Detection of structural variants and indels within exome data. Emre Karakoc,
Can Alkan, Brian J. O'Roak, Megan Y. Dennis, Laura Vives, Kenneth Mark, Mark J. Rieder, Deborah A. Nickerson, Evan E. Eichler.
Nature Methods, [Epub Dec 18, 2011], 9(2): 176-178, 2012.
Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee. Mario Ventura Claudia R. Catacchio,
Can Alkan, Tomas Marques-Bonet, Saba Sajjadian,
Tina A. Graves, Fereydoun Hormozdiari, Arcadi Navarro, Maika Malig, Carl Baker, Choli Lee, Emily H. Turner,
Lin Chen, Jeffrey M. Kidd, Nicoletta Archidiacono, Jay Shendure, Richard K. Wilson, Evan E. Eichler.
Genome Research, [Epub Jun 21], Oct;21(10):1640-9. 2011.
Sensitive and fast mapping of di-base encoded reads. Farhad Hormozdiari*, Faraz Hach*, S. Cenk Sahinalp, Evan E. Eichler,
Can Alkan.
Bioinformatics, [Epub May 17], Jul 15;27(14):1915-21, 2011.
Alu repeat discovery and characterization within human genomes. Fereydoun Hormozdiari*, Can Alkan*, Mario
Ventura*, Iman Hajirasouliha, Maika Malig, Faraz Hach, Deniz Yorukoglu,
Phuong Dao, Marzieh Bakshi, S. Cenk Sahinalp, Evan E. Eichler. Genome Research, [Epub Dec 3, 2010], Jun;21(6):840-9, 2011
.
Genome structural variation discovery and genotyping. Can Alkan, Bradley P. Coe, Evan E. Eichler.
Nature Reviews Genetics, [Epub Mar 1], May;12(5):363-76, 2011.
Mapping copy number
variation by population-scale genome sequencing. Ryan
E. Mills*, Klaudia Walter*, Chip Stewart*, Robert E. Handsaker*, Ken
Chen*,
Can
Alkan*, Alexej Abyzov*, Seungtai Chris Yoon*, Kai Ye*, R.
Keira
Cheetham, Asif Chinwalla, Donald F. Conrad, Yutao Fu, Fabian Grubert,
Iman Hajirasouliha, Fereydoun Hormozdiari, Lilia M. Iakoucheva, Zamin
Iqbal, Shuli Kang, Jeffrey M. Kidd, Miriam K. Konkel, Joshua Korn, Ekta
Khurana, Deniz Kural, Hugo Y. K. Lam, Jing Leng, Ruiqiang Li, Yingrui
Li, Chang-Yun Lin, Ruibang Luo, Xinmeng Jasmine Mu, James Nemesh,
Heather E. Peckham, Tobias Rausch, Aylwyn Scally, Xinghua Shi,
Michael P. Stromberg, Adrian M. Stütz, Alexander Eckehart Urban,
Jerilyn A. Walker, Jiantao Wu, Yujun Zhang, Zhengdong D. Zhang, Mark A.
Batzer, Li Ding, Gabor T. Marth, Gil McVean, Jonathan Sebat, Michael
Snyder, Jun Wang, Kenny Ye, Evan E. Eichler, Mark B. Gerstein, Matthew
E. Hurles, Charles Lee, Steven A. McCarroll, Jan O. Korbel& 1000
Genomes Project. Nature, 470(7332):59-65,
2011.
Genome-wide characterization of centromeric
satellites from multiple mammalian genomes. Can
Alkan*, Maria
Francesca Cardone*, Claudia Rita Catacchio, Francesca Antonacci,
Stephen J. O’Brien, Oliver A. Ryder, Stefania Purgato, Monica Zoli,
Giuliano Della Valle, Evan E. Eichler, and Mario Ventura. Genome Research, [Epub
Nov 16, 2010], 21(1): 137-145, 2011.
Limitations of
next-generation genome sequence assembly. Can Alkan, Saba
Sajjadian, Evan E. Eichler. Nature
Methods, [Epub Nov 21, 2010], 8(1):61-65,
2011.
* Highlighted
in Commentary, "Assemblies: the good, the bad, the ugly", E. Birney, Nature Methods, 8(1):59-60, 2011.
Diversity of human
copy number variation and multicopy genes. Peter H. Sudmant,
Jacob O. Kitzman, Francesca Antonacci,
Can Alkan,
Maika Malig, Anya Tsalenko, Nick Sampas, Laurakay Bruhn, Jay Shendure,
1000 Genomes Project, Evan E. Eichler.
Science, Oct 29;330(6004):641-6,
2010.
A map of human genome variation from
population-scale sequencing.
1000 Genomes Project Consortium.
Nature, Oct
28;467(7319):1061-73, 2010.
Detection and characterization of novel
sequence insertions using paired-end next-generation sequencing.
Iman Hajirasouliha*, Fereydoun Hormozdiari*, Can Alkan*,
Jeffrey M. Kidd, Inanc Birol, Evan E. Eichler, S. Cenk Sahinalp. Bioinformatics, May
15; 26(10):1277-83, 2010.
also in HiTSeq 2010: Conference on High Throughput
Sequencing Analysis and Algorithms, Special Interest Group of ISMB
2010: July 9-10 2010, Boston, MA, USA
Personalized copy
number and segmental duplication maps using next-generation sequencing.
Can Alkan,
Jeffrey M. Kidd, Tomas Marques-Bonet, Gozde Aksay, Francesca
Antonacci, Fereydoun Hormozdiari, Jacob O. Kitzman, Carl Baker, Maika
Malig, Onur Mutlu, S. Cenk Sahinalp, Richard A. Gibbs, Evan E. Eichler.
Nature Genetics, [Epub: Aug
30], Oct, 41(10):1061-1067
, 2009.
*
Highlighted in News and Views,
"Mapping duplicated sequences", DY Chiang and SA McCarroll, Nature Biotechnology,
Nov; 27(11):1001-2, 2009.
Combinatorial
algorithms for structural variation detection in high throughput
sequenced genomes. Fereydoun
Hormozdiari*, Can Alkan*,
Evan E. Eichler, S. Cenk Sahinalp. Genome
Research, Jul, 19(7):1270-8, 2009.
also
in Proc. of the Thirteenth
Annual International
Conference on Research in Computational Molecular Biology (RECOMB 2009),
May 18-21 2009, Tucson, AZ, USA
full list
