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
ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing. Gerald Quon, Quaid Morris Bioinformatics 25 2882-9 2009
Computation for ChIP-seq and RNA-seq studies. Shirley Pepke, Barbara Wold, Ali Mortazavi Nat Methods 6 S22-32 2009
The transcription unit architecture of the Escherichia coli genome. Byung-Kwan Cho, Karsten Zengler, Yu Qiu, Young Seoub Park, Eric M Knight, Christian L Barrett, Yuan Gao, Bernhard Ø Palsson Nat Biotechnol 27 1043-9 2009
Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. David Stephen Horner, Giulio Pavesi, Tiziana Castrignanò, Paolo DOnorio De Meo, Sabino Liuni, Michael Sammeth, Ernesto Picardi, Graziano Pesole Brief Bioinform 2009
BayesPeak: Bayesian analysis of ChIP-seq data. Christiana Spyrou, Rory Stark, Andy Lynch, Simon Tavare BMC Bioinformatics 10 299 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
Simultaneous alignment of short reads against multiple genomes. Korbinian Schneeberger, Jörg Hagmann, Stephan Ossowski, Norman Warthmann, Sandra Gesing, Oliver Kohlbacher, Detlef Weigel Genome Biol 10 R98 2009
Personalized copy number and segmental duplication maps using next-generation sequencing. Can Alkan, Jeffrey M Kidd, Tomas Marques-Bonet, Gozde Aksay, Francesca Antonacci, Fereydoun Hormozdiari, Jacob O Kitzman, Carl Baker, Maika Malig, Onur Mutlu, S Cenk Sahinalp, Richard A Gibbs, Evan E Eichler Nat Genet 41 1061-7 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
PIQA: pipeline for Illumina G1 genome analyzer data quality assessment. Summary A Martínez-Alcántara, E Ballesteros, C Feng, M Rojas, H Koshinsky, V Y Fofanov, P Havlak, Y Fofanov Bioinformatics 25 2438-9 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
Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Summary Chengjian Li, Vasily V Vagin, Soohyun Lee, Jia Xu, Shengmei Ma, Hualin Xi, Hervé Seitz, Michael D Horwich, Monika Syrzycka, Barry M Honda, Ellen L W Kittler, Maria L Zapp, Carla Klattenhoff, Nadine Schulz, William E Theurkauf, Zhiping Weng, Phillip D Zamore Cell 137 509-21 2009
Profiling model T-cell metagenomes with short reads. Summary Renè L Warren, Brad H Nelson, Robert A Holt Bioinformatics 25 458-464 2009
miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. Wei-Chi Wang, Feng-Mao Lin, Wen-Chi Chang, Kuan-Yu Lin, Hsien-Da Huang, Na-Sheng Lin BMC Bioinformatics 10 328 2009
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Raja Jothi, Suresh Cuddapah, Artem Barski, Kairong Cui, Keji Zhao Nucleic Acids Res 2008
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