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
Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Tim van Opijnen, Kip L Bodi, Andrew Camilli Nat Methods 6 767-72 2009
Relative power and sample size analysis on gene expression profiling data. M van Iterson, P t Hoen, P Pedotti, G Hooiveld, J den Dunnen, Gj van Ommen, J Boer, R Menezes BMC Genomics 10 439 2009
Sensitive and accurate detection of copy number variants using read depth of coverage. Seungtai Yoon, Zhenyu Xuan, Vladimir Makarov, Kenny Ye, Jonathan Sebat Genome Res 19 1586-92 2009
SOAP2: an improved ultrafast tool for short read alignment. Summary Ruiqiang Li, Chang Yu, Yingrui Li, Tak-Wah Lam, Siu-Ming Yiu, Karsten Kristiansen, Jun Wang Bioinformatics 25 1966-7 2009
De novo Transcriptome Assembly with ABySS. Summary Inanç Birol, Shaun D Jackman, Cydney Nielsen, Jenny Q Qian, Richard Varhol, Greg Stazyk, Ryan D Morin, Yongjun Zhao, Martin Hirst, Jacqueline E Schein, Doug E Horsman, Joseph M Connors, Randy D Gascoyne, Marco A Marra, Steven Jm Jones Bioinformatics 2009
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Summary Iwanka Kozarewa, Zemin Ning, Michael A Quail, Mandy J Sanders, Matthew Berriman, Daniel J Turner Nat Methods 6 291-5 2009
Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. H Alexander Ebhardt, Herbert H Tsang, Denny C Dai, Yifeng Liu, Babak Bostan, Richard P Fahlman Nucleic Acids Res 37 2461-70 2009
Massive transcriptional start site analysis of human genes in hypoxia cells. Summary Katsuya Tsuchihara, Yutaka Suzuki, Hiroyuki Wakaguri, Takuma Irie, Kousuke Tanimoto, Shin-ichi Hashimoto, Kouji Matsushima, Junko Mizushima-Sugano, Riu Yamashita, Kenta Nakai, David Bentley, Hiroyasu Esumi, Sumio Sugano Nucleic Acids Res 37 2249-63 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
De novo fragment assembly with short mate-paired reads: Does the read length matter? Mark J Chaisson, Dumitru Brinza, Pavel A Pevzner Genome Res 19 336-46 2009
Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. Ali Bashir, Stanislav Volik, Colin Collins, Vineet Bafna, Benjamin J Raphael PLoS Comput Biol 4 e1000051 2008