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
