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
Computation for ChIP-seq and RNA-seq studies. Shirley Pepke, Barbara Wold, Ali Mortazavi Nat Methods 6 S22-32 2009
CCCTC-binding factor and the transcription factor T-bet orchestrate T helper 1 cell-specific structure and function at the interferon-gamma locus. Masayuki Sekimata, Mercedes Pérez-Melgosa, Sara A Miller, Amy S Weinmann, Peter J Sabo, Richard Sandstrom, Michael O Dorschner, John A Stamatoyannopoulos, Christopher B Wilson Immunity 31 551-64 2009
Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Erez Lieberman-Aiden, Nynke L van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R Lajoie, Peter J Sabo, Michael O Dorschner, Richard Sandstrom, Bradley Bernstein, M A Bender, Mark Groudine, Andreas Gnirke, John Stamatoyannopoulos, Leonid A Mirny, Eric S Lander, Job Dekker Science 326 289-93 2009
Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factors. Akira Nishiyama, Li Xin, Alexei A Sharov, Marshall Thomas, Gregory Mowrer, Emily Meyers, Yulan Piao, Samir Mehta, Sarah Yee, Yuhki Nakatake, Carole Stagg, Lioudmila Sharova, Lina S Correa-Cerro, Uwem Bassey, Hien Hoang, Eugene Kim, Richard Tapnio, Yong Qian, Dawood Dudekula, Michal Zalzman, Manxiang Li, Geppino Falco, Hsih-Te Yang, Sung-Lim Lee, Manuela Monti, Ilaria Stanghellini, Md Nurul Islam, Ramaiah Nagaraja, Ilya Goldberg, Weidong Wang, Dan L Longo, David Schlessinger, Minoru S H Ko Cell Stem Cell 5 420-33 2009
Chromatin poises miRNA- and protein-coding genes for expression. Artem Barski, Raja Jothi, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Dustin E Schones, Keji Zhao Genome Res 19 1742-51 2009
Splice site strength-dependent activity and genetic buffering by poly-G runs. Xinshu Xiao, Zefeng Wang, Minyoung Jang, Razvan Nutiu, Eric T Wang, Christopher B Burge Nat Struct Mol Biol 16 1094-100 2009
BayesPeak: Bayesian analysis of ChIP-seq data. Christiana Spyrou, Rory Stark, Andy Lynch, Simon Tavare BMC Bioinformatics 10 299 2009
Selective epigenetic control of retrotransposition in Arabidopsis. Marie Mirouze, Jon Reinders, Etienne Bucher, Taisuke Nishimura, Korbinian Schneeberger, Stephan Ossowski, Jun Cao, Detlef Weigel, Jerzy Paszkowski, Olivier Mathieu Nature 461 427-30 2009
ChIP-seq: advantages and challenges of a maturing technology. Peter J Park Nat Rev Genet 10 669-80 2009
Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif. Young-Kyo Seo, Hansook Kim Chong, Aniello M Infante, Seung-Soon Im, Xiaohui Xie, Timothy F Osborne Proc Natl Acad Sci U S A 106 13765-9 2009
Chromatin architecture and transcription factor binding regulate expression of erythrocyte membrane protein genes. Laurie A Steiner, Yelena Maksimova, Vincent Schulz, Clara Wong, Debasish Raha, Milind C Mahajan, Sherman M Weissman, Patrick G Gallagher Mol Cell Biol 29 5399-412 2009
Open chromatin encoded in DNA sequence is the signature of master replication origins in human cells. Benjamin Audit, Lamia Zaghloul, Cédric Vaillant, Guillaume Chevereau, Yves dAubenton-Carafa, Claude Thermes, Alain Arneodo Nucleic Acids Res 2009
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Summary Yong Zhang, Zarmik Moqtaderi, Barbara P Rattner, Ghia Euskirchen, Michael Snyder, James T Kadonaga, X Shirley Liu, Kevin Struhl Nat Struct Mol Biol 16 847-52 2009
H3.3/H2A.Z double variant-containing nucleosomes mark nucleosome-free regions of active promoters and other regulatory regions. Chunyuan Jin, Chongzhi Zang, Gang Wei, Kairong Cui, Weiqun Peng, Keji Zhao, Gary Felsenfeld Nat Genet 41 941-5 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
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