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Lower prevalence but similar fitness in a parasitic fungus at higher radiation levels near Chernobyl.

Aguileta G, Badouin H, Hood ME, Møller AP, Le Prieur S, Snirc A, Siguenza S, Mousseau TA, Shykoff JA, Cuomo CA, Giraud T.

Mol Ecol. 2016 May 2. doi: 10.1111/mec.13675. [Epub ahead of print]


Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts.

Ma L, Chen Z, Huang da W, 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 JM, Handley G, Hu X, Huber C, Jiao X, Jones K, Levin JZ, Liu Y, Macdonald P, Melnikov A, Raley C, Sassi M, Sherman BT, Song X, Sykes S, Tran B, Walsh L, Xia Y, Yang J, Young S, Zeng Q, Zheng X, Stephens R, Nusbaum C, Birren BW, Azadi P, Lempicki RA, Cuomo CA, Kovacs JA.

Nat Commun. 2016 Feb 22;7:10740. doi: 10.1038/ncomms10740.


50 Years of Emmonsia Disease in Humans: The Dramatic Emergence of a Cluster of Novel Fungal Pathogens.

Schwartz IS, Kenyon C, Feng P, Govender NP, Dukik K, Sigler L, Jiang Y, Stielow JB, Muñoz JF, Cuomo CA, Botha A, Stchigel AM, de Hoog GS.

PLoS Pathog. 2015 Nov 19;11(11):e1005198. doi: 10.1371/journal.ppat.1005198. eCollection 2015. Review. No abstract available.


The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia.

Muñoz JF, Gauthier GM, Desjardins CA, Gallo JE, Holder J, Sullivan TD, Marty AJ, Carmen JC, Chen Z, Ding L, Gujja S, Magrini V, Misas E, Mitreva M, Priest M, Saif S, Whiston EA, Young S, Zeng Q, Goldman WE, Mardis ER, Taylor JW, McEwen JG, Clay OK, Klein BS, Cuomo CA.

PLoS Genet. 2015 Oct 6;11(10):e1005493. doi: 10.1371/journal.pgen.1005493. eCollection 2015 Oct.


Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii.

Farrer RA, Desjardins CA, Sakthikumar S, Gujja S, Saif S, Zeng Q, Chen Y, Voelz K, Heitman J, May RC, Fisher MC, Cuomo CA.

MBio. 2015 Sep 1;6(5):e00868-15. doi: 10.1128/mBio.00868-15.


Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus.

Perlin MH, Amselem J, Fontanillas E, Toh SS, 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 ME, Schultz DJ, Cuomo CA.

BMC Genomics. 2015 Jun 16;16:461. doi: 10.1186/s12864-015-1660-8.


Chaos of Rearrangements in the Mating-Type Chromosomes of the Anther-Smut Fungus Microbotryum lychnidis-dioicae.

Badouin H, Hood ME, Gouzy J, Aguileta G, Siguenza S, Perlin MH, Cuomo CA, Fairhead C, Branca A, Giraud T.

Genetics. 2015 Aug;200(4):1275-84. doi: 10.1534/genetics.115.177709. Epub 2015 Jun 3.


Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes.

Desjardins CA, Sanscrainte ND, Goldberg JM, Heiman D, Young S, Zeng Q, Madhani HD, Becnel JJ, Cuomo CA.

Nat Commun. 2015 May 13;6:7121. doi: 10.1038/ncomms8121.


Finding a Missing Gene: EFG1 Regulates Morphogenesis in Candida tropicalis.

Mancera E, Porman AM, Cuomo CA, Bennett RJ, Johnson AD.

G3 (Bethesda). 2015 Mar 9;5(5):849-56. doi: 10.1534/g3.115.017566.


Draft Genome Sequence of the Cellulolytic Fungus Chaetomium globosum.

Cuomo CA, Untereiner WA, Ma LJ, Grabherr M, Birren BW.

Genome Announc. 2015 Feb 26;3(1). pii: e00021-15. doi: 10.1128/genomeA.00021-15.


Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes.

Upadhyaya NM, Garnica DP, Karaoglu H, Sperschneider J, Nemri A, Xu B, Mago R, Cuomo CA, Rathjen JP, Park RF, Ellis JG, Dodds PN.

Front Plant Sci. 2015 Jan 8;5:759. doi: 10.3389/fpls.2014.00759. eCollection 2014.


Degeneration of the nonrecombining regions in the mating-type chromosomes of the anther-smut fungi.

Fontanillas E, Hood ME, Badouin H, Petit E, Barbe V, Gouzy J, de Vienne DM, Aguileta G, Poulain J, Wincker P, Chen Z, Toh SS, Cuomo CA, Perlin MH, Gladieux P, Giraud T.

Mol Biol Evol. 2015 Apr;32(4):928-43. doi: 10.1093/molbev/msu396. Epub 2014 Dec 21.


Genetic and phenotypic intra-species variation in Candida albicans.

Hirakawa MP, Martinez DA, Sakthikumar S, Anderson MZ, Berlin A, Gujja S, Zeng Q, Zisson E, Wang JM, Greenberg JM, Berman J, Bennett RJ, Cuomo CA.

Genome Res. 2015 Mar;25(3):413-25. doi: 10.1101/gr.174623.114. Epub 2014 Dec 11.


Genome update of the dimorphic human pathogenic fungi causing paracoccidioidomycosis.

Muñoz JF, Gallo JE, Misas E, Priest M, Imamovic A, Young S, Zeng Q, Clay OK, McEwen JG, Cuomo CA.

PLoS Negl Trop Dis. 2014 Dec 4;8(12):e3348. doi: 10.1371/journal.pntd.0003348. eCollection 2014 Dec.


Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.

Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM.

PLoS One. 2014 Nov 19;9(11):e112963. doi: 10.1371/journal.pone.0112963. eCollection 2014.


Genome Sequence of the Microsporidian Species Nematocida sp1 Strain ERTm6 (ATCC PRA-372).

Bakowski MA, Priest M, Young S, Cuomo CA, Troemel ER.

Genome Announc. 2014 Sep 18;2(5). pii: e00905-14. doi: 10.1128/genomeA.00905-14.


Fungi on the skin: dermatophytes and Malassezia.

White TC, Findley K, Dawson TL Jr, Scheynius A, Boekhout T, Cuomo CA, Xu J, Saunders CW.

Cold Spring Harb Perspect Med. 2014 Aug 1;4(8). pii: a019802. doi: 10.1101/cshperspect.a019802. Review.


Highly recombinant VGII Cryptococcus gattii population develops clonal outbreak clusters through both sexual macroevolution and asexual microevolution.

Billmyre RB, Croll D, Li W, Mieczkowski P, Carter DA, Cuomo CA, Kronstad JW, Heitman J.

MBio. 2014 Jul 29;5(4):e01494-14. doi: 10.1128/mBio.01494-14.


Analysis of a food-borne fungal pathogen outbreak: virulence and genome of a Mucor circinelloides isolate from yogurt.

Lee SC, Billmyre RB, Li A, Carson S, Sykes SM, Huh EY, Mieczkowski P, Ko DC, Cuomo CA, Heitman J.

MBio. 2014 Jul 8;5(4):e01390-14. doi: 10.1128/mBio.01390-14.


Ubiquitin-mediated response to microsporidia and virus infection in C. elegans.

Bakowski MA, Desjardins CA, Smelkinson MG, Dunbar TL, Lopez-Moyado IF, Rifkin SA, Cuomo CA, Troemel ER.

PLoS Pathog. 2014 Jun 19;10(6):e1004200. doi: 10.1371/journal.ppat.1004200. eCollection 2014 Jun. Erratum in: PLoS Pathog. 2014 Aug;10(8):e1004371. Dunbar, Tiffany A [corrected to Dunbar, Tiffany L].

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