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
Cooperation between the transcription factors p63 and IRF6 is essential to prevent cleft palate in mice. Helen A Thomason, Huiqing Zhou, Evelyn N Kouwenhoven, Gian-Paolo Dotto, Gaia Restivo, Bach-Cuc Nguyen, Hayley Little, Michael J Dixon, Hans van Bokhoven, Jill Dixon J Clin Invest 120 1561-9 2010
Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Hui Xiang, Jingde Zhu, Quan Chen, Fangyin Dai, Xin Li, Muwang Li, Hongyu Zhang, Guojie Zhang, Dong Li, Yang Dong, Li Zhao, Ying Lin, Daojun Cheng, Jian Yu, Jinfeng Sun, Xiaoyu Zhou, Kelong Ma, Yinghua He, Yangxing Zhao, Shicheng Guo, Mingzhi Ye, Guangwu Guo, Yingrui Li, Ruiqiang Li, Xiuqing Zhang, Lijia Ma, Karsten Kristiansen, Qiuhong Guo, Jianhao Jiang, Stephan Beck, Qingyou Xia, Wen Wang, Jun Wang Nat Biotechnol 28 516-20 2010
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, Lior Pachter Nat Biotechnol 28 511-5 2010
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Mitchell Guttman, Manuel Garber, Joshua Z Levin, Julie Donaghey, James Robinson, Xian Adiconis, Lin Fan, Magdalena J Koziol, Andreas Gnirke, Chad Nusbaum, John L Rinn, Eric S Lander, Aviv Regev Nat Biotechnol 28 503-10 2010
Characterization of missing human genome sequences and copy-number polymorphic insertions. Jeffrey M Kidd, Nick Sampas, Francesca Antonacci, Tina Graves, Robert Fulton, Hillary S Hayden, Can Alkan, Maika Malig, Mario Ventura, Giuliana Giannuzzi, Joelle Kallicki, Paige Anderson, Anya Tsalenko, N Alice Yamada, Peter Tsang, Rajinder Kaul, Richard K Wilson, Laurakay Bruhn, Evan E Eichler Nat Methods 7 365-71 2010
Pol II and its associated epigenetic marks are present at Pol III-transcribed noncoding RNA genes. Artem Barski, Iouri Chepelev, Dritan Liko, Suresh Cuddapah, Alastair B Fleming, Joanna Birch, Kairong Cui, Robert J White, Keji Zhao Nat Struct Mol Biol 17 629-34 2010
Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. Andrew J Oler, Ravi K Alla, Douglas N Roberts, Alexander Wong, Peter C Hollenhorst, Katherine J Chandler, Patrick A Cassiday, Cassie A Nelson, Curt H Hagedorn, Barbara J Graves, Bradley R Cairns Nat Struct Mol Biol 17 620-8 2010
Global survey of escape from X inactivation by RNA-sequencing in mouse. Fan Yang, Tomas Babak, Jay Shendure, Christine M Disteche Genome Res 20 614-22 2010
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Guojie Zhang, Guangwu Guo, Xueda Hu, Yong Zhang, Qiye Li, Ruiqiang Li, Ruhong Zhuang, Zhike Lu, Zengquan He, Xiaodong Fang, Li Chen, Wei Tian, Yong Tao, Karsten Kristiansen, Xiuqing Zhang, Songgang Li, Huanming Yang, Jian Wang, Jun Wang Genome Res 20 646-54 2010
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Aaron R Quinlan, Royden A Clark, Svetlana Sokolova, Mitchell L Leibowitz, Yujun Zhang, Matthew E Hurles, Joshua C Mell, Ira M Hall Genome Res 20 623-35 2010
Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs. Luigi Cicatiello, Margherita Mutarelli, Oli M V Grober, Ornella Paris, Lorenzo Ferraro, Maria Ravo, Roberta Tarallo, Shujun Luo, Gary P Schroth, Martin Seifert, Christian Zinser, Maria Luisa Chiusano, Alessandra Traini, Michele De Bortoli, Alessandro Weisz Am J Pathol 176 2113-30 2010
A CTCF-independent role for cohesin in tissue-specific transcription. Dominic Schmidt, Petra C Schwalie, Caryn S Ross-Innes, Antoni Hurtado, Gordon D Brown, Jason S Carroll, Paul Flicek, Duncan T Odom Genome Res 20 578-88 2010
Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity. Melanie J Filiatrault, Paul V Stodghill, Philip A Bronstein, Simon Moll, Magdalen Lindeberg, George Grills, Peter Schweitzer, Wei Wang, Gary P Schroth, Shujun Luo, Irina Khrebtukova, Yong Yang, Theodore Thannhauser, Bronwyn G Butcher, Samuel Cartinhour, David J Schneider J Bacteriol 192 2359-72 2010
Advancing RNA-Seq analysis. Brian J Haas, Michael C Zody Nat Biotechnol 28 421-3 2010
Constitutional translocation breakpoint mapping by genome-wide paired-end sequencing identifies HACE1 as a putative Wilms tumour susceptibility gene. I Slade, P Stephens, J Douglas, K Barker, L Stebbings, F Abbaszadeh, K Pritchard-Jones,    , R Cole, B Pizer, C Stiller, G Vujanic, R H Scott, M R Stratton, N Rahman J Med Genet 47 342-7 2010
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