Can Alkan

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Contact Information		Department of Genome Sciences University of Washington Box 355065 Foege Bulding S-413A 1705 NE Pacific St. Seattle, WA, 98195-5065 USA	Voice: (206) 543-9698 Fax:    (206) 543-6575 E-mail: calkan@u.washington.edu
Research Interests		Evolution of tandemly repeated DNA sequences, RNA-RNA interactions, RNA secondary structures, RNA secondary structure motifs, human structural variation, next-gen sequencing technologies, segmental duplications.
Education		Case Western Reserve University, Cleveland, Ohio, USA Department of EECS     Ph.D., Computer Science, August 2005 Dissertation Topic: "Computational Studies on Evolution and Functionality of Genomic Repeats" Advisor: Süleyman Cenk Şahinalp
		Bilkent University, Ankara, Turkey Department of Engineering     B.Sc., Computer Science, May 2000
Publications		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. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding.  K.J. McKernan, H.E. Peckham, G.L. Costa, S.F. McLaughlin, Y. Fu, E.F. Tsung, C.R. Clouser, C. Duncan, J.K. Ichikawa, C.C. Lee, Z. Zhang, S.S. Ranade, E.T. Dimalanta,  F.C. Hyland, T.D. Sokolsky, L. Zhang, J.A. Sheridan, H. Fu, C.L. Hendrickson, B. Li, L. Kotler, J.R. Stuart, J.A. Malek, J.M. Manning, A.A. Antipova, D.S. Perez, M.P. Moore, K.C. Hayashibara, M.R. Lyons, R.E. Beaudoin, B.E. Coleman, M.W. Laptewicz, A.E. Sannicandro, M.D. Rhodes, R.K. Gottimukkala, S. Yang, V. Bafna, A. Bashir, A. MacBride, C. Alkan, J.M. Kidd, E.E. Eichler, M.G. Reese, F.M. De La Vega, A.P. Blanchard. Genome Research, Sep, 19(9): 1527-1541, 2009. New Insights into Centromere Organization and Evolution from White-cheeked Gibbon and Marmoset, A. Cellamare,    C.R Catacchio,  C. Alkan, G. Giannuzzi, F. Antonacci, M.F. Cardone, G. Della Valle, M. Malig, M. Rocchi, E.E. Eichler, M. Ventura. Molecular Biology and Evolution, Aug; 26(8):1889-1900, 2009. MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions, Seunghak Lee, Fereydoun Hormozdiari, Can Alkan, Michael Brudno. Nature Methods,  Jul, 6(7):473-4, 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 Comparative analysis of Alu repeats in primate genomes, George E. Liu, Can Alkan, Lu Jiang, Shaying Zhao, Evan E. Eichler. Genome Research, 19(5):876-885, 2009. Death and resurrection of the human IRGM gene, Cemalettin Bekpen, Tomas Marques-Bonet, Can Alkan, Francesca Antonacci, Maria Bruna Leogrande, Mario Ventura, Jeffrey M. Kidd, Priscillia Siswara, Jonathan C. Howard, Evan E. Eichler. PLoS Genetics, 5(3):e1000403, March 2009. A burst of segmental duplications in the African Great Ape ancestor, Tomas Marques-Bonet, Jeffrey M. Kidd, Mario Ventura, Tina A. Graves, Ze Cheng, LaDeanna W. Hillier, Zhaoshi Jiang, Carl Baker, Ray Malfavon-Borja, Lucinda A. Fulton, Can Alkan, Gozde Aksay, Santhosh Girirajan, Priscillia Siswara, Lin Chen, Maria Francesca Cardone, Arcadi Navarro, Elaine R. Mardis, Richard K. Wilson, Evan E. Eichler. Nature, Feb 12 2009; 457(7231):877-881, 2009. Mapping and sequencing of structural variation from eight human genomes, Jeffrey M. Kidd, Gregory M. Cooper, William F. Donahue, Hillary S. Hayden, Nick Sampas, Tina Graves, Nancy Hansen, Brian Teague, Can Alkan, Francesca Antonacci, Eric Haugen, Troy Zerr, N. Alice Yamada, Peter Tsang, Tera L. Newman, Eray Tüzün, Ze Cheng, Heather M. Ebling, Nadeem Tusneem, Robert David, Will Gillett, Karen A. Phelps, Molly Weaver, David Saranga, Adrianne Brand, Wei Tao, Erik Gustafson, Kevin McKernan, Lin Chen, Maika Malig, Joshua D. Smith, Joshua M. Korn, Steven A. McCarroll, David A. Altshuler, Daniel A. Peiffer, Michael Dorschner, John Stamatoyannopoulos, David Schwartz, Deborah A. Nickerson, James C. Mullikin, Richard K. Wilson, Laurakay Bruhn, Maynard V. Olson, Rajinder Kaul, Douglas R. Smith, Evan E. Eichler. Nature 2008 May 1;453(7191):56-64, 2008. Optimal design of oligonucleotide microarrays for measurement of DNA copy number, Andrew J. Sharp, Andy Itsara, Ze Cheng, Can Alkan, Stuart Schwartz, Evan E. Eichler., Human Molecular Genetics, Nov 15; 16(22):2770-2779, 2007. Organization and Evolution of Primate Centromeric DNA from Whole Genome Shotgun Sequence Data, Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, S. Cenk Sahinalp, Evan E. Eichler., PLoS Computational Biology, 3(9): e181, September 2007. taveRNA: a web suite for RNA algorithms and applications, Cagri Aksay, Raheleh Salari, Emre Karakoç, Can Alkan, S. Cenk Sahinalp., Nucleic Acids Research, July 1, 2007; Vol. 35 (Web Server Issue): W325-329, 2007. RNA Secondary Structure Prediction via Energy Density Minimization, Can Alkan, Emre Karakoç, S. Cenk Şahinalp, Peter Unrau, H. Alexander Ebhardt, Kaizhong Zhang, Jeremy Buhler., Proc. of the Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2006 - LNBI 3909), pp. 130-142, April 2-5, 2006 Venice, Italy, 2006. RNA-RNA Interaction Prediction and Antisense RNA Target Search, Can Alkan, Emre Karakoç, Joe Nadeau, S. Cenk Şahinalp, Kaizhong Zhang., Journal of Computational Biology, March 2006, Vol. 13, No. 2: 267-282, 2006.     * also in Proc. of the Ninth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005 - LNBI 3500), pp. 152-171, May 14-18, 2005 Cambridge, MA, USA, 2005. Manipulating Multiple Sequence Alignments via MaM and WebMaM, Can Alkan, Eray Tüzün, Jerome Buard, Franck Lethiec, Evan E. Eichler, Jeffrey A. Bailey, S. Cenk Şahinalp., Nucleic Acids Research July 1; 33 (Web Server issue): W295-W298, 2005. The role of unequal crossover in alpha-satellite DNA evolution: a computational analysis, Can Alkan, Evan E. Eichler, Jeffrey A. Bailey, S. Cenk Şahinalp, Eray Tüzün., Journal of Computational Biology, Vol. 11, No.5: 933-944, 2004. The structure and evolution of centromeric transition regions within the human genome, She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C, Bailey JA, Şahinalp C, Rocchi M, Haussler D, Wilson RK, Miller W, Schwartz S, Eichler EE., Nature, 2004 Aug 19;430(7002):857-64, 2004 Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome, G. Liu, NISC Comparative Sequencing Program, S. Zhao, J. A. Bailey, S. C. Şahinalp, C. Alkan, E. Tüzün, E. D. Green, E. E. Eichler., Genome Research, 13(3):358-368, 2003. An algorithmic analysis of the role of unequal crossover in alpha-satellite DNA evolution, Can Alkan, Jeffrey A. Bailey, Evan E. Eichler, S. Cenk Şahinalp, Eray Tüzün., Genome Informatics, Tokyo, Japan, vol.18 pp 93-102, 2002. Divergent Origins and Concerted Expansion of Two Segmental Duplications on Chromosome 16, E. E. Eichler, M. E. Johnson, C. Alkan, E. Tüzün, C. Şahinalp, D. Misceo, N. Archidiacono, and M. Rocchi., Journal of Heredity, 2001 92: 462-468, 2001.
Academic Experience		Case Western Reserve University, Cleveland, Ohio, USA Graduate Student & Research Assistant August 2000 - August 2005     Includes Ph.D. research, Ph.D. level coursework and research projects, reviewing papers for bioinformatics, algorithms and database conferences and journals Teaching Assistant August 2000 - May 2001         Duties included grading homeworks, and office hours  Systems Programming, Fall 2000  Introduction to Bioinformatics, Fall 2001  Analysis of Algorithms, Spring 2001
Professional Experience		Department of Genome Sciences, University of Washington, Seattle, Washington, USA Postdoctoral Fellow October 2005 - present    Working with Evan E. Eichler on computational methods to reconstruct the evolutionary history of alpha-satellite DNA. School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada Research Assistant January 2004 - September 2005     Worked on RNA-RNA interaction algorithms, and RNA secondary structure motif discovery problems, collaborating with Peter Unrau, Kaizhong Zhang, and Jeremy Buhler. Department of EECS, Case Western Reserve University, Cleveland, Ohio, USA Research & Teaching Assistant August 2000 - December 2003     Worked on phylogenetic tree algorithms, sequence analysis, and RNA-RNA interaction algorithms, collaborating with Evan E. Eichler and Joe Nadeau. Department of Genetics, Case Western Reserve University, Cleveland, Ohio, USA Summer intern with Evan E. Eichler Summer 2001     Worked on phylogenetic and sequence analysis of alpha-satellite DNA. Implemented various tools including MaM for manipulating multiple sequence alignments.
Conference and Invited Talks		RNA-RNA Interactions and miRNA Target Prediction, MITACS-PIMS Pacific Northwest Bioinformatics Day, Simon Fraser University, Burnaby, BC, Canada, May 20, 2004. RNA-RNA Interaction Prediction and Antisense RNA Target Search, Ninth Annual Conference on Research in Computational Molecular Biology (RECOMB 2005), Cambridge, MA, USA, May 14, 2005. Towards a Model for the Evolution of Alpha-Satellite DNA, BC Genome Sciences Centre, Vancouver, BC, Canada April 12, 2006. Organization and evolution of primate centromeric DNA from whole genome shotgun sequence data, Bilkent University Center for Bioinformatics, Ankara, Turkey, July 20, 2007. Personalized Copy-Number and Segmental Duplication Maps using next-gen sequencing technology, Special Interest Group on Algorithms for Short Read Assembly, Alignment & Variation Analysis at the 16th Annual International Conference Intelligent Systems for Molecular Biology, Toronto, ON, Canada, July 19, 2008. Organization and evolution of primate centromeric DNA from whole genome shotgun sequence data, 16th Annual International Conference Intelligent Systems for Molecular Biology, Highlights Track, Toronto, ON, Canada, July 22, 2008. Characterization of structural variation and segmental duplications using next-gen sequencing technology, The Mediterranean Medical Genetics Meeting 2009, Ankara, Turkey, June 30, 2009.
Supervised Students and Interns		Kerry Hall: Undergraduate student at the Department of Computer Science, University ofWashington, Seattle, WA. Intern in 2006 Fereydoun Hormozdiari: Ph.D. student at the School of Computing Science, Simon Fraser University, Burnaby, BC, Canada. Intern between February to July 2008. Iman Hajirasouliha: Ph.D. student at the School of Computing Science, Simon Fraser University, Burnaby, BC, Canada. Intern between February 2009 to July 2009.
Honors and Awards		Ranked 36th among 1.2 million examinees in the Nationwide University Entrance Examinations in Turkey, 1996 Ranked 40th in the Nationwide Post-Graduate Education Examination in Turkey, 1999 Full Scholarship Awarded by Bilkent University, 1996-2000 Case Prime Fellowship, Case Western Reserve University, Cleveland, Ohio, USA, 2000
Service Activities		Session Co-Chair, Session on Personal Genomics at the Pacific Symposium for Biocomputing, January 4-8, 2010, The Big Island of Hawaii, USA. Member, 1000 Genomes Project Structural Variation Working Group, 2008-present PC Member, The IEEE 22nd International Conference on Advanced Information Networking and Applications 2008 (AINA-08). PC Member, The IEEE 21st International Conference on Advanced Information Networking and Applications 2007 (AINA-07). Reviewed papers for Nucleic Acids Research, Genome Research, PLoS Genetics, SODA (2002, 2003), FOCS (2003), ICDE (2003), CPM (2004,2005, 2009)
Professional Memberships		Member of the International Society for Computational Biology since 2002