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
Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. Beatriz Navarro, Vitantonio Pantaleo, Andreas Gisel, Simon Moxon, Tamas Dalmay, György Bisztray, Francesco Di Serio, József Burgyán PLoS One 4 e7686 2009
Genome-wide identification of Schistosoma japonicum microRNAs using a deep-sequencing approach. Jian Huang, Pei Hao, Hui Chen, Wei Hu, Qing Yan, Feng Liu, Ze-Guang Han PLoS One 4 e8206 2009
3 tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer. Yan W Asmann, Eric W Klee, E Aubrey Thompson, Edith A Perez, Sumit Middha, Ann L Oberg, Terry M Therneau, David I Smith, Gregory A Poland, Eric D Wieben, Jean-Pierre A Kocher BMC Genomics 10 531 2009
Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence-level analysis. Martin Trick, Soo-Jin Kwon, Su Ryun Choi, Fiona Fraser, Eleni Soumpourou, Nizar Drou, Zhi Wang, Seo Yeon Lee, Tae-Jin Yang, Jeong-Hwan Mun, Andrew H Paterson, Christopher D Town, J Chris Pires, Yong Pyo Lim, Beom-Seok Park, Ian Bancroft BMC Genomics 10 539 2009
Comparative transcripts profiling reveals new insight into molecular processes regulating lycopene accumulation in a sweet orange (Citrus sinensis) red-flesh mutant. Qiang Xu, Keqin Yu, Andan Zhu, Junli Ye, Qing Liu, Jianchen Zhang, Xiuxin Deng BMC Genomics 10 540 2009
Profiling critical cancer gene mutations in clinical tumor samples. Laura E MacConaill, Catarina D Campbell, Sarah M Kehoe, Adam J Bass, Charles Hatton, Lili Niu, Matt Davis, Keluo Yao, Megan Hanna, Chandrani Mondal, Lauren Luongo, Caroline M Emery, Alissa C Baker, Juliet Philips, Deborah J Goff, Michelangelo Fiorentino, Mark A Rubin, Kornelia Polyak, Jennifer Chan, Yuexiang Wang, Jonathan A Fletcher, Sandro Santagata, Gianni Corso, Franco Roviello, Ramesh Shivdasani, Mark W Kieran, Keith L Ligon, Charles D Stiles, William C Hahn, Matthew L Meyerson, Levi A Garraway PLoS One 4 e7887 2009
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. Wolfgang Gerlach, Sebastian Jünemann, Felix Tille, Alexander Goesmann, Jens Stoye BMC Bioinformatics 10 430 2009
Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. Daniel R Zerbino, Gayle K McEwen, Elliott H Margulies, Ewan Birney PLoS One 4 e8407 2009
Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa. Thomas Rio Frio, Sylwia Panek, Christian Iseli, Silvio Alessandro Di Gioia, Arun Kumar, Andreas Gal, Carlo Rivolta Mol Vis 15 2627-33 2009
A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. Teemu D Laajala, Sunil Raghav, Soile Tuomela, Riitta Lahesmaa, Tero Aittokallio, Laura L Elo BMC Genomics 10 618 2009
Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs. Haley F Oliver, Renato H Orsi, Lalit Ponnala, Uri Keich, Wei Wang, Qi Sun, Samuel W Cartinhour, Melanie J Filiatrault, Martin Wiedmann, Kathryn J Boor BMC Genomics 10 641 2009
Genome-wide dissection of globally emergent multi-drug resistant serotype 19A Streptococcus pneumoniae. Dylan R Pillai, Dea Shahinas, Alla Buzina, Remy A Pollock, Rachel Lau, Krishna Khairnar, Andrew Wong, David J Farrell, Karen Green, Allison McGeer, Donald E Low BMC Genomics 10 642 2009
High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach. Gilbert Greub, Carole Kebbi-Beghdadi, Claire Bertelli, François Collyn, Beat M Riederer, Camille Yersin, Antony Croxatto, Didier Raoult PLoS One 4 e8423 2009
Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Rossa W K Chiu, K C Allen Chan, Yuan Gao, Virginia Y M Lau, Wenli Zheng, Tak Y Leung, Chris H F Foo, Bin Xie, Nancy B Y Tsui, Fiona M F Lun, Benny C Y Zee, Tze K Lau, Charles R Cantor, Y M Dennis Lo Proc Natl Acad Sci U S A 105 20458-63 2008
Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Hairi Li, Michael T Lovci, Young-Soo Kwon, Michael G Rosenfeld, Xiang-Dong Fu, Gene W Yeo Proc Natl Acad Sci U S A 105 20179-84 2008
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