Publications
Conference Papers
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Ferhat Ay, Tamer Kahveci, Valerie de Crecy-Lagard,
Consistent alignment of metabolic pathways without any
abstraction in modeling,
CSB, 2008. (Abstract)
(PDF)
-
Jun Liu, Sanjay Ranka, Tamer Kahveci,
Classification and
Feature Selection Algorithms for Multi-class CGH data,
ISMB, 2008. (Abstract)
(PDF)
(PPT)
-
Padmavati Sridhar, Bin Song, Tamer Kahveci and Sanjay Ranka,
Mining metabolic networks for optimal drug targets,
PSB, 2008, 13: 291-302. (Abstract)
(PDF)
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Jun Liu, Sanjay Ranka, and Tamer Kahveci
A web server for
mining Comparative Genomic Hybridization (CGH) data,
Data
mining, systems analysis and optimization in biomedicine,
2007, pages 144-131 (PDF)
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Xu Zhang, Tamer Kahveci,
QOMA2: Optimizing the alignment
of many sequences,
BIBE, 2007. (Abstract)
(PDF)
-
Padmavati Sridhar, Tamer Kahveci, Sanjay Ranka
An
iterative algorithm for metabolic network-based drug target
identification,
PSB, 2007, 12:88-99. (Abstract)
(PDF) (PPT)
-
Xuehui Li, Tamer Kahveci,
Quality-based similarity search
for biological sequence databases,
BIOCOMP, 2007
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Jayendra Venkateswaran, Deepak Lachwani, Tamer Kahveci,
Christopher Jermaine
Reference-based Indexing of Sequence
Databases,
VLDB, 2006, pages 906-917. (Abstract)
(PDF)
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Jayendra Venkateswaran, Tamer Kahveci, Orhan Camoglu
Finding Data Broadness Via Generalized Nearest Neighbors,
EDBT, 2006, pages 645-663. (Abstract)
(PDF)
-
Xu Zhang, Tamer Kahveci
A New Approach for Alignment of
Multiple Proteins,
PSB, 2006, pages 339-350. (Abstract)
(PDF)
-
Yue Li, Lan Luo, Tao Li and Tamer Kahveci,
Microarchitecture
Characteristics and Implications of Alignment of Multiple
Bioinformatics Sequences,
Workshop on Unique Chips and Systems
(Held in conjunction with IEEE ISPASS), 2006.
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Tamer Kahveci, Venkatakrishnan Ramaswamy, Han Tao, Tao Li
Approximate Global Alignment of Sequences,
BIBE, 2005,
pages 81-88. (Abstract)
(PDF)
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Abhijit Pol, Tamer Kahveci
Highly Scalable and Accurate
Seeds for Subsequence Alignment,
BIBE, 2005, pages
27-31. (Abstract)
(PDF)
-
Yue Li, Tao Li, Tamer Kahveci, Jose Fortes
Workload
Characterization of Bioinformatics Applications on Pentium 4
Architecture,
MASCOTS, 2005, pages 15-22. (PDF)
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Xu Zhang, Tamer Kahveci
A New Approach for Multiple
Sequence Alignment,
RECOMB, 2005 (poster paper).
-
Arnab Bhattacharya, Tamer Kahveci, Ambuj K. Singh
Motif
Finding and Multiple Alignment through Vector-Space Embeddings
of Protein Sequences,
RECOMB, 2004 (poster paper).
-
Arnab Bhattacharya, Tolga Can, Tamer Kahveci, Ambuj K. Singh,
Yuan-Fang Wang
ProGreSS: Simultaneous Searching of
Protein Databases by Sequence and Structure,
PSB, 2004,
pages 264-275. (PDF)
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Orhan Camoglu, Tamer Kahveci, Ambuj K. Singh,
Towards
Index-based Similarity Search for Protein Structure
Databases,
CSB, 2003, pages 148-158.(PDF)
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Orhan Camoglu, Tamer Kahveci, Ambuj K. Singh,
PSI:
Indexing Protein Structures for Fast Similarity Search,
ISMB, 2003, pages 81-83 (also in Bioinformatics journal). (PDF)
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Tamer Kahveci, Ambuj K. Singh,
Fast Alignment of Large
Genome Databases,
ICDE, 2003 (demo paper), pages
768-770. (PDF)
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Tamer Kahveci, Christian Lang, Ambuj K. Singh,
Joining
Massive High-Dimensional Databases,
ICDE, 2003, pages
264-276. (Abstract)
(PDF)
(PPT)
(TR)
-
Tamer Kahveci, Ambuj K. Singh,
MAP: Searching Large
Genome Databases,
PSB, 2003, pages 303-314. (Abstract)
(PDF)
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Tamer Kahveci, Ambuj K. Singh, and Aliekber Gurel,
Similarity Searching for Multi-Attribute Sequences,
SSDBM, 2002. (Abstract)
(PDF)
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Tamer Kahveci, Ambuj K. Singh, and Aliekber Gurel,
An
Efficient Index Structure for Shift and Scale Invariant Search
of Multi-Attribute Time Sequences,
ICDE, 2002 (poster
paper), San Jose, CA. (Abstract)
(PDF)
(TR)
-
Tamer Kahveci and Ambuj K. Singh,
An Efficient Index
Structure for String Databases,
VLDB, 2001, pages
351-360. (Abstract)
(PDF)
(PPT)
(TR)
-
Tamer Kahveci and Ambuj K. Singh,
Variable Length Queries
for Time Series Data,
ICDE, 2001, pages 273-282. (Abstract)
(PDF)
(TR)
-
Tuba Yavuz-Kahveci, Tamer Kahveci and Ambuj K. Singh,
Buffering of Index Structures,
SPIE, 2000, October,
Boston. (Abstract)
(PDF)
Journal Papers
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Xuehui Li, Tamer Kahveci and Mark Settles,
A Novel
Genome-Scale Repeat Finder Geared towards Transposons,
Bioinformatics 24(4): 468-476, 2008. (Bioinformatics)
-
Jayendra Venkateswaran, Deepak Lachwani, Tamer Kahveci,
Christopher Jermaine
Reference-Based Indexing for Metric
Spaces with Costly Distance Measures,
the VLDB Journal,
17:5, pages 1231 - 1251, 2008. (SpringerLink)
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Bin Song, Padmavati Sridhar, Tamer Kahveci and Sanjay Ranka,
Double Iterative Optimization for Metabolic Network-Based
Drug Target Identification,
accepted to International
Journal of Data Mining and Bioinformatics, 2007. (Abstract)
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Jun Liu, Sanjay Ranka, Tamer Kahveci,
Markers improve
clustering of CGH data,
Bioinformatics, 23:4, pages
450-457, 2007. (PubMed)
(Bioinformatics)
-
Xu Zhang, Tamer Kahveci,
QOMA: Quasi-Optimal Multiple
Alignment of Protein Sequences,
Bioinformatics, 23:2,
pages 162-168, 2007. (PubMed)
(Bioinformatics)
-
Xuehui Li, Tamer Kahveci,
A novel algorithm for
identifying low-complexity regions in a protein sequence,
Bioinformatics, 22:24, pages 2980-2987, 2006. (PubMed)
(Bioinformatics)
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Jun Liu, Jaaved Mohammed, James Carter, Sanjay Ranka, Tamer
Kahveci, Michael Baudis,
Distance-based Clustering of CGH
Data,
Bioinformatics, 22:16, pages 1971-1978, 2006. (PubMed)
(Bioinformatics)
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Tamer Kahveci, Vebjorn Ljosa and Ambuj K. Singh,
Speeding
up Whole Genome Alignment by Indexing Frequency Vectors,
Bioinformatics, 20:13, pages 2122-2134, 2004. (PubMed)
(Bioinformatics)
-
Tamer Kahveci and Ambuj K. Singh,
Progressive Searching
of Biological Sequences,
IEEE Database Engineering
Bulletin, 27:3, pages 32-39, 2004. (PS)
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Orhan Camoglu, Tamer Kahveci and Ambuj K. Singh,
Towards
Index-based Similarity Search for Protein Structure Databases,
Journal of Bioinformatics and Computational Biology
(JBCB), 2:1, pages 99-126, 2004. (invited paper). (PubMed)
-
Tamer Kahveci and Ambuj K. Singh,
Optimizing Similarity
Search for Arbitrary Length Time Series Queries,
IEEE
Transactions on Knowledge and Data Engineering (TKDE), 16:4,
pages 418-433, 2004. (Digital
Library)
Book Chapters
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Tamer Kahveci, Ambuj K. Singh,
Index Structures for
Approximate Matching in Sequence Databases,
to appear in
"Handbook on Computational Biology", editor Srinivas Aluru,
CRC Press
Tamer Kahveci
Last modified: Tue Jul 29 09:50:17 EDT 2008