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
Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Robert Shoemaker, Jie Deng, Wei Wang, Kun Zhang Genome Res 2010
To infinium, and beyond! Karen D Wright, Richard J Gilbertson Cancer Cell 17 419-20 2010
Whole genome DNA methylation analysis based on high throughput sequencing technology. Ning Li, Mingzhi Ye, Yingrui Li, Zhixiang Yan, Lee M Butcher, Jihua Sun, Xu Han, Quan Chen, Xiuqing Zhang, Jun Wang Methods 2010
Conservation and divergence of methylation patterning in plants and animals. Suhua Feng, Shawn J Cokus, Xiaoyu Zhang, Pao-Yang Chen, Magnolia Bostick, Mary G Goll, Jonathan Hetzel, Jayati Jain, Steven H Strauss, Marnie E Halpern, Chinweike Ukomadu, Kirsten C Sadler, Sriharsa Pradhan, Matteo Pellegrini, Steven E Jacobsen Proc Natl Acad Sci U S A 107 8689-94 2010
Genome-wide analysis of histone modifications in human pancreatic islets. Reena Bhandare, Jonathan Schug, John Le Lay, Alan Fox, Olga Smirnova, Chengyang Liu, Ali Naji, Klaus H Kaestner Genome Res 20 428-33 2010
Principles and challenges of genome-wide DNA methylation analysis. Peter W Laird Nat Rev Genet 11 191-203 2010
Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Hongcang Gu, Christoph Bock, Tarjei S Mikkelsen, Natalie Jäger, Zachary D Smith, Eleni Tomazou, Andreas Gnirke, Eric S Lander, Alexander Meissner Nat Methods 7 133-6 2010
Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing. Yoshinao Ruike, Yukako Imanaka, Fumiaki Sato, Kazuharu Shimizu, Gozoh Tsujimoto BMC Genomics 11 137 2010
A first look at entire human methylomes. Joseph F Costello, Martin Krzywinski, Marco A Marra Nat Biotechnol 27 1130-2 2009
The human retinoblastoma gene is imprinted. Deniz Kanber, Tea Berulava, Ole Ammerpohl, Diana Mitter, Julia Richter, Reiner Siebert, Bernhard Horsthemke, Dietmar Lohmann, Karin Buiting PLoS Genet 5 e1000790 2009
Human DNA methylomes at base resolution show widespread epigenomic differences. Summary Ryan Lister, Mattia Pelizzola, Robert H Dowen, R David Hawkins, Gary Hon, Julian Tonti-Filippini, Joseph R Nery, Leonard Lee, Zhen Ye, Que-Minh Ngo, Lee Edsall, Jessica Antosiewicz-Bourget, Ron Stewart, Victor Ruotti, A Harvey Millar, James A Thomson, Bing Ren, Joseph R Ecker Nature 462 315-22 2009
Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Zhibin Wang, Chongzhi Zang, Kairong Cui, Dustin E Schones, Artem Barski, Weiqun Peng, Keji Zhao Cell 138 1019-31 2009
Sensitive digital quantification of DNA methylation in clinical samples. Summary Meng Li, Wei-Dong Chen, Nickolas Papadopoulos, Steven N Goodman, Niels Christian Bjerregaard, Søren Laurberg, Bernard Levin, Hartmut Juhl, Nadir Arber, Helen Moinova, Kris Durkee, Kerstin Schmidt, Yiping He, Frank Diehl, Victor E Velculescu, Shibin Zhou, Luis A Diaz, Kenneth W Kinzler, Sanford D Markowitz, Bert Vogelstein Nat Biotechnol 27 858-63 2009
High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Summary Emily Hodges, Andrew D Smith, Jude Kendall, Zhenyu Xuan, Kandasamy Ravi, Michelle Rooks, Michael Q Zhang, Kenny Ye, Arindam Bhattacharjee, Leonardo Brizuela, W Richard McCombie, Michael Wigler, Gregory J Hannon, James B Hicks Genome Res 19 1593-605 2009
Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression. Jesse D Hollister, Brandon S Gaut Genome Res 19 1419-28 2009
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