyces dendrorhous JO - BMC Microbiol VL - 11 UR - https://doi.org/10.1186/1471-2180-11-190 DO - 10.1186/1471-2180-11-190 ID - Marcoleta2011 ER - TY - JOUR AU - Wozniak, A. AU - Lozano, C. AU - Barahona, S. AU - Niklitschek, M. AU - Marcoleta, A. AU - Alcaíno, J. AU - Sepulveda, D. AU - Baeza, M. AU - Cifuentes, V. PY - 2011 DA - 2011// TI - Differential carotenoid production and gene expression in Xanthophyllomyces dendrorhous grown in a nonfermentable carbon source JO - FEMS Yeast Res VL - 11 UR - https://doi.org/10.1111/j.1567-1364.2010.00711.x DO - 10.1111/j.1567-1364.2010.00711.x ID - Wozniak2011 ER - TY - JOUR AU - Prado-Cabrero, A. AU - Scherzinger, D. AU - Avalos, J. AU - Al-Babili, S. PY - 2007 DA - 2007// TI - Retinal biosynthesis in fungi: characterization of the carotenoid oxygenase CarX from Fusarium fujikuroi JO - Eukaryot Cell VL - 6 UR - https://doi.org/10.1128/EC.00392-06 DO - 10.1128/EC.00392-06 ID - Prado-Cabrero2007 ER - TY - JOUR AU - Estrada, A. F. AU - Brefort, T. AU - Mengel, C. AU - Díaz-Sánchez, V. AU - Alder, A. AU - Al-Babili, S. AU - Avalos, J. PY - 2009 DA - 2009// TI - Ustilago maydis accumulates β-carotene at levels determined by a retinal-forming carotenoid oxygenase JO - Fungal Genet Biol VL - 46 UR - https://doi.org/10.1016/j.fgb.2009.06.011 DO - 10.1016/j.fgb.2009.06.011 ID - Estrada2009 ER - TY - JOUR AU - Spence, E. AU - Dunlap, W. C. AU - Shick, J. M. AU - Long, P. F. PY - 2012 DA - 2012// TI - Redundant pathways of sunscreen biosynthesis in a cyanobacterium JO - Chembiochem VL - 13 UR - https://doi.org/10.1002/cbic.201100737 DO - 10.1002/cbic.201100737 ID - Spence2012 ER - TY - JOUR AU - Colabella, F. AU - Moliné, M. AU - Libkind, D. PY - 2015 DA - 2015// TI - UV sunscreens of microbial origin: mycosporines and mycosporine-like aminoacids JO - Recent Pat Biotechnol VL - 8 UR - https://doi.org/10.2174/1872208309666150102104520 DO - 10.2174/1872208309666150102104520 ID - Colabella2015 ER - TY - JOUR AU - Balskus, E. P. AU - Walsh, C. T. PY - 2010 DA - 2010// TI - The genetic and molecular basis for sunscreen biosynthesis in cyanobacteria JO - Science VL - 329 UR - https://doi.org/10.1126/science.1193637 DO - 10.1126/science.1193637 ID - Balskus2010 ER - TY - JOUR AU - Libkind, D. AU - Sommaruga, R. AU - Zagarese, H. AU - Broock, M. PY - 2005 DA - 2005// TI - Mycosporines in carotenogenic yeasts JO - Syst Appl Microbiol VL - 28 UR - https://doi.org/10.1016/j.syapm.2005.05.005 DO - 10.1016/j.syapm.2005.05.005 ID - Libkind2005 ER - TY - JOUR AU - Contreras, G. AU - Barahona, S. AU - Sepúlveda, D. AU - Baeza, M. AU - Cifuentes, V. AU - Alcaíno, J. PY - 2015 DA - 2015// TI - Identification and analysis of metabolite production with biotechnological potential in Xanthophyllomyces dendrorhous isolates JO - World J Microbiol Biotechnol VL - 31 UR - https://doi.org/10.1007/s11274-015-1808-3 DO - 10.1007/s11274-015-1808-3 ID - Contreras2015 ER - TY - JOUR AU - Liu, Y. S. AU - Wu, J. Y. PY - 2006 DA - 2006// TI - Hydrogen peroxide-induced astaxanthin biosynthesis and catalase activity in Xanthophyllomyces dendrorhous JO - Appl Microbiol Biotechnol VL - 73 UR - https://doi.org/10.1007/s00253-006-0501-8 DO - 10.1007/s00253-006-0501-8 ID - Liu2006 ER - TY - JOUR AU - Hansberg, W. AU - Salas-Lizana, R. AU - Domínguez, L. PY - 2012 DA - 2012// TI - Fungal catalases: function, phylogenetic origin and structure JO - Arch Biochem Biophys VL - 525 UR - https://doi.org/10.1016/j.abb.2012.05.014 DO - 10.1016/j.abb.2012.05.014 ID - Hansberg2012 ER - TY - JOUR AU - Giles, S. S. AU - Stajich, J. E. AU - Nichols, C. AU - Gerrald, Q. D. AU - Alspaugh, J. A. AU - Dietrich, F. AU - Perfect, J. R. PY - 2006 DA - 2006// TI - The Cryptococcus neoformans catalase gene family and its role in antioxidant defense JO - Eukaryot Cell VL - 5 UR - https://doi.org/10.1128/EC.00098-06 DO - 10.1128/EC.00098-06 ID - Giles2006 ER - TY - JOUR AU - Zamocky, M. AU - Furtmüller, P. G. AU - Obinger, C. PY - 2008 DA - 2008// TI - Evolution of catalases from bacteria to humans JO - Antioxid Redox Signal VL - 10 UR - https://doi.org/10.1089/ars.2008.2046 DO - 10.1089/ars.2008.2046 ID - Zamocky2008 ER - TY - JOUR AU - Zámocký, M. AU - Gasselhuber, B. AU - Furtmüller, P. G. AU - Obinger, C. PY - 2012 DA - 2012// TI - Molecular evolution of hydrogen peroxide degrading enzymes JO - Arch Biochem Biophys VL - 525 UR - https://doi.org/10.1016/j.abb.2012.01.017 DO - 10.1016/j.abb.2012.01.017 ID - Zámocký2012 ER - TY - JOUR AU - Schroeder, W. A. AU - Johnson, E. PY - 1993 DA - 1993// TI - Antioxidant role of carotenoids in Phaffia rhodozyma JO - J Gen Microbiol VL - 139 UR - https://doi.org/10.1099/00221287-139-5-907 DO - 10.1099/00221287-139-5-907 ID - Schroeder1993 ER - TY - JOUR AU - Martinez-Moya, P. AU - Niehaus, K. AU - Alcaíno, J. AU - Baeza, M. AU - Cifuentes, V. PY - 2015 DA - 2015// TI - Proteomic and metabolomic analysis of the carotenogenic yeast Xanthophyllomyces dendrorhous using different carbon sources JO - BMC Genomics VL - 16 UR - https://doi.org/10.1186/s12864-015-1484-6 DO - 10.1186/s12864-015-1484-6 ID - Martinez-Moya2015 ER - TY - JOUR AU - Fridovich, I. PY - 1995 DA - 1995// TI - Superoxide radical and superoxide dismutases JO - Annu Rev Biochem VL - 64 UR - https://doi.org/10.1146/annurev.bi.64.070195.000525 DO - 10.1146/annurev.bi.64.070195.000525 ID - Fridovich1995 ER - TY - JOUR AU - Fréalle, E. AU - Noël, C. AU - Viscogliosi, E. AU - Camus, D. AU - Dei‐Cas, E. AU - Delhaes, L. PY - 2005 DA - 2005// TI - Manganese superoxide dismutase in pathogenic fungi: an issue with pathophysiological and phylogenetic involvements JO - FEMS Immunol Med Microbiol VL - 45 UR - https://doi.org/10.1016/j.femsim.2005.06.003 DO - 10.1016/j.femsim.2005.06.003 ID - Fréalle2005 ER - TY - JOUR AU - David-Palma, M. AU - Sampaio, J. P. AU - Gonçalves, P. PY - 2016 DA - 2016// TI - Genetic dissection of sexual reproduction in a primary homothallic basidiomycete JO - PLoS Genet VL - 12 UR - https://doi.org/10.1371/journal.pgen.1006110 DO - 10.1371/journal.pgen.1006110 ID - David-Palma2016 ER - TY - STD TI - Metin B, Findley K, Heitman J. The mating type locus (MAT) and sexual reproduction of Cryptococcus heveanensis: insights into the evolution of sex and sex-determining chromosomal regions in fungi. PLoS Genet. 2010;6: doi: 10.1371/journal.pgen.1000961. ID - ref50 ER - TY - JOUR AU - Guerreiro, M. A. AU - Springer, D. J. AU - Rodrigues, J. A. AU - Rusche, L. N. AU - Findley, K. AU - Heitman, J. AU - Fonseca, Á. PY - 2013 DA - 2013// TI - Molecular and genetic evidence for a tetrapolar mating system in the basidiomycetous yeast Kwoniella mangrovensis and two novel sibling species JO - Eukaryot Cell VL - 12 UR - https://doi.org/10.1128/EC.00065-13 DO - 10.1128/EC.00065-13 ID - Guerreiro2013 ER - TY - STD TI - Coelho MA, Sampaio JP, Gonçalves P. A deviation from the bipolar-tetrapolar mating paradigm in an early diverged basidiomycete. PLoS Genet. 2010;6: doi: 10.1371/journal.pgen.1001052. ID - ref52 ER - TY - JOUR AU - Maia, T. M. AU - Lopes, S. T. AU - Almeida, J. M. AU - Rosa, L. H. AU - Sampaio, J. P. AU - Gonçalves, P. AU - Coelho, M. A. PY - 2015 DA - 2015// TI - Evolution of mating systems in Basidiomycetes and the genetic architecture underlying mating-type determination in the yeast Leucosporidium scottii JO - Genetics VL - 201 UR - https://doi.org/10.1534/genetics.115.177717 DO - 10.1534/genetics.115.177717 ID - Maia2015 ER - TY - JOUR AU - Errede, B. AU - Ammerer, G. PY - 1989 DA - 1989// TI - STE12, a protein involved in cell-type-specific transcription and signal transduction in yeast, is part of protein-DNA complexes JO - Genes Dev VL - 3 UR - https://doi.org/10.1101/gad.3.9.1349 DO - 10.1101/gad.3.9.1349 ID - Errede1989 ER - TY - STD TI - Lin X, Jackson JC, Feretzaki M, Xue C, Heitman J. Transcription factors Mat2 and Znf2 operate cellular circuits orchestrating opposite-and same-sex mating in Cryptococcus neoformans. PLoS Genet. 2010;6: doi: 10.1371/journal.pgen.1000953. ID - ref55 ER - TY - JOUR AU - Kaffarnik, F. AU - Müller, P. AU - Leibundgut, M. AU - Kahmann, R. AU - Feldbrügge, M. PY - 2003 DA - 2003// TI - PKA and MAPK phosphorylation of Prf1 allows promoter discrimination in Ustilago maydis JO - EMBO J VL - 22 UR - https://doi.org/10.1093/emboj/cdg554 DO - 10.1093/emboj/cdg554 ID - Kaffarnik2003 ER - TY - STD TI - Gonçalves P, Valério E, Correia C, de Almeida JM, Sampaio JP. Evidence for divergent evolution of growth temperature preference in sympatric Saccharomyces species. PLoS One. 2011;6: doi:10.1371/journal.pone.0020739. ID - ref57 ER - TY - JOUR AU - Hittinger, C. T. AU - Gonçalves, P. AU - Sampaio, J. P. AU - Dover, J. AU - Johnston, M. AU - Rokas, A. PY - 2010 DA - 2010// TI - Remarkably ancient balanced polymorphisms in a multi-locus gene network JO - Nature VL - 464 UR - https://doi.org/10.1038/nature08791 DO - 10.1038/nature08791 ID - Hittinger2010 ER - TY - JOUR AU - Bankevich, A. AU - Nurk, S. AU - Antipov, D. AU - Gurevich, A. A. AU - Dvorkin, M. AU - Kulikov, A. S. AU - Lesin, V. M. AU - Nikolenko, S. I. AU - Pham, S. AU - Prjibelski, A. D. PY - 2012 DA - 2012// TI - SPAdes: a new genome assembly algorithm and its applications 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 - Kent, W. J. PY - 2002 DA - 2002// TI - BLAT—the BLAST-like alignment tool JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.229202. Article published online before March 2002 DO - 10.1101/gr.229202. Article published online before March 2002 ID - Kent2002 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schäffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - BOOK AU - Harris, R. S. PY - 2007 DA - 2007// TI - Improved pairwise alignment of genomic DNA: ProQuest ID - Harris2007 ER - TY - JOUR AU - Ter-Hovhannisyan, V. AU - Lomsadze, A. AU - Chernoff, Y. O. AU - Borodovsky, M. PY - 2008 DA - 2008// TI - Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.081612.108 DO - 10.1101/gr.081612.108 ID - Ter-Hovhannisyan2008 ER - TY - STD TI - Smit A, Hubley R, Green P. 1996–2010. RepeatMasker Open-3.0. http://www.repeatmasker.org. UR - http://www.repeatmasker.org/ ID - ref64 ER - TY - JOUR AU - Jurka, J. AU - Kapitonov, V. V. AU - Pavlicek, A. AU - Klonowski, P. AU - Kohany, O. AU - Walichiewicz, J. PY - 2005 DA - 2005// TI - Repbase update, a database of eukaryotic repetitive elements JO - Cytogenet Genome Res VL - 110 UR - https://doi.org/10.1159/000084979 DO - 10.1159/000084979 ID - Jurka2005 ER - TY - JOUR AU - Lowe, T. M. AU - Eddy, S. R. PY - 1997 DA - 1997// TI - tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.5.0955 DO - 10.1093/nar/25.5.0955 ID - Lowe1997 ER - TY - STD TI - Eddy SR, Rost B. A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput Biol. 2008;4: doi:10.1371/journal.pcbi.1000069. ID - ref67 ER - TY - JOUR AU - Conesa, A. AU - Götz, S. AU - García-Gómez, J. M. AU - Terol, J. AU - Talón, M. AU - Robles, M. PY - 2005 DA - 2005// TI - Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti610 DO - 10.1093/bioinformatics/bti610 ID - Conesa2005 ER - TY - JOUR AU - Katoh, K. AU - Kuma, K. -. i. AU - Toh, H. AU - Miyata, T. PY - 2005 DA - 2005// TI - MAFFT version 5: improvement in accuracy of multiple sequence alignment JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki198 DO - 10.1093/nar/gki198 ID - Katoh2005 ER - TY - JOUR AU - Claudel‐Renard, C. AU - Chevalet, C. AU - Faraut, T. AU - Kahn, D. PY - 2003 DA - 2003// TI - Enzyme‐specific profiles for genome annotation: PRIAM JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg847 DO - 10.1093/nar/gkg847 ID - Claudel‐Renard2003 ER - TY - JOUR AU - Finn, R. D. AU - Bateman, A. AU - Clements, J. AU - Coggill, P. AU - Eberhardt, R. Y. AU - Eddy, S. R. AU - Heger, A. AU - Hetherington, K. AU - Holm, L. AU - Mistry, J. PY - 2014 DA - 2014// TI - Pfam: the protein families database JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1223 DO - 10.1093/nar/gkt1223 ID - Finn2014 ER - TY - JOUR AU - Gremme, G. AU - Steinbiss, S. AU - Kurtz, S. PY - 2013 DA - 2013// TI - GenomeTools: a comprehensive software library for efficient processing of structured genome annotations JO - IEEE/ACM Trans Comput Biol Bioinform VL - 10 UR - https://doi.org/10.1109/TCBB.2013.68 DO - 10.1109/TCBB.2013.68 ID - Gremme2013 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: multiple sequence alignment with high accuracy 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 - Ronquist, F. AU - Teslenko, M. AU - Mark, P. AU - Ayres, D. L. AU - Darling, A. AU - Höhna, S. AU - Larget, B. AU - Liu, L. AU - Suchard, M. A. AU - Huelsenbeck, J. P. PY - 2012 DA - 2012// TI - MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space JO - Syst Biol VL - 61 UR - https://doi.org/10.1093/sysbio/sys029 DO - 10.1093/sysbio/sys029 ID - Ronquist2012 ER - TY - JOUR AU - Stamatakis, A. PY - 2006 DA - 2006// TI - RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl446 DO - 10.1093/bioinformatics/btl446 ID - Stamatakis2006 ER - TY - JOUR AU - Emanuelsson, O. AU - Nielsen, H. AU - Brunak, S. AU - Heijne, G. PY - 2000 DA - 2000// TI - Predicting subcellular localization of proteins based on their N-terminal amino acid sequence JO - J Mol Biol VL - 300 UR - https://doi.org/10.1006/jmbi.2000.3903 DO - 10.1006/jmbi.2000.3903 ID - Emanuelsson2000 ER - TY - STD TI - Feretzaki M, Heitman J. Genetic circuits that govern bisexual and unisexual reproduction in Cryptococcus neoformans. PLoS Genet. 2013;9: doi:10.1371/journal.pgen.1003688. ID - ref77 ER -