Can Alkan, Ph.D.
Postdoctoral Fellow @ Dept. of Genome Sciences, University of Washington

Department of Genome Sciences
University of Washington
Foege Building S-433D
Box 355065
1705 NE Pacific St
Seattle, WA, 98195-5065
USA

Email:
PGP Public Key:	publickey.txt
Phone:	+1-206-5437402
Fax :	+1-206-5436575 / +1-206-6857301

Pronunciation of my name:

Vita: PDF - HTML

Education

Ph.D., Computer Science, at Case Western Reserve University, Cleveland, OH, USA, August 2005
Supervisor: Assoc. Prof. Cenk Şahinalp
B.Sc., Computer Science, Bilkent University, Ankara, Turkey, May 2000

Research Interests

Bioinformatics and Computational biology:
- Analysis of tandemly repeated DNA sequence
- RNA-RNA interactions
- RNA secondary structure motif discovery
- Human structural variation detection
- Next-gen sequencing technologies

Contributed Software Projects

Multiple alignment Manipulator (MaM) with Eray Tüzün.
- Project web page
- Web interface implemented and hosted by LIRMM.

taveRNA: RNA suite for RNA folding, RNA-RNA interaction prediction and search
- Project web page

Selected 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

    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

    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, Oct 2004, 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, Jeff Bailey, Evan Eichler, S. Cenk Şahinalp, Eray Tüzün. Genome Informatics Workshop, 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.

Personal

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