Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement
Walker, Bruce J, Abeel, Thomas, Shea, Terrance, Priest, Margaret, Abouelliel, Amr, Sakthikumar, Sharadha, Cuomo, Christina A, Zeng, Qiandong, Wortman, Jennifer, Young, Sarah K, Earl, Ashlee M
Published in PloS one (19.11.2014)
Published in PloS one (19.11.2014)
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Journal Article
Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species
Muñoz, José F., Gade, Lalitha, Chow, Nancy A., Loparev, Vladimir N., Juieng, Phalasy, Berkow, Elizabeth L., Farrer, Rhys A., Litvintseva, Anastasia P., Cuomo, Christina A.
Published in Nature communications (17.12.2018)
Published in Nature communications (17.12.2018)
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Journal Article
The importance of antimicrobial resistance in medical mycology
Gow, Neil A. R., Johnson, Carolyn, Berman, Judith, Coste, Alix T., Cuomo, Christina A., Perlin, David S., Bicanic, Tihana, Harrison, Thomas S., Wiederhold, Nathan, Bromley, Mike, Chiller, Tom, Edgar, Keegan
Published in Nature communications (12.09.2022)
Published in Nature communications (12.09.2022)
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Journal Article
Threats Posed by the Fungal Kingdom to Humans, Wildlife, and Agriculture
Fisher, Matthew C, Gurr, Sarah J, Cuomo, Christina A, Blehert, David S, Jin, Hailing, Stukenbrock, Eva H, Stajich, Jason E, Kahmann, Regine, Boone, Charles, Denning, David W, Gow, Neil A R, Klein, Bruce S, Kronstad, James W, Sheppard, Donald C, Taylor, John W, Wright, Gerard D, Heitman, Joseph, Casadevall, Arturo, Cowen, Leah E
Published in mBio (05.05.2020)
Published in mBio (05.05.2020)
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Journal Article
Tracing the Evolutionary History and Global Expansion of Candida auris Using Population Genomic Analyses
Chow, Nancy A, Muñoz, José F, Gade, Lalitha, Berkow, Elizabeth L, Li, Xiao, Welsh, Rory M, Forsberg, Kaitlin, Lockhart, Shawn R, Adam, Rodney, Alanio, Alexandre, Alastruey-Izquierdo, Ana, Althawadi, Sahar, Araúz, Ana Belén, Ben-Ami, Ronen, Bharat, Amrita, Calvo, Belinda, Desnos-Ollivier, Marie, Escandón, Patricia, Gardam, Dianne, Gunturu, Revathi, Heath, Christopher H, Kurzai, Oliver, Martin, Ronny, Litvintseva, Anastasia P, Cuomo, Christina A
Published in mBio (28.04.2020)
Published in mBio (28.04.2020)
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Journal Article
RNAi is a critical determinant of centromere evolution in closely related fungi
Yadav, Vikas, Sun, Sheng, Billmyre, R. Blake, Thimmappa, Bhagya C., Shea, Terrance, Lintner, Robert, Bakkeren, Guus, Cuomo, Christina A., Heitman, Joseph, Sanyal, Kaustuv
Published in Proceedings of the National Academy of Sciences - PNAS (20.03.2018)
Published in Proceedings of the National Academy of Sciences - PNAS (20.03.2018)
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Journal Article
Coordinated host-pathogen transcriptional dynamics revealed using sorted subpopulations and single macrophages infected with Candida albicans
Muñoz, José F., Delorey, Toni, Ford, Christopher B., Li, Bi Yu, Thompson, Dawn A., Rao, Reeta P., Cuomo, Christina A.
Published in Nature communications (08.04.2019)
Published in Nature communications (08.04.2019)
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Journal Article
Best practices on the differential expression analysis of multi-species RNA-seq
Chung, Matthew, Bruno, Vincent M, Rasko, David A, Cuomo, Christina A, Muñoz, José F, Livny, Jonathan, Shetty, Amol C, Mahurkar, Anup, Dunning Hotopp, Julie C
Published in Genome Biology (29.04.2021)
Published in Genome Biology (29.04.2021)
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Journal Article
Titan cells formation in Cryptococcus neoformans is finely tuned by environmental conditions and modulated by positive and negative genetic regulators
Hommel, Benjamin, Mukaremera, Liliane, Cordero, Radames J B, Coelho, Carolina, Desjardins, Christopher A, Sturny-Leclère, Aude, Janbon, Guilhem, Perfect, John R, Fraser, James A, Casadevall, Arturo, Cuomo, Christina A, Dromer, Françoise, Nielsen, Kirsten, Alanio, Alexandre
Published in PLoS pathogens (18.05.2018)
Published in PLoS pathogens (18.05.2018)
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Journal Article
Ubiquitin-mediated response to microsporidia and virus infection in C. elegans
Bakowski, Malina A, Desjardins, Christopher A, Smelkinson, Margery G, Dunbar, Tiffany L, Dunbar, Tiffany A, Lopez-Moyado, Isaac F, Rifkin, Scott A, Cuomo, Christina A, Troemel, Emily R
Published in PLoS pathogens (01.06.2014)
Published in PLoS pathogens (01.06.2014)
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Journal Article
New approaches to tackle a rising problem: Large-scale methods to study antifungal resistance
Després, Philippe C, Shapiro, Rebecca S, Cuomo, Christina A
Published in PLoS pathogens (05.09.2024)
Published in PLoS pathogens (05.09.2024)
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Journal Article
Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi
Farrer, Rhys A., Martel, An, Verbrugghe, Elin, Abouelleil, Amr, Ducatelle, Richard, Longcore, Joyce E., James, Timothy Y., Pasmans, Frank, Fisher, Matthew C., Cuomo, Christina A.
Published in Nature communications (21.03.2017)
Published in Nature communications (21.03.2017)
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Journal Article
Antagonistic paralogs control a switch between growth and pathogen resistance in C. elegans
Reddy, Kirthi C, Dror, Tal, Underwood, Ryan S, Osman, Guled A, Elder, Corrina R, Desjardins, Christopher A, Cuomo, Christina A, Barkoulas, Michalis, Troemel, Emily R
Published in PLoS pathogens (01.01.2019)
Published in PLoS pathogens (01.01.2019)
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Journal Article
Diversity, multifaceted evolution, and facultative saprotrophism in the European Batrachochytrium salamandrivorans epidemic
Kelly, Moira, Pasmans, Frank, Muñoz, Jose F., Shea, Terrance P., Carranza, Salvador, Cuomo, Christina A., Martel, An
Published in Nature communications (18.11.2021)
Published in Nature communications (18.11.2021)
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Journal Article
Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans
Leach, Michelle D., Farrer, Rhys A., Tan, Kaeling, Miao, Zhengqiang, Walker, Louise A., Cuomo, Christina A., Wheeler, Robert T., Brown, Alistair J. P., Wong, Koon Ho, Cowen, Leah E.
Published in Nature communications (26.05.2016)
Published in Nature communications (26.05.2016)
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Journal Article
Gene Expression of Diverse Cryptococcus Isolates during Infection of the Human Central Nervous System
Yu, Chen-Hsin, Sephton-Clark, Poppy, Tenor, Jennifer L, Toffaletti, Dena L, Giamberardino, Charles, Haverkamp, Miriam, Cuomo, Christina A, Perfect, John R
Published in mBio (21.12.2021)
Published in mBio (21.12.2021)
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