(joint first authors are marked with * in case of equal
contribution)
Great ape
genetic diversity and population history. Javier
Prado-Martinez, Peter H. Sudmant, Jeffrey M. Kidd, Heng Li, Joanna L.
Kelley, Belen Lorente-Galdos, Krishna R. Veeramah, August E. Woerner,
Timothy D. O’Connor, Gabriel Santpere, Alexander Cagan, Christoph
Theunert, Ferran Casals, Hafid Laayouni, Kasper Munch, Asger Hobolth,
Anders E. Halager, Maika Malig, Jessica Hernandez-Rodriguez, Irene
Hernando-Herraez, Kay Prüfer, Marc Pybus, Laurel Johnstone, Michael
Lachmann,
Can Alkan, Dorina
Twigg, Natalia Petit , Carl Baker , Fereydoun Hormozdiari, Marcos
Fernandez-Callejo, Marc Dabad, Michael L. Wilson, Laurie Stevison,
Cristina Camprubí, Tiago Carvalho, Aurora Ruiz-Herrera, Laura Vives, Marta
Mele, Teresa Abello , Ivanela Kondova , Ronald E. Bontrop, Anne Pusey,
Felix Lankester, John A. Kiyang, Richard A. Bergl, Elizabeth Lonsdorf,
Simon Myers, Mario Ventura, Pascal Gagneux, David Comas, Hans Siegismund,
Julie Blanc, Lidia Agueda-Calpena, Marta Gut, Lucinda Fulton, Sarah A.
Tishkoff, James C. Mullikin, Richard K. Wilson, Ivo G. Gut, Mary Katherine
Gonder, Oliver A. Ryder, Beatrice H. Hahn, Arcadi Navarro,, Joshua M.
Akey, Jaume Bertranpetit, David Reich, Thomas Mailund, Mikkel H. Schierup,
Christina Hvilsom, Aida M. André s, Jeffrey D. Wall, Carlos D. Bustamante,
Michael F. Hammer, Evan E. Eichler, Tomas Marques-Bonet.
Nature,
499(7459):471-475,
2013.
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
