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
Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Tom Walsh, Ming K Lee, Silvia Casadei, Anne M Thornton, Sunday M Stray, Christopher Pennil, Alex S Nord, Jessica B Mandell, Elizabeth M Swisher, Mary-Claire King Proc Natl Acad Sci U S A 107 12629-33 2010
Sequencing of 50 human exomes reveals adaptation to high altitude. Science 329 75-8 2010
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Charles Plessy, Nicolas Bertin, Hazuki Takahashi, Roberto Simone, Md Salimullah, Timo Lassmann, Morana Vitezic, Jessica Severin, Signe Olivarius, Dejan Lazarevic, Nadine Hornig, Valerio Orlando, Ian Bell, Hui Gao, Jacqueline Dumais, Philipp Kapranov, Huaien Wang, Carrie A Davis, Thomas R Gingeras, Jun Kawai, Carsten O Daub, Yoshihide Hayashizaki, Stefano Gustincich, Piero Carninci Nat Methods 7 528-34 2010
Biases in Illumina transcriptome sequencing caused by random hexamer priming. Kasper D Hansen, Steven E Brenner, Sandrine Dudoit Nucleic Acids Res 38 e131 2010
Regulation of MicroRNA Expression and Abundance during Lymphopoiesis Stefan Kuchen, Wolfgang Resch, Arito Yamane, Nan Kuo, Zhiyu Li, Tirtha Chakraborty, Lai Wei, Arian Laurence, Tomoharu Yasuda, Siying Peng, Jane Hu-Li, Kristina Lu, Wendy Dubois, Yoshiaki Kitamura, Nicolas Charles, Hong-wei Sun, Stefan Muljo, Pamela L Schwartzberg, William E Paul, John OShea, Klaus Rajewsky, Rafael Casellas Immunity
Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Weibo Xie, Qi Feng, Huihui Yu, Xuehui Huang, Qiang Zhao, Yongzhong Xing, Sibin Yu, Bin Han, Qifa Zhang Proc Natl Acad Sci U S A 107 10578-83 2010
Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network. Aviva Presser Aiden, Miguel N Rivera, Esther Rheinbay, Manching Ku, Erik J Coffman, Thanh T Truong, Sara O Vargas, Eric S Lander, Daniel A Haber, Bradley E Bernstein Cell Stem Cell 6 591-602 2010
Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens. Henry M Wood, Ornella Belvedere, Caroline Conway, Catherine Daly, Rebecca Chalkley, Melissa Bickerdike, Claire McKinley, Phil Egan, Lisa Ross, Bruce Hayward, Joanne Morgan, Leslie Davidson, Ken Maclennan, Thian K Ong, Kostas Papagiannopoulos, Ian Cook, David J Adams, Graham R Taylor, Pamela Rabbitts Nucleic Acids Res 38 e151 2010
Microbes and Health Sackler Colloquium: Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. J Gregory Caporaso, Christian L Lauber, William A Walters, Donna Berg-Lyons, Catherine A Lozupone, Peter J Turnbaugh, Noah Fierer, Rob Knight Proc Natl Acad Sci U S A 2010
Novel multi-nucleotide polymorphisms in the human genome characterized by whole genome and exome sequencing. Jeffrey A Rosenfeld, Anil K Malhotra, Todd Lencz Nucleic Acids Res 2010
Challenges of sequencing human genomes. Daniel C Koboldt, Li Ding, Elaine R Mardis, Richard K Wilson Brief Bioinform 2010
Natural selection on cis and trans regulation in yeasts. J J Emerson, Li-Ching Hsieh, Huang-Mo Sung, Tzi-Yuan Wang, Chih-Jen Huang, Henry Horng-Shing Lu, Mei-Yeh Jade Lu, Shu-Hsing Wu, Wen-Hsiung Li Genome Res 20 826-36 2010
mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain. Paul Hammer, Michaela S Banck, Ronny Amberg, Cheng Wang, Gabriele Petznick, Shujun Luo, Irina Khrebtukova, Gary P Schroth, Peter Beyerlein, Andreas S Beutler Genome Res 20 847-60 2010
Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene. Nara L M Sobreira, Elizabeth T Cirulli, Dimitrios Avramopoulos, Elizabeth Wohler, Gretchen L Oswald, Eric L Stevens, Dongliang Ge, Kevin V Shianna, Jason P Smith, Jessica M Maia, Curtis E Gumbs, Jonathan Pevsner, George Thomas, David Valle, Julie E Hoover-Fong, David B Goldstein PLoS Genet 6 e1000991 2010
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Arttu Jolma, Teemu Kivioja, Jarkko Toivonen, Lu Cheng, Gonghong Wei, Martin Enge, Mikko Taipale, Juan M Vaquerizas, Jian Yan, Mikko J Sillanp??, Martin Bonke, Kimmo Palin, Shaheynoor Talukder, Timothy R Hughes, Nicholas M Luscombe, Esko Ukkonen, Jussi Taipale Genome Res 20 861-73 2010
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