SOFTWARE:
Multiple Alignment Manipulator with Can Alkan
MaM is a software tool that processes and
manipulates multiple
alignments of genomic sequences.
Written in C. Web based version
WebMaM
RESEARCH:
* Finding Intermediate Structural Variation in Human Genome
* Finding
recent segmental duplications in Rat
PUBLICATIONS:
* Fine-Scale Structural Variation of the Human Genome
Tuzun E, 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; [Epub ahead of print]
*
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.
* 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.
* 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.
* 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
* 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.
* "Information Architecture for a Variable-Feedback Tutoring Knowledge Base"
Eray Tuzun and Dave Smith
U.S Provisional Patent Pending (2003)
-Eray 02.20.2006
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