Publications

Publications:

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

Closing gaps in the human genome with fosmid resources generated from multiple individuals. Bovee. et al., Nat Genet, 40(1):96–101, January 2008.

Mapping and sequencing of structural variation from eight human genomes.
Kidd. et al. Nature. 2008 May 1;453(7191):56-64.

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 Tuzun, 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 Tuzun, 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

International Human Genome Sequencing Consortium. (2004).

Finishing the euchromatic sequence of the human genome. Nature Oct;431(7011):931-45.

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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