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
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
Challenges of sequencing human genomes. Daniel C Koboldt, Li Ding, Elaine R Mardis, Richard K Wilson Brief Bioinform 2010
Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Robert Shoemaker, Jie Deng, Wei Wang, Kun Zhang Genome Res 2010
Characterization of missing human genome sequences and copy-number polymorphic insertions. Jeffrey M Kidd, Nick Sampas, Francesca Antonacci, Tina Graves, Robert Fulton, Hillary S Hayden, Can Alkan, Maika Malig, Mario Ventura, Giuliana Giannuzzi, Joelle Kallicki, Paige Anderson, Anya Tsalenko, N Alice Yamada, Peter Tsang, Rajinder Kaul, Richard K Wilson, Laurakay Bruhn, Evan E Eichler Nat Methods 7 365-71 2010
Capture and sequence analysis of RNAs with terminal 2,3-cyclic phosphates. Kevin Schutz, Jay R Hesselberth, Stanley Fields RNA 16 621-31 2010
Copy number variant detection in inbred strains from short read sequence data. Jared T Simpson, Rebecca E McIntyre, David J Adams, Richard Durbin Bioinformatics 26 565-7 2010
FRT-seq: amplification-free, strand-specific transcriptome sequencing. Lira Mamanova, Robert M Andrews, Keith D James, Elizabeth M Sheridan, Peter D Ellis, Cordelia F Langford, Tobias W B Ost, John E Collins, Daniel J Turner Nat Methods 7 130-2 2010
Parallel, tag-directed assembly of locally derived short sequence reads. Joseph B Hiatt, Rupali P Patwardhan, Emily H Turner, Choli Lee, Jay Shendure Nat Methods 7 119-22 2010
Mind the gaps. Steven L Salzberg Nat Methods 7 105-6 2010
A new strategy for genome assembly using short sequence reads and reduced representation libraries. Andrew L Young, Hatice Ozel Abaan, Daniel Zerbino, James C Mullikin, Ewan Birney, Elliott H Margulies Genome Res 20 249-56 2010
Deep sequencing of target linkage assay-identified regions in familial breast cancer: methods, analysis pipeline and troubleshooting. Juan Manuel Rosa-Rosa, Francisco Javier Gracia-Azn?rez, Emily Hodges, Guillermo Pita, Michelle Rooks, Zhenyu Xuan, Arindam Bhattacharjee, Leonardo Brizuela, Jos? M Silva, Gregory J Hannon, Javier Benitez PLoS One 5 e9976 2010
Sensitivity of noninvasive prenatal detection of fetal aneuploidy from maternal plasma using shotgun sequencing is limited only by counting statistics. H Christina Fan, Stephen R Quake PLoS One 5 e10439 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
Inferring binding energies from selected binding sites. Yue Zhao, David Granas, Gary D Stormo PLoS Comput Biol 5 e1000590 2009
Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens. Charles Cunningham, Derek Gatherer, Birgitta Hilfrich, Katarina Baluchova, Derrick J Dargan, Marian Thomson, Paul D Griffiths, Gavin W G Wilkinson, Thomas F Schulz, Andrew J Davison J Gen Virol 91 605-15 2010
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