Can ALKAN - calkan -

MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions, Seunghak Lee, Fereydoun Hormozdiari, Can Alkan, Michael Brudno. Nature Methods, May 31 [Epub ahead of print], 2009.

Combinatorial algorithms for structural variation detection in high throughput sequenced genomes, Fereydoun Hormozdiari*, Can Alkan*, Evan E. Eichler, S. Cenk Sahinalp. Genome Research, May 15 [Epub ahead of print], 2009.
        *also in Proc. of the Thirteenth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2009), to appear, May 18-21, 2009 Tucson, AZ, USA

New Insights into Centromere Organization and Evolution from White-cheeked Gibbon and Marmoset, A. Cellamare,    C.R Cataccio, 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, May 8, [Epub ahead of print], 2009.

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 May 1 2008;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.
       *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

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, 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.

Session on Personal Genomics at the Pacific Symposium on Biocomputing 2010

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