Chapter 18.15 References and further reading

Chapter 18.15 References and further reading

Aebersold, R. (2003). Quantitative proteome analysis: methods and applications. Journal of Infectious Diseases, 187: S315-S320. DOI:

Ahuactzin-Pérez, M., Tlecuitl-Beristain, S., García-Dávila, J., Santacruz-Juárez, E., González-Pérez, M., Gutiérrez-Ruíz, M.C. & Sánchez, C. (2018). A novel biodegradation pathway of the endocrine-disruptor di(2-ethyl hexyl) phthalate by Pleurotus ostreatus based on quantum chemical investigation. Ecotoxicology and Environmental Safety, 147: 494-499. DOI:

Albertin, W. & Marullo, P. (2012). Polyploidy in fungi: evolution after whole-genome duplication. Proceedings of the Royal Society B: Biological Sciences, 279: 2497-2509. DOI:

Anonymous editorial (2011). Method of the Year 2011. Nature Methods, 9: 1. DOI:

Appasani, K. (2018). Genome Editing and Engineering: From TALENs, ZFNs and CRISPRs to Molecular Surgery. Cambridge, UK: Cambridge University Press. ISBN: 9781107170377. VIEW on Amazon.

Aurrecoechea, C., Barreto, A., Basenko, E.Y., Brestelli, J., Brunk, B.P. and 30 others. (2017). EuPathDB: the eukaryotic pathogen genomics database resource. Nucleic Acids Research, 45: D581–D591. DOI:

Austin, H.P., Allen, M.D., Donohoe, B.S., Rorrer, N.A., Kearns, F.L. and 16 others. (2018). Characterisation and engineering of a plastic-degrading aromatic polyesterase. Proceedings of the National Academy of Sciences of the United States of America, 115: E4350-E4357. DOI:

Baker, S.E., Thykaer, J., Adney, W.S., Brettin, T.S., Brockman, F.J., d’Haeseleer, P., Martinez, A.D., Miller, R.M., Rokhsar, D.S., Schadt, C.W., Torok, T., Tuskan, G., Bennett, J., Berka, R.M., Briggs, S.P., Heitman, J., Taylor, J., Turgeon, B.G., Werner-Washburne, M. & Himmel, M.E. (2008). Fungal genome sequencing and bioenergy. Fungal Biology Reviews, 22: 1-5. DOI:

Balba, H. (2007). Review of strobilurin fungicide chemicals. Journal of Environmental Science and Health, Part B, 42: 441-451. DOI:

Ballance, D.J., Buxton F.P. & Turner, G. (1983). Transformation of Aspergillus nidulans by the orotidine-5′-phosphate decarboxylase gene of Neurospora crassa. Biochemical and Biophysical Research Communications, 112: 284-289. DOI:

Bartlett, D.W., Clough, J.M., Godwin, J.R., Hall, A.A., Hamer, M., Parr-Dobrzanski, B. (2002). The strobilurin fungicides. Pest Management Science, 58: 649-662. DOI:

Belanger, E.S., Yang, E. & Forrest, G.N. (2015). Combination antifungal therapy: when, where, and why. Current Fungal Infection Reports, 2: 67-75.

Berovic, M. & Podgornik, B.B. (2015). Cultivation of medicinal fungi in bioreactors. In: Mushroom Biotechnology: Developments and Applications, (ed M. Petre), pp. 155-171. London: Academic Press, an imprint of Elsevier Inc. 242 pp. ISBN: 9780128027943. DOI:

Bhadauria, V., Zhao, W.-S., Wang, L.-X., Zhang, Y., Liu, J.-H., Yang, J., Kong, L.-A. & Peng, Y.-L. (2007). Advances in fungal proteomics. Microbiological Research, 162: 193-200. DOI:

Boucher, H.W., Groll, A.H., Chiou, C.C. & Walsh, T.J. (2004). Newer systemic antifungal agents: pharmacokinetics, safety and efficacy. Drugs, 64: 1997-2020. DOI:

Bowman, S.M. & Free, S.J. (2006). The structure and synthesis of the fungal cell wall. BioEssays, 28: 799-808. DOI:

Brent, K.J. & Hollomon, D.W. (2007). Fungicide resistance in crop pathogens: how can it be managed? FRAC Monograph No. 1 (second, revised edition). 60 pp. Brussels, Belgium: Published by the Fungicide Resistance Action Committee, a Technical Sub-Group of Croplife International. ISBN 90-72398-07-6. URL:

Bunnik, E.M. & Le Roch, K.G. (2013). An introduction to functional genomics and systems biology. Advances in Wound Care, 2: 490-498. DOI:

Burnie, J.P., Carter, T.L., Hodgetts, S.J. & Matthews, R.C. (2006). Fungal heat-shock proteins in human disease. FEMS Microbiology Reviews, 30: 53-88. DOI:

Buxton, F.P., Gwynne, D.I. & Davies, R.W. (1985). Transformation of Aspergillus niger using the argB gene of Aspergillus nidulans. Gene, 37: 207−214. DOI:

Camacho-Morales, R.L. & Sánchez, J.E. (2015). Biotechnological use of fungi for the degradation of recalcitrant agro-pesticides. In: Mushroom Biotechnology: Developments and Applications, (ed M. Petre), pp. 203-214. London: Academic Press, an imprint of Elsevier Inc. 242 pp. ISBN: 9780128027943. DOI:

Caracuel-Rios, Z. & Talbot, N.J. (2008). Silencing the crowd: high-throughput functional genomics in Magnaporthe oryzae. Molecular Microbiology, 68: 1341–1344. DOI:

Case, M.E., Schweizer, M., Kushner, S.R. & Giles, N.H. (1979). Efficient transformation of Neurospora crassa by utilizing hybrid plasmid DNA. Proceedings of the National Academy of Sciences of the United States of America, 76: 5259-5263. URL:

Castanera, R., López-Varas, L., Borgognone, A. LaButti, K., Lapidus, A., Schmutz, J., Grimwood, J., Pérez, G., Pisabarro, A.G., Grigoriev, I.V., Stajich, J.E. & Ramírez, L. (2016). Transposable elements versus the fungal genome: impact on whole-genome architecture and transcriptional profiles. PLoS Genetics, 12: article e1006108. DOI:

Ceccaldi, R., Rondinelli, B. & D’Andrea, A.D. (2016). Repair pathway choices and consequences at the double-strand break. Trends in Cell Biology, 26: 52-64. DOI:

Cecil, J.A. & Wenzel, R.P. (2009). Voriconazole: a broad-spectrum triazole for the treatment of invasive fungal infections. Expert Review of Hematology, 2: 237-254. DOI:

Chen, J., Lai, Y., Wang, L., Zhai, S., Zou, G., Zhou, Z., Cui, C. & Wang, S. (2017). CRISPR/Cas9-mediated efficient genome editing via blastospore-based transformation in entomopathogenic fungus Beauveria bassiana. Scientific Reports, 7: article 45763. DOI:

Chiu, S.W., Wang, Z.M., Leung, T.M. & Moore, D. (2000). Nutritional value of Ganoderma extract and assessment of its genotoxicity and anti-genotoxicity using comet assays of mouse lymphocytes. Food and Chemical Toxicology, 38: 173-178. DOI: CLICK HERE to download a full-text PDF.

Cho, Y., Davis, J.W., Kim, K.-H., Wang, J., Sun, Q.-H., Cramer, R.A. Jr, Lawrence, C.B. (2006). A high throughput targeted gene disruption method for Alternaria brassicicola functional genomics using linear minimal element (LME) constructs. Molecular Plant-Microbe Interactions, 19: 7-15. DOI:

Courtecuisse, R. (2001). Current trends and perspectives for the global conservation of fungi. In: Fungal Conservation: Issues and Solutions (eds D. Moore, M. M. Nauta, S.E. Evans & M. Rotheroe), pp. 7-18. Cambridge, UK: Cambridge University Press. ISBN-10: 0521048184, ISBN-13: 978-0521048187. VIEW on Amazon.

Cowen, L.E. (2008). The evolution of fungal drug resistance: modulating the trajectory from genotype to phenotype. Nature Reviews Microbiology, 6: 187-198. DOI:

Da Silva Ferreira, M.E., Colombo, A.L., Paulsen, I., Ren, Q., Wortman, J., Huang, J., Goldman, M.H.S. & Goldman, G.H. (2005). The ergosterol biosynthesis pathway, transporter genes, and azole resistance in Aspergillus fumigatus. Medical Mycology, 43: S313-S319. DOI:

Delneri, D., Brancia, F.L. & Oliver, S.G. (2001). Towards a truly integrative biology through the functional genomics of yeast. Current Opinion in Biotechnology, 12: 87-91. DOI:

Dominguez, J.M., Kelly, V.A., Kinsman, O.S., Marriott, M.S., Gomez de las Heras, F. & Martin, J.J. (1998). Sordarins: a new class of antifungals with selective inhibition of the protein synthesis elongation cycle in yeasts. Antimicrobial Agents and Chemotherapy, 42: 2274-2278. URL:

Doudna, J.A. & Charpentier, E. (2014). The new frontier of genome engineering with CRISPR-Cas9. Science, 346: article 1258096. DOI:

Dunn, D.A. & Pinkert, C.A. (2014). Gene editing. In: Transgenic Animal Technology. A Laboratory Handbook (3rd edition), (ed C.A. Pinkert), pp. 229-248. London: Elsevier Inc. ISBN 9780124104907. DOI:

Dupont, S., Lemetais, G., Ferreira, T., Cayot, P., Gervais, P. & Beney, L. (2012). Ergosterol biosynthesis: a fungal pathway for life on land? Evolution, 66: 2961-2968. DOI:

Dyer, P.S., Munro, C.A. & Bradshaw, R.E. (2017). Fungal genetics. Chapter 5 in: Oxford Textbook of Medical Mycology, (eds C.C. Kibbler,‎ R. Barton,‎ N.A.R. Gow,‎ S. Howell,‎ D.M. MacCallum & R.J. Manuel), pp. 35-42. Oxford, UK: Oxford University Press. 400 pp. ISBN-10: 0198755384, ISBN-13: 978-0198755388. VIEW on Amazon.

Fernández, F.J. & Vega, M.C. (2013). Technologies to keep an eye on: alternative hosts for protein production in structural biology. Current Opinion in Structural Biology, 23: 365-373. DOI:

Ferrer-Parra, L., López-Nicolás, D.I., Martínez-Castillo, R., Montiel-Cina, J.P., Morales-Hernández, A.R., Ocaña-Romo, E., González Márquez, A., Portillo-Ojeda, M., Sánchez-Sánchez, D.F. & Sánchez, C. (2018). Partial characterization of esterases from Fusarium culmorum grown in media supplemented with di (2-ethyl hexyl phthalate) in solid-state and submerged fermentation. Mexican Journal of Biotechnology, 3: 82-94. DOI:

Fisher, M.C., Gow, N.A.R. & Gurr, S.J. (2016). Tackling emerging fungal threats to animal health, food security and ecosystem resilience. Philosophical Transactions of the Royal Society B: Biological Sciences, 371: 20160332. DOI:

Foster, S.J., Monahan, B.J., Bradshaw, R.E. (2006). Genomics of the filamentous fungi – moving from the shadow of the bakers yeast. Mycologist, 20: 10-14. DOI:

Galagan, J.E., Henn, M.R., Ma, L.-J., Cuomo, C.A. & Birren, B. (2005). Genomics of the fungal kingdom: insights into eukaryotic biology. Genome Research, 15: 1620-1631. DOI:

Gao, D. & Wen, Z.-D. (2015). Phthalate esters in the environment: a critical review of their occurrence, biodegradation, and removal during wastewater treatment processes. The Science Of The Total Environment, 541: 986-1001. DOI:

Garbati, M.A., Alasmari, F.A., Al-Tannir, M.A. & Tleyjeh, I.M. (2012). The role of combination antifungal therapy in the treatment of invasive aspergillosis: a systematic review. International Journal of Infectious Diseases, 16: e76-e81. DOI:

Garcia-Rubio, R., Cuenca-Estrella, M. & Mellado, E. (2017). Triazole resistance in Aspergillus species: an emerging problem. Drugs, 77: 599-613. DOI:

Gauthier, G.M. (2015). Dimorphism in fungal pathogens of mammals, plants, and insects. PLoS Pathogens, 11: e1004608 (7 pp). DOI:

Gehrmann, T., Pelkmans, J.F., Lugones, L.G., Wösten, H.A.B., Abeel, T. & Reinders, M.J.T. (2016). Schizophyllum commune has an extensive and functional alternative splicing repertoire. Scientific Reports, 6: article 33640. DOI:

Ghosh, J.S. (2016). Solid state fermentation and food processing: a short review. Journal of Nutrition & Food Sciences, 6: 453 (7 pages). DOI:

Gibson, G. & Muse, S. (2009). A Primer of Genome Science, 3rd Edn.  Basingstoke, UK: Sinauer Associates, Inc./Macmillan Publishers Limited. Pp.350. ISBN-10: 0878932364, ISBN-13: 978-0878932368. VIEW on Amazon.

Gladyshev, E. (2017). Repeat-Induced Point mutation (RIP) and other genome defense mechanisms in fungi. Microbiology Spectrum, 5: FUNK-0042-2017. DOI:

Gow, N.A.R., Latge, J.-P. & Munro, C.A. (2017). The fungal cell wall: structure, biosynthesis, and function. Microbiology Spectrum, 5: FUNK-0035-2016. DOI:

Gressler, M., Hortschansky, P., Geib, E. & Brock, M. (2015). A new high-performance heterologous fungal expression system based on regulatory elements from the Aspergillus terreus terrein gene cluster. Frontiers in Microbiology, 6: 184. DOI:

Grigoriev, I.V., Nikitin, R., Haridas, S., Kuo, A., Ohm, R., Otillar, R., Riley, R., Salamov, A., Zhao, X., Korzeniewski, F., Smirnova, T., Nordberg, H., Dubchak, I. & Shabalov, I. (2014). MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Research, 42: D699-D704. DOI:

Grützmann, K., Szafranski, K., Pohl, M., Voigt, K., Petzold, A. & Schuster, S. (2014). Fungal alternative splicing is associated with multicellular complexity and virulence: a genome-wide multi-species study. DNA Research, 21: 27-39. DOI:

Gumber, K., Sidhu, A. & Sharma, V.K. (2017). In silico rationalized novel low molecular weight 1,2,4-triazolyldithiocarbamates: design, synthesis, and mycocidal potential. Russian Journal of Applied Chemistry, 90: 993-1004. DOI:

Hauser, R. & Calafat, A.M. (2005). Phthalates and human health. Occupational and Environmental Medicine, 62: 806-818. DOI:

Heitman, J., Howlett, B.J., Crous, P.W., Stukenbrock, E.H., James, T.Y. & Gow, N.A.R. (2017). The Fungal Kingdom. Washington, DC: ASM Press. ISBN: 9781555819576. DOI:

Hibbett, D.S., Stajich, J.E. & Spatafora, J.W. (2013). Toward genome-enabled mycology. Mycologia, 105: 1339-1349. DOI:

Honda, S. & Selker, E.U. (2009). Tools for fungal proteomics: multifunctional Neurospora vectors for gene replacement, protein expression and protein purification. Genetics, 182: 11-23. DOI:

Horgan, R.P. & Kenny, L.C. (2011). ‘Omic’ technologies: genomics, transcriptomics, proteomics and metabolomics. The Obstetrician & Gynaecologist, 13: 189-195. DOI:

Howard, S.J. & Arendrup, M.C. (2011). Acquired antifungal drug resistance in Aspergillus fumigatus: epidemiology and detection. Medical Mycology, 49: S90-S95. DOI:

Idnurm, A., Bailey, A.M., Cairns, T.C., Elliott, C.E., Foster, G.D., Ianiri, G. & Jeon, J. (2017). A silver bullet in a golden age of functional genomics: the impact of Agrobacterium-mediated transformation of fungi. Fungal Biology and Biotechnology, 4: 6. DOI:

Irimia, M. & Roy, S.W. (2014). Origin of spliceosomal introns and alternative splicing. Cold Spring Harbor Perspectives in Biology, 6: article a016071. DOI:

Jewett, M.C., Hofmann, G. & Nielsen, J. (2006). Fungal metabolite analysis in genomics and phenomics. Current Opinion in Biotechnology, 17: 191-197. DOI:

Jin, L., Li, G., Yu, D., Huang, W., Cheng, C., Liao, S., Wu, Q. & Zhang, Y. (2017). Transcriptome analysis reveals the complexity of alternative splicing regulation in the fungus Verticillium dahlia. BMC Genomics, 18: 130. DOI:

Johnson, M.D. & Perfect, J.R. (2010). Use of antifungal combination therapy: agents, order, and timing. Current Fungal Infection Reports, 4: 87-95. DOI:

Jones, M.G. (2007). The first filamentous fungal genome sequences: Aspergillus leads the way for essential everyday resources or dusty museum specimens? Microbiology, 153: 1–6. DOI:

Karagiosis, S.A. & Baker, S.E. (2012). Fungal Cell Factories. In: Food and Industrial Bioproducts and Bioprocessing, (ed N. T. Dunford). Oxford, UK: Wiley-Blackwell. DOI:

Kaznessis, Y.N. (2007).  Models for synthetic biology. BMC Systems Biology, 1: 47 doi:10.1186/1752-0509-1-47. Open source online at: DOI:

Kelly, M.K. & Hynes, M.J. (1985). Transformation of Aspergillus niger by the amdS gene of Aspergillus nidulans. EMBO Journal, 4: 475-479. URL:

Kempken, F. & Kück, U. (1998). Transposons in filamentous fungi - facts and perspectives. BioEssays, 20: 652-659. DOI:<652::AID-BIES8>3.0.CO;2-K.

Khan, A.A., Bacha, N., Ahmad, B., Lutfullah, G., Farooq, U. & Cox, R.J. (2014). Fungi as chemical industries and genetic engineering for the production of biologically active secondary metabolites. Asian Pacific Journal of Tropical Biomedicine, 4: 859-870. DOI:

Klipp, E., Liebermeister, W., Wierling, C., Kowald, A., Lehrach, H. & Herwig, R. (2009). Systems Biology: A Textbook. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KgaA. ISBN-10: 3527318747, ISBN-13: 978-3527318742. VIEW on Amazon.

Krappmann, S. (2007). Gene targeting in filamentous fungi: the benefits of impaired repair. Fungal Biology Reviews, 21: 25-29. DOI:

Krishnan, B.R., James, K.D., Polowy, K., Bryant, B.J., Vaidya, A., Smith, S. & Laudeman, C.P. (2017). CD101, a novel echinocandin with exceptional stability properties and enhanced aqueous solubility. The Journal of Antibiotics, 70: 130-135. DOI:

Lamoth, F., Juvvadi, P.R. & Steinbach, W.J. (2016). Heat shock protein 90 (Hsp90): A novel antifungal target against Aspergillus fumigatus. Critical Reviews in Microbiology, 42: 310-321. DOI:

Li, L., An, M., Shen, H., Huang, X., Yao, X., Liu, J., Zhu, F., Zhang, S., Chen, S., He, L., Zhang, J., Zou, Z. & Jiang, Y. (2015). The non-Geldanamycin Hsp90 inhibitors enhanced the antifungal activity of fluconazole. American Journal of Translational Research, 7: 2589-2602. URL:

Lipshutz, R.J., Fodor, S.P., Gingeras, T.R. & Lockhart, D.J. (1999). High density synthetic oligonucleotide arrays. Nature Genetics, 21 (January supplement): 20-24. DOI:

Mares, D., Romagnoli, C., Andreotti, E., Forlani, G., Guccione, S. & Vicentini, C.B. (2006). Emerging antifungal azoles and effects on Magnaporthe grisea. Mycological Research, 110: 686-696. DOI:

Mast, N., Zheng, W., Stout, C.D. & Pikuleva, I.A. (2013). Antifungal azoles: structural insights into undesired tight binding to cholesterol-metabolizing CYP46A1. Molecular Pharmacology, 84: 86-94. DOI:

Mazu, T.K., Bricker, B.A., Flores-Rozas, H. & Ablordeppey, S.Y. (2016). The mechanistic targets of antifungal agents: an overview. Mini-Reviews in Medicinal Chemistry, 16: 555-578. DOI:

McCluskey, K. & Baker, S.E. (2017). Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era. Mycology, 8: 67-83. DOI:

McNutt, M. (2015). Editorial: breakthrough to genome editing. Science, 350: 1445. DOI:

Meyer, V., Nevoigt, E. & Wiemann, P. (2016). The art of design. Fungal Genetics and Biology, 89: 1-2. DOI:

Meyer, V., Wanka, F., van Gent, J., Arentshorst, M., van den Hondel, C.A.M.J.J. & Ram, A.F.J. (2011). Fungal gene expression on demand: an inducible, tunable, and metabolism-independent expression system for Aspergillus niger. Applied and Environmental Microbiology, 77: 2975-2983. DOI:

Michielse, C.B., Hooykaas, P.J.J., van den Hondel, C.A.M.J.J. & Ram, A.F.J. (2005). Agrobacterium-mediated transformation as a tool for functional genomics in fungi. Current Genetics, 48: 1-17. DOI:

Minter, D.W. (2001). Fungal conservation in Cuba. In: Fungal Conservation: Issues and Solutions (eds D. Moore, M. M. Nauta, S.E. Evans & M. Rotheroe), pp. 182-196. Cambridge, UK: Cambridge University Press. ISBN-10: 0521048184, ISBN-13: 978-0521048187. VIEW on Amazon.

Mishra, N.C. & Tatum, E.L. (1973). Non-Mendelian inheritance of DNA-induced inositol independence in Neurospora. Proceedings of the National Academy of Sciences of the United States of America, 70: 3875-3879. URL:

Mohanta, T.K., Bashir, T., Hashem, A., Abd-Allah, E.F. & Bae, H. (2017). Genome editing tools in plants. Genes, 8: 399. DOI:

Monk, B.C. & Goffeau, A. (2008). Outwitting multidrug resistance to antifungals. Science, 321: 367-369. DOI:

Moore, D. & Novak Frazer, L. (2002). Essential Fungal Genetics. New York: Springer-Verlag Inc. ISBN-10: 0387953671, ISBN-13: 978-0387953670. VIEW on Amazon.

Morton, V. & Staub, T. (2008). A short history of fungicides. This is an American Phytopathological Society APSnet feature available online at this DOI:

Muszewska, A., Steczkiewicz, K., Stepniewska-Dziubinska, M. & Ginalski, K. (2017). Cut-and-paste transposons in fungi with diverse lifestyles. Genome Biology and Evolution, 9: 3463-3477. DOI:

Nagasaki, M., Saito, A., Doi, A., Matsuno, H. & Miyano, S. (2009). Foundations of Systems Biology. London: Springer-Verlag. ISBN-10: 1848820224, ISBN-13: 978-1848820227. VIEW on Amazon.

Nevalainen, H. & Peterson, R. (2014). Making recombinant proteins in filamentous fungi - are we expecting too much? Frontiers in Microbiology, 5: 75. DOI:

Nielsen, J.C. & Nielsen, J. (2017). Development of fungal cell factories for the production of secondary metabolites: linking genomics and metabolism. Synthetic and Systems Biotechnology, 2: 5-12. DOI:

Nigg, M. & Bernier, L. (2016). From yeast to hypha: defining transcriptomic signatures of the morphological switch in the dimorphic fungal pathogen Ophiostoma novo-ulmi. BMC Genomics, 17: 920 (16 pp). DOI:

Nødvig, C.S., Nielsen, J.B., Kogle, M.E. & Mortensen, U.H. (2015). A CRISPR-Cas9 system for genetic engineering of filamentous fungi. PLoS ONE, 10: article e0133085. DOI:

Nowrousian, M. (2007). Of patterns and pathways: microarray technologies for the analysis of filamentous fungi. Fungal Biology Reviews, 21: 171-178. DOI:

Nowrousian, M. (2014a). Genomics and transcriptomics to analyze fruiting body development. In: The Mycota, Fungal Genomics, XIII: (2nd ed.) (ed M. Nowrousian), pp. 149-172.  Berlin, Heidelberg: Springer-Verlag.  ISBN: 978-3-642-45217-8. DOI:

Nowrousian, M. (ed) (2014b). In: The Mycota, Fungal Genomics, XIII (2nd ed.), Fungal Genomics. Berlin, Heidelberg: Springer-Verlag.  ISBN: 978-3-642-45217-8. DOI:

Oakley, C.E., Ahuja, M., Sun, W.-W., Entwistle, R., Akashi, T., Yaegashi, J., Guo, C.-J., Cerqueira, G.C., Russo, W.J., Wang, C.C.C., Chiang, Y.-M. & Oakley, B.R. (2016). Discovery of McrA, a master regulator of Aspergillus secondary metabolism. Molecular Microbiology, 103: 347-365. DOI:

Odds, F.C. (2001). Sordarin antifungal agents. Expert Opinion on Therapeutic Patents, 11: 283-294. DOI:

Panaretou, B. & Zhai, C. (2008). The heat shock proteins: their roles as multi-component machines for protein folding. Fungal Biology Reviews, 22: 110-119. DOI:

Parnell, L.D., Lindenbaum, P., Shameer, K., Dall’Olio, G.M., Swan, D.C., Jensen, L.J., Cockell, S.J., Pedersen, B.S., Mangan, M.E., Miller, C.A. & Albert, I. (2011). BioStar: an online question & answer resource for the bioinformatics community. PLoS Computational Biology, 7: article e1002216. DOI:

Pastore, A. & Puccio, H. (2013). Frataxin: a protein in search for a function. Journal of Neurochemistry, 126: 43-52. DOI:

Peter, J., De Chiara, M., Friedrich, A., Yue, J.-X., Pflieger, D. and 16 others. (2018). Genome evolution across 1,011 Saccharomyces cerevisiae isolates. Nature, 556: 339-344. DOI:

Petre, M. (ed) (2015). Mushroom Biotechnology: Developments and Applications. London: Academic Press, an imprint of Elsevier Inc. 242 pp. ISBN: 9780128027943. VIEW on Amazon.

Phasha, M.M., Wingfield, B.D., Coetzee, M.P.A., Santana, Q.C., Fourie, G. & Steenkamp, E.T. (2017). Architecture and distribution of introns in core genes of four Fusarium species. G3: Genes, Genomes, Genetics, 7: 3809-3820. DOI:

Pritham, E.J. (2009). Transposable elements and factors influencing their success in eukaryotes. Journal of Heredity, 100: 648-655. DOI:

Pudake, R.N., Kumari, M., Sahu, B.B. & Sultan, E. (2017). Targeted gene disruption tools for fungal genomics. In:  Modern Tools and Techniques to Understand Microbes, (eds A.Varma & A. Sharma), pp 81-102. Cham, Switzerland: Springer Inc. ISBN 978-3-319-49195-0. DOI:

Purnomo, A.S., Mori, T., Takagi, K. & Kondo, R. (2011). Bioremediation of DDT contaminated soil using brown-rot fungi. International Biodeterioration & Biodegradation, 65: 691-695. DOI:

Ranatunga, W., Gakh, O., Galeano, B.K., Smith, D.Y., Söderberg, C.A.G., Al-Karadaghi, S., Thompson, J.R. & Isaya, G. (2016). Architecture of the yeast mitochondrial iron-sulfur cluster assembly machinery: the sub-complex formed by the iron donor, Yfh1 protein, and the scaffold, Isu1 protein. Journal of Biological Chemistry, 291: 10378-10398. DOI:

Richards, T.A., Leonard, G., Soanes, D.M. & Talbot, N.J. (2011). Gene transfer into the fungi. Fungal Biology Reviews, 25: 98-110. DOI: Roberts, S.E. & Gladfelter, A.S. (2016) Nuclear dynamics and cell growth in fungi. In: The Mycota, Vol. I. Growth, Differentiation and Sexuality, 3rd edn, (ed J. Wendland), pp. 27-46. Cham, Switzerland: Springer International Publishing. ISBN: 978-3-319-25842-3. DOI:

Rokas, A. (2009). The effect of domestication on the fungal proteome. Trends in Genetics, 25: 60-63. DOI:

Roper, M., Simonin, A., Hickey, P.C., Leeder, A. & Glass, N.L. (2013). Nuclear dynamics in a fungal chimera. Proceedings of the National Academy of Sciences of the United States of America, 110: 12875-12880. DOI:

Ross-Macdonald, P., Coelho, P.S., Roemer, T., Agarwal, S., Kumar, A., Jansen, R., Cheung, K.H., Sheehan, A., Symoniatis, D., Umansky, L., Heidtman, M., Nelson, F.K., Iwasaki, H., Hager, K., Gerstein, M., Miller, P., Roeder, G.S. & Snyder, M. (1999). Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature, 402: 413-418. DOI:

Sant, D.G., Tupe, S.G., Ramana, C.V. & Deshpande, M.V. (2016). Fungal cell membrane - promising drug target for antifungal therapy. Journal of Applied Microbiology, 121: 1498-1510. DOI:

Satyanarayana, T., Deshmukh, S. & Johri, B.N. (2017). Developments in Fungal Biology and Applied Mycology. Singapore: Springer Nature Singapore Pte Ltd. ISBN: 978-981-10-4767-1. DOI:

Sauter, H., Steglich, W. & Anke, T. (1999). Strobilurins: evolution of a new class of active substances. Angewandte Chemie International Edition, 38: 1328-1349. DOI:<1328::AID-ANIE1328>3.0.CO;2-1.

Scharf, D.H. & Brakhage, A.A. (2013). Engineering fungal secondary metabolism: a roadmap to novel compounds. Journal of Biotechnology, 163: 179-183. DOI:

Semighini, C.P. & Heitman, J. (2009). Dynamic duo takes down fungal villains. Proceedings of the National Academy of Sciences of the U.S.A., 106: 2971-2972. DOI: Shah, S.U. (2012). Importance of genotoxicity & S2A guidelines for. IOSR Journal of Pharmacy and Biological Sciences, 1: 43-54. DOI:

Sharma, K.K. (2015). Fungal genome sequencing: basic biology to biotechnology. Critical Reviews in Biotechnology, 36: 743-759. DOI:

Sharman, A. (2001). The many uses of a genome sequence. Genome Biology, 2: reports 4013.1-4013.4. DOI:

Silver, P.A., Way, J.C., Arnold, F.H. & Meyerowitz, J.T. (2014). Engineering explored. Nature, 509: 166-167. DOI:

Sims, A.H., Gent, M.E., Robson, G.D., Dunn-Coleman, N.S. & Oliver, S.G. (2004). Combining transcriptome data with genomic and cDNA sequence alignments to make confident functional assignments for Aspergillus nidulans genes. Mycological Research, 108: 853-857. DOI:

Slot, J.C., Townsend, J.P. & Wang, Z. (2017). Fungal gene cluster diversity and evolution. Advances in Genetics, 100: 141-178. DOI:

Stajich, J.E., Dietrich, F.S. & Roy, S.W. (2007). Comparative genomic analysis of fungal genomes reveals intron-rich ancestors. Genome Biology, 8: R223. DOI:

Stajich, J.E, Harris, T., Brunk, B.P., Brestelli, J., Fischer, S., Harb, O.S., Kissinger, J.C., Li, W., Nayak, V., Pinney, D.F., Stoeckert, C.J. & Roos, D.S. (2012). FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Research, 40: D675-D681. DOI:

Steenkamp, E.T., Wingfield, M.J., McTaggart, A.R. & Wingfield, B.D. (2018). Fungal species and their boundaries matter - definitions, mechanisms and practical implications. Fungal Biology Reviews, 32: 104-116. DOI:

Strom, N.B. & Bushley, K.E. (2016). Two genomes are better than one: history, genetics, and biotechnological applications of fungal heterokaryons. Fungal Biology and Biotechnology, 3: 4. DOI:

Stukenbrock, E.H. & Croll, D. (2014). The evolving fungal genome. Fungal Biology Reviews, 28: 1-12. DOI:

Sudheer, S., Alzorqi, I., Manickam, S. & Ali, A. (2018). Bioactive compounds of the wonder medicinal mushroom ‘Ganoderma lucidum’. In: Bioactive Molecules in Food. Reference Series in Phytochemistry, (eds J.M. Mérillon & K. Ramawat), pp 1-31. Cham, Switzerland: Springer International Publishing AG. ISBN: 978-3-319-54528-8. DOI:

Sugui, J.A., Chang, Y.C. & Kwon-Chung, K.J. (2005). Agrobacterium tumefaciens-mediated transformation of Aspergillus fumigatus: an efficient tool for insertional mutagenesis and targeted gene disruption. Applied and Environmental Microbiology, 71: 1798-1802. DOI:–1802.2005.

Tada, R., Latge, J.-P. & Aimanianda, V. (2013). Undressing the fungal cell wall/cell membrane - the antifungal drug targets. Current Pharmaceutical Design, 19: 3738-3747. DOI:

Taylor, J.W., Branco, S., Gao, C., Hann-Soden, C., Montoya, L., Sylvain, I. & Gladieux, P. (2017). Sources of fungal genetic variation and associating it with phenotypic diversity. Microbiology Spectrum, 5: FUNK-0057-2016. DOI:

Thangadurai, D., Sangeetha, J. & David, M. (2016). Fundamentals of Molecular Mycology. Waretown, NJ: Apple Academic Press. 194 pp. ISBN: 978-1771882538. VIEW on Amazon.

Todd, R., Forche, A. & Selmecki, A. (2017). Ploidy variation in fungi: polyploidy, aneuploidy, and genome evolution. Microbiology Spectrum, 5: FUNK-0051-2016. DOI:

Vicente, F., Basilio, A., Platas, G., Collado, J., Bills, G.F., González Del Val, A., Martín, J., Tormo, J.R., Harris, G.H., Zink, D.L., Justice, M., Nielsen Kahn, J. & Peláez, F. (2009). Distribution of the antifungal agents sordarins across filamentous fungi. Mycological Research, 113: 754-770. DOI:

Vincelli, P. (2012). QoI (Strobilurin) Fungicides: Benefits and Risks. An American Phytopathological Society Topics in Plant Pathology Feature Article available online at this DOI:

Ward, O.P. (2012). Production of recombinant proteins by filamentous fungi. Biotechnology Advances, 30: 1119-1139. DOI:

Weld, R.J., Plummer, K.M., Carpenter, M.A., Ridgway, H.J. (2006). Approaches to functional genomics in filamentous fungi. Cell Research, 16: 31-44.  DOI:

Winzeler, E.A., Shoemaker, D.D., Astromoff, A., Liang, H., Anderson, K. and 46 others. (1999). Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science, 285: 901-906. DOI:

Yandell, M. & Ence, D. (2012). A beginner’s guide to eukaryotic genome annotation. Nature Reviews Genetics, 13: 329-342. DOI:

Yan, Y.-M., Wang, X.-L., Luo, Q., Jiang, L.-P., Yang, C.-P., Hou, B., Zuo, Z.-L., Chen, Y.-B. & Cheng, Y.-X. (2015). Metabolites from the mushroom Ganoderma lingzhi as stimulators of neural stem cell proliferation. Phytochemistry, 114: 155-162. DOI:

Yang, H., Tong, J., Lee, C.W., Ha, S., Eom, S.H. & Im, Y.J. (2015). Structural mechanism of ergosterol regulation by fungal sterol transcription factor Upc2. Nature Communications, 6: article 6129. DOI:

Yoshida, S., Hiraga, K., Takehana, T., Taniguchi, I., Yamaji, H., Maeda, Y., Toyohara, K., Miyamoto, K., Kimura, Y. & Oda, K. (2016). A bacterium that degrades and assimilates poly(ethylene terephthalate). Science, 351: 1196-1199. DOI:

Zheng, Y.-M., Lin, F.-L., Gao, H., Zou, G., Zhang, J.-W., Wang, G.-Q., Chen, G.-D., Zhou, Z.-H., Yao, X.-S. & Hu, D. (2017). Development of a versatile and conventional technique for gene disruption in filamentous fungi based on CRISPR-Cas9 technology. Scientific Reports, 7: 9250. DOI:

Updated July, 2018