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
High-throughput sequence analysis of variants of human cytomegalovirus strains Towne and AD169. Amanda J Bradley, Nell S Lurain, Peter Ghazal, Urmi Trivedi, Charles Cunningham, Katarina Baluchova, Derek Gatherer, Gavin W G Wilkinson, Derrick J Dargan, Andrew J Davison J Gen Virol 90 2375-80 2009
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. Summary Vladimir Lazarevic, Katrine Whiteson, Susan Huse, David Hernandez, Laurent Farinelli, Magne Osterås, Jacques Schrenzel, Patrice François J Microbiol Methods 79 266-71 2009
Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. Richard Stabler, Miao He, Lisa Dawson, Melissa Martin, Esmeralda Valiente, Craig Corton, Trevor Lawley, Mohammed Sebaihia, Michael Quail, Graham Rose, Dale Gerding, Maryse Gibert, Michel Popoff, Julian Parkhill, Gordon Dougan, Brendan Wren Genome Biol 10 R102 2009
Distinct extremely abundant siRNAs associated with cosuppression in petunia. Emanuele De Paoli, Ana Dorantes-Acosta, Jixian Zhai, Monica Accerbi, Dong-Hoon Jeong, Sunhee Park, Blake C Meyers, Richard A Jorgensen, Pamela J Green RNA 15 1965-70 2009
Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing. Stéphane Le Crom, Wendy Schackwitz, Len Pennacchio, Jon K Magnuson, David E Culley, James R Collett, Joel Martin, Irina S Druzhinina, Hugues Mathis, Frédéric Monot, Bernhard Seiboth, Barbara Cherry, Michael Rey, Randy Berka, Christian P Kubicek, Scott E Baker, Antoine Margeot Proc Natl Acad Sci U S A 106 16151-6 2009
A genome-wide view of Caenorhabditis elegans base-substitution mutation processes. Dee R Denver, Peter C Dolan, Larry J Wilhelm, Way Sung, J Ignacio Lucas-Lledó, Dana K Howe, Samantha C Lewis, Kazu Okamoto, W Kelley Thomas, Michael Lynch, Charles F Baer Proc Natl Acad Sci U S A 106 16310-4 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
Selective epigenetic control of retrotransposition in Arabidopsis. Marie Mirouze, Jon Reinders, Etienne Bucher, Taisuke Nishimura, Korbinian Schneeberger, Stephan Ossowski, Jun Cao, Detlef Weigel, Jerzy Paszkowski, Olivier Mathieu Nature 461 427-30 2009
De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Scott Diguistini, Nancy Liao, Darren Platt, Gordon Robertson, Michael Seidel, Simon Chan, T Roderick Docking, Inanc Birol, Robert Holt, Martin Hirst, Elaine Mardis, Marco Marra, Richard Hamelin, Jörg Bohlmann, Colette Breuil, Steven Jones Genome Biol 10 R94 2009
Loss of cardiac microRNA-mediated regulation leads to dilated cardiomyopathy and heart failure. Prakash K Rao, Yumiko Toyama, H Rosaria Chiang, Sumeet Gupta, Michael Bauer, Rostislav Medvid, Ferenc Reinhardt, Ronglih Liao, Monty Krieger, Rudolf Jaenisch, Harvey F Lodish, Robert Blelloch Circ Res 105 585-94 2009
Targeted capture and massively parallel sequencing of 12 human exomes. Summary Sarah B Ng, Emily H Turner, Peggy D Robertson, Steven D Flygare, Abigail W Bigham, Choli Lee, Tristan Shaffer, Michelle Wong, Arindam Bhattacharjee, Evan E Eichler, Michael Bamshad, Deborah A Nickerson, Jay Shendure Nature 461 272-6 2009
ChIP-seq: advantages and challenges of a maturing technology. Peter J Park Nat Rev Genet 10 669-80 2009
The B cell mutator AID promotes B lymphoid blast crisis and drug resistance in chronic myeloid leukemia. Lars Klemm, Cihangir Duy, Ilaria Iacobucci, Stefan Kuchen, Gregor von Levetzow, Niklas Feldhahn, Nadine Henke, Zhiyu Li, Thomas K Hoffmann, Yong-mi Kim, Wolf-Karsten Hofmann, Hassan Jumaa, John Groffen, Nora Heisterkamp, Giovanni Martinelli, Michael R Lieber, Rafael Casellas, Markus Müschen Cancer Cell 16 232-45 2009
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