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Udvalgte publikationer af partnerne

(More on the way…)

Whole-Exome Sequencing of 2,000 Danish Individuals and the Role of Rare Coding Variants in Type 2 Diabetes
Kirk E. Lohmueller, Thomas Sparsø, Qibin Li, Ehm Andersson, Thorfinn Korneliussen, Anders Albrechtsen, Karina Banasik, Niels Grarup, Ingileif Hallgrimsdottir, Kristoffer Kiil, Tuomas O. Kilpeläinen, Nikolaj T. Krarup, Tune H. Pers, Gaston Sanchez, Youna Hu, Michael DeGiorgio, Torben Jørgensen, Annelli Sandbæk, Torsten Lauritzen, Søren Brunak, Karsten Kristiansen, Yingrui Li, Torben Hansen, Jun Wang, Rasmus Nielsen, and Oluf Pedersen.
The American Journal of Human Genetics 93, 1072–1086, December 5, 2013, p. 1072.

A short-read multiplex sequencing method for reliable, cost-effective and high-throughput genotyping in large-scale studies
Cao H, Wang Y, Zhang W, Chai X, Zhang X, Chen S, Yang F, Zhang C, Guo Y, Liu Y, Tang Z, Chen C, Xue Y, Zhen H, Xu Y, Rao B, Liu T, Zhao M, Zhang W, Li Y, Zhang X, Tellier LC, Krogh A, Kristiansen K, Wang J, Li J.
Hum Mutat. 2013 Dec; 34(12):1715-20.

Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing
Alquezar-Planas DE, Mourier T, Bruhn CA, Hansen AJ, Vitcetz SN, Mørk S, Gorodkin J, Nielsen HA, Guo Y, Sethuraman A, Paxinos EE, Shan T, Delwart EL, and Nielsen LP.
Nature Scientific Reports 2013; 3:2468.

Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma
Kan Z, Zheng H, Liu X, Li S, Barber TD, Gong Z, Gao H, Hao K, Willard MD, Xu J, Hauptschein R, Rejto PA, Fernandez J, Wang G, Zhang Q, Wang B, Chen R, Wang J, Lee NP, Zhou W, Lin Z, Peng Z, Yi K, Chen S, Li L, Fan X, Yang J, Ye R, Ju J, Wang K, Estrella H, Deng S, Wei P, Qiu M, Wulur IH, Liu J, Ehsani ME, Zhang C, Loboda A, Sung WK, Aggarwal A, Poon RT, Fan ST, Wang J, Hardwick J, Reinhard C, Dai H, Li Y, Luk JM, and Mao M.
Genome Res. 2013 Sep; 23(9):1422-33.

Richness of human gut microbiome correlates with metabolic markers
Emmanuelle Le Chatelier, Trine Nielsen, Junjie Qin, Edi Prifti, Falk Hildebrand, Gwen Falony, Mathieu Almeida, Manimozhiyan Arumugam, Jean-Michel Batto, Sean Kennedy, Pierre Leonard, Junhua, Kristoffer Burgdorf, Niels Grarup, Torben Jørgensen, Ivan Brandslund, Henrik Bjørn Nielsen, Agnieszka S. Juncker, Marcelo Bertalan, Florence Levenez, Nicolas Pons, Simon Rasmussen, Shinichi Sunagawa, Julien Tap, Sebastian Tims, Erwin G. Zoetendal, Søren Brunak, Karine Clément, Joël Dore, Michiel Kleerebezem, Karsten Kristiansen, Pierre Renault, Thomas Sicheritz-Ponten, Willem M. de Vos, Jean-Daniel Zucker, Jeroen Raes, Torben Hansen, JunWang, S. Dusko Ehrlich, and Oluf Pedersen.
NATURE, Vol 500, 29 August 2013, p. 541.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis E, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, and Korf IF.
Gigascience. 2013 Jul 22; 2(1):10.

Genetic Architecture of Vitamin B12 and Folate Levels Uncovered Applying Deeply Sequenced Large Dataset
Niels Grarup, Patrick Sulem, Camilla H. Sandholt, Gudmar Thorleifsson, Tarunveer S. Ahluwalia, Valgerdur Steinthorsdottir, Helgi Bjarnason, Daniel F. Gudbjartsson, Olafur T. Magnusson, Thomas Sparsø, Anders Albrechtsen, Augustine Kong, Gisli Masson, Geng Tian, Hongzhi Cao, Chao Nie, Karsten Kristiansen, Lise Lotte Husemoen, Betina Thuesen, Yingrui Li, Rasmus Nielsen, Allan Linneberg, Isleifur Olafsson, Gudmundur I. Eyjolfsson, Torben Jørgensen, Jun Wang, Torben Hansen, Unnur Thorsteinsdottir, Kari Stefansson, and Oluf Pedersen.
PLOS Genetics, June 2013, Volume 9, Issue 6.

Genetic diversity among pandemic 2009 influenza viruses isolated from a transmission chain
Sarah L Fordyce, Karoline Bragstad, Svend Stenvang Pedersen, Thøger G Jensen, Bente Gahrn-Hansen, Rod Daniels, Alan Hay, Marie-Louise Kampmann, Christian AW Bruhn, J Victor Moreno-Mayar, María C Ávila-Arcos, M Thomas P Gilbert, Lars P Nielsen.
Virol J. 2013; 10: 116.

Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes
A. Albrechtsen, N. Grarup, Y. Li, T. Sparsø,G. Tian, H. Cao, T. Jiang, S. Y. Kim, T. Korneliussen, Q. Li, C. Nie, R. Wu, L. Skotte, A. P. Morris, C. Ladenvall, S. Cauchi, A. Stancáková, G. Andersen, A. Astrup, K. Banasik, A. J. Bennett, L. Bolund, G. Charpentier, Y. Chen, J. M. Dekker, A. S. F. Doney, M. Dorkhan, T. Forsen, T. M. Frayling, C. J. Groves, Y. Gui, G. Hallmans, A. T. Hattersley, K. He, G. A. Hitman, J. Holmkvist, S. Huang, H. Jiang, X. Jin, J. M. Justesen, K. Kristiansen, J. Kuusisto, M. Lajer, O. Lantieri, W. Li, H. Liang, Q. Liao, X. Liu, T. Ma, X. Ma, M. P. Manijak, M. Marre, J. Mokrosinski, A. D. Morris, B. Mu, A. A. Nielsen, G. Nijpels, P. Nilsson, C. N. A. Palmer, N. W. Rayner, F. Renström, R. Ribel-Madsen, N. Robertson, O. Rolandsson, P. Rossing, T. W. Schwartz, P. E. Slagboom, M. Sterner, D.E.S.I.R. Study Group, M. Tang, L. Tarnow, the DIAGRAM Consortium, T. Tuomi, E. van’t Riet, N. van Leeuwen, T. V. Varga, M. A. Vestmar, M. Walker, B. Wang, Y. Wang, H. Wu, F. Xi, L. Yengo, C. Yu, X. Zhang, J. Zhang, Q. Zhang, W. Zhang, H. Zheng, Y. Zhou, D. Altshuler, L. M. ‘t Hart, P.W. Franks, B. Balkau, P. Froguel, M. I. McCarthy, M. Laakso, L. Groop, C. Christensen, I. Brandslund, T. Lauritzen, D. R. Witte, A. Linneberg, T. Jørgensen, T. Hansen, J. Wang, R. Nielsen, and O. Pedersen.
Diabetologia (2013) 56:298–310.

Ametagenome-wide association study of gut microbiota in type 2 diabetes
Junjie Qin, Yingrui Li, Zhiming Cai, Shenghui Li, Jianfeng Zhu, Fan Zhang, Suisha Liang, Wenwei Zhang, Yuanlin Guan, Dongqian Shen, Yangqing Peng, Dongya Zhang, Zhuye Jie, WenxianWu, Youwen Qin, Wenbin Xue, Junhua Li, Lingchuan Han, Donghui Lu, PeixianWu, Yali Dai, Xiaojuan Sun, Zesong Li, Aifa Tang, Shilong Zhong, Xiaoping Li, Weineng Chen, Ran Xu, MingbangWang, Qiang Feng, Meihua Gong, Jing Yu, Yanyan Zhang1, Ming Zhang, Torben Hansen, Gaston Sanchez, Jeroen Raes, Gwen Falony, Shujiro Okuda, Mathieu Almeida, Emmanuelle LeChatelier, Pierre Renault, Nicolas Pons, Jean-Michel Batto, Zhaoxi Zhang, Hua Chen, Ruifu Yang, Weimou Zheng, Songgang Li, Huanming Yang, JianWang, S. Dusko Ehrlich, Rasmus Nielsen, Oluf Pedersen, Karsten Kristiansen, and Jun Wang.
NATURE Vol 490, 4 October 2012, p. 55.

Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer
Yingrui Li, Xun Xu, Luting Song, Yong Hou, Zesong Li, Shirley Tsang, Fuqiang L, Kate McGee Im, Kui Wu, Hanjie Wu, Xiaofei Ye, Guibo Li, Linlin Wang, Bo Zhang, Jie Liang, Wei Xie, Renhua Wu, Hui Jiang, Xiao Liu, Chang Yu, Hancheng Zheng, Min Jian, Liping Nie, Lei Wan, Min Shi, Xiaojuan Sun, Aifa Tang, Guangwu Guo, Yaoting Gui, Zhiming Cai, Jingxiang Li, Wen Wang, Zuhong Lu, Xiuqing Zhang, Lars Bolund, Karsten Kristiansen, Jian Wang, Huanming Yang, Michael Dean and Jun Wang.
GigaScience 2012, 1:12 [Aug12]

Probable transmission of coxsackie B3 virus from human to chimpanzee, Denmark
Nielsen SC, Mourier T, Baandrup U, Søland TM, Bertelsen MF, Gilbert MT, and Nielsen LP.
Emerg Infect Dis. 2012 Jul; 18(7):1163-5.

Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor
Xun Xu, Yong Hou, Xuyang Yin, Li Bao, Aifa Tang, Luting Song, Fuqiang Li, Shirley Tsang, Kui Wu, Hanjie Wu, Weiming He, Liang Zeng, Manjie Xing, Renhua Wu, Hui Jiang, Xiao Liu, Dandan Cao, Guangwu Guo, Xueda Hu, Yaoting Gui, Zesong Li, Wenyue Xie, Xiaojuan Sun, Min Shi, Zhiming Cai, Bin Wang, Meiming Zhong, Jingxiang Li, Zuhong Lu, Ning Gu, Xiuqing Zhang, Laurie Goodman, Lars Bolund, Jian Wang, Huanming Yang, Karsten Kristiansen, Michael Dean, Yingrui Li, and Jun Wang.
Cell 148, 886–895, March 2, 2012, p. 886.

Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm
Yong Hou, Luting Song, Ping Zhu, Bo Zhang, Ye Tao, Xun Xu, Fuqiang Li, Kui Wu, Jie Liang, Di Shao, Hanjie Wu, Xiaofei Ye, Chen Ye, Renhua Wu, Min Jian, Yan Chen, Wei Xie, Ruren Zhang, Lei Chen, Xin Liu, Xiaotian Yao, Hancheng Zheng, Chang Yu, Qibin Li, Zhuolin Gong, Mao Mao, Xu Yang, Lin Yang, Jingxiang Li, Wen Wang, Zuhong Lu, Ning Gu, Goodman Laurie, Lars Bolund, Karsten Kristiansen, Jian Wang, Huanming Yang, Yingrui Li, Xiuqing Zhang, and Jun Wang.
Cell 148, 873–885, March 2, 2012.

Serious invasive Saffold virus infections in children, 2009
Nielsen AC, Böttiger B, Banner J, Hoffmann T, and Nielsen LP.
Emerg Infect Dis. 2012 Jan; 18(1):7-12.

A simple method for the parallel deep sequencing of full influenza A genomes
Kampmann ML, Fordyce SL, Avila-Arcos MC, Rasmussen M, Willerslev E, Nielsen LP, and Gilbert MT.
J Virol Methods. 2011; 178:243-8.