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
Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes
Sakthikumar, Sharadha, Roy, Ananya, Haseeb, Lulu, Pettersson, Mats E, Sundström, Elisabeth, Marinescu, Voichita D, Lindblad-Toh, Kerstin, Forsberg-Nilsson, Karin
Published in Genome Biology (09.06.2020)
Published in Genome Biology (09.06.2020)
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Journal Article
Comparative Genomics Reveals Shared Mutational Landscape in Canine Hemangiosarcoma and Human Angiosarcoma
Megquier, Kate, Turner-Maier, Jason, Swofford, Ross, Kim, Jong-Hyuk, Sarver, Aaron L, Wang, Chao, Sakthikumar, Sharadha, Johnson, Jeremy, Koltookian, Michele, Lewellen, Mitzi, Scott, Milcah C, Schulte, Ashley J, Borst, Luke, Tonomura, Noriko, Alfoldi, Jessica, Painter, Corrie, Thomas, Rachael, Karlsson, Elinor K, Breen, Matthew, Modiano, Jaime F, Elvers, Ingegerd, Lindblad-Toh, Kerstin
Published in Molecular cancer research (01.12.2019)
Published in Molecular cancer research (01.12.2019)
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Journal Article
SETD2 Is Recurrently Mutated in Whole-Exome Sequenced Canine Osteosarcoma
Sakthikumar, Sharadha, Elvers, Ingegerd, Kim, Jaegil, Arendt, Maja L, Thomas, Rachael, Turner-Maier, Jason, Swofford, Ross, Johnson, Jeremy, Schumacher, Steven E, Alföldi, Jessica, Axelsson, Erik, Couto, C Guillermo, Kisseberth, William C, Pettersson, Mats E, Getz, Gad, Meadows, Jennifer R S, Modiano, Jaime F, Breen, Matthew, Kierczak, Marcin, Forsberg-Nilsson, Karin, Marinescu, Voichita D, Lindblad-Toh, Kerstin
Published in Cancer research (Chicago, Ill.) (01.07.2018)
Published in Cancer research (Chicago, Ill.) (01.07.2018)
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Journal Article
PIK3CA is recurrently mutated in canine mammary tumors, similarly to in human mammary neoplasia
Arendt, Maja Louise, Sakthikumar, Sharadha, Melin, Malin, Elvers, Ingegerd, Rivera, Patricio, Larsen, Majbritt, Saellström, Sara, Lingaas, Frode, Rönnberg, Henrik, Lindblad-Toh, Kerstin
Published in Scientific reports (12.01.2023)
Published in Scientific reports (12.01.2023)
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Journal Article
Novel genomic prognostic biomarkers for dogs with cancer
Chon, Esther, Sakthikumar, Sharadha, Tang, Min, Hamilton, Matthew J., Vaughan, Andrew, Smith, Ashley, Sommer, Breann, Robat, Cecilia, Manley, Christina, Mullin, Christine, Ohashi, Emi, Manor, Emily, Custis, James, Intile, Joanne, Shiu, Kai Biu, Parshley, Lisa, Bergman, Noelle, Sheppard‐Olivares, Sabina, Hafeman, Scott, Wright, Zachary, Haworth, David, Hendricks, William, Wang, Guannan
Published in Journal of veterinary internal medicine (01.11.2023)
Published in Journal of veterinary internal medicine (01.11.2023)
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Journal Article
Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii
Farrer, Rhys A, Desjardins, Christopher A, Sakthikumar, Sharadha, Gujja, Sharvari, Saif, Sakina, Zeng, Qiandong, Chen, Yuan, Voelz, Kerstin, Heitman, Joseph, May, Robin C, Fisher, Matthew C, Cuomo, Christina A
Published in mBio (01.09.2015)
Published in mBio (01.09.2015)
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Journal Article
Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci
Cuomo, Christina A, Bakkeren, Guus, Khalil, Hala Badr, Panwar, Vinay, Joly, David, Linning, Rob, Sakthikumar, Sharadha, Song, Xiao, Adiconis, Xian, Fan, Lin, Goldberg, Jonathan M, Levin, Joshua Z, Young, Sarah, Zeng, Qiandong, Anikster, Yehoshua, Bruce, Myron, Wang, Meinan, Yin, Chuntao, McCallum, Brent, Szabo, Les J, Hulbert, Scot, Chen, Xianming, Fellers, John P
Published in G3 : genes - genomes - genetics (01.02.2017)
Published in G3 : genes - genomes - genetics (01.02.2017)
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Journal Article
Whole-genome sequencing of multiple isolates of Puccinia triticina reveals asexual lineages evolving by recurrent mutations
Fellers, John P, Sakthikumar, Sharadha, He, Fei, McRell, Katie, Bakkeren, Guus, Cuomo, Christina A, Kolmer, James A
Published in G3 : genes - genomes - genetics (06.09.2021)
Published in G3 : genes - genomes - genetics (06.09.2021)
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Journal Article
Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides
Muñoz, José F, Farrer, Rhys A, Desjardins, Christopher A, Gallo, Juan E, Sykes, Sean, Sakthikumar, Sharadha, Misas, Elizabeth, Whiston, Emily A, Bagagli, Eduardo, Soares, Celia M A, Teixeira, Marcus de M, Taylor, John W, Clay, Oliver K, McEwen, Juan G, Cuomo, Christina A
Published in mSphere (01.09.2016)
Published in mSphere (01.09.2016)
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Journal Article
Identification of the Mating-Type (MAT) Locus That Controls Sexual Reproduction of Blastomyces dermatitidis
Li, Wenjun, Sullivan, Thomas D, Walton, Eric, Averette, Anna Floyd, Sakthikumar, Sharadha, Cuomo, Christina A, Klein, Bruce S, Heitman, Joseph
Published in Eukaryotic Cell (01.01.2013)
Published in Eukaryotic Cell (01.01.2013)
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Journal Article
Genetic and phenotypic intra-species variation in Candida albicans
Hirakawa, Matthew P, Martinez, Diego A, Sakthikumar, Sharadha, Anderson, Matthew Z, Berlin, Aaron, Gujja, Sharvari, Zeng, Qiandong, Zisson, Ethan, Wang, Joshua M, Greenberg, Joshua M, Berman, Judith, Bennett, Richard J, Cuomo, Christina A
Published in Genome research (01.03.2015)
Published in Genome research (01.03.2015)
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Journal Article
Genomic tumor analysis provides clinical guidance for the management of diagnostically challenging cancers in dogs
Chon, Esther, Wang, Guannan, Whitley, Derick, Sakthikumar, Sharadha, Warrier, Manisha, Wong, Shukmei, Duran, Natalie, Adkins, Jonathan, Boateng, Martin, Zhu, Zhanyang, Facista, Salvatore, Haworth, David, Hendricks, William
Published in Journal of the American Veterinary Medical Association (01.05.2023)
Published in Journal of the American Veterinary Medical Association (01.05.2023)
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Journal Article
CNSC-40. HARNESSING EVOLUTIONARY CONSTRAINT IDENTIFIES POTENTIAL NON-CODING DRIVERS IN BRAIN TUMORS
Roy, Ananya, Pensch, Raphaela, Sakthikumar, Sharadha, Kozyrev, Sergey V, Nordin, Jessika, Mäkeläinen, Suvi, Jansson, Ylva, Pettersson, Mats, Karlsson, Elinor, Lindblad-Toh, Kerstin, Forsberg-Nilsson, Karin
Published in Neuro-oncology (Charlottesville, Va.) (10.11.2023)
Published in Neuro-oncology (Charlottesville, Va.) (10.11.2023)
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Journal Article
Tracing Genetic Exchange and Biogeography of Cryptococcus neoformans var. grubii at the Global Population Level
Rhodes, Johanna, Desjardins, Christopher A, Sykes, Sean M, Beale, Mathew A, Vanhove, Mathieu, Sakthikumar, Sharadha, Chen, Yuan, Gujja, Sharvari, Saif, Sakina, Chowdhary, Anuradha, Lawson, Daniel John, Ponzio, Vinicius, Colombo, Arnaldo Lopes, Meyer, Wieland, Engelthaler, David M, Hagen, Ferry, Illnait-Zaragozi, Maria Teresa, Alanio, Alexandre, Vreulink, Jo-Marie, Heitman, Joseph, Perfect, John R, Litvintseva, Anastasia P, Bicanic, Tihana, Harrison, Thomas S, Fisher, Matthew C, Cuomo, Christina A
Published in Genetics (Austin) (01.09.2017)
Published in Genetics (Austin) (01.09.2017)
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Journal Article
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium
Ma, Li-Jun, Does, H. Charlotte van der, Borkovich, Katherine A, Coleman, Jeffrey J, Daboussi, Marie-Josée, Di Pietro, Antonio, Dufresne, Marie, Freitag, Michael, Grabherr, Manfred, Breakspear, Andrew, Brown, Daren W, Butchko,Robert A.E, Gale, Liane R, Hilburn, Karen, Proctor, Robert H, Kistler, H. Corby
Published in Nature (London) (18.03.2010)
Published in Nature (London) (18.03.2010)
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Journal Article
Obligate biotrophy features unraveled by the genomic analysis of rust fungi
Duplessis, Sébastien, Cuomo, Christina A, Lin, Yao-Cheng, Aerts, Andrea, Tisserant, Emilie, Veneault-Fourrey, Claire, Joly, David L, Hacquard, Stéphane, Amselem, Joëlle, Cantarel, Brandi L, Chiu, Readman, Coutinho, Pedro M, Feau, Nicolas, Field, Matthew, Frey, Pascal, Gelhaye, Eric, Goldberg, Jonathan, Grabherr, Manfred G, Kodira, Chinnappa D, Kohler, Annegret, Kües, Ursula, Lindquist, Erika A, Lucas, Susan M, Mago, Rohit, Mauceli, Evan, Morin, Emmanuelle, Murat, Claude, Pangilinan, Jasmyn L, Park, Robert, Pearson, Matthew, Quesneville, Hadi, Rouhier, Nicolas, Sakthikumar, Sharadha, Salamov, Asaf A, Schmutz, Jeremy, Selles, Benjamin, Shapiro, Harris, Tanguay, Philippe, Tuskan, Gerald A, Henrissat, Bernard, Peer, Yves Van de, Rouzé, Pierre, Ellis, Jeffrey G, Dodds, Peter N, Schein, Jacqueline E, Zhong, Shaobin, Hamelin, Richard C, Grigoriev, Igor V, Szabo, Les J, Martin, Francis
Published in Proceedings of the National Academy of Sciences - PNAS (31.05.2011)
Published in Proceedings of the National Academy of Sciences - PNAS (31.05.2011)
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Journal Article
Evolution of pathogenicity and sexual reproduction in eight Candida genomes
Butler, Geraldine, Kellis, Manolis, Cuomo, Christina A, Rasmussen, Matthew D, Lin, Michael F, Santos, Manuel A. S, Sakthikumar, Sharadha, Munro, Carol A, Rheinbay, Esther, Grabherr, Manfred, Forche, Anja, Reedy, Jennifer L, Agrafioti, Ino, Arnaud, Martha B, Bates, Steven, Brown, Alistair J. P, Brunke, Sascha, Costanzo, Maria C, Fitzpatrick, David A, de Groot, Piet W. J, Harris, David, Hoyer, Lois L, Hube, Bernhard, Klis, Frans M, Kodira, Chinnappa, Lennard, Nicola, Logue, Mary E, Martin, Ronny, Neiman, Aaron M, Nikolaou, Elissavet, Quail, Michael A, Quinn, Janet, Santos, Maria C, Schmitzberger, Florian F, Sherlock, Gavin, Shah, Prachi, Silverstein, Kevin A. T, Skrzypek, Marek S, Soll, David, Staggs, Rodney, Stansfield, Ian, Stumpf, Michael P. H, Sudbery, Peter E, Srikantha, Thyagarajan, Zeng, Qiandong, Berman, Judith, Berriman, Matthew, Heitman, Joseph, Gow, Neil A. R, Lorenz, Michael C, Birren, Bruce W
Published in Nature (04.06.2009)
Published in Nature (04.06.2009)
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Journal Article
Microevolution of Serial Clinical Isolates of Cryptococcus neoformans var. grubii and C. gattii
Chen, Yuan, Farrer, Rhys A, Giamberardino, Charles, Sakthikumar, Sharadha, Jones, Alexander, Yang, Timothy, Tenor, Jennifer L, Wagih, Omar, Van Wyk, Marelize, Govender, Nelesh P, Mitchell, Thomas G, Litvintseva, Anastasia P, Cuomo, Christina A, Perfect, John R
Published in mBio (07.03.2017)
Published in mBio (07.03.2017)
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Journal Article
Comparative Genomics Integrated with Association Analysis Identifies Candidate Effector Genes Corresponding to Lr20 in Phenotype-Paired Puccinia triticina Isolates from Australia
Wu, Jing Qin, Sakthikumar, Sharadha, Dong, Chongmei, Zhang, Peng, Cuomo, Christina A, Park, Robert F
Published in Frontiers in plant science (09.02.2017)
Published in Frontiers in plant science (09.02.2017)
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Journal Article