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
Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing. Graham A Heap, Jennie H M Yang, Kate Downes, Barry C Healy, Karen A Hunt, Nicholas Bockett, Lude Franke, Patrick C Dubois, Charles A Mein, Richard J Dobson, Thomas J Albert, Matthew J Rodesch, David G Clayton, John A Todd, David A van Heel, Vincent Plagnol Hum Mol Genet 19 122-34 2010
Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Erez Lieberman-Aiden, Nynke L van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R Lajoie, Peter J Sabo, Michael O Dorschner, Richard Sandstrom, Bradley Bernstein, M A Bender, Mark Groudine, Andreas Gnirke, John Stamatoyannopoulos, Leonid A Mirny, Eric S Lander, Job Dekker Science 326 289-93 2009
Endogenous, tissue-specific short interfering RNAs silence the chalcone synthase gene family in glycine max seed coats. Jigyasa H Tuteja, Gracia Zabala, Kranthi Varala, Matthew Hudson, Lila O Vodkin Plant Cell 21 3063-77 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
Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factors. Akira Nishiyama, Li Xin, Alexei A Sharov, Marshall Thomas, Gregory Mowrer, Emily Meyers, Yulan Piao, Samir Mehta, Sarah Yee, Yuhki Nakatake, Carole Stagg, Lioudmila Sharova, Lina S Correa-Cerro, Uwem Bassey, Hien Hoang, Eugene Kim, Richard Tapnio, Yong Qian, Dawood Dudekula, Michal Zalzman, Manxiang Li, Geppino Falco, Hsih-Te Yang, Sung-Lim Lee, Manuela Monti, Ilaria Stanghellini, Md Nurul Islam, Ramaiah Nagaraja, Ilya Goldberg, Weidong Wang, Dan L Longo, David Schlessinger, Minoru S H Ko Cell Stem Cell 5 420-33 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 28 3400-12 2009
Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility. Julius Gudmundsson, Patrick Sulem, Daniel F Gudbjartsson, Thorarinn Blondal, Arnaldur Gylfason, Bjarni A Agnarsson, Kristrun R Benediktsdottir, Droplaug N Magnusdottir, Gudbjorg Orlygsdottir, Margret Jakobsdottir, Simon N Stacey, Asgeir Sigurdsson, Tiina Wahlfors, Teuvo Tammela, Joan P Breyer, Kate M McReynolds, Kevin M Bradley, Berta Saez, Javier Godino, Sebastian Navarrete, Fernando Fuertes, Laura Murillo, Eduardo Polo, Katja K Aben, Inge M van Oort, Brian K Suarez, Brian T Helfand, Donghui Kan, Carlo Zanon, Michael L Frigge, Kristleifur Kristjansson, Jeffrey R Gulcher, Gudmundur V Einarsson, Eirikur Jonsson, William J Catalona, Jose I Mayordomo, Lambertus A Kiemeney, Jeffrey R Smith, Johanna Schleutker, Rosa B Barkardottir, Augustine Kong, Unnur Thorsteinsdottir, Thorunn Rafnar, Kari Stefansson Nat Genet 41 1122-6 2009
Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Tim van Opijnen, Kip L Bodi, Andrew Camilli Nat Methods 6 767-72 2009
Chromatin poises miRNA- and protein-coding genes for expression. Artem Barski, Raja Jothi, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Dustin E Schones, Keji Zhao Genome Res 19 1742-51 2009
Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression. Marlon Stoeckius, Jonas Maaskola, Teresa Colombo, Hans-Peter Rahn, Marc R Friedländer, Na Li, Wei Chen, Fabio Piano, Nikolaus Rajewsky Nat Methods 6 745-51 2009
The non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAs. Helena Persson, Anders Kvist, Johan Vallon-Christersson, Patrik Medstrand, Ake Borg, Carlos Rovira Nat Cell Biol 11 1268-71 2009
Splice site strength-dependent activity and genetic buffering by poly-G runs. Xinshu Xiao, Zefeng Wang, Minyoung Jang, Razvan Nutiu, Eric T Wang, Christopher B Burge Nat Struct Mol Biol 16 1094-100 2009
Analysis of human alphaherpesvirus microRNA expression in latently infected human trigeminal ganglia. Jennifer L Umbach, Maria A Nagel, Randall J Cohrs, Donald H Gilden, Bryan R Cullen J Virol 83 10677-83 2009
Quantifying adaptive evolution in the Drosophila immune system. Darren J Obbard, John J Welch, Kang-Wook Kim, Francis M Jiggins PLoS Genet 5 e1000698 2009
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