| Contact Information |
Department
of Genome Sciences University of Washington Box 355065 Foege Bulding S-433D 1705 NE Pacific St. Seattle, WA, 98195-5065 USA |
Voice:
(206) 543-7402 Fax: (206) 543-6575 E-mail: calkan@gs.washington.edu |
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| 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. |
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| Education |
Case Western Reserve University,
Cleveland, Ohio, USA Department of EECS Ph.D., Computer Science, August 2005
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| Bilkent University, Ankara, Turkey Department of Engineering B.Sc., Computer Science, May 2000 |
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| Publications |
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. 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. RNA-RNA Interaction Prediction and Antisense RNA Target Search, Can Alkan, Emre Karakoç, Joe Nadeau, S. Cenk Şahinalp, Kaizhong Zhang., 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. 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 Conference, 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. MaM: Multiple Alignment Manipulator, Can Alkan, Eray Tüzün, Evan Eichler, Jeff Bailey, S. Cenk Şahinalp., Currents in Computational Molecular Biology, April 18-21, 2002 (RECOMB poster) |
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| Academic Experience |
Case Western Reserve University,
Cleveland, Ohio, USA
Includes Ph.D. research, Ph.D. level coursework and research projects, reviewing papers for bioinformatics, algorithms and database conferences and journals
Duties included grading homeworks, and office hours
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| Professional Experience |
Department of Genome Sciences, University
of Washington, Seattle, Washington, USA
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
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
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
Worked on phylogenetic and sequence analysis of alpha-satellite DNA. Implemented various tools including MaM for manipulating multiple sequence alignments. |
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| Computer Skills |
Languages:
C, Java, Pascal, Unix shell scripts, SQL, MPI parallel processing
library. Applications: LATEX, Unix tools. Operating Systems: Unix/Linux, Windows. |
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| 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 |
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