The Bioinformatics Lab

Journal Papers

• Michael Dang, Ferhat Ay, Tamer Kahveci
  Metabolic network alignment in large scale by network compression
  BMC Bioinformatics vol 13, 2012.
• Gunhan Gulsoy, Bhavik Gandhi, Tamer Kahveci
  TOPAC: Alignment of gene regulatory networks using topology aware coloring
  Journal of Bioinformatics and Computational Biology (JBCB) to appear
• Nirmalya Bandyopadhyay, Manas Somaiya, Sanjay Ranka, Tamer Kahveci
  CMRF : Analyzing Differential Gene Regulation in Two Group Perturbation Experiments
  BMC Genomics, accepted for publication.
• 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.
• 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

• 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

• 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)