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
Neandertal genomics. Tales of a prehistoric human genome. Elizabeth Pennisi Science 323 866-71 2009
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Summary Nicholas T Ingolia, Sina Ghaemmaghami, John R S Newman, Jonathan S Weissman Science 324 218-23 2009
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Mitchell Guttman, Ido Amit, Manuel Garber, Courtney French, Michael F Lin, David Feldser, Maite Huarte, Or Zuk, Bryce W Carey, John P Cassady, Moran N Cabili, Rudolf Jaenisch, Tarjei S Mikkelsen, Tyler Jacks, Nir Hacohen, Bradley E Bernstein, Manolis Kellis, Aviv Regev, John L Rinn, Eric S Lander Nature 458 223-7 2009
De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. Rhys A Farrer, Eric Kemen, Jonathan D G Jones, David J Studholme FEMS Microbiol Lett 291 103-11 2009
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Ladeana W Hillier, Valerie Reinke, Philip Green, Martin Hirst, Marco A Marra, Robert H Waterston Genome Res 19 657-66 2009
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. Philippe Lefrancois, Ghia Euskirchen, Raymond Auerbach, Joel Rozowsky, Theodore Gibson, Christopher Yellman, Mark Gerstein, Michael Snyder BMC Genomics 10 37 2009
Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust. Yuanyuan Wei, Shuang Chen, Pengcheng Yang, Zongyuan Ma, Le Kang Genome Biol 10 R6 2009
Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Martin Trick, Yan Long, Jinling Meng, Ian Bancroft Plant Biotechnol J 7 334-46 2009
De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Josephine A Reinhardt, David A Baltrus, Marc T Nishimura, William R Jeck, Corbin D Jones, Jeffery L Dangl Genome Res 19 294-305 2009
Transcriptome sequencing to detect gene fusions in cancer. Summary Christopher A Maher, Chandan Kumar-Sinha, Xuhong Cao, Shanker Kalyana-Sundaram, Bo Han, Xiaojun Jing, Lee Sam, Terrence Barrette, Nallasivam Palanisamy, Arul M Chinnaiyan Nature 458 97-101 2009
Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing. Brad G Hoffman, Steven J M Jones J Endocrinol 201 1-13 2009
A regulatory interplay between miR-27a and Runx1 during megakaryopoiesis. Oren Ben-Ami, Niv Pencovich, Joseph Lotem, Ditsa Levanon, Yoram Groner Proc Natl Acad Sci U S A 106 238-43 2009
H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Florian M Pauler, Mathew A Sloane, Ru Huang, Kakkad Regha, Martha V Koerner, Ido Tamir, Andreas Sommer, Andras Aszodi, Thomas Jenuwein, Denise P Barlow Genome Res 19 221-33 2009
Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Chad Nusbaum, Toshiro K Ohsumi, James Gomez, John Aquadro, Thomas C Victor, Robert M Warren, Deborah T Hung, Bruce W Birren, Eric S Lander, David B Jaffe Nat Methods 6 67-9 2009
A draft genome sequence of Pseudomonas syringae pv. tomato T1 reveals a type III effector repertoire significantly divergent from that of Pseudomonas syringae pv. tomato DC3000. Nalvo F Almeida, Shuangchun Yan, Magdalen Lindeberg, David J Studholme, David J Schneider, Bradford Condon, Haijie Liu, Carlos J Viana, Andrew Warren, Clive Evans, Eric Kemen, Dan Maclean, Aurelie Angot, Gregory B Martin, Jonathan D Jones, Alan Collmer, Joao C Setubal, Boris A Vinatzer Mol Plant Microbe Interact 22 52-62 2009
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