Comparative Genomic and Transcriptomic Analysis of Wangiella dermatitidis, A Major Cause of Phaeohyphomycosis and a Model Black Yeast Human Pathogen

por Chen, Zehua, Martinez, Diego A., Gujja, Sharvari, Sykes, Sean M., Zeng, Qiandong, Szaniszlo, Paul J., Wang, Zheng, Cuomo, Christina A.
Publicado 2014

Sequence Analysis of a 101-Kilobase Plasmid Required for Agar Degradation by a Microscilla Isolate

por Zhong, Zhenping, Toukdarian, Aresa, Helinski, Donald, Knauf, Vic, Sykes, Sean, Wilkinson, Jane E., O'Bryne, Colleen, Shea, Terry, DeLoughery, Craig, Caspi, Ron
Publicado 2001

Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities

por Martin, John, Sykes, Sean, Young, Sarah, Kota, Karthik, Sanka, Ravi, Sheth, Nihar, Orvis, Joshua, Sodergren, Erica, Wang, Zhengyuan, Weinstock, George M., Mitreva, Makedonka
Publicado 2012

Analysis of a Food-Borne Fungal Pathogen Outbreak: Virulence and Genome of a Mucor circinelloides Isolate from Yogurt

por Lee, Soo Chan, Billmyre, R. Blake, Li, Alicia, Carson, Sandra, Sykes, Sean M., Huh, Eun Young, Mieczkowski, Piotr, Ko, Dennis C., Cuomo, Christina A., Heitman, Joseph
Publicado 2014

Sequencing and characterization of the complete mitochondrial genomes of three Pneumocystis species provide new insights into divergence between human and rodent Pneumocystis

por Ma, Liang, Huang, Da-Wei, Cuomo, Christina A., Sykes, Sean, Fantoni, Giovanna, Das, Biswajit, Sherman, Brad T., Yang, Jun, Huber, Charles, Xia, Yun, Davey, Emma, Kutty, Geetha, Bishop, Lisa, Sassi, Monica, Lempicki, Richard A., Kovacs, Joseph A.
Publicado 2013

Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans

por Desjardins, Christopher A., Giamberardino, Charles, Sykes, Sean M., Yu, Chen-Hsin, Tenor, Jennifer L., Chen, Yuan, Yang, Timothy, Jones, Alexander M., Sun, Sheng, Haverkamp, Miriam R., Heitman, Joseph, Litvintseva, Anastasia P., Perfect, John R., Cuomo, Christina A.
Publicado en Genome Res (2017)

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

por 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.
Publicado en mSphere (2016)

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

por Gnerre, Sante, MacCallum, Iain, Przybylski, Dariusz, Ribeiro, Filipe J., Burton, Joshua N., Walker, Bruce J., Sharpe, Ted, Hall, Giles, Shea, Terrance P., Sykes, Sean, Berlin, Aaron M., Aird, Daniel, Costello, Maura, Daza, Riza, Williams, Louise, Nicol, Robert, Gnirke, Andreas, Nusbaum, Chad, Lander, Eric S., Jaffe, David B.
Publicado 2011

The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum

por Neafsey, Daniel E., Galinsky, Kevin, Jiang, Rays H. Y., Young, Lauren, Sykes, Sean M., Saif, Sakina, Gujja, Sharvari, Goldberg, Jonathan M., Young, Sarah, Zeng, Qiandong, Chapman, Sinéad B., Dash, Aditya P., Anvikar, Anupkumar R., Sutton, Patrick L., Birren, Bruce W., Escalante, Ananias A., Barnwell, John W., Carlton, Jane M.
Publicado 2012

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

por Fisher, Sheila, Barry, Andrew, Abreu, Justin, Minie, Brian, Nolan, Jillian, Delorey, Toni M, Young, Geneva, Fennell, Timothy J, Allen, Alexander, Ambrogio, Lauren, Berlin, Aaron M, Blumenstiel, Brendan, Cibulskis, Kristian, Friedrich, Dennis, Johnson, Ryan, Juhn, Frank, Reilly, Brian, Shammas, Ramy, Stalker, John, Sykes, Sean M, Thompson, Jon, Walsh, John, Zimmer, Andrew, Zwirko, Zac, Gabriel, Stacey, Nicol, Robert, Nusbaum, Chad
Publicado 2011

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

por 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.
Publicado en Genetics (2017)

Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control

por Neafsey, Daniel E., Barker, Bridget M., Sharpton, Thomas J., Stajich, Jason E., Park, Daniel J., Whiston, Emily, Hung, Chiung-Yu, McMahan, Cody, White, Jared, Sykes, Sean, Heiman, David, Young, Sarah, Zeng, Qiandong, Abouelleil, Amr, Aftuck, Lynne, Bessette, Daniel, Brown, Adam, FitzGerald, Michael, Lui, Annie, Macdonald, J. Pendexter, Priest, Margaret, Orbach, Marc J., Galgiani, John N., Kirkland, Theo N., Cole, Garry T., Birren, Bruce W., Henn, Matthew R., Taylor, John W., Rounsley, Steven D.
Publicado 2010

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

por Grad, Yonatan H., Lipsitch, Marc, Feldgarden, Michael, Arachchi, Harindra M., Cerqueira, Gustavo C., FitzGerald, Michael, Godfrey, Paul, Haas, Brian J., Murphy, Cheryl I., Russ, Carsten, Sykes, Sean, Walker, Bruce J., Wortman, Jennifer R., Young, Sarah, Zeng, Qiandong, Abouelleil, Amr, Bochicchio, James, Chauvin, Sara, DeSmet, Timothy, Gujja, Sharvari, McCowan, Caryn, Montmayeur, Anna, Steelman, Scott, Frimodt-Møller, Jakob, Petersen, Andreas M., Struve, Carsten, Krogfelt, Karen A., Bingen, Edouard, Weill, François-Xavier, Lander, Eric S., Nusbaum, Chad, Birren, Bruce W., Hung, Deborah T., Hanage, William P.
Publicado 2012

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

por Ma, Liang, Chen, Zehua, Huang, Da Wei, Kutty, Geetha, Ishihara, Mayumi, Wang, Honghui, Abouelleil, Amr, Bishop, Lisa, Davey, Emma, Deng, Rebecca, Deng, Xilong, Fan, Lin, Fantoni, Giovanna, Fitzgerald, Michael, Gogineni, Emile, Goldberg, Jonathan M., Handley, Grace, Hu, Xiaojun, Huber, Charles, Jiao, Xiaoli, Jones, Kristine, Levin, Joshua Z., Liu, Yueqin, Macdonald, Pendexter, Melnikov, Alexandre, Raley, Castle, Sassi, Monica, Sherman, Brad T., Song, Xiaohong, Sykes, Sean, Tran, Bao, Walsh, Laura, Xia, Yun, Yang, Jun, Young, Sarah, Zeng, Qiandong, Zheng, Xin, Stephens, Robert, Nusbaum, Chad, Birren, Bruce W., Azadi, Parastoo, Lempicki, Richard A., Cuomo, Christina A., Kovacs, Joseph A.
Publicado en Nat Commun (2016)

Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen Saprolegnia parasitica

por Jiang, Rays H. Y., de Bruijn, Irene, Haas, Brian J., Belmonte, Rodrigo, Löbach, Lars, Christie, James, van den Ackerveken, Guido, Bottin, Arnaud, Bulone, Vincent, Díaz-Moreno, Sara M., Dumas, Bernard, Fan, Lin, Gaulin, Elodie, Govers, Francine, Grenville-Briggs, Laura J., Horner, Neil R., Levin, Joshua Z., Mammella, Marco, Meijer, Harold J. G., Morris, Paul, Nusbaum, Chad, Oome, Stan, Phillips, Andrew J., van Rooyen, David, Rzeszutek, Elzbieta, Saraiva, Marcia, Secombes, Chris J., Seidl, Michael F., Snel, Berend, Stassen, Joost H. M., Sykes, Sean, Tripathy, Sucheta, van den Berg, Herbert, Vega-Arreguin, Julio C., Wawra, Stephan, Young, Sarah K., Zeng, Qiandong, Dieguez-Uribeondo, Javier, Russ, Carsten, Tyler, Brett M., van West, Pieter
Publicado 2013

Comparative Genomic Analysis of Human Fungal Pathogens Causing Paracoccidioidomycosis

por Desjardins, Christopher A., Champion, Mia D., Holder, Jason W., Muszewska, Anna, Goldberg, Jonathan, Bailão, Alexandre M., Brigido, Marcelo Macedo, Ferreira, Márcia Eliana da Silva, Garcia, Ana Maria, Grynberg, Marcin, Gujja, Sharvari, Heiman, David I., Henn, Matthew R., Kodira, Chinnappa D., León-Narváez, Henry, Longo, Larissa V. G., Ma, Li-Jun, Malavazi, Iran, Matsuo, Alisson L., Morais, Flavia V., Pereira, Maristela, Rodríguez-Brito, Sabrina, Sakthikumar, Sharadha, Salem-Izacc, Silvia M., Sykes, Sean M., Teixeira, Marcus Melo, Vallejo, Milene C., Walter, Maria Emília Machado Telles, Yandava, Chandri, Young, Sarah, Zeng, Qiandong, Zucker, Jeremy, Felipe, Maria Sueli, Goldman, Gustavo H., Haas, Brian J., McEwen, Juan G., Nino-Vega, Gustavo, Puccia, Rosana, San-Blas, Gioconda, Soares, Celia Maria de Almeida, Birren, Bruce W., Cuomo, Christina A.
Publicado 2011

Comparative Functional Genomics of the Fission Yeasts

por Rhind, Nicholas, Chen, Zehua, Yassour, Moran, Thompson, Dawn A, Haas, Brian J, Habib, Naomi, Wapinski, Ilan, Roy, Sushmita, Lin, Michael F., Heiman, David I, Young, Sarah K, Furuya, Kanji, Guo, Yabin, Pidoux, Alison, Chen, Huei Mei, Robbertse, Barbara, Goldberg, Jonathan M., Aoki, Keita, Bayne, Elizabeth H., Berlin, Aaron M, Desjardins, Christopher A., Dobbs, Edward, Dukaj, Livio, Fan, Lin, FitzGerald, Michael G, French, Courtney, Gujja, Sharvari, Hansen, Klavs, Keifenheim, Dan, Levin, Joshua Z., Mosher, Rebecca A., Müller, Carolin A., Pfiffner, Jenna, Priest, Margaret, Russ, Carsten, Smialowska, Agata, Swoboda, Peter, Sykes, Sean M, Vaughn, Matthew, Vengrova, Sonya, Yoder, Ryan, Zeng, Qiandong, Allshire, Robin, Baulcombe, David, Birren, Bruce W., Brown, William, Ekwall, Karl, Kellis, Manolis, Leatherwood, Janet, Levin, Henry, Margalit, Hanah, Martienssen, Rob, Nieduszynski, Conrad A., Spatafora, Joseph W., Friedman, Nir, Dalgaard, Jacob Z., Baumann, Peter, Niki, Hironori, Regev, Aviv, Nusbaum, Chad
Publicado 2011

Erratum: The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

por Klenk, Hans-Peter, Clayton, Rebecca A., Tomb, Jean-Francois, White, Owen, Nelson, Karen E., Ketchum, Karen A., Dodson, Robert J., Gwinn, Michelle, Hickey, Erin K., Peterson, Jeremy D., Richardson, Delwood L., Kerlavage, Anthony R., Graham, David E., Kyrpides, Nikos C., Fleischmann, Robert D., Quackenbush, John, Lee, Norman H., Sutton, Granger G., Gill, Steven, Kirkness, Ewen F., Dougherty, Brian A., McKenney, Keith, Adams, Mark D., Loftus, Brendan, Peterson, Scott, Reich, Claudia I., McNeil, Leslie K., Badger, Jonathan H., Glodek, Anna, Zhou, Lixin, Overbeek, Ross, Gocayne, Jeannine D., Weidman, Janice F., McDonald, Lisa, Utterback, Teresa, Cotton, Matthew D., Spriggs, Tracy, Artiach, Patricia, Kaine, Brian P., Sykes, Sean M., Sadow, Paul W., D'Andrea, Kurt P., Bowman, Cheryl, Fujii, Claire, Garland, Stacey A., Mason, Tanya M., Olsen, Gary J., Fraser, Claire M., Smith, Hamilton O., Woese, Carl R., Venter, J. Craig
Publicado en Nature (1998)

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

por Ma, Li-Jun, van der Does, H. Charlotte, Borkovich, Katherine A., Coleman, Jeffrey J., Daboussi, Marie-Josée, Di Pietro, Antonio, Dufresne, Marie, Freitag, Michael, Grabherr, Manfred, Henrissat, Bernard, Houterman, Petra M., Kang, Seogchan, Shim, Won-Bo, Woloshuk, Charles, Xie, Xiaohui, Xu, Jin-Rong, Antoniw, John, Baker, Scott E., Bluhm, Burton H., Breakspear, Andrew, Brown, Daren W., Butchko, Robert A. E., Chapman, Sinead, Coulson, Richard, Coutinho, Pedro M., Danchin, Etienne G. J., Diener, Andrew, Gale, Liane R., Gardiner, Donald M., Goff, Stephen, Hammond-Kosack, Kim E., Hilburn, Karen, Hua-Van, Aurélie, Jonkers, Wilfried, Kazan, Kemal, Kodira, Chinnappa D., Koehrsen, Michael, Kumar, Lokesh, Lee, Yong-Hwan, Li, Liande, Manners, John M., Miranda-Saavedra, Diego, Mukherjee, Mala, Park, Gyungsoon, Park, Jongsun, Park, Sook-Young, Proctor, Robert H., Regev, Aviv, Ruiz-Roldan, M. Carmen, Sain, Divya, Sakthikumar, Sharadha, Sykes, Sean, Schwartz, David C., Turgeon, B. Gillian, Wapinski, Ilan, Yoder, Olen, Young, Sarah, Zeng, Qiandong, Zhou, Shiguo, Galagan, James, Cuomo, Christina A., Kistler, H. Corby, Rep, Martijn
Publicado 2010

A framework for human microbiome research

por Methé, Barbara A., Nelson, Karen E., Pop, Mihai, Creasy, Heather H., Giglio, Michelle G., Huttenhower, Curtis, Gevers, Dirk, Petrosino, Joseph F., Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Vivien Bonazzi, J., Brooks, Paul, Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Wm. Michael, Durkin, A. Scott, Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry, Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, Kinder-Haake, Susan, King, Nicholas B., Knight, Rob, Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, R. Dwayne, Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavrommatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Pamela Sankar, J., Sathirapongsasuti, Fah, Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Chris S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, Yuan Qing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Weinstock, George M., Wilson, Richard K., White, Owen
Publicado 2012