At Illumina, we enjoy seeing how researchers are successfully using our products for a wide range of genetic analysis applications. We are proud to share this list of publications from the growing community of Illumina customers, collaborators, and internal scientists. If we missed one, please send the citation to publications@illumina.com.

Title Authors Source Year
Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Weibo Xie, Qi Feng, Huihui Yu, Xuehui Huang, Qiang Zhao, Yongzhong Xing, Sibin Yu, Bin Han, Qifa Zhang Proc Natl Acad Sci U S A 107 10578-83 2010
Genome-wide SNP detection in the great tit Parus major using high throughput sequencing. Nikkie E M van Bers, Kees van Oers, Hindrik H D Kerstens, Bert W Dibbits, Richard P M A Crooijmans, Marcel E Visser, Martien A M Groenen Mol Ecol 19 Suppl 1 89-99 2010
New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. Thomas D Otto, Daniel Wilinski, Sammy Assefa, Thomas M Keane, Louis R Sarry, Ulrike B?hme, Jacob Lemieux, Bart Barrell, Arnab Pain, Matthew Berriman, Chris Newbold, Manuel Llin?s Mol Microbiol 76 12-24 2010
High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. David L Hyten, Steven B Cannon, Qijian Song, Nathan Weeks, Edward W Fickus, Randy C Shoemaker, James E Specht, Andrew D Farmer, Gregory D May, Perry B Cregan BMC Genomics 11 38 2010
De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. Minou Nowrousian, Jason E Stajich, Meiling Chu, Ines Engh, Eric Espagne, Karen Halliday, Jens Kamerewerd, Frank Kempken, Birgit Knab, Hsiao-Che Kuo, Heinz D Osiewacz, Stefanie P?ggeler, Nick D Read, Stephan Seiler, Kristina M Smith, Denise Zickler, Ulrich K?ck, Michael Freitag PLoS Genet 6 e1000891 2010
De novo assembly of human genomes with massively parallel short read sequencing. Ruiqiang Li, Hongmei Zhu, Jue Ruan, Wubin Qian, Xiaodong Fang, Zhongbin Shi, Yingrui Li, Shengting Li, Gao Shan, Karsten Kristiansen, Songgang Li, Huanming Yang, Jian Wang, Jun Wang Genome Res 20 265-72 2010
The sequence and de novo assembly of the giant panda genome. Ruiqiang Li, Wei Fan, Geng Tian, Hongmei Zhu, Lin He, Jing Cai, Quanfei Huang, Qingle Cai, Bo Li, Yinqi Bai, Zhihe Zhang, Yaping Zhang, Wen Wang, Jun Li, Fuwen Wei, Heng Li, Min Jian, Jianwen Li, Zhaolei Zhang, Rasmus Nielsen, Dawei Li, Wanjun Gu, Zhentao Yang, Zhaoling Xuan, Oliver A Ryder, Frederick Chi-Ching Leung, Yan Zhou, Jianjun Cao, Xiao Sun, Yonggui Fu, Xiaodong Fang, Xiaosen Guo, Bo Wang, Rong Hou, Fujun Shen, Bo Mu, Peixiang Ni, Runmao Lin, Wubin Qian, Guodong Wang, Chang Yu, Wenhui Nie, Jinhuan Wang, Zhigang Wu, Huiqing Liang, Jiumeng Min, Qi Wu, Shifeng Cheng, Jue Ruan, Mingwei Wang, Zhongbin Shi, Ming Wen, Binghang Liu, Xiaoli Ren, Huisong Zheng, Dong Dong, Kathleen Cook, Gao Shan, Hao Zhang, Carolin Kosiol, Xueying Xie, Zuhong Lu, Hancheng Zheng, Yingrui Li, Cynthia C Steiner, Tommy Tsan-Yuk Lam, Siyuan Lin, Qinghui Zhang, Guoqing Li, Jing Tian, Timing Gong, Hongde Liu, Dejin Zhang, Lin Fang, Chen Ye, Juanbin Zhang, Wenbo Hu, Anlong Xu, Yuanyuan Ren, Guojie Zhang, Micha Nature 463 311-7 2010
Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens. Charles Cunningham, Derek Gatherer, Birgitta Hilfrich, Katarina Baluchova, Derrick J Dargan, Marian Thomson, Paul D Griffiths, Gavin W G Wilkinson, Thomas F Schulz, Andrew J Davison J Gen Virol 91 605-15 2010
The genome of the cucumber, Cucumis sativus L. Nat Genet 41 1275-81 2009
De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Scott Diguistini, Nancy Liao, Darren Platt, Gordon Robertson, Michael Seidel, Simon Chan, T Roderick Docking, Inanc Birol, Robert Holt, Martin Hirst, Elaine Mardis, Marco Marra, Richard Hamelin, Jörg Bohlmann, Colette Breuil, Steven Jones Genome Biol 10 R94 2009
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Summary Iwanka Kozarewa, Zemin Ning, Michael A Quail, Mandy J Sanders, Matthew Berriman, Daniel J Turner Nat Methods 6 291-5 2009
De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. Rhys A Farrer, Eric Kemen, Jonathan D G Jones, David J Studholme FEMS Microbiol Lett 291 103-11 2009
De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Josephine A Reinhardt, David A Baltrus, Marc T Nishimura, William R Jeck, Corbin D Jones, Jeffery L Dangl Genome Res 19 294-305 2009
Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey. Hindrik H D Kerstens, Richard P M A Crooijmans, Albertine Veenendaal, Bert W Dibbits, Thomas F C Chin-A-Woeng, Johan T den Dunnen, Martien A M Groenen BMC Genomics 10 479 2009