Journal Papers
- Rasha Elhesha, Benjamin Baiser, Tamer
Kahveci.
Motif Centrality in Food Web Networks.
Complex Networks. 2016. to appear
- Yuanfang Ren, Qiyao Wang, Mahmudul Hasan, Ahmet Ay, Tamer
Kahveci.
Identifying the topology of signaling networks
from partial RNAi data.
BMC Systems Biology. 2016. to
appear
- Sebo Kim, Varsha Sundaresan, Lei Zhou, Tamer Kahveci.
Integrating domain specific knowledge and network
analysis to predict drug sensitivity of cancer cell lines.
PLoS Journal. 2016. to appear
- Rasha Elhesha, Tamer Kahveci.
Identification of large disjoint motifs in biological networks.
BMC Bioinformatics. 2016. to appear
- Benjamin Baiser, Rasha Elhesha, Tamer Kahveci.
Motifs in the assembly of food web networks.
OIKOS Journal. 125:4. 480-491. 2016.
- Haitham Gabr, Juan Carlos Rivera-Mulia, David M. Gilbert,
Tamer Kahveci.
Computing interaction probabilities in
signaling networks.
EURASIP Journal on Bioinformatics
and Systems Biology. 1:1. 2015.
- Md Mahmudul Hasan and Tamer Kahveci.
Indexing a protein-protein interaction network expedites network alignment.
BMC Bioinformatics. 16:326. 2015.
- Juan Carlos Rivera-Mulia, Quinton Buckley, Takayo Sasaki,
Jared Zimmerman, Ruth A. Didier, Kristopher Nazor, Jeanne
F. Loring, Zheng Lian, Sherman Weissman, Allan J. Robins, Thomas
C. Schulz, Laura Menendez, Michael J. Kulik, Stephen Dalton,
Haitham Gabr, Tamer Kahveci, David M. Gilbert.
Dynamic
changes in replication timing and gene expression during human
development
Genome Research. 25:8. 1091-1103. 2015.
- Haitham Gabr, Tamer Kahveci.
Signal reachability
facilitates characterization of probabilistic signaling
networks.
BMC Bioinformatics. 16 Suppl 17:S6. 2015.
- Ahmet Ay, Dihong Gong, Tamer Kahveci.
Hierarchical
Decomposition of Dynamically Evolving Regulatory Networks.
BMC Bioinformatics. 16:161. 2015. (PDF)
- Mouse ENCODE Consortium.
A comparative
encyclopedia of DNA elements in the mouse genome.
Nature. 515: 355-364. 2014. (Nature)
- Benjamin D. Pope, Tyrone Ryba, Vishnu Dileep, Feng Yue,
Weisheng Wu, Olgert Denas, Daniel L. Vera, Yanli Wang, R. Scott
Hansen, Theresa K. Canfield, Robert E. Thurman, Yong Cheng,
Günhan Gülsoy, Jonathan H. Dennis, Michael P. Snyder, John
A. Stamatoyannopoulos, James Taylor, Ross C. Hardison, Tamer
Kahveci, Bing Ren and David M. Gilbert.
Topologically-associating domains are stable units of
replication-timing regulation.
Nature. 515:
402-405. 2014 (Nature)
- Haitham Gabr, Andrei Todor, Alin Dobra, Tamer Kahveci
Reachability analysis in probabilistic biological
networks.
IEEE/ACM Transactions on Computational
Biology and Bioinformatics (IEEE/ACM TCBB). 12:1. pages
53-66. 2014 (PDF)
- Ahmet Ay, Dihong Gong, Tamer Kahveci
Network-based prediction of cancer under genetic
storm.
Cancer Informatics. Suppl. 3:
15-31. 2014.(PDF)
- Andrei Todor, Haitham Gabr, Alin Dobra, Tamer Kahveci
Large scale analysis of signal reachability.
Bioinformatics. 12: i96-i104. 2014. (International Conference on
Intelligent Systems for Molecular Biology (ISMB), 2014)
- Andrei Todor, Alin Dobra, Tamer Kahveci.
Characterizing topology of probabilistic biological
networks.
IEEE/ACM Transactions on Computational
Biology and Bioinformatics Journal (IEEE/ACM
TCBB). 10:4. 2013. (PDF)
- Mahmudul Hasan, Yusuf Kavurucu and Tamer Kahveci.
A
scalable method for discovering significant subnetworks,
BMC Systems Biology. 7: S3. 2013. (PDF)
- Saad Sheikh, Tamer Kahveci, Sanjay Ranka, Gordon
Burleigh.
Stability Analysis of Phylogenetic Trees,
Bioinformatics. 29 (2): 166-174. 2013. (PDF)
(Project
page)
- Jesse F. Gregory III, Youngja Park, Yvonne Lamers, Nirmalya
Bandyopadhyay, Yueh-Yun Chi, Kichen Lee, Steven Kim, Vanessa da
Silva, Nicholas Hove, Sanjay Ranka, Tamer Kahveci, Keith
E. Muller, Robert D. Stevens, Christopher B. Newgard, Peter
W. Stacpoole, and Dean P. Jones.
Metabolomic Analysis
Reveals Extended Metabolic Consequences of Marginal Vitamin B-6
Deficiency in Healthy Human Subjects.
PLoS ONE.
8:6, 2013. (PDF)
- Andrei Todor, Alin Dobra, Tamer Kahveci.
Probabilistic Biological Network Alignment,
IEEE/ACM
Transactions on Computational Biology and Bioinformatics Journal
(IEEE/ACM TCBB). 10:1, 2013. (PDF)
(Project
page)
- Seyedsasan Hashemikhabir, Eyup Serdar Ayaz, Yusuf Kavurucu,
Tolga Can, Tamer Kahveci
Large scale signaling network
reconstruction
IEEE/ACM Transactions on Computational
Biology and Bioinformatics Journal (IEEE/ACM TCBB). 9:6,
2012. (PDF)
- Daniel Marbach, Sushmita Roy, Ferhat Ay, Patrick E Meyer,
Rogerio Candeias, Tamer Kahveci, Christopher A Bristow, Manolis
Kellis
Predictive regulatory models in Drosophila
melanogaster by integrative inference of transcriptional
networks
Genome Research, 7:22, 2012.
- Gunhan Gulsoy, Nirmalya Bandhyopadhyay, Tamer Kahveci
HIDEN: Hierarchical decomposition of regulatory networks
BMC Bioinformatics, 13:250, 2012.
(PDF)
- Avinash Ramu, Gordon Burleigh, Tamer Kahveci
A
scalable method for identifying frequent subtrees in sets of
large phylogenetic trees
BMC Bioinformatics, 13:256,
2012.
(PDF)
- Gunhan Gulsoy, Bhavik Gandhi, Tamer Kahveci
TOPAC:
Alignment of gene regulatory networks using topology aware
coloring
Journal of Bioinformatics and Computational
Biology (JBCB), Vol. 10:1, 2012.
(PDF)
- Ferhat Ay, Michael Dang, Tamer Kahveci
Metabolic
network alignment in large scale by network compression
BMC Bioinformatics vol 13, 2012. (HTML+PDF)
- Nirmalya Bandyopadhyay, Manas Somaiya, Sanjay Ranka, Tamer
Kahveci
CMRF : Analyzing Differential Gene Regulation in
Two Group Perturbation Experiments
BMC Genomics, Vol
13:2, 2012 (HTML+PDF)
- Gunhan Gulsoy, Tamer Kahveci
RINQ: Reference-based
Indexing for Network Queries,
Bioinformatics, 27 (13):
i149-i158. (International Conference on Intelligent Systems for
Molecular Biology (ISMB), 2011) (HTML+PDF)
- Basma El Yacoubi, Isabelle Hatin, Christopher Deutsch,
Tamer Kahveci, Jean-Pierre Rousset, Dirk Iwata-Reuyl, Alexey G
Murzin and Valerie de Crecy-Lagard,
A role for the
universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification,
The EMBO Journal advance online publication 1 February
2011; doi:10.1038/emboj.2010.363 (Nature)
- Ferhat Ay, Manolis Kellis, Tamer Kahveci
SubMAP:
Aligning metabolic pathways with subnetwork mappings,
Journal of Computational Biology, 18(3):1-17, 2011. (PDF)
(SubMAP server)
-
Nirmalya Bandyopadhyay, Sanjay Ranka, Y. Sun, Steve Goodison,
Tamer Kahveci
Pathway based Feature Selection for
Cancer Microarray Data
Journal of Advances in
Bioinformatics, accepted for publication.
-
Bin Song, I. Esra Buyuktahtakin, Sanjay Ranka, Tamer Kahveci,
Manipulating the steady state of metabolic pathways
IEEE/ACM Transactions on Computational Biology and
Bioinformatics (IEEE TCBB), 8(3), pages 732-747, 2011. (IEEE
TCBB)
-
Nirmalya Bandyopadhyay, Tamer Kahveci
GBA Manager : An
online tool for querying low complexity regions in proteins
Journal of Computational Biology, 17(1):73-7, 2010.
(PDF)
-
Jayendra Venkateswaran, Bin Song, Tamer Kahveci, Christopher
Jermaine
TRIAL: A Tool for Finding Distant Structural
Similarities
IEEE/ACM Transactions on Computational
Biology and Bioinformatics (IEEE TCBB), 8(3), pages
819-831. (IEEE
TCBB)
-
Ferhat Ay, Fei Xu, Tamer Kahveci,
Scalable Steady
State Analysis of Boolean Biological Regulatory Networks,
PLoS ONE 4(12), pages e7992, 2009. (PLoS)
-
Jun Liu, Nirmalya Bandyopadhyay, Sanjay Ranka, Michael Baudis,
Tamer Kahveci
Inferring Progression Models for CGH data
Bioinformatics, 25:17, pages 2208-2215, 2009. (Bioinformatics)
-
Ferhat Ay, Tamer Kahveci, Valerie de Crecy-Lagard,
A
Fast And Accurate Algorithm For Comparative Analysis Of
Metabolic Pathways
Journal of Bioinformatics and
Computational Biology (JBCB), 7:3, pages 389-428, 2009. (PDF)
-
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,
3:2, pages 145-159, 2009. (Abstract)
-
Jun Liu, Sanjay Ranka, Tamer Kahveci,
Classification and
Feature Selection Algorithms for Multi-class CGH data,
Bioinformatics, 24 (13): i86-i95. (International Conference on
Intelligent Systems for Molecular Biology (ISMB), 86-95, 2008)
(HTML+PDF) (PPT)
-
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)
-
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)
-
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)
-
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)
-
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)
-
Orhan Camoglu, Tamer Kahveci, Ambuj K. Singh,
PSI:
Indexing Protein Structures for Fast Similarity Search,
Bioinformatics (2003) 19: i81-i83. (International Conference
on Intelligent Systems for Molecular Biology (ISMB), pages
81-83, 2003) (HTML+PDF)
Conference Papers
- Aisharjya Sarkar, Yuanfang Ren, Rasha Elhesa, and
Tamer Kahveci
Counting independent motifs in
probabilistic networks .
International Conference
on Bioinformatics and Computational Biology (ACM-BCB)
2016.
- Qiyao Wang, Yuanfang Ren, Md Mahmudul Hasan, Ahmet
Ay, and Tamer Kahveci
Construction of signaling
networks with incomplete RNAi data.
IEEE
International Conference on Bioinformatics and Biomedicine
(BIBM). 2015.
- Haitham Gabr, Alin Dobra and Tamer Kahveci
Estimating Reachability in Dense Biological Networks.
International Conference on Bioinformatics and
Computational Biology (ACM-BCB) 2015.
- Andrei Todor, Alin Dobra and Tamer Kahveci
Counting Motifs in Probabilistic Biological Networks.
International Conference on Bioinformatics and
Computational Biology (ACM-BCB) 2015.
- Md Abdul Alim, Ahmet Ay, Md Mahmudul Hasan, My Thai
and Tamer Kahveci
Multiple Reference Networks
Improve Accuracy of Signaling Network Construction.
International Conference on Bioinformatics and
Computational Biology (ACM-BCB) 2015.
- Md Mahmudul Hasan and Tamer Kahveci
Incremental Network Querying in Biological Networks.
8th International Workshop on Biomolecular Network
Analysis (IWBNA 2014) at ACM-BCB 2014.
- Rasha Elhesha, Ryan Cobb, Gordon Burleigh and Tamer
Kahveci
Extracting phylogenetic signals from gene
trees and its significance for species tree
construction.
International Conference on
Bioinformatics and Computational Biology (ACM-BCB) 2014.
- Haitham Gabr and Tamer Kahveci
Characterization of probabilistic signaling networks
through signal propagation.
IEEE International
Conference on Computational Advances in Bio and Medical
Sciences (IEEE ICCABS) 2014.
- Mahmudul Hasan, Tamer Kahveci,
Color
distribution can accelerate network alignment.
International Conference On Bioinformatics and
Computational Biology (ACM-BCB), 2013.
- Haitham Gabr, Andrei Todor, Helia Zandi, Alin Dobra,
Tamer Kahveci,
PReach: Reachability in
Probabilistic Signaling Networks.
International
Conference On Bioinformatics and Computational Biology
(ACM-BCB), 2013.
- Haitham Gabr, Alin Dobra, Tamer Kahveci,
From
uncertain protein interaction networks to signaling
pathways through intensive color coding,
Pacific
Symposium on Biocomputing (PSB), 2013.
- Gunhan Gulsoy, Tamer Kahveci,
Inferring gene
functions from metabolic reactions
IEEE
International Workshop on Genomic Signal Processing and
Statistics (GENSIPS), 2012.
- Andrei Todor, Alin Dobra, Tamer Kahveci,
Uncertain interactions affect degree distribution of
biological networks
International Conference On
Bioinformatics and Computational Biology (IEEE-BIBM),
2012.(PDF)
- Mahmudul Hasan, Yusuf Kavurucu, Tamer Kahveci,
SiS: Significant Subnetworks in Massive Number of Network
Topologies
International Conference On Bioinformatics
and Computational Biology (IEEE-BIBM), 2012. (PDF)
- Nirmalya Bandyopadhyay, Manas Somiya, Sanjay Ranka,
Tamer Kahveci,
SSLPred : Predicting Synthetic
Sickness Lethality,
Pacific Symposium on
Biocomputing (PSB), 2012.
- Gunhan Gulsoy, Bhavik Gandhi, Tamer Kahveci,
Topology aware coloring of gene regulatory networks
International Conference On Bioinformatics and
Computational Biology (ACM-BCB), 2011.
- Michael Dang, Ferhat Ay, Tamer Kahveci,
A Novel
Framework for Large Scale Metabolic Network Alignments by
Compression,
International Conference On
Bioinformatics and Computational Biology (ACM-BCB),
2011. (PDF)
(PPTX)
(Honorary best paper)
- Nirmalya Bandyopadhyay, Manas Somiya, Sanjay Ranka,
Tamer Kahveci,
Identifying Differentially Regulated
Genes ,
IEEE International Conference on
Computational Advances in Bio and medical Sciences
(ICCABS), 2011. (PDF)
- Ferhat Ay, Gunhan Gulsoy, Tamer Kahveci,
Finding
Steady States of Large Scale Regulatory Networks through
Partitioning,
IEEE International Workshop on Genomic
Signal Processing and Statistics (GENSIPS), 2010. (PDF)
- Nirmalya Bandyopadhyay, Manas Somiya, Sanjay Ranka,
Tamer Kahveci,
Modeling Perturbations using Gene
Networks,
International Conference on Computational
Systems Biology (CSB), 2010. (PDF)
- Bin Song, Sanjay Ranka, Tamer Kahveci,
Enzymatic
target identification with dynamic states,
International Conference On Bioinformatics and
Computational Biology (ACM-BCB), 2010. (PDF)
(Best student paper)
- Ferhat Ay, Tamer Kahveci,
Functional
Similarities of Reaction Sets in Metabolic Pathways,
International Conference On Bioinformatics and
Computational Biology (ACM-BCB), 2010. (PDF)
- Nirmalya Bandyopadhyay, Mark Settles, Tamer Kahveci,
RepFrag: A Graph based Method for Finding Repeats and
Transposons from Fragmented Genomes,
International
Conference On Bioinformatics and Computational Biology
(ACM-BCB), 2010. (PDF)
- Ferhat Ay, Thang N. Dinh, My T. Thai, Tamer Kahveci,
Finding Dynamic Modules of Biological Regulatory
Networks
IEEE International Conference on
Bioinformatics and Bioengineering (BIBE), 2010. (PDF)
- Ferhat Ay, Tamer Kahveci,
SubMAP: Aligning
metabolic pathways with subnetwork mappings,
International Conference on Research in Computational
Biology (RECOMB), 2010. (Abstract)
(PDF)
(SubMAP server)
- Fei Xu, Ravi Jampani, Mingxi Wu, Chris Jermaine,
Tamer Kahveci,
Surrogate Ranking for Very Expensive
Similarity Queries
International Conference on Data
Engineering (ICDE), 848-859, 2010. (Abstract)
(PDF)
- Ferhat Ay, Fei Xu, Tamer Kahveci,
Scalable
Steady State Analysis of Boolean Biological Regulatory
Networks,
RECOMB RG, 2009. (Abstract)
(PDF)
- Ferhat Ay, Tamer Kahveci, Valerie de Crecy-Lagard,
Consistent alignment of metabolic pathways without
any abstraction in modeling,
International Conference
on Computational Systems Biology (CSB), 2008. (Abstract)
(PDF)
(PPT)
(Best paper)
- Padmavati Sridhar, Bin Song, Tamer Kahveci and Sanjay
Ranka,
Mining metabolic networks for optimal drug
targets,
Pacific Symposium on Biocomputing (PSB), 13:
291-302, 2008. (Abstract)
(PDF)
- 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, pages 144-131, 2007. (PDF)
- Xu Zhang, Tamer Kahveci,
QOMA2: Optimizing the
alignment of many sequences,
IEEE International
Conference on Bioinformatics and Bioengineering (BIBE),
780-787, 2007. (Abstract)
(PDF)
- Padmavati Sridhar, Tamer Kahveci, Sanjay Ranka
An iterative algorithm for metabolic network-based drug
target identification,
Pacific Symposium on
Biocomputing (PSB), 12:88-99, 2007. (Abstract)
(PDF)
(PPT)
- Xuehui Li, Tamer Kahveci,
Quality-based
similarity search for biological sequence databases,
BIOCOMP, 567-573, 2007
- Jayendra Venkateswaran, Deepak Lachwani, Tamer
Kahveci, Christopher Jermaine
Reference-based
Indexing of Sequence Databases,
International
Conference on Very Large Databases (VLDB), 906-917, 2006.
(Abstract)
(PDF)
- Jayendra Venkateswaran, Tamer Kahveci, Orhan Camoglu
Finding Data Broadness Via Generalized Nearest
Neighbors,
International Conference on Extending
Database Technologies (EDBT), 645-663, 2006. (Abstract)
(PDF)
- Xu Zhang, Tamer Kahveci
A New Approach for
Alignment of Multiple Proteins,
Pacific Symposium on
Biocomputing (PSB), pages 339-350, 2006. (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.
- Tamer Kahveci, Venkatakrishnan Ramaswamy, Han Tao,
Tao Li
Approximate Global Alignment of Sequences,
IEEE International Conference on Bioinformatics and
Bioengineering (BIBE), pages 81-88, 2005. (Abstract)
(PDF)
- Abhijit Pol, Tamer Kahveci
Highly Scalable and
Accurate Seeds for Subsequence Alignment,
IEEE
International Conference on Bioinformatics and
Bioengineering (BIBE), pages 27-31, 2005. (Abstract)
(PDF)
- Yue Li, Tao Li, Tamer Kahveci, Jose Fortes
Workload Characterization of Bioinformatics Applications
on Pentium 4 Architecture,
MASCOTS, pages 15-22,
2005. (PDF)
- Arnab Bhattacharya, Tolga Can, Tamer Kahveci, Ambuj
K. Singh, Yuan-Fang Wang
ProGreSS: Simultaneous
Searching of Protein Databases by Sequence and Structure,
Pacific Symposium on Biocomputing (PSB), pages
264-275, 2004. (PDF)
- Orhan Camoglu, Tamer Kahveci, Ambuj K. Singh,
Towards Index-based Similarity Search for Protein
Structure Databases,
International Conference on
Computational Systems Biology (CSB), pages 148-158,
2003.(PDF)
- Tamer Kahveci, Christian Lang, Ambuj K. Singh,
Joining Massive High-Dimensional Databases,
International Conference on Data Engineering (ICDE), pages
264-276, 2003. (Abstract)
(PDF)
(PPT)
(TR)
- Tamer Kahveci, Ambuj K. Singh,
MAP: Searching
Large Genome Databases,
Pacific Symposium on
Biocomputing (PSB), pages 303-314, 2003. (Abstract)
(PDF)
- Tamer Kahveci, Ambuj K. Singh, and Aliekber Gurel,
Similarity Searching for Multi-Attribute Sequences,
Statistical and Scientific Database Management
(SSDBM), 2002. (Abstract)
(PDF)
- Tamer Kahveci and Ambuj K. Singh,
An Efficient
Index Structure for String Databases,
International
Conference on Very Large Databases (VLDB), 2001, pages
351-360. (Abstract)
(PDF)
(PPT)
(TR)
- Tamer Kahveci and Ambuj K. Singh,
Variable
Length Queries for Time Series Data,
International
Conference on Data Engineering (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)
Book Chapters
-
Mahmudul Hasan, Gunhan Gulsoy, Yusuf Kavurucu, Tamer Kahveci,
Indexing for Similarity Queries in Biological Networks,
in "Biological Data Mining and its Applications in
Healthcare Bioinformatics", editor Xiao Li, See-Kiong Ng and
Jason T. L. Wang, World Scientific
-
Ferhat Ay, Gunhan Gulsoy, Tamer Kahveci,
Mining
biological networks for similar patterns,
in "DATA
MINING: Foundations and Intelligent Paradigms-- Volume 3",
editor Dawn E. Holmes and Lakhmi Jain, Springer
-
Bin Song, I. Esra Büyüktahtakin, Nirmalya Bandyopadhyay, Sanjay Ranka and Tamer Kahveci,
Identifying Enzyme Knockout Strategies on Multiple Enzyme Associations,
Bioinformatics - Trends and Methodologies, Mahmood A. Mahdavi (Ed.), ISBN: 978-953-307-282-1, InTech 2011.
(PDF)
-
Tamer Kahveci, Ambuj K. Singh,
Index Structures for
Approximate Matching in Sequence Databases,
in "Handbook
on Computational Biology", editor Srinivas Aluru, CRC Press
Other Publications
-
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).
-
Tamer Kahveci, Ambuj K. Singh,
Fast Alignment of Large
Genome Databases,
International Conference on Data
Engineering (ICDE), pages 768-770, 2003 (demo paper). (PDF)
-
Tamer Kahveci, Ambuj K. Singh, and Aliekber Gurel,
An
Efficient Index Structure for Shift and Scale Invariant Search
of Multi-Attribute Time Sequences,
International Conference on Data Engineering (ICDE), 2002 (poster
paper), San Jose, CA. (Abstract)
(PDF)
(TR)