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| Publications: Multidimensional Classification Approach for Defining Product Line Engineering Transition Strategies B. Tekinerdoğan, E. Tüzün, E. Şaykol. Proc. of the 14th International Software Product Line Conference (SPLC 2010), Korea LNCS 6287, pp. 461–465, September 2010. Exploring the Business Case for Transitioning from a Framework-based Approach to a Software Product Line Engineering Approach B. Tekinerdoğan, E. Tüzün, E. Şaykol. Proc. of the 14th International Software Product Line Conference, Vol. 2, Industrial Track, pp. 251-255, September 2010. Yazılım Klonları, Oluşum Nedenleri ve Mücadele Yöntemleri Üzerine Bir İnceleme Eray Tüzün, Emre Er, Buyurman Baykal. 2. Yazılım Kalitesi ve Yazılım Geliştirme Araçları Sempozyumu 2010
A Data-Centric Framework for Network Enabled C4ISR Software Systems Karaca, H.N., Yüksel M., Tüzün E., Kılınç, I., Baykal B. Lectures Notes in Electrical Engineering ISCIS 2010, Springer Belin, Volume 62, 978-90-481-9793-4, pp 173-176, October 24, 2010. Using Continuous Integration and Automated Test Techniques for a Robust C4ISR System H. Mehmet Yüksel, Eray Tüzün, Erdoğan Gelirli, Emrah Bıyıklı, Buyurman Baykal, 14-16 September 2009, ISCIS 2009
Population stratification of a common APOBEC gene deletion polymorphism Kidd JM, Newman TL, Tuzun E, Kaul R, Eichler EE. PLoS Genet. 2007;3:e63. Molecular refinement of gibbon genome rearrangements Roberta Roberto, Oronzo Capozzi, Richard K. Wilson, Elaine R. Mardis, Mariana Lomiento, Eray Tuzun, Ze Cheng, Alan R. Mootnick, Nicoletta Archidiacono, Mariano Rocchi, and Evan E. Eichler. Genome Res. 2007 February; 17(2): 249–257. Initial sequence of the chimpanzee genome and comparison with the human genome
Chimpanzee Sequencing and Analysis Consortium. Nature. 2005 Sep 1;437(7055):50-1.
Manipulating multiple sequence alignments via MaM and WebMam
Can Alkan, Eray Tüzün, Jerome Buard, Franck Lethiec, Evan Eicher, Jeff Bailey, S. Cenk Sahinalp
Nucleic Acids Research, July 1;33 (Web server issue): W295-W298, 2005
Fine-Scale Structural Variation of the Human Genome
Eray Tüzün, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, Olson MV, Eichler EE. Nature Genetics 2005, May 15 A genome-wide survey of structural variation between human and chimpanzee Newman, T.L., Tuzun, E., Morrison, V.A., Hayden, K.E., Ventura, M., McGrath, S.D., Rocchi, M., Eichler, E.E.(2005), Genome Res. 15:1344–1356. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
International Chicken Genome Sequencing Consortium
Nature. 2004 Dec 9;432(7018):695-716. Erratum in: Nature. 2005 Feb 17;433(7027):777. 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. October 2004, 11(5): 933-944. Shotgun sequence assembly and recent segmental duplications within the human genome She X, Jiang Z, Clark RA, Liu G, Cheng Z, Tuzun E, Church DM, Sutton G, Halpern AL, Eichler EE. Nature 2004 Oct 21;431(7011):927-30 Recent segmental duplications in the working draft assembly of the brown norway rat Tuzun, E, Bailey, J. A,Eichler, EE. Genome Research 2004 Apr;14(4):493-506. Genome Sequence of the Brown Norway Rat yields insights into mammalian evolution
Rat Genome Sequencing Project Consortium (2004) Nature. 2004 Apr 1;428(6982):493-521. Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome Liu G, Program NI, Zhao S, Bailey JA, Sahinalp SC, Alkan C, Tuzun E, Green ED, Eichler EE. Genome Research, 2003 Mar 1; 13(3): 358-368. An algorithmic analysis of the role of unequal crossover in alpha-satellite DNA evolution
Can Alkan, Jeff Bailey, Evan Eichler, S. Cenk Sahinalp, Eray Tuzun Genome Informatics Workshop 2002, Tokyo, Japan, 2002 Divergent Origins and Concerted Expansion of Two Segmental Duplications on Chromosome 16 E. E. Eichler, M. E. Johnson, C. Alkan, E. Tuzun, C. Sahinalp, D. Misceo, N. Archidiacono, and M. Rocchi Journal of Heredity 2001 92: 462-468.
Software: Multiple Alignment Manipulator: MaM is a software tool that processes and manipulates multiple alignments. Written in C. WebMaM: Web version of MaM Patents:
Information Architecture for a Variable-Feedback Tutoring Knowledge Base Eray Tuzun and Dave Smith U.S Provisional Patent Pending (2003)
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