Finding the missing honey bee genes: lessons learned from a genome upgrade
Elsik, Christine G, Worley, Kim C, Bennett, Anna K, Beye, Martin, Camara, Francisco, Childers, Christopher P, de Graaf, Dirk C, Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D, Foster, Leonard J, Graur, Dan, Guigo, Roderic, Hoff, Katharina Jasmin, Holder, Michael E, Hudson, Matthew E, Hunt, Greg J, Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L, Ma, Jian, Maleszka, Ryszard, Moritz, Robin F A, Munoz-Torres, Monica C, Murphy, Terence D, Muzny, Donna M, Newsham, Irene F, Reese, Justin T, Robertson, Hugh M, Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M, Vaerenbergh, Matthias Van, Waterhouse, Robert M, Weaver, Daniel B, Whitfield, Charles W, Wu, Yuanqing, Zdobnov, Evgeny M, Zhang, Lan, Zhu, Dianhui, Gibbs, Richard A
Published in BMC genomics (30.01.2014)
Published in BMC genomics (30.01.2014)
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Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds
Gibbs, Richard A, Taylor, Jeremy F, Van Tassell, Curtis P, Barendse, William, Eversole, Kellye A, Gill, Clare A, Green, Ronnie D, Hamernik, Debora L, Kappes, Steven M, Lien, Sigbjørn, Matukumalli, Lakshmi K, McEwan, John C, Nazareth, Lynne V, Schnabel, Robert D, Weinstock, George M, Wheeler, David A, Ajmone-Marsan, Paolo, Boettcher, Paul J, Caetano, Alexandre R, Garcia, Jose Fernando, Hanotte, Olivier, Mariani, Paola, Skow, Loren C, Sonstegard, Tad S, Williams, John L, Diallo, Boubacar, Hailemariam, Lemecha, Martinez, Mario L, Morris, Chris A, Silva, Luiz O C, Spelman, Richard J, Mulatu, Woudyalew, Zhao, Keyan, Abbey, Colette A, Agaba, Morris, Araujo, Flábio R, Bunch, Rowan J, Burton, James, Gorni, Chiara, Olivier, Hanotte, Harrison, Blair E, Luff, Bill, Machado, Marco A, Mwakaya, Joel, Plastow, Graham, Sim, Warren, Smith, Timothy, Thomas, Merle B, Valentini, Alessio, Williams, Paul, Womack, James, Woolliams, John A, Liu, Yue, Qin, Xiang, Worley, Kim C, Gao, Chuan, Jiang, Huaiyang, Moore, Stephen S, Ren, Yanru, Song, Xing-Zhi, Bustamante, Carlos D, Hernandez, Ryan D, Muzny, Donna M, Patil, Shobha, San Lucas, Anthony, Fu, Qing, Kent, Matthew P, Vega, Richard, Matukumalli, Aruna, McWilliam, Sean, Sclep, Gert, Bryc, Katarzyna, Choi, Jungwoo, Gao, Hong, Grefenstette, John J, Murdoch, Brenda, Stella, Alessandra, Villa-Angulo, Rafael, Wright, Mark, Aerts, Jan, Jann, Oliver, Negrini, Riccardo, Goddard, Mike E, Hayes, Ben J, Bradley, Daniel G, Barbosa da Silva, Marcos, Lau, Lilian P L, Liu, George E, Lynn, David J, Panzitta, Francesca, Dodds, Ken G
Published in Science (American Association for the Advancement of Science) (24.04.2009)
Published in Science (American Association for the Advancement of Science) (24.04.2009)
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Comparative validation of the D. melanogaster modENCODE transcriptome annotation
Chen, Zhen-Xia, Sturgill, David, Qu, Jiaxin, Jiang, Huaiyang, Park, Soo, Boley, Nathan, Suzuki, Ana Maria, Fletcher, Anthony R, Plachetzki, David C, FitzGerald, Peter C, Artieri, Carlo G, Atallah, Joel, Barmina, Olga, Brown, James B, Blankenburg, Kerstin P, Clough, Emily, Dasgupta, Abhijit, Gubbala, Sai, Han, Yi, Jayaseelan, Joy C, Kalra, Divya, Kim, Yoo-Ah, Kovar, Christie L, Lee, Sandra L, Li, Mingmei, Malley, James D, Malone, John H, Mathew, Tittu, Mattiuzzo, Nicolas R, Munidasa, Mala, Muzny, Donna M, Ongeri, Fiona, Perales, Lora, Przytycka, Teresa M, Pu, Ling-Ling, Robinson, Garrett, Thornton, Rebecca L, Saada, Nehad, Scherer, Steven E, Smith, Harold E, Vinson, Charles, Warner, Crystal B, Worley, Kim C, Wu, Yuan-Qing, Zou, Xiaoyan, Cherbas, Peter, Kellis, Manolis, Eisen, Michael B, Piano, Fabio, Kionte, Karin, Fitch, David H, Sternberg, Paul W, Cutter, Asher D, Duff, Michael O, Hoskins, Roger A, Graveley, Brenton R, Gibbs, Richard A, Bickel, Peter J, Kopp, Artyom, Carninci, Piero, Celniker, Susan E, Oliver, Brian, Richards, Stephen
Published in Genome research (01.07.2014)
Published in Genome research (01.07.2014)
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Bos taurus genome assembly
Liu, Yue, Qin, Xiang, Song, Xing-Zhi Henry, Jiang, Huaiyang, Shen, Yufeng, Durbin, K James, Lien, Sigbjørn, Kent, Matthew Peter, Sodeland, Marte, Ren, Yanru, Zhang, Lan, Sodergren, Erica, Havlak, Paul, Worley, Kim C, Weinstock, George M, Gibbs, Richard A
Published in BMC genomics (24.04.2009)
Published in BMC genomics (24.04.2009)
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Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF
Bourgogne, Agathe, Garsin, Danielle A, Qin, Xiang, Singh, Kavindra V, Sillanpaa, Jouko, Yerrapragada, Shailaja, Ding, Yan, Dugan-Rocha, Shannon, Buhay, Christian, Shen, Hua, Chen, Guan, Williams, Gabrielle, Muzny, Donna, Maadani, Arash, Fox, Kristina A, Gioia, Jason, Chen, Lei, Shang, Yue, Arias, Cesar A, Nallapareddy, Sreedhar R, Zhao, Meng, Prakash, Vittal P, Chowdhury, Shahreen, Jiang, Huaiyang, Gibbs, Richard A, Murray, Barbara E, Highlander, Sarah K, Weinstock, George M
Published in Genome biology (08.07.2008)
Published in Genome biology (08.07.2008)
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Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus
Highlander, Sarah K, Hultén, Kristina G, Qin, Xiang, Jiang, Huaiyang, Yerrapragada, Shailaja, Mason, Jr, Edward O, Shang, Yue, Williams, Tiffany M, Fortunov, Régine M, Liu, Yamei, Igboeli, Okezie, Petrosino, Joseph, Tirumalai, Madhan, Uzman, Akif, Fox, George E, Cardenas, Ana Maria, Muzny, Donna M, Hemphill, Lisa, Ding, Yan, Dugan, Shannon, Blyth, Peter R, Buhay, Christian J, Dinh, Huyen H, Hawes, Alicia C, Holder, Michael, Kovar, Christie L, Lee, Sandra L, Liu, Wen, Nazareth, Lynne V, Wang, Qiaoyan, Zhou, Jianling, Kaplan, Sheldon L, Weinstock, George M
Published in BMC microbiology (06.11.2007)
Published in BMC microbiology (06.11.2007)
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Complete Genome Sequence of Rickettsia typhi and Comparison with Sequences of Other Rickettsiae
MCLEOD, Michael P, XIANG QIN, HAWES, Alicia C, SODERGREN, Erica, GILL, Rachel, HUME, Jennifer, MORGAN, Maggie, GUANGWEI FAN, AMIN, Anita G, GIBBS, Richard A, CHAO HONG, YU, Xue-Jie, KARPATHY, Sandor E, WALKER, David H, WEINSTOCK, George M, GIOIA, Jason, HIGHLANDER, Sarah K, FOX, George E, MCNEILL, Thomas Z, HUAIYANG JIANG, MUZNY, Donna, JACOB, Leni S
Published in Journal of Bacteriology (01.09.2004)
Published in Journal of Bacteriology (01.09.2004)
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Chromosome Rearrangement and Diversification of Francisella tularensis Revealed by the Type B (OSU18) Genome Sequence
PETROSINO, Joseph F, QIN XIANG, UZMAN, Akif, FOX, George E, HIGHLANDER, Sarah, REICHARD, Mason, MORTON, Rebecca J, CLINKENBEARD, Kenneth D, WEINSTOCK, George M, KARPATHY, Sandor E, HUAIYANG JIANG, YERRAPRAGADA, Shailaja, YAMEI LIU, GIOIA, Jason, HEMPHILL, Lisa, GONZALEZ, Arely, RAGHAVAN, T. M
Published in Journal of Bacteriology (01.10.2006)
Published in Journal of Bacteriology (01.10.2006)
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The Genome Sequence of Mannheimia haemolytica A1: Insights into Virulence, Natural Competence, and Pasteurellaceae Phylogeny
GIOIA, Jason, XIANG QIN, HEMPHILL, Lisa, SODERGREN, Erica, QIAOYAN WANG, MUZNY, Donna M, HOMSI, Farah J, WEINSTOCK, George M, HIGHLANDER, Sarah K, HUAIYANG JIANG, CLINKENBEARD, Kenneth, LO, Reggie, YAMEI LIU, FOX, George E, YERRAPRAGADA, Shailaja, MCLEOD, Michael P, MCNEILL, Thomas Z
Published in Journal of Bacteriology (01.10.2006)
Published in Journal of Bacteriology (01.10.2006)
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Genome sequence of Fusobacterium nucleatum subspecies polymorphum - a genetically tractable fusobacterium
Karpathy, Sandor E, Qin, Xiang, Gioia, Jason, Jiang, Huaiyang, Liu, Yamei, Petrosino, Joseph F, Yerrapragada, Shailaja, Fox, George E, Haake, Susan Kinder, Weinstock, George M, Highlander, Sarah K
Published in PloS one (01.08.2007)
Published in PloS one (01.08.2007)
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Community annotation: Procedures, protocols, and supporting tools: Table 1
Elsik, Christine G., Worley, Kim C., Zhang, Lan, Milshina, Natalia V., Jiang, Huaiyang, Reese, Justin T., Childs, Kevin L., Venkatraman, Anand, Dickens, C. Michael, Weinstock, George M., Gibbs, Richard A.
Published in Genome research (01.11.2006)
Published in Genome research (01.11.2006)
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Gene variants identified by whole-exome sequencing in 33 French women with premature ovarian insufficiency
Yang, Xiang, Touraine, Philippe, Desai, Swapna, Humphreys, Gregory, Jiang, Huaiyang, Yatsenko, Alexander, Rajkovic, Aleksandar
Published in Journal of assisted reproduction and genetics (01.01.2019)
Published in Journal of assisted reproduction and genetics (01.01.2019)
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Importance of complete phenotyping in prenatal whole exome sequencing
Aarabi, Mahmoud, Sniezek, Olivia, Jiang, Huaiyang, Saller, Devereux N., Bellissimo, Daniel, Yatsenko, Svetlana A., Rajkovic, Aleksandar
Published in Human genetics (01.02.2018)
Published in Human genetics (01.02.2018)
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Exome sequencing reveals MCM8 mutation underlies ovarian failure and chromosomal instability
AlAsiri, Saleh, Basit, Sulman, Wood-Trageser, Michelle A, Yatsenko, Svetlana A, Jeffries, Elizabeth P, Surti, Urvashi, Ketterer, Deborah M, Afzal, Sibtain, Ramzan, Khushnooda, Faiyaz-Ul Haque, Muhammad, Jiang, Huaiyang, Trakselis, Michael A, Rajkovic, Aleksandar
Published in The Journal of clinical investigation (01.01.2015)
Published in The Journal of clinical investigation (01.01.2015)
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MCM8 and MCM9 Nucleotide Variants in Women with Primary Ovarian Insufficiency
Desai, Swapna, Wood-Trageser, Michelle, Matic, Jelena, Chipkin, Jaqueline, Jiang, Huaiyang, Bachelot, Anne, Dulon, Jerome, Sala, Cinzia, Barbieri, Caterina, Cocca, Massimiliano, Toniolo, Daniela, Philippe, Touraine, Witchel, Selma, Rajkovic, Aleksandar
Published in The journal of clinical endocrinology and metabolism (01.02.2017)
Published in The journal of clinical endocrinology and metabolism (01.02.2017)
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MCM9 Mutations Are Associated with Ovarian Failure, Short Stature, and Chromosomal Instability
Wood-Trageser, Michelle A., Gurbuz, Fatih, Yatsenko, Svetlana A., Jeffries, Elizabeth P., Kotan, L. Damla, Surti, Urvashi, Ketterer, Deborah M., Matic, Jelena, Chipkin, Jacqueline, Jiang, Huaiyang, Trakselis, Michael A., Topaloglu, A. Kemal, Rajkovic, Aleksandar
Published in American journal of human genetics (04.12.2014)
Published in American journal of human genetics (04.12.2014)
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X-linked ADGRG2 mutation and obstructive azoospermia in a large Pakistani family
Khan, Muhammad Jaseem, Pollock, Nijole, Jiang, Huaiyang, Castro, Carlos, Nazli, Rubina, Ahmed, Jawad, Basit, Sulman, Rajkovic, Aleksandar, Yatsenko, Alexander N.
Published in Scientific reports (02.11.2018)
Published in Scientific reports (02.11.2018)
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Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, Inanç, Boisvert, Sébastien, Chapman, Jarrod A, Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T Roderick, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A, Ganapathy, Ganeshkumar, Gibbs, Richard A, Gnerre, Sante, Godzaridis, Elénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B, Ho, Isaac Y, Howard, Jason, Hunt, Martin, Jackman, Shaun D, Jaffe, David B, Jarvis, Erich D, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J, Kitzman, Jacob O, Knight, James R, Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, Maccallum, Iain, Macmanes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Naquin, Delphine, Ning, Zemin, Otto, Thomas D, Paten, Benedict, Paulo, Octávio S, Phillippy, Adam M, Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S, Ruby, J Graham, Scalabrin, Simone, Schatz, Michael C, Schwartz, David C, Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I, Shendure, Jay, Shi, Yujian, Simpson, Jared T, Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Vieira, Bruno M, Wang, Jun, Worley, Kim C, Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, Korf, Ian F
Published in Gigascience (22.07.2013)
Published in Gigascience (22.07.2013)
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Genomic Signatures of Cooperation and Conflict in the Social Amoeba
Ostrowski, Elizabeth A., Shen, Yufeng, Tian, Xiangjun, Sucgang, Richard, Jiang, Huaiyang, Qu, Jiaxin, Katoh-Kurasawa, Mariko, Brock, Debra A., Dinh, Christopher, Lara-Garduno, Fremiet, Lee, Sandra L., Kovar, Christie L., Dinh, Huyen H., Korchina, Viktoriya, Jackson, LaRonda, Patil, Shobha, Han, Yi, Chaboub, Lesley, Shaulsky, Gad, Muzny, Donna M., Worley, Kim C., Gibbs, Richard A., Richards, Stephen, Kuspa, Adam, Strassmann, Joan E., Queller, David C.
Published in Current biology (15.06.2015)
Published in Current biology (15.06.2015)
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