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Novel taxa of thermally dimorphic systemic pathogens in the Ajellomycetaceae (Onygenales).
K. Dukik, Muñoz, J. F. , Jiang, Y. , Feng, P. , Sigler, L. , J Stielow, B. , Freeke, J. , Jamalian, A. , van den Ende, B. Gerrits, McEwen, J. G. , Clay, O. K. , Schwartz, I. S. , Govender, N. P. , Maphanga, T. G. , Cuomo, C. A. , Moreno, L. F. , Kenyon, C. , Borman, A. M. , and de Hoog, S. , “Novel taxa of thermally dimorphic systemic pathogens in the Ajellomycetaceae (Onygenales).”, Mycoses, vol. 60, no. 5, pp. 296-309, 2017.
Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi.
R. A. Farrer, Martel, A. , Verbrugghe, E. , Abouelleil, A. , Ducatelle, R. , Longcore, J. E. , James, T. Y. , Pasmans, F. , Fisher, M. C. , and Cuomo, C. A. , “Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi.”, Nat Commun, vol. 8, p. 14742, 2017.
Microevolution of Serial Clinical Isolates of Cryptococcus neoformans var. grubii and C. gattii.
Y. Chen, Farrer, R. A. , Giamberardino, C. , Sakthikumar, S. , Jones, A. , Yang, T. , Tenor, J. L. , Wagih, O. , Van Wyk, M. , Govender, N. P. , Mitchell, T. G. , Litvintseva, A. P. , Cuomo, C. A. , and Perfect, J. R. , “Microevolution of Serial Clinical Isolates of Cryptococcus neoformans var. grubii and C. gattii.”, MBio, vol. 8, no. 2, 2017.
Exploring the genomic diversity of black yeasts and relatives (Chaetothyriales, Ascomycota).
M. M. Teixeira, Moreno, L. F. , Stielow, B. J. , Muszewska, A. , Hainaut, M. , Gonzaga, L. , Abouelleil, A. , Patané, J. S. L. , Priest, M. , Souza, R. , Young, S. , Ferreira, K. S. , Zeng, Q. , da Cunha, M. M. L. , Gladki, A. , Barker, B. , Vicente, V. A. , de Souza, E. M. , Almeida, S. , Henrissat, B. , Vasconcelos, A. T. R. , Deng, S. , Voglmayr, H. , Moussa, T. A. A. , Gorbushina, A. , Felipe, M. S. S. , Cuomo, C. A. , and G de Hoog, S. , “Exploring the genomic diversity of black yeasts and relatives (Chaetothyriales, Ascomycota).”, Stud Mycol, vol. 86, pp. 1-28, 2017.
Paracoccidioides spp. catalases and their role in antioxidant defense against host defense responses.
D. Tamayo, Muñoz, J. F. , Almeida, A. J. , Puerta, J. D. , Restrepo, Á. , Cuomo, C. A. , McEwen, J. G. , and Hernández, O. , “Paracoccidioides spp. catalases and their role in antioxidant defense against host defense responses.”, Fungal Genet Biol, vol. 100, pp. 22-32, 2017.
Whole Genome Sequence of the Heterozygous Clinical Isolate Candida krusei 81-B-5.
C. A. Cuomo, Shea, T. , Yang, B. , Rao, R. , and Forche, A. , “Whole Genome Sequence of the Heterozygous Clinical Isolate Candida krusei 81-B-5.”, G3 (Bethesda), 2017.
Tracing Genetic Exchange and Biogeography of Cryptococcus neoformans var. grubii at the Global Population Level.
J. Rhodes, Desjardins, C. A. , Sykes, S. M. , Beale, M. A. , Vanhove, M. , Sakthikumar, S. , Chen, Y. , Gujja, S. , Saif, S. , Chowdhary, A. , Lawson, D. John, Ponzio, V. , Colombo, A. Lopes, Meyer, W. , Engelthaler, D. M. , Hagen, F. , Illnait-Zaragozi, M. Teresa, Alanio, A. , Vreulink, J. - M. , Heitman, J. , Perfect, J. R. , Litvintseva, A. , Bicanic, T. , Harrison, T. S. , Fisher, M. C. , and Cuomo, C. A. , “Tracing Genetic Exchange and Biogeography of Cryptococcus neoformans var. grubii at the Global Population Level.”, Genetics, 2017.
Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans.
C. A. Desjardins, Giamberardino, C. , Sykes, S. M. , Yu, C. - H. , Tenor, J. L. , Chen, Y. , Yang, T. , Jones, A. M. , Sun, S. , Haverkamp, M. R. , Heitman, J. , Litvintseva, A. P. , Perfect, J. R. , and Cuomo, C. A. , “Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans.”, Genome Res, vol. 27, no. 7, pp. 1207-1219, 2017.
The Case for Adopting the "Species Complex" Nomenclature for the Etiologic Agents of Cryptococcosis.
K. J. Kwon-Chung, Bennett, J. E. , Wickes, B. L. , Meyer, W. , Cuomo, C. A. , Wollenburg, K. R. , Bicanic, T. A. , Castañeda, E. , Chang, Y. C. , Chen, J. , Cogliati, M. , Dromer, F. , Ellis, D. , Filler, S. G. , Fisher, M. C. , Harrison, T. S. , Holland, S. M. , Kohno, S. , Kronstad, J. W. , Lazera, M. , Levitz, S. M. , Lionakis, M. S. , May, R. C. , Ngamskulrongroj, P. , Pappas, P. G. , Perfect, J. R. , Rickerts, V. , Sorrell, T. C. , Walsh, T. J. , Williamson, P. R. , Xu, J. , Zelazny, A. M. , and Casadevall, A. , “The Case for Adopting the "Species Complex" Nomenclature for the Etiologic Agents of Cryptococcosis.”, mSphere, vol. 2, no. 1, 2017.
Transcriptional analysis of mating and pre-infection stages of the anther smut, Microbotryum lychnidis-dioicae.
S. San Toh, Chen, Z. , Schultz, D. J. , Cuomo, C. A. , and Perlin, M. H. , “Transcriptional analysis of mating and pre-infection stages of the anther smut, Microbotryum lychnidis-dioicae.”, Microbiology, 2017.
Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses.
S. R. Lockhart, Etienne, K. A. , Vallabhaneni, S. , Farooqi, J. , Chowdhary, A. , Govender, N. P. , Colombo, A. Lopes, Calvo, B. , Cuomo, C. A. , Desjardins, C. A. , Berkow, E. L. , Castanheira, M. , Magobo, R. E. , Jabeen, K. , Asghar, R. J. , Meis, J. F. , Jackson, B. , Chiller, T. , and Litvintseva, A. P. , “Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses.”, Clin Infect Dis, vol. 64, no. 2, pp. 134-140, 2017.
Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci.
C. A. Cuomo, Bakkeren, G. , Khalil, H. Badr, Panwar, V. , Joly, D. , Linning, R. , Sakthikumar, S. , Song, X. , Adiconis, X. , Fan, L. , Goldberg, J. M. , Levin, J. Z. , Young, S. , Zeng, Q. , Anikster, Y. , Bruce, M. , Wang, M. , Yin, C. , McCallum, B. , Szabo, L. J. , Hulbert, S. , Chen, X. , and Fellers, J. P. , “Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci.”, G3 (Bethesda), vol. 7, no. 2, pp. 361-376, 2017.
Zinc Cluster Transcription Factors Alter Virulence in Candida albicans.
L. Issi, Farrer, R. A. , Pastor, K. , Landry, B. , Delorey, T. , Bell, G. W. , Thompson, D. A. , Cuomo, C. A. , and Rao, R. P. , “Zinc Cluster Transcription Factors Alter Virulence in Candida albicans.”, Genetics, vol. 205, no. 2, pp. 559-576, 2017.
Comparative Genomics Integrated with Association Analysis Identifies Candidate Effector Genes Corresponding to Lr20 in Phenotype-Paired Puccinia triticina Isolates from Australia.
J. Qin Wu, Sakthikumar, S. , Dong, C. , Zhang, P. , Cuomo, C. A. , and Park, R. F. , “Comparative Genomics Integrated with Association Analysis Identifies Candidate Effector Genes Corresponding to Lr20 in Phenotype-Paired Puccinia triticina Isolates from Australia.”, Front Plant Sci, vol. 8, p. 148, 2017.
Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides.
J. F. Muñoz, Farrer, R. A. , Desjardins, C. A. , Gallo, J. E. , Sykes, S. , Sakthikumar, S. , Misas, E. , Whiston, E. A. , Bagagli, E. , Soares, C. M. A. , Teixeira, Mde M. , Taylor, J. W. , Clay, O. K. , McEwen, J. G. , and Cuomo, C. A. , “Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides.”, mSphere, vol. 1, no. 5, 2016.
A Multistate Toggle Switch Defines Fungal Cell Fates and Is Regulated by Synergistic Genetic Cues.
M. Z. Anderson, Porman, A. M. , Wang, N. , Mancera, E. , Huang, D. , Cuomo, C. A. , and Bennett, R. J. , “A Multistate Toggle Switch Defines Fungal Cell Fates and Is Regulated by Synergistic Genetic Cues.”, PLoS Genet, vol. 12, no. 10, p. e1006353, 2016.
Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans.
M. D. Leach, Farrer, R. A. , Tan, K. , Miao, Z. , Walker, L. A. , Cuomo, C. A. , Wheeler, R. T. , Brown, A. J. P. , Wong, K. Ho, and Cowen, L. E. , “Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans.”, Nat Commun, vol. 7, p. 11704, 2016.
Use of Multiple Sequencing Technologies To Produce a High-Quality Genome of the Fungus Pseudogymnoascus destructans, the Causative Agent of Bat White-Nose Syndrome.
K. P. Drees, Palmer, J. M. , Sebra, R. , Lorch, J. M. , Chen, C. , Wu, C. - C. , Bok, J. Woo, Keller, N. P. , Blehert, D. S. , Cuomo, C. A. , Lindner, D. L. , and Foster, J. T. , “Use of Multiple Sequencing Technologies To Produce a High-Quality Genome of the Fungus Pseudogymnoascus destructans, the Causative Agent of Bat White-Nose Syndrome.”, Genome Announc, vol. 4, no. 3, 2016.
Intracellular Action of a Secreted Peptide Required for Fungal Virulence.
C. M. Homer, Summers, D. K. , Goranov, A. I. , Clarke, S. C. , Wiesner, D. L. , Diedrich, J. K. , Moresco, J. J. , Toffaletti, D. , Upadhya, R. , Caradonna, I. , Petnic, S. , Pessino, V. , Cuomo, C. A. , Lodge, J. K. , Perfect, J. , Yates, J. R. , Nielsen, K. , Craik, C. S. , and Madhani, H. D. , “Intracellular Action of a Secreted Peptide Required for Fungal Virulence.”, Cell Host Microbe, vol. 19, no. 6, pp. 849-64, 2016.
Lower prevalence but similar fitness in a parasitic fungus at higher radiation levels near Chernobyl.
G. Aguileta, Badouin, H. , Hood, M. E. , Møller, A. P. , Le Prieur, S. , Snirc, A. , Siguenza, S. , Mousseau, T. A. , Shykoff, J. A. , Cuomo, C. A. , and Giraud, T. , “Lower prevalence but similar fitness in a parasitic fungus at higher radiation levels near Chernobyl.”, Mol Ecol, vol. 25, no. 14, pp. 3370-83, 2016.
Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts.
L. Ma, Chen, Z. , Huang, D. Wei, Kutty, G. , Ishihara, M. , Wang, H. , Abouelleil, A. , Bishop, L. , Davey, E. , Deng, R. , Deng, X. , Fan, L. , Fantoni, G. , Fitzgerald, M. , Gogineni, E. , Goldberg, J. M. , Handley, G. , Hu, X. , Huber, C. , Jiao, X. , Jones, K. , Levin, J. Z. , Liu, Y. , Macdonald, P. , Melnikov, A. , Raley, C. , Sassi, M. , Sherman, B. T. , Song, X. , Sykes, S. , Tran, B. , Walsh, L. , Xia, Y. , Yang, J. , Young, S. , Zeng, Q. , Zheng, X. , Stephens, R. , Nusbaum, C. , Birren, B. W. , Azadi, P. , Lempicki, R. A. , Cuomo, C. A. , and Kovacs, J. A. , “Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts.”, Nat Commun, vol. 7, p. 10740, 2016.
Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus Cryptococcus gattii.
R. A. Farrer, Voelz, K. , Henk, D. A. , Johnston, S. A. , Fisher, M. C. , May, R. C. , and Cuomo, C. A. , “Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus Cryptococcus gattii.”, Philos Trans R Soc Lond B Biol Sci, vol. 371, no. 1709, 2016.
Genome Sequence of Spizellomyces punctatus.
C. Russ, B Lang, F. , Chen, Z. , Gujja, S. , Shea, T. , Zeng, Q. , Young, S. , Cuomo, C. A. , and Nusbaum, C. , “Genome Sequence of Spizellomyces punctatus.”, Genome Announc, vol. 4, no. 4, 2016.
Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii.
R. A. Farrer, Desjardins, C. A. , Sakthikumar, S. , Gujja, S. , Saif, S. , Zeng, Q. , Chen, Y. , Voelz, K. , Heitman, J. , May, R. C. , Fisher, M. C. , and Cuomo, C. A. , “Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii.”, MBio, vol. 6, no. 5, pp. e00868-15, 2015.
The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia.
J. F. Muñoz, Gauthier, G. M. , Desjardins, C. A. , Gallo, J. E. , Holder, J. , Sullivan, T. D. , Marty, A. J. , Carmen, J. C. , Chen, Z. , Ding, L. , Gujja, S. , Magrini, V. , Misas, E. , Mitreva, M. , Priest, M. , Saif, S. , Whiston, E. A. , Young, S. , Zeng, Q. , Goldman, W. E. , Mardis, E. R. , Taylor, J. W. , McEwen, J. G. , Clay, O. K. , Klein, B. S. , and Cuomo, C. A. , “The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia.”, PLoS Genet, vol. 11, no. 10, p. e1005493, 2015.
Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes.
C. A. Desjardins, Sanscrainte, N. D. , Goldberg, J. M. , Heiman, D. , Young, S. , Zeng, Q. , Madhani, H. D. , Becnel, J. J. , and Cuomo, C. A. , “Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes.”, Nat Commun, vol. 6, p. 7121, 2015.
Finding a Missing Gene: EFG1 Regulates Morphogenesis in Candida tropicalis.
E. Mancera, Porman, A. M. , Cuomo, C. A. , Bennett, R. J. , and Johnson, A. D. , “Finding a Missing Gene: EFG1 Regulates Morphogenesis in Candida tropicalis.”, G3 (Bethesda), vol. 5, no. 5, pp. 849-56, 2015.
Genetic and phenotypic intra-species variation in Candida albicans.
M. P. Hirakawa, Martinez, D. A. , Sakthikumar, S. , Anderson, M. Z. , Berlin, A. , Gujja, S. , Zeng, Q. , Zisson, E. , Wang, J. M. , Greenberg, J. M. , Berman, J. , Bennett, R. J. , and Cuomo, C. A. , “Genetic and phenotypic intra-species variation in Candida albicans.”, Genome Res, vol. 25, no. 3, pp. 413-25, 2015.
Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus.
M. H. Perlin, Amselem, J. , Fontanillas, E. , San Toh, S. , Chen, Z. , Goldberg, J. , Duplessis, S. , Henrissat, B. , Young, S. , Zeng, Q. , Aguileta, G. , Petit, E. , Badouin, H. , Andrews, J. , Razeeq, D. , Gabaldón, T. , Quesneville, H. , Giraud, T. , Hood, M. E. , Schultz, D. J. , and Cuomo, C. A. , “Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus.”, BMC Genomics, vol. 16, p. 461, 2015.
Draft Genome Sequence of the Cellulolytic Fungus Chaetomium globosum.
C. A. Cuomo, Untereiner, W. A. , Ma, L. - J. , Grabherr, M. , and Birren, B. W. , “Draft Genome Sequence of the Cellulolytic Fungus Chaetomium globosum.”, Genome Announc, vol. 3, no. 1, 2015.
The evolution of drug resistance in clinical isolates of Candida albicans.
C. B. Ford, Funt, J. M. , Abbey, D. , Issi, L. , Guiducci, C. , Martinez, D. A. , Delorey, T. , Li, B. Yu, White, T. C. , Cuomo, C. , Rao, R. P. , Berman, J. , Thompson, D. A. , and Regev, A. , “The evolution of drug resistance in clinical isolates of Candida albicans.”, Elife, vol. 4, p. e00662, 2015.
Degeneration of the nonrecombining regions in the mating-type chromosomes of the anther-smut fungi.
E. Fontanillas, Hood, M. E. , Badouin, H. , Petit, E. , Barbe, V. , Gouzy, J. , de Vienne, D. M. , Aguileta, G. , Poulain, J. , Wincker, P. , Chen, Z. , San Toh, S. , Cuomo, C. A. , Perlin, M. H. , Gladieux, P. , and Giraud, T. , “Degeneration of the nonrecombining regions in the mating-type chromosomes of the anther-smut fungi.”, Mol Biol Evol, vol. 32, no. 4, pp. 928-43, 2015.
50 Years of Emmonsia Disease in Humans: The Dramatic Emergence of a Cluster of Novel Fungal Pathogens.
I. S. Schwartz, Kenyon, C. , Feng, P. , Govender, N. P. , Dukik, K. , Sigler, L. , Jiang, Y. , J Stielow, B. , Muñoz, J. F. , Cuomo, C. A. , Botha, A. , Stchigel, A. M. , and G de Hoog, S. , “50 Years of Emmonsia Disease in Humans: The Dramatic Emergence of a Cluster of Novel Fungal Pathogens.”, PLoS Pathog, vol. 11, no. 11, p. e1005198, 2015.
Genome Sequence of the Microsporidian Species Nematocida sp1 Strain ERTm6 (ATCC PRA-372).
M. A. Bakowski, Priest, M. , Young, S. , Cuomo, C. A. , and Troemel, E. R. , “Genome Sequence of the Microsporidian Species Nematocida sp1 Strain ERTm6 (ATCC PRA-372).”, Genome Announc, vol. 2, no. 5, 2014.
Genome Sequence of the Pathogenic Fungus Sporothrix schenckii (ATCC 58251).
C. A. Cuomo, Del Valle, N. Rodriguez-, Perez-Sanchez, L. , Abouelleil, A. , Goldberg, J. , Young, S. , Zeng, Q. , and Birren, B. W. , “Genome Sequence of the Pathogenic Fungus Sporothrix schenckii (ATCC 58251).”, Genome Announc, vol. 2, no. 3, 2014.
Ubiquitin-mediated response to microsporidia and virus infection in C. elegans.
M. A. Bakowski, Desjardins, C. A. , Smelkinson, M. G. , Dunbar, T. L. , Dunbar, T. A. , Lopez-Moyado, I. F. , Rifkin, S. A. , Cuomo, C. A. , and Troemel, E. R. , “Ubiquitin-mediated response to microsporidia and virus infection in C. elegans.”, PLoS Pathog, vol. 10, no. 6, p. e1004200, 2014.
Highly recombinant VGII Cryptococcus gattii population develops clonal outbreak clusters through both sexual macroevolution and asexual microevolution.
B. R Billmyre, Croll, D. , Li, W. , Mieczkowski, P. , Carter, D. A. , Cuomo, C. A. , Kronstad, J. W. , and Heitman, J. , “Highly recombinant VGII Cryptococcus gattii population develops clonal outbreak clusters through both sexual macroevolution and asexual microevolution.”, MBio, vol. 5, no. 4, pp. e01494-14, 2014.
Analysis of a food-borne fungal pathogen outbreak: virulence and genome of a Mucor circinelloides isolate from yogurt.
S. Chan Lee, R Billmyre, B. , Li, A. , Carson, S. , Sykes, S. M. , Huh, E. Young, Mieczkowski, P. , Ko, D. C. , Cuomo, C. A. , and Heitman, J. , “Analysis of a food-borne fungal pathogen outbreak: virulence and genome of a Mucor circinelloides isolate from yogurt.”, MBio, vol. 5, no. 4, pp. e01390-14, 2014.
Using transcription of six Puccinia triticina races to identify the effective secretome during infection of wheat.
M. Bruce, Neugebauer, K. A. , Joly, D. L. , Migeon, P. , Cuomo, C. A. , Wang, S. , Akhunov, E. , Bakkeren, G. , Kolmer, J. A. , and Fellers, J. P. , “Using transcription of six Puccinia triticina races to identify the effective secretome during infection of wheat.”, Front Plant Sci, vol. 4, p. 520, 2014.
Genome update of the dimorphic human pathogenic fungi causing paracoccidioidomycosis.
J. F. Muñoz, Gallo, J. E. , Misas, E. , Priest, M. , Imamovic, A. , Young, S. , Zeng, Q. , Clay, O. K. , McEwen, J. G. , and Cuomo, C. A. , “Genome update of the dimorphic human pathogenic fungi causing paracoccidioidomycosis.”, PLoS Negl Trop Dis, vol. 8, no. 12, p. e3348, 2014.
Fungi on the skin: dermatophytes and Malassezia.
T. C. White, Findley, K. , Dawson, T. L. , Scheynius, A. , Boekhout, T. , Cuomo, C. A. , Xu, J. , and Saunders, C. W. , “Fungi on the skin: dermatophytes and Malassezia.”, Cold Spring Harb Perspect Med, vol. 4, no. 8, 2014.
Comparative genomic and transcriptomic analysis of wangiella dermatitidis, a major cause of phaeohyphomycosis and a model black yeast human pathogen.
Z. Chen, Martinez, D. A. , Gujja, S. , Sykes, S. M. , Zeng, Q. , Szaniszlo, P. J. , Wang, Z. , and Cuomo, C. A. , “Comparative genomic and transcriptomic analysis of wangiella dermatitidis, a major cause of phaeohyphomycosis and a model black yeast human pathogen.”, G3 (Bethesda), vol. 4, no. 4, pp. 561-78, 2014.
Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.
G. Janbon, Ormerod, K. L. , Paulet, D. , Byrnes, E. J. , Yadav, V. , Chatterjee, G. , Mullapudi, N. , Hon, C. - C. , R Billmyre, B. , Brunel, F. , Bahn, Y. - S. , Chen, W. , Chen, Y. , Chow, E. W. L. , Coppée, J. - Y. , Floyd-Averette, A. , Gaillardin, C. , Gerik, K. J. , Goldberg, J. , Gonzalez-Hilarion, S. , Gujja, S. , Hamlin, J. L. , Hsueh, Y. - P. , Ianiri, G. , Jones, S. , Kodira, C. D. , Kozubowski, L. , Lam, W. , Marra, M. , Mesner, L. D. , Mieczkowski, P. A. , Moyrand, F. , Nielsen, K. , Proux, C. , Rossignol, T. , Schein, J. E. , Sun, S. , Wollschlaeger, C. , Wood, I. A. , Zeng, Q. , Neuvéglise, C. , Newlon, C. S. , Perfect, J. R. , Lodge, J. K. , Idnurm, A. , Stajich, J. E. , Kronstad, J. W. , Sanyal, K. , Heitman, J. , Fraser, J. A. , Cuomo, C. A. , and Dietrich, F. S. , “Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.”, PLoS Genet, vol. 10, no. 4, p. e1004261, 2014.
Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
B. J. Walker, Abeel, T. , Shea, T. , Priest, M. , Abouelliel, A. , Sakthikumar, S. , Cuomo, C. A. , Zeng, Q. , Wortman, J. , Young, S. K. , and Earl, A. M. , “Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.”, PLoS One, vol. 9, no. 11, p. e112963, 2014.
Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes.
N. M. Upadhyaya, Garnica, D. P. , Karaoglu, H. , Sperschneider, J. , Nemri, A. , Xu, B. , Mago, R. , Cuomo, C. A. , Rathjen, J. P. , Park, R. F. , Ellis, J. G. , and Dodds, P. N. , “Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes.”, Front Plant Sci, vol. 5, p. 759, 2014.
One fungus, one name: defining the genus Fusarium in a scientifically robust way that preserves longstanding use.
D. M. Geiser, Aoki, T. , Bacon, C. W. , Baker, S. E. , Bhattacharyya, M. K. , Brandt, M. E. , Brown, D. W. , Burgess, L. W. , Chulze, S. , Coleman, J. J. , Correll, J. C. , Covert, S. F. , Crous, P. W. , Cuomo, C. A. , G de Hoog, S. , Di Pietro, A. , Elmer, W. H. , Epstein, L. , Frandsen, R. J. N. , Freeman, S. , Gagkaeva, T. , Glenn, A. E. , Gordon, T. R. , Gregory, N. F. , Hammond-Kosack, K. E. , Hanson, L. E. , Jímenez-Gasco, M. Del Mar, Kang, S. , H Kistler, C. , Kuldau, G. A. , Leslie, J. F. , Logrieco, A. , Lu, G. , Lysøe, E. , Ma, L. - J. , McCormick, S. P. , Migheli, Q. , Moretti, A. , Munaut, F. , O'donnell, K. , Pfenning, L. , Ploetz, R. C. , Proctor, R. H. , Rehner, S. A. , Robert, V. A. R. G. , Rooney, A. P. , Bin Salleh, B. , Scandiani, M. Mercedes, Scauflaire, J. , Short, D. P. G. , Steenkamp, E. , Suga, H. , Summerell, B. A. , Sutton, D. A. , Thrane, U. , Trail, F. , Van Diepeningen, A. , Vanetten, H. D. , Viljoen, A. , Waalwijk, C. , Ward, T. J. , Wingfield, M. J. , Xu, J. - R. , Yang, X. - B. , Yli-Mattila, T. , and Zhang, N. , “One fungus, one name: defining the genus Fusarium in a scientifically robust way that preserves longstanding use.”, Phytopathology, vol. 103, no. 5, pp. 400-8, 2013.
Sequencing and characterization of the complete mitochondrial genomes of three Pneumocystis species provide new insights into divergence between human and rodent Pneumocystis.
L. Ma, Huang, D. - W. , Cuomo, C. A. , Sykes, S. , Fantoni, G. , Das, B. , Sherman, B. T. , Yang, J. , Huber, C. , Xia, Y. , Davey, E. , Kutty, G. , Bishop, L. , Sassi, M. , Lempicki, R. A. , and Kovacs, J. A. , “Sequencing and characterization of the complete mitochondrial genomes of three Pneumocystis species provide new insights into divergence between human and rodent Pneumocystis.”, FASEB J, vol. 27, no. 5, pp. 1962-72, 2013.
Isolation of Blastomyces dermatitidis yeast from lung tissue during murine infection for in vivo transcriptional profiling.
A. J. Marty, Wüthrich, M. , Carmen, J. C. , Sullivan, T. D. , Klein, B. S. , Cuomo, C. A. , and Gauthier, G. M. , “Isolation of Blastomyces dermatitidis yeast from lung tissue during murine infection for in vivo transcriptional profiling.”, Fungal Genet Biol, vol. 56, pp. 1-8, 2013.
Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements.
J. P. Fellers, Soltani, B. M. , Bruce, M. , Linning, R. , Cuomo, C. A. , Szabo, L. J. , and Bakkeren, G. , “Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements.”, BMC Genomics, vol. 14, p. 60, 2013.
Identification of the mating-type (MAT) locus that controls sexual reproduction of Blastomyces dermatitidis.
W. Li, Sullivan, T. D. , Walton, E. , Averette, A. Floyd, Sakthikumar, S. , Cuomo, C. A. , Klein, B. S. , and Heitman, J. , “Identification of the mating-type (MAT) locus that controls sexual reproduction of Blastomyces dermatitidis.”, Eukaryot Cell, vol. 12, no. 1, pp. 109-17, 2013.
Complete genome sequences from three genetically distinct strains reveal high intraspecies genetic diversity in the microsporidian Encephalitozoon cuniculi.
J. - F. Pombert, Xu, J. , Smith, D. R. , Heiman, D. , Young, S. , Cuomo, C. A. , Weiss, L. M. , and Keeling, P. J. , “Complete genome sequences from three genetically distinct strains reveal high intraspecies genetic diversity in the microsporidian Encephalitozoon cuniculi.”, Eukaryot Cell, vol. 12, no. 4, pp. 503-11, 2013.
Novel, panzootic and hybrid genotypes of amphibian chytridiomycosis associated with the bullfrog trade.
L. M. Schloegel, Toledo, L. Felipe, Longcore, J. E. , Greenspan, S. E. , Vieira, C. Augusto, Lee, M. , Zhao, S. , Wangen, C. , Ferreira, C. Maris, Hipolito, M. , Davies, A. J. , Cuomo, C. A. , Daszak, P. , and James, T. Y. , “Novel, panzootic and hybrid genotypes of amphibian chytridiomycosis associated with the bullfrog trade.”, Mol Ecol, vol. 21, no. 21, pp. 5162-77, 2012.
Linkage to the mating-type locus across the genus Microbotryum: insights into nonrecombining chromosomes.
E. Petit, Giraud, T. , de Vienne, D. M. , Coelho, M. A. , Aguileta, G. , Amselem, J. , Kreplak, J. , Poulain, J. , Gavory, F. , Wincker, P. , Young, S. K. , Cuomo, C. , Perlin, M. H. , and Hood, M. E. , “Linkage to the mating-type locus across the genus Microbotryum: insights into nonrecombining chromosomes.”, Evolution, vol. 66, no. 11, pp. 3519-33, 2012.
Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth.
C. A. Cuomo, Desjardins, C. A. , Bakowski, M. A. , Goldberg, J. , Ma, A. T. , Becnel, J. J. , Didier, E. S. , Fan, L. , Heiman, D. I. , Levin, J. Z. , Young, S. , Zeng, Q. , and Troemel, E. R. , “Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth.”, Genome Res, vol. 22, no. 12, pp. 2478-88, 2012.
Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection.
D. A. Martinez, Oliver, B. G. , Gräser, Y. , Goldberg, J. M. , Li, W. , Martinez-Rossi, N. M. , Monod, M. , Shelest, E. , Barton, R. C. , Birch, E. , Brakhage, A. A. , Chen, Z. , Gurr, S. J. , Heiman, D. , Heitman, J. , Kosti, I. , Rossi, A. , Saif, S. , Samalova, M. , Saunders, C. W. , Shea, T. , Summerbell, R. C. , Xu, J. , Young, S. , Zeng, Q. , Birren, B. W. , Cuomo, C. A. , and White, T. C. , “Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection.”, MBio, vol. 3, no. 5, pp. e00259-12, 2012.
Adaptation of the black yeast Wangiella dermatitidis to ionizing radiation: molecular and cellular mechanisms.
K. L. Robertson, Mostaghim, A. , Cuomo, C. A. , Soto, C. M. , Lebedev, N. , Bailey, R. F. , and Wang, Z. , “Adaptation of the black yeast Wangiella dermatitidis to ionizing radiation: molecular and cellular mechanisms.”, PLoS One, vol. 7, no. 11, p. e48674, 2012.
Approaches to Fungal Genome Annotation.
B. J. Haas, Zeng, Q. , Pearson, M. D. , Cuomo, C. A. , and Wortman, J. R. , “Approaches to Fungal Genome Annotation.”, Mycology, vol. 2, no. 3, pp. 118-141, 2011.
Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis.
C. A. Desjardins, Champion, M. D. , Holder, J. W. , Muszewska, A. , Goldberg, J. , Bailão, A. M. , Brigido, M. Macedo, Ferreira, M. Eliana da, Garcia, A. Maria, Grynberg, M. , Gujja, S. , Heiman, D. I. , Henn, M. R. , Kodira, C. D. , León-Narváez, H. , Longo, L. V. G. , Ma, L. - J. , Malavazi, I. , Matsuo, A. L. , Morais, F. V. , Pereira, M. , Rodríguez-Brito, S. , Sakthikumar, S. , Salem-Izacc, S. M. , Sykes, S. M. , Teixeira, M. Melo, Vallejo, M. C. , Walter, M. Emília Ma, Yandava, C. , Young, S. , Zeng, Q. , Zucker, J. , Felipe, M. Sueli, Goldman, G. H. , Haas, B. J. , McEwen, J. G. , Nino-Vega, G. , Puccia, R. , San-Blas, G. , Soares, C. Maria de A. , Birren, B. W. , and Cuomo, C. A. , “Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis.”, PLoS Genet, vol. 7, no. 10, p. e1002345, 2011.
Obligate biotrophy features unraveled by the genomic analysis of rust fungi.
S. Duplessis, Cuomo, C. A. , Lin, Y. - C. , Aerts, A. , Tisserant, E. , Veneault-Fourrey, C. , Joly, D. L. , Hacquard, S. , Amselem, J. , Cantarel, B. L. , Chiu, R. , Coutinho, P. M. , Feau, N. , Field, M. , Frey, P. , Gelhaye, E. , Goldberg, J. , Grabherr, M. G. , Kodira, C. D. , Kohler, A. , Kües, U. , Lindquist, E. A. , Lucas, S. M. , Mago, R. , Mauceli, E. , Morin, E. , Murat, C. , Pangilinan, J. L. , Park, R. , Pearson, M. , Quesneville, H. , Rouhier, N. , Sakthikumar, S. , Salamov, A. A. , Schmutz, J. , Selles, B. , Shapiro, H. , Tanguay, P. , Tuskan, G. A. , Henrissat, B. , Van de Peer, Y. , Rouzé, P. , Ellis, J. G. , Dodds, P. N. , Schein, J. E. , Zhong, S. , Hamelin, R. C. , Grigoriev, I. V. , Szabo, L. J. , and Martin, F. , “Obligate biotrophy features unraveled by the genomic analysis of rust fungi.”, Proc Natl Acad Sci U S A, vol. 108, no. 22, pp. 9166-71, 2011.
Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens.
S. J. Klosterman, Subbarao, K. V. , Kang, S. , Veronese, P. , Gold, S. E. , Thomma, B. P. H. J. , Chen, Z. , Henrissat, B. , Lee, Y. - H. , Park, J. , Garcia-Pedrajas, M. D. , Barbara, D. J. , Anchieta, A. , de Jonge, R. , Santhanam, P. , Maruthachalam, K. , Atallah, Z. , Amyotte, S. G. , Paz, Z. , Inderbitzin, P. , Hayes, R. J. , Heiman, D. I. , Young, S. , Zeng, Q. , Engels, R. , Galagan, J. , Cuomo, C. A. , Dobinson, K. F. , and Ma, L. - J. , “Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens.”, PLoS Pathog, vol. 7, no. 7, p. e1002137, 2011.
Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea.
J. Amselem, Cuomo, C. A. , van Kan, J. A. L. , Viaud, M. , Benito, E. P. , Couloux, A. , Coutinho, P. M. , de Vries, R. P. , Dyer, P. S. , Fillinger, S. , Fournier, E. , Gout, L. , Hahn, M. , Kohn, L. , Lapalu, N. , Plummer, K. M. , Pradier, J. - M. , Quévillon, E. , Sharon, A. , Simon, A. , Have, Aten, Tudzynski, B. , Tudzynski, P. , Wincker, P. , Andrew, M. , Anthouard, V. , Beever, R. E. , Beffa, R. , Benoit, I. , Bouzid, O. , Brault, B. , Chen, Z. , Choquer, M. , Collémare, J. , Cotton, P. , Danchin, E. G. , Da Silva, C. , Gautier, A. , Giraud, C. , Giraud, T. , Gonzalez, C. , Grossetete, S. , Güldener, U. , Henrissat, B. , Howlett, B. J. , Kodira, C. , Kretschmer, M. , Lappartient, A. , Leroch, M. , Levis, C. , Mauceli, E. , Neuvéglise, C. , Oeser, B. , Pearson, M. , Poulain, J. , Poussereau, N. , Quesneville, H. , Rascle, C. , Schumacher, J. , Segurens, B. , Sexton, A. , Silva, E. , Sirven, C. , Soanes, D. M. , Talbot, N. J. , Templeton, M. , Yandava, C. , Yarden, O. , Zeng, Q. , Rollins, J. A. , Lebrun, M. - H. , and Dickman, M. , “Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea.”, PLoS Genet, vol. 7, no. 8, p. e1002230, 2011.
Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts.
C. A. D'Souza, Kronstad, J. W. , Taylor, G. , Warren, R. , Yuen, M. , Hu, G. , Jung, W. H. , Sham, A. , Kidd, S. E. , Tangen, K. , Lee, N. , Zeilmaker, T. , Sawkins, J. , McVicker, G. , Shah, S. , Gnerre, S. , Griggs, A. , Zeng, Q. , Bartlett, K. , Li, W. , Wang, X. , Heitman, J. , Stajich, J. E. , Fraser, J. A. , Meyer, W. , Carter, D. , Schein, J. , Krzywinski, M. , Kwon-Chung, K. J. , Varma, A. , Wang, J. , Brunham, R. , Fyfe, M. , Ouellette, B. F. F. , Siddiqui, A. , Marra, M. , Jones, S. , Holt, R. , Birren, B. W. , Galagan, J. E. , and Cuomo, C. A. , “Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts.”, MBio, vol. 2, no. 1, pp. e00342-10, 2011.
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium.
L. - J. Ma, H van der Does, C. , Borkovich, K. A. , Coleman, J. J. , Daboussi, M. - J. , Di Pietro, A. , Dufresne, M. , Freitag, M. , Grabherr, M. , Henrissat, B. , Houterman, P. M. , Kang, S. , Shim, W. - B. , Woloshuk, C. , Xie, X. , Xu, J. - R. , Antoniw, J. , Baker, S. E. , Bluhm, B. H. , Breakspear, A. , Brown, D. W. , Butchko, R. A. E. , Chapman, S. , Coulson, R. , Coutinho, P. M. , Danchin, E. G. J. , Diener, A. , Gale, L. R. , Gardiner, D. M. , Goff, S. , Hammond-Kosack, K. E. , Hilburn, K. , Hua-Van, A. , Jonkers, W. , Kazan, K. , Kodira, C. D. , Koehrsen, M. , Kumar, L. , Lee, Y. - H. , Li, L. , Manners, J. M. , Miranda-Saavedra, D. , Mukherjee, M. , Park, G. , Park, J. , Park, S. - Y. , Proctor, R. H. , Regev, A. , M Ruiz-Roldan, C. , Sain, D. , Sakthikumar, S. , Sykes, S. , Schwartz, D. C. , B Turgeon, G. , Wapinski, I. , Yoder, O. , Young, S. , Zeng, Q. , Zhou, S. , Galagan, J. , Cuomo, C. A. , H Kistler, C. , and Rep, M. , “Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium.”, Nature, vol. 464, no. 7287, pp. 367-73, 2010.
SREB, a GATA transcription factor that directs disparate fates in Blastomyces dermatitidis including morphogenesis and siderophore biosynthesis.
G. M. Gauthier, Sullivan, T. D. , Gallardo, S. S. , T Brandhorst, T. , Wymelenberg, A. J. Vanden, Cuomo, C. A. , Suen, G. , Currie, C. R. , and Klein, B. S. , “SREB, a GATA transcription factor that directs disparate fates in Blastomyces dermatitidis including morphogenesis and siderophore biosynthesis.”, PLoS Pathog, vol. 6, no. 4, p. e1000846, 2010.
The fungal genome initiative and lessons learned from genome sequencing.
C. A. Cuomo and Birren, B. W. , “The fungal genome initiative and lessons learned from genome sequencing.”, Methods Enzymol, vol. 470, pp. 833-55, 2010.
Evolution of pathogenicity and sexual reproduction in eight Candida genomes.
G. Butler, Rasmussen, M. D. , Lin, M. F. , Santos, M. A. S. , Sakthikumar, S. , Munro, C. A. , Rheinbay, E. , Grabherr, M. , Forche, A. , Reedy, J. L. , Agrafioti, I. , Arnaud, M. B. , Bates, S. , Brown, A. J. P. , Brunke, S. , Costanzo, M. C. , Fitzpatrick, D. A. , de Groot, P. W. J. , Harris, D. , Hoyer, L. L. , Hube, B. , Klis, F. M. , Kodira, C. , Lennard, N. , Logue, M. E. , Martin, R. , Neiman, A. M. , Nikolaou, E. , Quail, M. A. , Quinn, J. , Santos, M. C. , Schmitzberger, F. F. , Sherlock, G. , Shah, P. , Silverstein, K. A. T. , Skrzypek, M. S. , Soll, D. , Staggs, R. , Stansfield, I. , Stumpf, M. P. H. , Sudbery, P. E. , Srikantha, T. , Zeng, Q. , Berman, J. , Berriman, M. , Heitman, J. , Gow, N. A. R. , Lorenz, M. C. , Birren, B. W. , Kellis, M. , and Cuomo, C. A. , “Evolution of pathogenicity and sexual reproduction in eight Candida genomes.”, Nature, vol. 459, no. 7247, pp. 657-62, 2009.
Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication.
L. - J. Ma, Ibrahim, A. S. , Skory, C. , Grabherr, M. G. , Burger, G. , Butler, M. , Elias, M. , Idnurm, A. , B Lang, F. , Sone, T. , Abe, A. , Calvo, S. E. , Corrochano, L. M. , Engels, R. , Fu, J. , Hansberg, W. , Kim, J. - M. , Kodira, C. D. , Koehrsen, M. J. , Liu, B. , Miranda-Saavedra, D. , O'Leary, S. , Ortiz-Castellanos, L. , Poulter, R. , Rodriguez-Romero, J. , Ruiz-Herrera, J. , Shen, Y. - Q. , Zeng, Q. , Galagan, J. , Birren, B. W. , Cuomo, C. A. , and Wickes, B. L. , “Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication.”, PLoS Genet, vol. 5, no. 7, p. e1000549, 2009.
The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization.
C. A. Cuomo, Güldener, U. , Xu, J. - R. , Trail, F. , B Turgeon, G. , Di Pietro, A. , Walton, J. D. , Ma, L. - J. , Baker, S. E. , Rep, M. , Adam, G. , Antoniw, J. , Baldwin, T. , Calvo, S. , Chang, Y. - L. , DeCaprio, D. , Gale, L. R. , Gnerre, S. , Goswami, R. S. , Hammond-Kosack, K. , Harris, L. J. , Hilburn, K. , Kennell, J. C. , Kroken, S. , Magnuson, J. K. , Mannhaupt, G. , Mauceli, E. , Mewes, H. - W. , Mitterbauer, R. , Muehlbauer, G. , Münsterkötter, M. , Nelson, D. , O'donnell, K. , Ouellet, T. , Qi, W. , Quesneville, H. , M Roncero, I. G. , Seong, K. - Y. , Tetko, I. V. , Urban, M. , Waalwijk, C. , Ward, T. J. , Yao, J. , Birren, B. W. , and H Kistler, C. , “The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization.”, Science, vol. 317, no. 5843, pp. 1400-2, 2007.
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae.
J. E. Galagan, Calvo, S. E. , Cuomo, C. , Ma, L. - J. , Wortman, J. R. , Batzoglou, S. , Lee, S. - I. , Baştürkmen, M. , Spevak, C. C. , Clutterbuck, J. , Kapitonov, V. , Jurka, J. , Scazzocchio, C. , Farman, M. , Butler, J. , Purcell, S. , Harris, S. , Braus, G. H. , Draht, O. , Busch, S. , D'Enfert, C. , Bouchier, C. , Goldman, G. H. , Bell-Pedersen, D. , Griffiths-Jones, S. , Doonan, J. H. , Yu, J. , Vienken, K. , Pain, A. , Freitag, M. , Selker, E. U. , Archer, D. B. , Peñalva, M. A. , Oakley, B. R. , Momany, M. , Tanaka, T. , Kumagai, T. , Asai, K. , Machida, M. , Nierman, W. C. , Denning, D. W. , Caddick, M. , Hynes, M. , Paoletti, M. , Fischer, R. , Miller, B. , Dyer, P. , Sachs, M. S. , Osmani, S. A. , and Birren, B. W. , “Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae.”, Nature, vol. 438, no. 7071, pp. 1105-15, 2005.