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
Assembly algorithms for next-generation sequencing data. Jason R Miller, Sergey Koren, Granger Sutton Genomics 95 315-27 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
Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Kin Fai Au, Hui Jiang, Lan Lin, Yi Xing, Wing Hung Wong Nucleic Acids Res 38 4570-8 2010
A SNP discovery method to assess variant allele probability from next-generation resequencing data. Yufeng Shen, Zhengzheng Wan, Cristian Coarfa, Rafal Drabek, Lei Chen, Elizabeth A Ostrowski, Yue Liu, George M Weinstock, David A Wheeler, Richard A Gibbs, Fuli Yu Genome Res 20 273-80 2010
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Hugo Y K Lam, Xinmeng Jasmine Mu, Adrian M Stütz, Andrea Tanzer, Philip D Cayting, Michael Snyder, Philip M Kim, Jan O Korbel, Mark B Gerstein Nat Biotechnol 28 47-55 2010
Effects of Alu elements on global nucleosome positioning in the human genome. Yoshiaki Tanaka, Riu Yamashita, Yutaka Suzuki, Kenta Nakai BMC Genomics 11 309 2010
Second generation sequencing of the mesothelioma tumor genome. Raphael Bueno, Assunta De Rienzo, Lingsheng Dong, Gavin J Gordon, Colin F Hercus, William G Richards, Roderick V Jensen, Arif Anwar, Gautam Maulik, Lucian R Chirieac, Kim-Fong Ho, Bruce E Taillon, Cynthia L Turcotte, Robert G Hercus, Steven R Gullans, David J Sugarbaker PLoS One 5 e10612 2010
Index-free de novo assembly and deconvolution of mixed mitochondrial genomes. Bennet J McComish, Simon F K Hills, Patrick J Biggs, David Penny Genome Biol Evol 2 410-24 2010
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 11 181-97 2010
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
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