TY - JOUR AU - Pildain, M. B. AU - Frisvad, J. C. AU - Vaamonde, G. AU - Cabral, D. AU - Varga, J. AU - Samson, R. A. PY - 2008 DA - 2008// TI - Two novel aflatoxin-producing Aspergillus species from Argentinean peanuts JO - Int J Syst Evol Microbiol VL - 58 UR - https://doi.org/10.1099/ijs.0.65123-0 DO - 10.1099/ijs.0.65123-0 ID - Pildain2008 ER - TY - JOUR AU - Varga, J. AU - Frisvad, J. C. AU - Samson, R. A. PY - 2011 DA - 2011// TI - Two new aflatoxin producing species, and an overview of Aspergillus section Flavi JO - Stud Mycol VL - 69 UR - https://doi.org/10.3114/sim.2011.69.05 DO - 10.3114/sim.2011.69.05 ID - Varga2011 ER - TY - JOUR AU - Gonçalves, S. S. AU - Stchigel, A. M. AU - Cano, J. F. AU - Godoy-Martinez, P. C. AU - Colombo, A. L. AU - Guarro, J. PY - 2012 DA - 2012// TI - Aspergillus novoparasiticus: a new clinical species of the section Flavi JO - Med Mycol VL - 50 UR - https://doi.org/10.3109/13693786.2011.593564 DO - 10.3109/13693786.2011.593564 ID - Gonçalves2012 ER - TY - JOUR AU - Soares, C. AU - Rodrigues, P. AU - Peterson, S. W. AU - Lima, N. AU - Venâncio, A. PY - 2012 DA - 2012// TI - Three new species of Aspergillus section Flavi isolated from almonds and maize in Portugal JO - Mycologia VL - 104 UR - https://doi.org/10.3852/11-088 DO - 10.3852/11-088 ID - Soares2012 ER - TY - STD TI - Santini A, Ritieni A. Aflatoxins: risk, exposure and remediation. In: Razzaghi-Abyaneh M, editor. Rijeka: Aflatoxins - recent advances and future prospects: InTech; 2013. https://doi.org/10.5772/52866. ID - ref5 ER - TY - JOUR AU - Gonçalves, J. S. AU - Ferracin, L. M. AU - Carneiro Vieira, M. L. AU - Iamanaka, B. T. AU - Taniwaki, M. H. AU - Pelegrinelli Fungaro, M. H. PY - 2012 DA - 2012// TI - Molecular analysis of Aspergillus section Flavi isolated from Brazil nuts JO - World J Microbiol Biotechnol VL - 28 UR - https://doi.org/10.1007/s11274-011-0956-3 DO - 10.1007/s11274-011-0956-3 ID - Gonçalves2012 ER - TY - JOUR AU - Negri, C. E. AU - Gonçalves, S. S. AU - Xafranski, H. AU - Bergamasco, M. D. AU - Aquinob, V. R. AU - Castroc, P. T. O. AU - Colomboa, A. L. PY - 2014 DA - 2014// TI - Cryptic and rare Aspergillus species in Brazil: prevalence in clinical samples and in vitro susceptibility to triazoles JO - J Clin Microbiol VL - 52 UR - https://doi.org/10.1128/JCM.01582-14 DO - 10.1128/JCM.01582-14 ID - Negri2014 ER - TY - JOUR AU - Viaro, H. P. AU - da Silva, J. J. AU - de Souza Ferranti, L. AU - Bordini, J. G. AU - Massi, F. P. AU - Pelegrinelli Fungaro, M. H. PY - 2017 DA - 2017// TI - The first report of A. novoparasiticus, A. arachidicola and A. pseudocaelatus in Brazilian corn kernels JO - Int J Food Microbiol VL - 243 UR - https://doi.org/10.1016/j.ijfoodmicro.2016.12.002 DO - 10.1016/j.ijfoodmicro.2016.12.002 ID - Viaro2017 ER - TY - JOUR AU - Olarte, R. A. AU - Worthington, C. J. AU - Horn, B. W. AU - Moore, G. G. AU - Singh, R. AU - Monacell, J. T. AU - Dorner, J. W. AU - Stone, E. A. AU - Xie, D. -. Y. AU - Carbone, I. PY - 2015 DA - 2015// TI - Enhanced diversity and aflatoxigenicity in interspecific hybrids of Aspergillus flavus and Aspergillus parasiticus JO - Mol Ecol VL - 24 UR - https://doi.org/10.1111/mec.13153 DO - 10.1111/mec.13153 ID - Olarte2015 ER - TY - JOUR AU - Frisvad, J. C. AU - Skouboe, P. AU - Samson, R. A. PY - 2005 DA - 2005// TI - Taxonomic comparison of three different groups of aflatoxin producers and a new efficient producer of aflatoxin B1, sterigmatocystin and 3-O-methylsterigmatocystin, Aspergillus rambellii sp. nov JO - Syst Appl Microbiol VL - 28 UR - https://doi.org/10.1016/j.syapm.2005.02.012 DO - 10.1016/j.syapm.2005.02.012 ID - Frisvad2005 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 - Linz, J. E. AU - Wee, J. AU - Roze, L. V. PY - 2014 DA - 2014// TI - Aspergillus parasiticus SU-1 genome sequence, predicted chromosome structure, and comparative gene expression under aflatoxin-inducing conditions: evidence that differential expression contributes to species phenotype JO - Eukaryot Cell VL - 13 UR - https://doi.org/10.1128/EC.00108-14 DO - 10.1128/EC.00108-14 ID - Linz2014 ER - TY - JOUR AU - Machida, M. AU - Asai, K. AU - Sano, M. AU - Tanaka, T. AU - Kumagai, T. AU - Terai, G. AU - Kusumoto, K. -. I. AU - Arima, T. AU - Akita, O. AU - Kashiwagi, Y. AU - Abe, K. AU - Gomi, K. AU - Horiuchi, H. AU - Kitamoto, K. AU - Kobayashi, T. AU - Takeuchi, M. AU - Denning, D. W. AU - Galagan, J. E. AU - Nierman, W. C. AU - Yu, J. AU - Archer, D. B. AU - Bennett, J. W. AU - Bhatnagar, D. AU - Cleveland, T. E. AU - Fedorova, N. D. AU - Gotoh, O. AU - Horikawa, H. AU - Hosoyama, A. AU - Ichinomiya, M. AU - Igarashi, R. PY - 2005 DA - 2005// TI - Genome sequencing and analysis of Aspergillus oryzae JO - Nature VL - 438 UR - https://doi.org/10.1038/nature04300 DO - 10.1038/nature04300 ID - Machida2005 ER - TY - JOUR AU - Payne, G. A. AU - Nierman, W. C. AU - Wortman, J. R. AU - Pritchard, B. L. AU - Brown, D. AU - Dean, R. A. AU - Bhatnagar, D. AU - Cleveland, T. E. AU - Machida, M. AU - Yu, J. PY - 2006 DA - 2006// TI - Whole genome comparison of Aspergillus flavus and A. oryzae JO - Med Mycol VL - 44 UR - https://doi.org/10.1080/13693780600835716 DO - 10.1080/13693780600835716 ID - Payne2006 ER - TY - JOUR AU - Moore, G. G. AU - Mack, B. M. AU - Beltz, S. B. PY - 2015 DA - 2015// TI - Genomic sequence of the aflatoxigenic filamentous fungus Aspergillus nomius JO - BMC Genomics VL - 16 UR - https://doi.org/10.1186/s12864-015-1719-6 DO - 10.1186/s12864-015-1719-6 ID - Moore2015 ER - TY - JOUR AU - Moore, G. G. AU - Mack, B. M. AU - Beltz, S. B. AU - Gilbert, M. K. PY - 2016 DA - 2016// TI - Draft genome sequence of an aflatoxigenic Aspergillus species, A. bombycis JO - Genome Biol Evol VL - 8 UR - https://doi.org/10.1093/gbe/evw238 DO - 10.1093/gbe/evw238 ID - Moore2016 ER - TY - JOUR AU - Hua, S. T. AU - Mcalpin, C. E. AU - Chang, P. -. K. AU - Sarreal, S. L. PY - 2012 DA - 2012// TI - Characterization of toxigenic and atoxigenic Aspergillus flavus isolates from pistachio JO - Mycotoxin Res VL - 28 UR - https://doi.org/10.1007/s12550-011-0117-4 DO - 10.1007/s12550-011-0117-4 ID - Hua2012 ER - TY - BOOK AU - Klich, M. A. PY - 2002 DA - 2002// TI - Identification of common aspergillus species PB - Utrecht CY - Centraalbureau voor Shimmelcultures ID - Klich2002 ER - TY - JOUR AU - Li, M. AU - Rollins, J. A. PY - 2009 DA - 2009// TI - The development-specific protein (Ssp1) from Sclerotinia sclerotiorum is encoded by a novel gene expressed exclusively in sclerotium tissues JO - Mycologia VL - 101 UR - https://doi.org/10.3852/08-114 DO - 10.3852/08-114 ID - Li2009 ER - TY - JOUR AU - Rollins, J. A. PY - 2003 DA - 2003// TI - The Sclerotinia sclerotiorum pac1 gene is required for sclerotial development and virulence JO - Mol Plant-Microbe Interact VL - 16 UR - https://doi.org/10.1094/MPMI.2003.16.9.785 DO - 10.1094/MPMI.2003.16.9.785 ID - Rollins2003 ER - TY - JOUR AU - Jin, F. J. AU - Takahashi, T. AU - Matsushima, K. -. I. AU - Hara, S. AU - Shinohara, Y. AU - Maruyama, J. AU - Kitamoto, K. AU - Koyama, Y. PY - 2011 DA - 2011// TI - SclR, a basic helix-loop-helix transcription factor, regulates hyphal morphology and promotes sclerotial formation in Aspergillus oryzae JO - Eukaryot Cell VL - 10 UR - https://doi.org/10.1128/EC.00013-11 DO - 10.1128/EC.00013-11 ID - Jin2011 ER - TY - JOUR AU - Chang, P. -. K. AU - Scharfenstein, L. L. AU - Ehrlich, K. C. AU - Diana Di Mavungu, J. PY - 2016 DA - 2016// TI - The Aspergillus flavus fluP-associated metabolite promotes sclerotial production JO - Fungal Biol VL - 120 UR - https://doi.org/10.1016/j.funbio.2016.07.010 DO - 10.1016/j.funbio.2016.07.010 ID - Chang2016 ER - TY - JOUR AU - Chang, P. -. K. AU - Scharfenstein, L. L. AU - Li, R. W. AU - Arroyo-Manzanares, N. AU - De Saeger, S. AU - Di Mavungu, J. D. PY - 2017 DA - 2017// TI - Aspergillus flavus aswA, a gene homolog of Aspergillus nidulans oefC, regulates sclerotial development and biosynthesis of sclerotium-associated secondary metabolites JO - Fungal Genet Biol VL - 104 UR - https://doi.org/10.1016/j.fgb.2017.04.006 DO - 10.1016/j.fgb.2017.04.006 ID - Chang2017 ER - TY - JOUR AU - Calvo, A. M. AU - Bok, J. AU - Brooks, W. AU - Keller, N. P. PY - 2004 DA - 2004// TI - veA is required for toxin and sclerotial production in Aspergillus parasiticus JO - Appl Environ Microbiol VL - 70 UR - https://doi.org/10.1128/AEM.70.8.4733-4739.2004 DO - 10.1128/AEM.70.8.4733-4739.2004 ID - Calvo2004 ER - TY - JOUR AU - Medema, M. H. AU - Blin, K. AU - Cimermancic, P. AU - de Jager, V. AU - Zakrzewski, P. AU - Michael, A. AU - Fischbach, M. A. AU - Weber, T. AU - Takano, E. AU - Breitling, R. PY - 2011 DA - 2011// TI - antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkr466 DO - 10.1093/nar/gkr466 ID - Medema2011 ER - TY - JOUR AU - Khaldi, N. AU - Seifuddin, F. T. AU - Turner, G. AU - Haft, D. AU - Nierman, W. C. AU - Wolfe, K. H. AU - Fedorova, N. D. PY - 2010 DA - 2010// TI - SMURF: genomic mapping of fungal secondary metabolite clusters JO - Fungal Genet Biol VL - 47 UR - https://doi.org/10.1016/j.fgb.2010.06.003 DO - 10.1016/j.fgb.2010.06.003 ID - Khaldi2010 ER - TY - JOUR AU - Chang, P. -. K. AU - Ehrlich, K. C. PY - 2011 DA - 2011// TI - Cyclopiazonic acid biosynthesis by Aspergillus flavus JO - Toxin Rev VL - 30 UR - https://doi.org/10.3109/15569543.2011.576795 DO - 10.3109/15569543.2011.576795 ID - Chang2011 ER - TY - JOUR AU - Holzapfel, C. W. PY - 1968 DA - 1968// TI - The isolation and structure of cyclopiazonic acid, a toxic metabolite of Penicillium cyclopium Westling JO - Tetrahedron VL - 24 UR - https://doi.org/10.1016/0040-4020(68)88113-X DO - 10.1016/0040-4020(68)88113-X ID - Holzapfel1968 ER - TY - JOUR AU - Chang, P. -. K. AU - Horn, B. W. AU - Dorner, J. W. PY - 2009 DA - 2009// TI - Clustered genes involved in cyclopiazonic acid production are next to the aflatoxin biosynthesis gene cluster in Aspergillus flavus JO - Fungal Genet Biol VL - 46 UR - https://doi.org/10.1016/j.fgb.2008.11.002 DO - 10.1016/j.fgb.2008.11.002 ID - Chang2009 ER - TY - JOUR AU - Chang, P. K. AU - Abbas, H. K. AU - Weaver, M. A. AU - Ehrlich, K. C. AU - Scharfenstein, L. L. AU - Cotty, P. J. PY - 2012 DA - 2012// TI - Identification of genetic defects in the atoxigenic biocontrol strain Aspergillus flavus K49 reveals the presence of a competitive recombinant group in field populations JO - Int J Food Microbiol VL - 154 UR - https://doi.org/10.1016/j.ijfoodmicro.2012.01.005 DO - 10.1016/j.ijfoodmicro.2012.01.005 ID - Chang2012 ER - TY - JOUR AU - Wollenberg, R. D. AU - Saei, W. AU - Westphal, K. R. AU - Klitgaard, C. S. AU - Nielsen, K. L. AU - Lysøe, E. AU - Gardiner, D. M. AU - Wimmer, R. AU - Sondergaard, T. E. AU - Sørensen, J. L. PY - 2017 DA - 2017// TI - Chrysogine biosynthesis is mediated by a two-module nonribosomal peptide synthetase JO - J Nat Prod VL - 80 UR - https://doi.org/10.1021/acs.jnatprod.6b00822 DO - 10.1021/acs.jnatprod.6b00822 ID - Wollenberg2017 ER - TY - JOUR AU - Shah, A. J. AU - Tilburn, J. AU - Adlard, M. W. AU - Arst Jr, H. N. PY - 1991 DA - 1991// TI - pH regulation of penicillin production in Aspergillus nidulans JO - FEMS Microbiol Lett VL - 77 UR - https://doi.org/10.1111/j.1574-6968.1991.tb04349.x DO - 10.1111/j.1574-6968.1991.tb04349.x ID - Shah1991 ER - TY - JOUR AU - Lopez-Diam, T. M. AU - Flannigan, B. PY - 1997 DA - 1997// TI - Production of patulin and cytochalasin E by Aspergillus clavatus during malting of barley and wheat JO - Int J Food Microbiol VL - 35 UR - https://doi.org/10.1016/S0168-1605(96)01211-1 DO - 10.1016/S0168-1605(96)01211-1 ID - Lopez-Diam1997 ER - TY - JOUR AU - Zargar, S. PY - 2014 DA - 2014// TI - Inhibitory effect of various aqueous medicinal plant extracts on citrinin production a fungal biomass by Penicillium notatum and Aspergillus niger JO - IAIM VL - 1 ID - Zargar2014 ER - TY - JOUR AU - Wang, X. AU - Wang, J. AU - Lai, D. AU - Wang, W. AU - Dai, J. AU - Zhou, L. AU - Liu, Y. PY - 2017 DA - 2017// TI - Ustiloxin G, a new cyclopeptide mycotoxin from rice false smut balls JO - Toxins VL - 9 UR - https://doi.org/10.3390/toxins9020054 DO - 10.3390/toxins9020054 ID - Wang2017 ER - TY - JOUR AU - Umemura, M. AU - Nagano, N. AU - Koike, H. AU - Kawano, J. AU - Ishii, T. AU - Miyamura, Y. AU - Kikuchi, M. AU - Tamano, K. AU - Yu, J. AU - Shin-ya, K. AU - Machida, M. PY - 2014 DA - 2014// TI - Characterization of the biosynthetic gene cluster for the ribosomally synthesized cyclic peptide ustiloxin B in Aspergillus flavus JO - Fungal Genet Biol VL - 68 UR - https://doi.org/10.1016/j.fgb.2014.04.011 DO - 10.1016/j.fgb.2014.04.011 ID - Umemura2014 ER - TY - JOUR AU - Ha, G. T. AU - Wong, R. K. AU - Zhang, Y. PY - 2011 DA - 2011// TI - Huperzine a as potential treatment of Alzheimer's disease: an assessment on chemistry, pharmacology, and clinical studies JO - Chem Biodivers VL - 8 UR - https://doi.org/10.1002/cbdv.201000269 DO - 10.1002/cbdv.201000269 ID - Ha2011 ER - TY - JOUR AU - Holm, D. K. AU - Peterson, L. M. AU - Klitgaard, A. AU - Knudsen, P. B. AU - Jarczynska, Z. D. AU - Nielsen, K. F. AU - Gotfredsen, C. H. AU - Larsen, T. O. AU - Mortensen, U. H. PY - 2014 DA - 2014// TI - Molecular and chemical characterization of the biosynthesis of the 6-MSA-derived meroterpenoid Yanuthone D in Aspergillus niger JO - Chem Biol VL - 21 UR - https://doi.org/10.1016/j.chembiol.2014.01.013 DO - 10.1016/j.chembiol.2014.01.013 ID - Holm2014 ER - TY - JOUR AU - Sunderhaus, J. D. AU - Sherman, D. H. AU - Williams, R. M. PY - 2011 DA - 2011// TI - Studies on the biosynthesis of the stephacidin and notoamide natural products: a stereochemical and genetic conundrum JO - Israel J Chem VL - 51 UR - https://doi.org/10.1002/ijch.201100016 DO - 10.1002/ijch.201100016 ID - Sunderhaus2011 ER - TY - JOUR AU - TePaske, M. R. AU - Gloer, J. B. AU - Wicklow, D. T. AU - Dowd, P. F. PY - 1992 DA - 1992// TI - Aflavarin and β-Aflatrem: new anti-insectan metabolites from the sclerotia of Aspergillus flavus JO - J Nat Prod VL - 55 UR - https://doi.org/10.1021/np50086a008 DO - 10.1021/np50086a008 ID - TePaske1992 ER - TY - JOUR AU - Cary, J. W. AU - Han, Z. AU - Yin, Y. AU - Lohmar, J. M. AU - Shantappa, S. AU - Harris-Coward, P. Y. AU - Mack, B. AU - Ehrlich, K. C. AU - Wei, Q. AU - Arroyo-Manzanares, N. AU - Uka, V. AU - Vanhaecke, L. AU - Bhatnagar, D. AU - Yu, J. AU - Nierman, W. C. AU - Johns, M. A. AU - Sorensen, D. AU - Shen, H. AU - De Saeger, S. AU - Diana Di Mavungu, J. AU - Calvo, A. M. PY - 2015 DA - 2015// TI - Transcriptome analysis of Aspergillus flavus reveals veA-dependent regulation of secondary metabolite gene clusters, including the novel aflavarin cluster JO - Eukaryot Cell VL - 14 UR - https://doi.org/10.1128/EC.00092-15 DO - 10.1128/EC.00092-15 ID - Cary2015 ER - TY - JOUR AU - Ramirez-Prado, J. H. AU - Moore, G. G. AU - Horn, B. W. AU - Carbone, I. PY - 2008 DA - 2008// TI - Characterization and population analysis of the mating-type genes in Aspergillus flavus and Aspergillus parasiticus JO - Fungal Genet Biol VL - 45 UR - https://doi.org/10.1016/j.fgb.2008.06.007 DO - 10.1016/j.fgb.2008.06.007 ID - Ramirez-Prado2008 ER - TY - JOUR AU - Tsui, C. K. -. M. AU - DiGuistini, S. AU - Wang, Y. AU - Feau, N. AU - Dhillon, B. AU - Bohlmann, J. AU - Hamelin, R. C. PY - 2013 DA - 2013// TI - Unequal recombination and evolution of the mating-type (MAT) loci in the pathogenic fungus Grosmannia clavigera and relatives JO - G3-Genes Genom Genet VL - 3 ID - Tsui2013 ER - TY - JOUR AU - Metzenberg, R. L. AU - Glass, N. L. PY - 1990 DA - 1990// TI - Mating type and mating strategies in Neurospora JO - BioEssays VL - 12 UR - https://doi.org/10.1002/bies.950120202 DO - 10.1002/bies.950120202 ID - Metzenberg1990 ER - TY - JOUR AU - Chang, P. -. K. AU - Ehrlich, K. C. PY - 2010 DA - 2010// TI - What does genetic diversity of Aspergillus flavus tell us about Aspergillus oryzae? JO - Int J Food Microbiol VL - 138 UR - https://doi.org/10.1016/j.ijfoodmicro.2010.01.033 DO - 10.1016/j.ijfoodmicro.2010.01.033 ID - Chang2010 ER - TY - JOUR AU - Ehrlich, K. C. AU - Chang, P. -. K. AU - Yu, J. AU - Cotty, P. J. PY - 2004 DA - 2004// TI - Aflatoxin biosynthesis cluster gene cypA is required for G aflatoxin formation JO - Appl Environ Microb VL - 70 UR - https://doi.org/10.1128/AEM.70.11.6518-6524.2004 DO - 10.1128/AEM.70.11.6518-6524.2004 ID - Ehrlich2004 ER - TY - JOUR AU - Breitenbach, M. AU - Weber, M. AU - Rinnerthaler, M. AU - Karl, T. AU - Breitenbach-Koller, L. PY - 2015 DA - 2015// TI - Oxidative stress in fungi: its function in signal transduction, interaction with plant hosts, and lignocellulose degradation JO - Biomol Ther VL - 5 ID - Breitenbach2015 ER - TY - JOUR AU - Ichinose, H. AU - Wariishi, H. PY - 2012 DA - 2012// TI - Heterologous expression and mechanistic investigation of a fungal cytochrome P450 (CYP5150A2): involvement of alternative redox partners JO - Arch Biochem Biophys VL - 518 UR - https://doi.org/10.1016/j.abb.2011.12.010 DO - 10.1016/j.abb.2011.12.010 ID - Ichinose2012 ER - TY - JOUR AU - Caza, M. AU - Kronstad, J. W. PY - 2013 DA - 2013// TI - Shared and distinct mechanisms of iron acquisition by bacterial and fungal pathogens of humans JO - Front Cell Infect Microbiol VL - 3 UR - https://doi.org/10.3389/fcimb.2013.00080 DO - 10.3389/fcimb.2013.00080 ID - Caza2013 ER - TY - STD TI - Horn BW, Gell RM, Singh R, Sorensen RB, Carbone I. Sexual reproduction in Aspergillus flavus sclerotia: acquisition of novel alleles from soil populations and uniparental mitochondrial inheritance. PLoS One. 2016; https://doi.org/10.1371/journal.pone.0146169. ID - ref50 ER - TY - JOUR AU - Garbelotto, M. AU - Gonthier, P. AU - Nicolotti, G. PY - 2007 DA - 2007// TI - Ecological constraints limit the fitness of fungal hybrids in the Heterobasidion annosum species complex JO - Appl Environ Microbiol VL - 73 UR - https://doi.org/10.1128/AEM.01135-07 DO - 10.1128/AEM.01135-07 ID - Garbelotto2007 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. AU - Pyshkin, A. V. AU - Sirotkin, L. V. AU - Vyahhi, N. AU - Tesler, G. AU - Alekseyev, M. A. AU - Pevzner, P. A. 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 - Cantarel, B. L. AU - Korf, I. AU - Robb, S. M. C. AU - Parra, G. AU - Ross, E. AU - Moore, B. AU - Holt, C. AU - Sánchez Alvarado, A. AU - Yandell, M. PY - 2008 DA - 2008// TI - MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.6743907 DO - 10.1101/gr.6743907 ID - Cantarel2008 ER - TY - JOUR AU - Lomsadze, A. AU - Ter-Hovhannisyan, V. AU - Chernoff, Y. O. AU - Borodovsky, M. PY - 2005 DA - 2005// TI - Gene identification in novel eukaryotic genomes by self-training algorithm JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki937 DO - 10.1093/nar/gki937 ID - Lomsadze2005 ER - TY - JOUR AU - Stanke, M. AU - Waack, S. PY - 2003 DA - 2003// TI - Gene prediction with a hidden Markov model and a new intron submodel JO - Bioinformatics VL - 19-Suppl 2 ID - Stanke2003 ER - TY - JOUR AU - Lechner, M. AU - Findeiss, S. AU - Steiner, L. AU - Marz, M. AU - Stadler, P. F. AU - Prohaska, S. J. PY - 2011 DA - 2011// TI - Proteinortho: detection of (co-) orthologs in large-scale analysis JO - BMC Bioinformatics VL - 12 UR - https://doi.org/10.1186/1471-2105-12-124 DO - 10.1186/1471-2105-12-124 ID - Lechner2011 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 - 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 - 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 - Young, M. D. AU - Wakefield, M. J. AU - Smyth, G. K. AU - Oshlack, A. PY - 2010 DA - 2010// TI - Gene ontology analysis for RNA-seq: accounting for selection bias JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-2-r14 DO - 10.1186/gb-2010-11-2-r14 ID - Young2010 ER - TY - JOUR AU - Tarailo-Graovac, M. AU - Chen, N. PY - 2009 DA - 2009// TI - Using RepeatMasker to identify repetitive elements in genomic sequences JO - Curr Protoc Bioinform VL - 25 ID - Tarailo-Graovac2009 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 -