TY - JOUR AU - Hibbett, D. S. AU - Binder, M. AU - Bischoff, J. F. AU - Blackwell, M. AU - Cannon, P. F. AU - Eriksson, O. E. PY - 2007 DA - 2007// TI - A higher-level phylogenetic classification of the fungi JO - Mycol Res VL - 111 UR - https://doi.org/10.1016/j.mycres.2007.03.004 DO - 10.1016/j.mycres.2007.03.004 ID - Hibbett2007 ER - TY - JOUR AU - Walther, G. AU - Pawłowska, J. AU - Alastruey-Izquierdo, A. AU - Wrzosek, M. AU - Rodriguez-Tudela, J. L. AU - Dolatabadi, S. PY - 2013 DA - 2013// TI - DNA barcoding in Mucorales: an inventory of biodiversity JO - Persoonia VL - 30 UR - https://doi.org/10.3767/003158513X665070 DO - 10.3767/003158513X665070 ID - Walther2013 ER - TY - JOUR AU - Hoffmann, K. AU - Pawłowska, J. AU - Walther, G. AU - Wrzosek, M. AU - Hoog, G. S. AU - Benny, G. L. PY - 2013 DA - 2013// TI - The family structure of the Mucorales: a synoptic revision based on comprehensive multigene-genealogies JO - Persoonia VL - 30 UR - https://doi.org/10.3767/003158513X666259 DO - 10.3767/003158513X666259 ID - Hoffmann2013 ER - TY - JOUR AU - Spatafora, J. W. AU - Chang, Y. AU - Benny, G. L. AU - Lazarus, K. AU - Smith, M. E. AU - Berbee, M. L. PY - 2016 DA - 2016// TI - A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data JO - Mycologia VL - 108 UR - https://doi.org/10.3852/16-042 DO - 10.3852/16-042 ID - Spatafora2016 ER - TY - JOUR AU - Ribes, J. A. AU - Vanover-Sams, C. L. AU - Baker, D. J. PY - 2000 DA - 2000// TI - Zygomycetes in human disease JO - Clin Microbiol Rev VL - 13 UR - https://doi.org/10.1128/CMR.13.2.236-301.2000 DO - 10.1128/CMR.13.2.236-301.2000 ID - Ribes2000 ER - TY - JOUR AU - Roden, M. M. AU - Zaoutis, T. E. AU - Buchanan, W. L. AU - Knudsen, T. A. AU - Sarkisova, T. A. AU - Schaufele, R. L. PY - 2005 DA - 2005// TI - Epidemiology and outcome of zygomycosis: a review of 929 reported cases JO - Clin Infect Dis VL - 41 UR - https://doi.org/10.1086/432579 DO - 10.1086/432579 ID - Roden2005 ER - TY - JOUR AU - Skiada, A. AU - Pagano, L. AU - Groll, A. AU - Zimmerli, S. AU - Dupont, B. AU - Lagrou, K. PY - 2011 DA - 2011// TI - Zygomycosis in Europe: analysis of 230 cases accrued by the registry of the European Confederation of Medical Mycology (ECMM) working group on Zygomycosis between 2005 and 2007 JO - Clin Microbiol Infect VL - 17 UR - https://doi.org/10.1111/j.1469-0691.2010.03456.x DO - 10.1111/j.1469-0691.2010.03456.x ID - Skiada2011 ER - TY - JOUR AU - Petrikkos, G. AU - Skiada, A. AU - Drogari-Apiranthitou, M. PY - 2014 DA - 2014// TI - Epidemiology of mucormycosis in Europe JO - Clin Microbiol Infect VL - 8 UR - https://doi.org/10.1111/1469-0691.12563 DO - 10.1111/1469-0691.12563 ID - Petrikkos2014 ER - TY - JOUR AU - Chakrabarti, A. AU - Chatterjee, S. S. AU - Das, A. AU - Panda, N. AU - Shivaprakash, M. R. AU - Kaur, A. PY - 2009 DA - 2009// TI - Invasive zygomycosis in India: experience in a tertiary care hospital JO - Postgrad Med J VL - 85 UR - https://doi.org/10.1136/pgmj.2008.076463 DO - 10.1136/pgmj.2008.076463 ID - Chakrabarti2009 ER - TY - JOUR AU - Bala, K. AU - Chander, J. AU - Handa, U. AU - Punia, R. S. AU - Attri, A. K. PY - 2015 DA - 2015// TI - A prospective study of mucormycosis in north India: experience from a tertiary care hospital JO - Med Mycol VL - 53 UR - https://doi.org/10.1093/mmy/myu086 DO - 10.1093/mmy/myu086 ID - Bala2015 ER - TY - JOUR AU - Chakrabarti, A. AU - Shivaprakash, M. R. AU - Curfs-Breuker, I. AU - Baghela, A. AU - Klaassen, C. H. AU - Meis, J. F. PY - 2010 DA - 2010// TI - Apophysomyces elegans: epidemiology, amplified fragment length polymorphism typing, and in vitro antifungal susceptibility pattern JO - J Clin Microbiol VL - 48 UR - https://doi.org/10.1128/JCM.01420-10 DO - 10.1128/JCM.01420-10 ID - Chakrabarti2010 ER - TY - JOUR AU - Misra, P. C. AU - Srivastava, K. J. AU - Lata, K. PY - 1979 DA - 1979// TI - Apophysomyces, a new genus of the Mucorales JO - Mycotaxon VL - 8 ID - Misra1979 ER - TY - JOUR AU - Prakash, H. AU - Ghosh, A. AU - Rudramurthy, S. AU - Paul, R. AU - Gupta, S. AU - Negi, V. PY - 2016 DA - 2016// TI - The environmental source of emerging apophysomyces variabilis infection in india JO - Med Mycol VL - 54 UR - https://doi.org/10.1093/mmy/myw014 DO - 10.1093/mmy/myw014 ID - Prakash2016 ER - TY - JOUR AU - Alvarez, E. AU - Stchigel, A. M. AU - Cano, J. AU - Sutton, D. A. AU - Fothergill, A. W. AU - Chander, J. PY - 2010 DA - 2010// TI - Molecular phylogenetic diversity of the emerging mucoralean fungus Apophysomyces: proposal of three new species JO - Rev Iberoam Micol VL - 27 UR - https://doi.org/10.1016/j.riam.2010.01.006 DO - 10.1016/j.riam.2010.01.006 ID - Alvarez2010 ER - TY - JOUR AU - Bonifaz, A. AU - Stchigel, A. M. AU - Guarro, J. AU - Guevara, E. AU - Pintos, L. AU - Sanchis, M. PY - 2014 DA - 2014// TI - Primary cutaneous mucormycosis produced by the new species Apophysomyces mexicanus JO - J Clin Microbiol VL - 52 UR - https://doi.org/10.1128/JCM.02138-14 DO - 10.1128/JCM.02138-14 ID - Bonifaz2014 ER - TY - JOUR AU - Guarro, J. AU - Chander, J. AU - Alvarez, E. AU - Stchigel, A. M. AU - Robin, K. AU - Dalal, U. PY - 2011 DA - 2011// TI - Apophysomyces variabilis infections in humans JO - Emerg Infect Dis VL - 17 UR - https://doi.org/10.3201/eid1701.101139 DO - 10.3201/eid1701.101139 ID - Guarro2011 ER - TY - JOUR AU - Chander, J. AU - Miguel, A. AU - Alastruey-izquierdo, A. AU - Jayant, M. AU - Bala, K. AU - Rani, H. PY - 2015 DA - 2015// TI - Fungal necrotizing fasciitis, an emerging infectious disease caused by Apophysomyces ( Mucorales ) JO - Rev Iberoam Micol VL - 32 UR - https://doi.org/10.1016/j.riam.2014.06.005 DO - 10.1016/j.riam.2014.06.005 ID - Chander2015 ER - TY - JOUR AU - Etienne, K. A. AU - Gillece, J. AU - Hilsabeck, R. AU - Schupp, J. M. AU - Colman, R. AU - Lockhart, S. R. PY - 2012 DA - 2012// TI - Whole genome sequence typing to investigate the Apophysomyces outbreak following a tornado in Joplin, Missouri, 2011 JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0049989 DO - 10.1371/journal.pone.0049989 ID - Etienne2012 ER - TY - JOUR AU - Neblett Fanfair, R. AU - Benedict, K. AU - Bos, J. AU - Bennett, S. D. AU - Lo, Y. -. C. AU - Adebanjo, T. PY - 2012 DA - 2012// TI - Necrotizing cutaneous mucormycosis after a tornado in Joplin, Missouri, in 2011 JO - N Engl J Med VL - 367 UR - https://doi.org/10.1056/NEJMoa1204781 DO - 10.1056/NEJMoa1204781 ID - Neblett Fanfair2012 ER - TY - JOUR AU - Chibucos, M. C. AU - Soliman, S. AU - Gebremariam, T. AU - Lee, H. AU - Daugherty, S. AU - Orvis, J. PY - 2016 DA - 2016// TI - An integrated genomic and transcriptomic survey of mucormycosis-causing fungi JO - Nat Commun VL - 7 UR - https://doi.org/10.1038/ncomms12218 DO - 10.1038/ncomms12218 ID - Chibucos2016 ER - TY - JOUR AU - Ma, L. J. AU - Ibrahim, A. S. AU - Skory, C. AU - Grabherr, M. G. AU - Burger, G. AU - Butler, M. PY - 2009 DA - 2009// TI - Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication JO - PLoS Genet VL - 5 UR - https://doi.org/10.1371/journal.pgen.1000549 DO - 10.1371/journal.pgen.1000549 ID - Ma2009 ER - TY - JOUR AU - Schwartze, V. U. AU - Winter, S. AU - Shelest, E. AU - Marcet-Houben, M. AU - Horn, F. AU - Wehner, S. PY - 2014 DA - 2014// TI - Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina) JO - PLoS Genet VL - 10 UR - https://doi.org/10.1371/journal.pgen.1004496 DO - 10.1371/journal.pgen.1004496 ID - Schwartze2014 ER - TY - JOUR AU - Zhou, P. AU - Zhang, G. AU - Chen, S. AU - Jiang, Z. AU - Tang, Y. AU - Henrissat, B. PY - 2014 DA - 2014// TI - Genome sequence and transcriptome analyses of the thermophilic zygomycete fungus Rhizomucor miehei JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-294 DO - 10.1186/1471-2164-15-294 ID - Zhou2014 ER - TY - JOUR AU - Castanera, R. AU - López-Varas, L. AU - Borgognone, A. AU - LaButti, K. AU - Lapidus, A. AU - Schmutz, J. PY - 2016 DA - 2016// TI - Transposable elements versus the fungal genome: impact on whole-genome architecture and transcriptional profiles JO - PLoS Genet VL - 12 UR - https://doi.org/10.1371/journal.pgen.1006108 DO - 10.1371/journal.pgen.1006108 ID - Castanera2016 ER - TY - JOUR AU - Santana, M. F. AU - Queiroz, M. V. PY - 2015 DA - 2015// TI - Transposable elements in fungi: a genomic approach JO - Scientific J Genetics Gen Ther VL - 1 ID - Santana2015 ER - TY - JOUR AU - Kellis, M. AU - Birren, B. W. AU - Lander, E. S. PY - 2004 DA - 2004// TI - Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces Cerevisiae JO - Nature VL - 428 UR - https://doi.org/10.1038/nature02424 DO - 10.1038/nature02424 ID - Kellis2004 ER - TY - JOUR AU - Wolfe, K. H. AU - Shields, D. C. PY - 1997 DA - 1997// TI - Molecular evidence for an ancient duplication of the entire yeast genome JO - Nature VL - 387 UR - https://doi.org/10.1038/42711 DO - 10.1038/42711 ID - Wolfe1997 ER - TY - JOUR AU - Lewis, R. E. AU - Lortholary, O. AU - Spellberg, B. AU - Roilides, E. AU - Kontoyiannis, D. P. AU - Walsh, T. J. PY - 2012 DA - 2012// TI - How does antifungal pharmacology differ for mucormycosis versus aspergillosis? JO - Clin Infect Dis VL - 54 UR - https://doi.org/10.1093/cid/cir884 DO - 10.1093/cid/cir884 ID - Lewis2012 ER - TY - JOUR AU - Corrochano, L. M. AU - Kuo, A. AU - Marcet-Houben, M. AU - Polaino, S. AU - Salamov, A. AU - Villalobos-Escobedo, J. M. PY - 2016 DA - 2016// TI - Expansion of signal transduction pathways in fungi by extensive genome duplication JO - Curr Biol VL - 26 UR - https://doi.org/10.1016/j.cub.2016.04.038 DO - 10.1016/j.cub.2016.04.038 ID - Corrochano2016 ER - TY - JOUR AU - Kosti, I. AU - Mandel-Gutfreund, Y. AU - Glaser, F. AU - Horwitz, B. A. PY - 2010 DA - 2010// TI - Comparative analysis of fungal protein kinases and associated domains JO - BMC Genomics VL - 11 UR - https://doi.org/10.1186/1471-2164-11-133 DO - 10.1186/1471-2164-11-133 ID - Kosti2010 ER - TY - JOUR AU - Fortwendel, J. R. PY - 2015 DA - 2015// TI - Orchestration of morphogenesis in filamentous fungi: conserved roles for Ras signaling networks JO - Fungal Biol Rev VL - 29 UR - https://doi.org/10.1016/j.fbr.2015.04.003 DO - 10.1016/j.fbr.2015.04.003 ID - Fortwendel2015 ER - TY - JOUR AU - Spellberg, B. AU - Edwards, J. AU - Ibrahim, A. PY - 2005 DA - 2005// TI - Novel perspectives on mucormycosis: pathophysiology, presentation, and management JO - Clin Microbiol Rev VL - 18 UR - https://doi.org/10.1128/CMR.18.3.556-569.2005 DO - 10.1128/CMR.18.3.556-569.2005 ID - Spellberg2005 ER - TY - JOUR AU - Ibrahim, A. S. PY - 2011 DA - 2011// TI - Host cell invasion in mucormycosis: role of iron JO - Curr Opin Microbiol VL - 14 UR - https://doi.org/10.1016/j.mib.2011.07.004 DO - 10.1016/j.mib.2011.07.004 ID - Ibrahim2011 ER - TY - JOUR AU - Ibrahim, A. AU - Spellberg, B. AU - Edwards, J. J. PY - 2008 DA - 2008// TI - Iron acquisition: a novel prospective on Mucormycosis pathogenesis and treatment JO - Curr Opin Infect Dis VL - 21 UR - https://doi.org/10.1097/QCO.0b013e3283165fd1 DO - 10.1097/QCO.0b013e3283165fd1 ID - Ibrahim2008 ER - TY - JOUR AU - Ibrahim, A. S. AU - Gebremariam, T. AU - Lin, L. AU - Luo, G. AU - Husseiny, M. I. AU - Skory, C. D. PY - 2010 DA - 2010// TI - The high affinity iron permease is a key virulence factor required for Rhizopus oryzae pathogenesis JO - Mol Microbiol VL - 77 UR - https://doi.org/10.1111/j.1365-2958.2010.07234.x DO - 10.1111/j.1365-2958.2010.07234.x ID - Ibrahim2010 ER - TY - JOUR AU - Liu, M. AU - Lin, L. AU - Gebremariam, T. AU - Luo, G. AU - Skory, C. D. AU - French, S. W. PY - 2015 DA - 2015// TI - Fob1 And Fob2 proteins are virulence determinants of Rhizopus oryzae via facilitating iron uptake from Ferrioxamine JO - PLoS Pathog VL - 11 ID - Liu2015 ER - TY - JOUR AU - Liu, M. AU - Spellberg, B. AU - Phan, Q. T. AU - Fu, Y. Y. AU - Fu, Y. Y. AU - Lee, A. S. PY - 2010 DA - 2010// TI - The endothelial cell receptor GRP78 is required for mucormycosis pathogenesis in diabetic mice JO - J Clin Invest VL - 120 UR - https://doi.org/10.1172/JCI42164 DO - 10.1172/JCI42164 ID - Liu2010 ER - TY - JOUR AU - Gebremariam, T. AU - Liu, M. AU - Luo, G. AU - Bruno, V. AU - Phan, Q. T. AU - Waring, A. J. PY - 2014 DA - 2014// TI - CotH3 Mediates fungal invasion of host cells during mucormycosis JO - J Clin Invest VL - 124 UR - https://doi.org/10.1172/JCI71349 DO - 10.1172/JCI71349 ID - Gebremariam2014 ER - TY - JOUR AU - Mélida, H. AU - Sain, D. AU - Stajich, J. E. AU - Bulone, V. PY - 2015 DA - 2015// TI - Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches JO - Environ Microbiol VL - 17 UR - https://doi.org/10.1111/1462-2920.12601 DO - 10.1111/1462-2920.12601 ID - Mélida2015 ER - TY - JOUR AU - Yin, Y. AU - Mao, X. AU - Yang, J. AU - Chen, X. AU - Mao, F. AU - Xu, Y. PY - 2012 DA - 2012// TI - DbCAN: a web resource for automated carbohydrate-active enzyme annotation JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gks479 DO - 10.1093/nar/gks479 ID - Yin2012 ER - TY - CHAP AU - Lee, S. B. AU - Taylor, J. W. ED - Innis, M. A. ED - Gelfand, D. H. ED - Sninsky, J. J. ED - White, T. J. PY - 1990 DA - 1990// TI - Isolation of DNA from fungal mycelia and single spores BT - PCR protocols: a guide to methods and applications PB - Academic Press CY - California ID - Lee1990 ER - TY - JOUR AU - Nieuwerburgh, F. AU - Thompson, R. C. AU - Ledesma, J. AU - Deforce, D. AU - Gaasterland, T. AU - Ordoukhanian, P. PY - 2012 DA - 2012// TI - Illumina mate-paired DNA sequencing-library preparation using Cre-lox recombination JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr1000 DO - 10.1093/nar/gkr1000 ID - Nieuwerburgh2012 ER - TY - JOUR AU - Bolger, A. M. AU - Lohse, M. AU - Usadel, B. PY - 2014 DA - 2014// TI - Trimmomatic: a flexible trimmer for Illumina sequence data JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu170 DO - 10.1093/bioinformatics/btu170 ID - Bolger2014 ER - TY - JOUR AU - Luo, R. AU - Liu, B. AU - Xie, Y. AU - Li, Z. AU - Huang, W. AU - Yuan, J. PY - 2012 DA - 2012// TI - SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler JO - Gigascience VL - 1 UR - https://doi.org/10.1186/2047-217X-1-18 DO - 10.1186/2047-217X-1-18 ID - Luo2012 ER - TY - STD TI - Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010:265–72. ID - ref45 ER - TY - JOUR AU - Stanke, M. AU - Steinkamp, R. AU - Waack, S. AU - Morgenstern, B. PY - 2004 DA - 2004// TI - AUGUSTUS: a web server for gene finding in eukaryotes JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh379 DO - 10.1093/nar/gkh379 ID - Stanke2004 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schäffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. 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 - JOUR AU - Boutet, E. AU - Lieberherr, D. AU - Tognolli, M. AU - Schneider, M. AU - Bansal, P. AU - Bridge, A. J. PY - 2016 DA - 2016// TI - UniProtKB/Swiss-Prot, the manually annotated section of the UniProt KnowledgeBase: how to use the entry view JO - Methods Mol Biol VL - 1374 UR - https://doi.org/10.1007/978-1-4939-3167-5_2 DO - 10.1007/978-1-4939-3167-5_2 ID - Boutet2016 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. AU - Butler, H. AU - Cherry, J. M. PY - 2000 DA - 2000// TI - Gene ontology: tool for the unification of biology JO - The Gene Ontology Consortium Nat Genet VL - 25 ID - Ashburner2000 ER - TY - JOUR AU - Mistry, J. AU - Bateman, A. AU - Finn, R. D. PY - 2007 DA - 2007// TI - Predicting active site residue annotations in the Pfam database JO - BMC Bioinformatics VL - 8 UR - https://doi.org/10.1186/1471-2105-8-298 DO - 10.1186/1471-2105-8-298 ID - Mistry2007 ER - TY - JOUR AU - Finn, R. D. AU - Coggill, P. AU - Eberhardt, R. Y. AU - Eddy, S. R. AU - Mistry, J. AU - Mitchell, A. L. PY - 2016 DA - 2016// TI - The Pfam protein families database: towards a more sustainable future JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1344 DO - 10.1093/nar/gkv1344 ID - Finn2016 ER - TY - JOUR AU - Nawrocki, E. P. AU - Burge, S. W. AU - Bateman, A. AU - Daub, J. AU - Eberhardt, R. Y. AU - Eddy, S. R. PY - 2015 DA - 2015// TI - Rfam 12.0: Updates to the RNA families database JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1063 DO - 10.1093/nar/gku1063 ID - Nawrocki2015 ER - TY - JOUR AU - Rawlings, N. D. AU - Barrett, A. J. AU - Finn, R. PY - 2016 DA - 2016// TI - Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1118 DO - 10.1093/nar/gkv1118 ID - Rawlings2016 ER - TY - JOUR AU - Lee, S. A. AU - Wormsley, S. AU - Kamoun, S. AU - Lee, A. F. S. AU - Joiner, K. AU - Wong, B. PY - 2003 DA - 2003// TI - An analysis of the Candida Albicans genome database for soluble secreted proteins using computer-based prediction algorithms JO - Yeast VL - 20 UR - https://doi.org/10.1002/yea.988 DO - 10.1002/yea.988 ID - Lee2003 ER - TY - JOUR AU - Pellegrin, C. AU - Morin, E. AU - Martin, F. M. AU - Veneault-Fourrey, C. PY - 2015 DA - 2015// TI - Comparative analysis of secretomes from ectomycorrhizal fungi with an emphasis on small-secreted proteins JO - Front Microbiol VL - 6 UR - https://doi.org/10.3389/fmicb.2015.01278 DO - 10.3389/fmicb.2015.01278 ID - Pellegrin2015 ER - TY - JOUR AU - Petersen, T. N. AU - Brunak, S. AU - Heijne, G. AU - Nielsen, H. PY - 2011 DA - 2011// TI - SignalP 4.0: Discriminating signal peptides from transmembrane regions JO - Nat Methods VL - 8 UR - https://doi.org/10.1038/nmeth.1701 DO - 10.1038/nmeth.1701 ID - Petersen2011 ER - TY - JOUR AU - Krogh, A. AU - Larsson, B. AU - Heijne, G. AU - Sonnhammer, E. L. PY - 2001 DA - 2001// TI - Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes JO - J Mol Biol VL - 305 UR - https://doi.org/10.1006/jmbi.2000.4315 DO - 10.1006/jmbi.2000.4315 ID - Krogh2001 ER - TY - JOUR AU - Emanuelsson, O. AU - Brunak, S. AU - Heijne, G. AU - Nielsen, H. PY - 2007 DA - 2007// TI - Locating proteins in the cell using TargetP, SignalP and related tools JO - Nat Protoc VL - 2 UR - https://doi.org/10.1038/nprot.2007.131 DO - 10.1038/nprot.2007.131 ID - Emanuelsson2007 ER - TY - JOUR AU - Castro, E. AU - Sigrist, C. J. A. AU - Gattiker, A. AU - Bulliard, V. AU - Langendijk-Genevaux, P. S. AU - Gasteiger, E. PY - 2006 DA - 2006// TI - ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkl124 DO - 10.1093/nar/gkl124 ID - Castro2006 ER - TY - JOUR AU - Sigrist, C. J. A. AU - Castro, E. AU - Cerutti, L. AU - Cuche, B. A. AU - Hulo, N. AU - Bridge, A. PY - 2013 DA - 2013// TI - New and continuing developments at PROSITE JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks1067 DO - 10.1093/nar/gks1067 ID - Sigrist2013 ER - TY - JOUR AU - Fischer, M. AU - Pleiss, J. PY - 2003 DA - 2003// TI - The lipase engineering database: a navigation and analysis tool for protein families JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg015 DO - 10.1093/nar/gkg015 ID - Fischer2003 ER - TY - JOUR AU - Winnenburg, R. AU - Baldwin, T. K. AU - Urban, M. AU - Rawlings, C. AU - Köhler, J. AU - Hammond-Kosack, K. E. PY - 2006 DA - 2006// TI - PHI-base: a new database for pathogen host interactions JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj047 DO - 10.1093/nar/gkj047 ID - Winnenburg2006 ER - TY - JOUR AU - Chen, F. AU - Mackey, A. J. AU - Stoeckert, C. J. AU - Roos, D. S. PY - 2006 DA - 2006// TI - OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj123 DO - 10.1093/nar/gkj123 ID - Chen2006 ER - TY - JOUR AU - Li, L. AU - Stoeckert, C. J. J. AU - Roos, D. S. PY - 2003 DA - 2003// TI - OrthoMCL: identification of Ortholog groups for eukaryotic genomes JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1224503 DO - 10.1101/gr.1224503 ID - Li2003 ER - TY - JOUR AU - Simão, F. A. AU - Waterhouse, R. M. AU - Ioannidis, P. AU - Kriventseva, E. V. AU - Zdobnov, E. M. PY - 2015 DA - 2015// TI - BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv351 DO - 10.1093/bioinformatics/btv351 ID - Simão2015 ER - TY - JOUR AU - Katoh, K. AU - Misawa, K. AU - Kuma, K. AU - Miyata, T. PY - 2002 DA - 2002// TI - MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/gkf436 DO - 10.1093/nar/gkf436 ID - Katoh2002 ER - TY - JOUR AU - Castresana, J. PY - 2000 DA - 2000// TI - Selection of conserved blocks from multiple alignments for their use in Phylogenetic analysis JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026334 DO - 10.1093/oxfordjournals.molbev.a026334 ID - Castresana2000 ER - TY - JOUR AU - Guindon, S. AU - Dufayard, J. F. AU - Lefort, V. AU - Anisimova, M. AU - Hordijk, W. AU - Gascuel, O. PY - 2010 DA - 2010// TI - New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0 JO - Syst Biol VL - 59 UR - https://doi.org/10.1093/sysbio/syq010 DO - 10.1093/sysbio/syq010 ID - Guindon2010 ER - TY - JOUR AU - Le, S. Q. AU - Gascuel, O. PY - 2008 DA - 2008// TI - An improved general amino acid replacement matrix JO - Mol Biol Evol VL - 25 UR - https://doi.org/10.1093/molbev/msn067 DO - 10.1093/molbev/msn067 ID - Le2008 ER -