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
Biases in Illumina transcriptome sequencing caused by random hexamer priming. Kasper D Hansen, Steven E Brenner, Sandrine Dudoit Nucleic Acids Res 38 e131 2010
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Charles Plessy, Nicolas Bertin, Hazuki Takahashi, Roberto Simone, Md Salimullah, Timo Lassmann, Morana Vitezic, Jessica Severin, Signe Olivarius, Dejan Lazarevic, Nadine Hornig, Valerio Orlando, Ian Bell, Hui Gao, Jacqueline Dumais, Philipp Kapranov, Huaien Wang, Carrie A Davis, Thomas R Gingeras, Jun Kawai, Carsten O Daub, Yoshihide Hayashizaki, Stefano Gustincich, Piero Carninci Nat Methods 7 528-34 2010
Regulation of MicroRNA Expression and Abundance during Lymphopoiesis Stefan Kuchen, Wolfgang Resch, Arito Yamane, Nan Kuo, Zhiyu Li, Tirtha Chakraborty, Lai Wei, Arian Laurence, Tomoharu Yasuda, Siying Peng, Jane Hu-Li, Kristina Lu, Wendy Dubois, Yoshiaki Kitamura, Nicolas Charles, Hong-wei Sun, Stefan Muljo, Pamela L Schwartzberg, William E Paul, John OShea, Klaus Rajewsky, Rafael Casellas Immunity
Regulatory divergence in Drosophila revealed by mRNA-seq. C Joel McManus, Joseph D Coolon, Michael O Duff, Jodi Eipper-Mains, Brenton R Graveley, Patricia J Wittkopp Genome Res 20 816-25 2010
Natural selection on cis and trans regulation in yeasts. J J Emerson, Li-Ching Hsieh, Huang-Mo Sung, Tzi-Yuan Wang, Chih-Jen Huang, Henry Horng-Shing Lu, Mei-Yeh Jade Lu, Shu-Hsing Wu, Wen-Hsiung Li Genome Res 20 826-36 2010
mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain. Paul Hammer, Michaela S Banck, Ronny Amberg, Cheng Wang, Gabriele Petznick, Shujun Luo, Irina Khrebtukova, Gary P Schroth, Peter Beyerlein, Andreas S Beutler Genome Res 20 847-60 2010
Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq. Qiang Gan, Iouri Chepelev, Gang Wei, Lama Tarayrah, Kairong Cui, Keji Zhao, Xin Chen Cell Res 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
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
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
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
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
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
Advancing RNA-Seq analysis. Brian J Haas, Michael C Zody Nat Biotechnol 28 421-3 2010
Endogenous short RNAs generated by Dicer 2 and RNA-dependent RNA polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides. Francisco Esteban Nicolas, Simon Moxon, Juan P de Haro, Silvia Calo, Igor V Grigoriev, Santiago Torres-Mart?nez, Vincent Moulton, Rosa M Ruiz-V?zquez, Tamas Dalmay Nucleic Acids Res 2010
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