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
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 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. 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
Multiplex padlock targeted sequencing reveals human hypermutable CpG variations. Summary Jin Billy Li, Yuan Gao, John Aach, Kun Zhang, Gregory V Kryukov, Bin Xie, Annika Ahlford, Jung-Ki Yoon, Abraham M Rosenbaum, Alexander Wait Zaranek, Emily Leproust, Shamil R Sunyaev, George M Church Genome Res 19 1606-15 2009
Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Summary Mary Gehring, Kerry L Bubb, Steven Henikoff Science 324 1447-51 2009
Genome-wide demethylation of Arabidopsis endosperm. Summary Tzung-Fu Hsieh, Christian A Ibarra, Pedro Silva, Assaf Zemach, Leor Eshed-Williams, Robert L Fischer, Daniel Zilberman Science 324 1451-4 2009
High-throughput bisulfite sequencing in mammalian genomes. Summary Zachary D Smith, Hongcang Gu, Christoph Bock, Andreas Gnirke, Alexander Meissner Methods 48 226-32 2009
Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Summary Madeleine P Ball, Jin Billy Li, Yuan Gao, Je-Hyuk Lee, Emily M LeProust, In-Hyun Park, Bin Xie, George Q Daley, George M Church Nat Biotechnol 27 361-8 2009
Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Summary Jie Deng, Robert Shoemaker, Bin Xie, Athurva Gore, Emily M LeProust, Jessica Antosiewicz-Bourget, Dieter Egli, Nimet Maherali, In-Hyun Park, Junying Yu, George Q Daley, Kevin Eggan, Konrad Hochedlinger, James Thomson, Wei Wang, Yuan Gao, Kun Zhang Nat Biotechnol 27 353-60 2009
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Summary Alayne L Brunner, David S Johnson, Si Wan Kim, Anton Valouev, Timothy E Reddy, Norma F Neff, Elizabeth Anton, Catherine Medina, Loan Nguyen, Eric Chiao, Chuba B Oyolu, Gary P Schroth, Devin M Absher, Julie C Baker, Richard M Myers Genome Res 19 1044-56 2009
An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines. Jian Li, Fei Gao, Ning Li, Shengting Li, Guangliang Yin, Geng Tian, Shangang Jia, Kai Wang, Xiuqing Zhang, Huanming Yang, Anders Lade Nielsen, Lars Bolund BMC Genomics 10 223 2009
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Alexander Meissner, Tarjei S Mikkelsen, Hongcang Gu, Marius Wernig, Jacob Hanna, Andrey Sivachenko, Xiaolan Zhang, Bradley E Bernstein, Chad Nusbaum, David B Jaffe, Andreas Gnirke, Rudolf Jaenisch, Eric S Lander Nature 454 766-70 2008
Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Ryan Lister, Ronan C OMalley, Julian Tonti-Filippini, Brian D Gregory, Charles C Berry, A Harvey Millar, Joseph R Ecker Cell 133 523-36 2008
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