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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)
Tamer Kahveci
Last modified: Thu Sep 22 17:18:39 EDT 2016