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

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Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes von Sakthikumar, Sharadha, Roy, Ananya, Haseeb, Lulu, Pettersson, Mats E., Sundstrom, Elisabeth, Marinescu, Voichita D., Lindblad-Toh, Kerstin, Forsberg-Nilsson, Karin

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Comparative Genomics Reveals Shared Mutational Landscape in Canine Hemangiosarcoma and Human Angiosarcoma von 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

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SETD2 Is Recurrently Mutated in Whole-Exome Sequenced Canine Osteosarcoma von 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

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PIK3CA is recurrently mutated in canine mammary tumors, similarly to in human mammary neoplasia von Arendt, Maja Louise, Sakthikumar, Sharadha, Melin, Malin, Elvers, Ingegerd, Rivera, Patricio, Larsen, Majbritt, Saellström, Sara, Lingaas, Frode, Rönnberg, Henrik, Lindblad-Toh, Kerstin

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Novel genomic prognostic biomarkers for dogs with cancer von 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

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

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Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci von 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

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Whole-genome sequencing of multiple isolates of Puccinia triticina reveals asexual lineages evolving by recurrent mutations von Fellers, John P., Sakthikumar, Sharadha, He, Fei, McRell, Katie, Bakkeren, Guus, Cuomo, Christina A., Kolmer, James A.

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Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides von 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

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Identification of the Mating-Type (MAT) Locus That Controls Sexual Reproduction of Blastomyces dermatitidis von Li, Wenjun, Sullivan, Thomas D, Walton, Eric, Averette, Anna Floyd, Sakthikumar, Sharadha, Cuomo, Christina A, Klein, Bruce S, Heitman, Joseph

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Genetic and phenotypic intra-species variation in Candida albicans von 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

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CNSC-40. HARNESSING EVOLUTIONARY CONSTRAINT IDENTIFIES POTENTIAL NON-CODING DRIVERS IN BRAIN TUMORS von 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

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Tracing Genetic Exchange and Biogeography of Cryptococcus neoformans var. grubii at the Global Population Level von 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

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Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium von 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

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Obligate biotrophy features unraveled by the genomic analysis of rust fungi von 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

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Characterizing the spectrum of somatic alterations in canine and human cancers von Sakthikumar, Sharadha

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Characterizing the spectrum of somatic alterations in canine and human cancers von Sakthikumar, Sharadha

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Evolution of pathogenicity and sexual reproduction in eight Candida genomes von 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

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Microevolution of Serial Clinical Isolates of Cryptococcus neoformans var. grubii and C. gattii von 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

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