Can Alkan, Ph.D.
Assistant Professor @ Dept. of Computer Engineering, Bilkent University
PI, Lab for Bioinformatics & Computational Genomics

Department of Computer Engineering
Bilkent University
Engineering Building, EA-509
Bilkent, Ankara 06800
Turkey

Email:
Phone: +90-312-290-2912
Fax    : +90-312-266-4047

Graduate students wanted. Contact me if you are interested in computational genomics.
Click here for implementation based projects for undergraduate students and summer interns.


Pronunciation of my name: pronunciation
Vita: PDF

Education

Postdoctoral Fellow, Genome Sciences at University of Washington, Seattle, WA, USA, October 2005 to December 2011
                            Supervisor: Prof. Evan E. Eichler
Ph.D.,  Computer Science, at Case Western Reserve University, Cleveland, OH, USA, August 2005
                            Supervisor: Prof. Cenk Şahinalp
B.Sc.,  Computer Science, Bilkent University, Ankara, Turkey, May 2000


Research Interests
Teaching
Contributed Software Projects
Selected Publications

(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

Researcher ID



calkan

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