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
Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. Bas E Dutilh, Martijn A Huynen, Marc Strous Bioinformatics 25 2878-81 2009
ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing. Gerald Quon, Quaid Morris Bioinformatics 25 2882-9 2009
Next generation sequence analysis for mitochondrial disorders. Valeria Vasta, Sarah Ng, Emily Turner, Jay Shendure, Si Houn Hahn Genome Med 1 100 2009
Genome evolution and adaptation in a long-term experiment with Escherichia coli. Jeffrey E Barrick, Dong Su Yu, Sung Ho Yoon, Haeyoung Jeong, Tae Kwang Oh, Dominique Schneider, Richard E Lenski, Jihyun F Kim Nature 2009
Disease progression and solid tumor survival: A transcriptome decoherence model. Adrian E Platts, Claudia Lalancette, Benjamin R Emery, Douglas T Carrell, Stephen A Krawetz Mol Cell Probes 2009
Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels. Ian Sudbery, Jim Stalker, Jared Simpson, Thomas Keane, Alistair Rust, Matthew Hurles, Klaudia Walter, Dee Lynch, Lydia Teboul, Steve Brown, Heng Li, Zemin Ning, Joseph Nadeau, Colleen Croniger, Richard Durbin, David Adams Genome Biol 10 R112 2009
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Sohrab P Shah, Ryan D Morin, Jaswinder Khattra, Leah Prentice, Trevor Pugh, Angela Burleigh, Allen Delaney, Karen Gelmon, Ryan Guliany, Janine Senz, Christian Steidl, Robert A Holt, Steven Jones, Mark Sun, Gillian Leung, Richard Moore, Tesa Severson, Greg A Taylor, Andrew E Teschendorff, Kane Tse, Gulisa Turashvili, Richard Varhol, René L Warren, Peter Watson, Yongjun Zhao, Carlos Caldas, David Huntsman, Martin Hirst, Marco A Marra, Samuel Aparicio Nature 461 809-13 2009
Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions. Nicolas Corradi, Karen Haag, Jean-Francois Pombert, Dieter Ebert, Patrick Keeling Genome Biol 10 R106 2009
Failed gene conversion leads to extensive end processing and chromosomal rearrangements in fission yeast. Helen Tinline-Purvis, Andrew P Savory, Jason K Cullen, Anoushka Davé, Jennifer Moss, Wendy L Bridge, Samuel Marguerat, Jürg Bähler, Jiannis Ragoussis, Richard Mott, Carol A Walker, Timothy C Humphrey EMBO J 2009
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
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
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
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
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
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