Variable Length Queries for Time Series Data. - Tamer Kahveci; Ambuj K. Singh (ICDE, 2001)

Efficient Index Structures for String Databases. - Tamer Kahveci; Ambuj K. Singh (VLDB, 2001)

An Efficient Index Structure for Shift and Scale Invariant Search of Multi-Attribute Time Sequences. - Tamer Kahveci; Ambuj K. Singh; Aliekber Gürel (ICDE, 2002)

Similarity Searching for Multi-Attribute Sequences. - Tamer Kahveci; Ambuj K. Singh; Aliekber Gürel (SSDBM, 2002)

Towards Index-based Similarity Search for Protein Structure Databases. - Orhan Çamoglu; Tamer Kahveci; Ambuj K. Singh (CSB, 2003)

Genome on Demand: Interactive Substring Searching. - Tamer Kahveci; Ambuj K. Singh (CSB, 2003)

Joining Massive High-Dimensional Datasets. - Tamer Kahveci; Christian A. Lang; Ambuj K. Singh (ICDE, 2003)

Fast alignment of large genome databases. - Tamer Kahveci; Ambuj K. Singh (ICDE, 2003)

PSI: indexing protein structures for fast similarity search. - Orhan Çamoglu; Tamer Kahveci; Ambuj K. Singh (ISMB (Supplement of Bioinformatics), 2003)

MAP: Searching Large Genome Databases. - Tamer Kahveci; Ambuj K. Singh (Pacific Symposium on Biocomputing, 2003)

ProGreSS: Simultaneous Searching of Protein Databases by Sequence and Structure. - Arnab Bhattacharya 001; Tolga Can; Tamer Kahveci; Ambuj K. Singh; Yuan-Fang Wang (Pacific Symposium on Biocomputing, 2004)

Speeding up whole-genome alignment by indexing frequency vectors. - Tamer Kahveci; Vebjorn Ljosa; Ambuj K. Singh (Bioinform., 2004)

Progressive Searching of Biological Sequences. - Tamer Kahveci; Ambuj K. Singh (IEEE Data Eng. Bull., 2004)

Index-based Similarity Search for Protein Structure Databases. - Orhan Çamoglu; Tamer Kahveci; Ambuj K. Singh (J. Bioinform. Comput. Biol., 2004)

Optimizing Similarity Search for Arbitrary Length Time Series Queries. - Tamer Kahveci; Ambuj K. Singh (IEEE Trans. Knowl. Data Eng., 2004)

Approximate Global Alignment of Sequences. - Tamer Kahveci; Venkatakrishnan Ramaswamy; Han Tao; Tao Li 006 (BIBE, 2005)

Highly Scalable and Accurate Seeds for Subsequence Alignment. - Abhijit Pol; Tamer Kahveci (BIBE, 2005)

Workload Characterization of Bioinformatics Applications. - Yue Li; Tao Li 006; Tamer Kahveci; José A. B. Fortes (MASCOTS, 2005)

Finding Data Broadness Via Generalized Nearest Neighbors. - Jayendra Venkateswaran; Tamer Kahveci; Orhan Çamoglu (EDBT, 2006)

A New Approach for Alignment of Multiple Proteins. - Xu Zhang; Tamer Kahveci (Pacific Symposium on Biocomputing, 2006)

Reference-based Indexing of Sequence Databases. - Jayendra Venkateswaran; Deepak Lachwani; Tamer Kahveci; Christopher M. Jermaine (VLDB, 2006)

A Novel algorithm for identifying low-complexity regions in a protein sequence. - Xuehui Li; Tamer Kahveci (Bioinform., 2006)

Distance-based clustering of CGH data. - Jun Liu; Jaaved Mohammed; James Carter; Sanjay Ranka; Tamer Kahveci; Michael Baudis (Bioinform., 2006)

QOMA2: Optimizing the alignment of many sequences. - Xu Zhang; Tamer Kahveci (BIBE, 2007)

Quality-Based Similarity Search for Biological Sequence Databases. - Xuehui Li; Tamer Kahveci (BIOCOMP, 2007)

An Iterative Algorithm for Metabolic Network-Based Drug Target Identification. - Padmavati Sridhar; Tamer Kahveci; Sanjay Ranka (Pacific Symposium on Biocomputing, 2007)

Markers improve clustering of CGH data. - Jun Liu; Sanjay Ranka; Tamer Kahveci (Bioinform., 2007)

QOMA: quasi-optimal multiple alignment of protein sequences. - Xu Zhang; Tamer Kahveci (Bioinform., 2007)

Classification and feature selection algorithms for multi-class CGH data. - Jun Liu; Sanjay Ranka; Tamer Kahveci (ISMB, 2008)

Mining Metabolic Networks for Optimal Drug Targets. - Padmavati Sridhar; Bin Song 009; Tamer Kahveci; Sanjay Ranka (Pacific Symposium on Biocomputing, 2008)

A novel genome-scale repeat finder geared towards transposons. - Xuehui Li; Tamer Kahveci; A. Mark Settles (Bioinform., 2008)

Reference-based indexing for metric spaces with costly distance measures. - Jayendra Venkateswaran; Tamer Kahveci; Christopher M. Jermaine; Deepak Lachwani (VLDB J., 2008)

Pathway-Based Feature Selection Algorithm for Cancer Microarray Data. - Nirmalya Bandyopadhyay; Tamer Kahveci; Steve Goodison; Yijun Sun; Sanjay Ranka (Adv. Bioinformatics, 2009)

Inferring progression models for CGH data. - Jun Liu; Nirmalya Bandyopadhyay; Sanjay Ranka; Michael Baudis; Tamer Kahveci (Bioinform., 2009)

Double iterative optimisation for metabolic network-based drug target identification. - Bin Song 009; Padmavati Sridhar; Tamer Kahveci; Sanjay Ranka (Int. J. Data Min. Bioinform., 2009)

A Fast and Accurate Algorithm for Comparative Analysis of metabolic Pathways. - Ferhat Ay; Tamer Kahveci; Valérie de Crécy-Lagard (J. Bioinform. Comput. Biol., 2009)

Index Structures for Biological Sequences. - Tamer Kahveci (Encyclopedia of Database Systems, 2009)

Functional similarities of reaction sets in metabolic pathways. - Ferhat Ay; Tamer Kahveci (BCB, 2010)

RepFrag: a graph based method for finding repeats and transposons from fragmented genomes. - Nirmalya Bandyopadhyay; A. Mark Settles; Tamer Kahveci (BCB, 2010)

Enzymatic target identification with dynamic states. - Bin Song 009; Sanjay Ranka; Tamer Kahveci (BCB, 2010)

Finding Dynamic Modules of Biological Regulatory Networks. - Ferhat Ay; Thang N. Dinh; My T. Thai; Tamer Kahveci (BIBE, 2010)

Finding steady states of large scale regulatory networks through partitioning. - Ferhat Ay; Günhan Gülsoy; Tamer Kahveci (GENSiPS, 2010)

Surrogate ranking for very expensive similarity queries. - Fei Xu; Ravi Jampani; Mingxi Wu; Chris Jermaine; Tamer Kahveci (ICDE, 2010)

SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings. - Ferhat Ay; Tamer Kahveci (RECOMB, 2010)

GBA Manager: An Online Tool for Querying Low-Complexity Regions in Proteins. - Nirmalya Bandyopadhyay; Tamer Kahveci (J. Comput. Biol., 2010)

A novel framework for large scale metabolic network alignments by compression. - Michael Dang; Ferhat Ay; Tamer Kahveci (BCB, 2011)

Topology aware coloring of gene regulatory networks. - Günhan Gülsoy; Bhavik Gandhi; Tamer Kahveci (BCB, 2011)

Identifying differentially regulated genes. - Nirmalya Bandyopadhyay; Manas Somaiya; Sanjay Ranka; Tamer Kahveci (ICCABS, 2011)

RINQ: Reference-based Indexing for Network Queries. - Günhan Gülsoy; Tamer Kahveci (Bioinform., 2011)

SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings. - Ferhat Ay; Manolis Kellis; Tamer Kahveci (J. Comput. Biol., 2011)

Manipulating the Steady State of Metabolic Pathways. - Bin Song 009; I. Esra Büyüktahtakin; Sanjay Ranka; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

TRIAL: A Tool for Finding Distant Structural Similarities. - Jayendra Venkateswaran; Bin Song 009; Tamer Kahveci; Chris Jermaine (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

SiS: Significant subnetworks in massive number of network topologies. - Md Mahmudul Hasan; Yusuf Kavurucu; Tamer Kahveci (BIBM, 2012)

Uncertain interactions affect degree distribution of biological networks. - Andrei Todor; Alin Dobra; Tamer Kahveci (BIBM, 2012)

Inferring gene functions from metabolic reactions. - Günhan Gülsoy; Tamer Kahveci (GENSiPS, 2012)

SSLPred : Predicting Synthetic Sickness Lethality. - Nirmalya Bandyopadhyay; Sanjay Ranka; Tamer Kahveci (Pacific Symposium on Biocomputing, 2012)

Metabolic network alignment in large scale by network compression. - Ferhat Ay; Michael Dang; Tamer Kahveci (BMC Bioinform., 2012)

HIDEN: Hierarchical decomposition of regulatory networks. - Günhan Gülsoy; Nirmalya Bandyopadhyay; Tamer Kahveci (BMC Bioinform., 2012)

A scalable method for identifying frequent subtrees in sets of large phylogenetic trees. - Avinash Ramu; Tamer Kahveci; J. Gordon Burleigh (BMC Bioinform., 2012)

Topac: Alignment of gene Regulatory Networks Using Topology-Aware Coloring. - Günhan Gülsoy; Bhavik Gandhi; Tamer Kahveci (J. Bioinform. Comput. Biol., 2012)

Large-Scale Signaling Network Reconstruction. - Seyedsasan Hashemikhabir; Eyüp Serdar Ayaz; Yusuf Kavurucu; Tolga Can; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

PReach: Reachability in Probabilistic Signaling Networks. - Haitham Gabr; Andrei Todor; Helia Zandi; Alin Dobra; Tamer Kahveci (BCB, 2013)

Color distribution can accelerate network alignment. - Md Mahmudul Hasan; Tamer Kahveci (BCB, 2013)

Reachability analysis in large probabilistic biological networks. - Andrei Todor; Haitham Gabr; Alin Dobra; Tamer Kahveci (BCB, 2013)

From Uncertain Protein Interaction Networks to Signaling Pathways Through Intensive Color Coding. - Haitham Gabr; Alin Dobra; Tamer Kahveci (Pacific Symposium on Biocomputing, 2013)

Stability analysis of phylogenetic trees. - Saad I. Sheikh; Tamer Kahveci; Sanjay Ranka; J. Gordon Burleigh (Bioinform., 2013)

A scalable method for discovering significant subnetworks. - Md Mahmudul Hasan; Yusuf Kavurucu; Tamer Kahveci (BMC Syst. Biol., 2013)

Making massive probabilistic databases practical. - Andrei Todor; Alin Dobra; Tamer Kahveci; Christopher Dudley (CoRR, 2013)

Guest Editorial for ACM BCB. - Tamer Kahveci; Mona Singh 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Probabilistic Biological Network Alignment. - Andrei Todor; Alin Dobra; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Characterizing the Topology of Probabilistic Biological Networks. - Andrei Todor; Alin Dobra; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Extracting phylogenetic signals from multi-labeled gene trees and its significance for species tree construction. - Ryan Cobb; Rasha Elhesha; J. Gordon Burleigh; Tamer Kahveci (BCB, 2014)

Incremental network querying in biological networks. - Md Mahmudul Hasan; Tamer Kahveci (BCB, 2014)

Characterization of probabilistic signaling networks through signal propagation. - Haitham Gabr; Tamer Kahveci (ICCABS, 2014)

Large scale analysis of signal reachability. - Andrei Todor; Haitham Gabr; Alin Dobra; Tamer Kahveci (Bioinform., 2014)

Topologically associating domains are stable units of replication-timing regulation Open. - Benjamin D. Pope; Tyrone Ryba; Vishnu Dileep; Feng Yue; Wei-Sheng Wu; Olgert Denas; Daniel L. Vera; Yanli Wang; R. Scott Hansen; Theresa K. Canfield; Robert E. Thurman; Yong Cheng; et al. (Nat., 2014)

Multiple reference networks improve accuracy of signaling network construction. - Md Abdul Alim; Ahmet Ay; Md Mahmudul Hasan; My T. Thai; Tamer Kahveci (BCB, 2015)

Estimating reachability in dense biological networks. - Haitham Gabr; Alin Dobra; Tamer Kahveci (BCB, 2015)

Counting motifs in probabilistic biological networks. - Andrei Todor; Alin Dobra; Tamer Kahveci (BCB, 2015)

Construction of signaling networks with incomplete RNAi data. - Qiyao Wang; Yuanfang Ren; Md Mahmudul Hasan; Ahmet Ay; Tamer Kahveci (BIBM, 2015)

Hierarchical decomposition of dynamically evolving regulatory networks. - Ahmet Ay; Dihong Gong; Tamer Kahveci (BMC Bioinform., 2015)

Indexing a protein-protein interaction network expedites network alignment. - Md Mahmudul Hasan; Tamer Kahveci (BMC Bioinform., 2015)

Computing interaction probabilities in signaling networks. - Haitham Gabr; Juan Carlos Rivera-Mulia; David M. Gilbert; Tamer Kahveci (EURASIP J. Bioinform. Syst. Biol., 2015)

Reachability Analysis in Probabilistic Biological Networks. - Haitham Gabr; Andrei Todor; Alin Dobra; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Signal reachability facilitates characterization of probabilistic signaling networks. - Haitham Gabr; Tamer Kahveci (BMC Bioinform., 2015)

Counting independent motifs in probabilistic networks. - Aisharjya Sarkar; Yuanfang Ren; Rasha Elhesha; Tamer Kahveci (BCB, 2016)

Identification of large disjoint motifs in biological networks. - Rasha Elhesha; Tamer Kahveci (BMC Bioinform., 2016)

Identifying the topology of signaling networks from partial RNAi data. - Yuanfang Ren; Qiyao Wang; Md Mahmudul Hasan; Ahmet Ay; Tamer Kahveci (BMC Syst. Biol., 2016)

Highlights Talks at ACM BCB 2017. - Amarda Shehu; Tamer Kahveci; Giuseppe Pozzi (BCB, 2017)

CNB-MAC'17: The Fourth International Workshop on Computational Network Biology: Modeling, Analysis, and Control. - Byung-Jun Yoon; Xiaoning Qian; Tamer Kahveci (BCB, 2017)

Selected research articles from the 2016 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). - Byung-Jun Yoon; Xiaoning Qian; Tamer Kahveci (BMC Bioinform., 2017)

Motif centrality in food web networks. - Rasha Elhesha; Tamer Kahveci; Benjamin Baiser (J. Complex Networks, 2017)

ANCA: Alignment-based Network Construction Algorithm. - Kevin Chow; Ahmet Ay; Rasha Elhesha; Tamer Kahveci (BCB, 2018)

Identification of Co-evolving Temporal Networks. - Rasha Elhesha; Aisharjya Sarkar; Christina Boucher 001; Tamer Kahveci (BCB, 2018)

Shortest path counting in probabilistic biological networks. - Yuanfang Ren; Ahmet Ay; Tamer Kahveci (BMC Bioinform., 2018)

ProMotE: an efficient algorithm for counting independent motifs in uncertain network topologies. - Yuanfang Ren; Aisharjya Sarkar; Tamer Kahveci (BMC Bioinform., 2018)

Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). - Byung-Jun Yoon; Xiaoning Qian; Tamer Kahveci; Ranadip Pal (BMC Bioinform., 2018)

Counting motifs in dynamic networks. - Kingshuk Mukherjee; Md Mahmudul Hasan; Christina Boucher 001; Tamer Kahveci (BMC Syst. Biol., 2018)

Identification of jointly correlated gene sets. - Yuanfang Ren; Ahmet Ay; Travis A. Gerke; Tamer Kahveci (J. Bioinform. Comput. Biol., 2018)

Construction of Signaling Pathways with RNAi Data and Multiple Reference Networks. - Md Abdul Alim; Ahmet Ay; Md Mahmudul Hasan; My T. Thai; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Index Structures for Biological Sequences. - Tamer Kahveci (Encyclopedia of Database Systems (2nd ed.), 2018)

Co-evolving Patterns in Temporal Networks of Varying Evolution. - Rasha Elhesha; Aisharjya Sarkar; Pietro Cinaglia; Christina Boucher 001; Tamer Kahveci (BCB, 2019)

Finding Conserved Patterns in Multilayer Networks. - Yuanfang Ren; Aisharjya Sarkar; Ahmet Ay; Alin Dobra; Tamer Kahveci (BCB, 2019)

Aligning optical maps to de Bruijn graphs. - Kingshuk Mukherjee; Bahar Alipanahi; Tamer Kahveci; Leena Salmela; Christina Boucher 001 (Bioinform., 2019)

Characterizing building blocks of resource constrained biological networks. - Yuanfang Ren; Ahmet Ay; Alin Dobra; Tamer Kahveci (BMC Bioinform., 2019)

Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). - Byung-Jun Yoon; Xiaoning Qian; Tamer Kahveci; Ranadip Pal (BMC Bioinform., 2019)

A New Algorithm for Counting Independent Motifs in Probabilistic Networks. - Aisharjya Sarkar; Yuanfang Ren; Rasha Elhesha; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Guest Editorial for the ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. - Amarda Shehu; Giuseppe Pozzi; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Guest Editorial on the Special Issue on Informatics on Biomedical Data Learning, Reasoning, and Representation. - Tamer Kahveci; Giuseppe Pozzi; Amarda Shehu; May Dongmei Wang (IEEE J. Biomed. Health Informatics, 2019)

A method to assess COVID-19 infected numbers in Italy during peak pandemic period. - Giuseppe Tradigo; Pietro Hiram Guzzi; Tamer Kahveci; Pierangelo Veltri (BIBM, 2020)

Stability Analysis of Biological Networks' Diffusion State. - Volkan Altuntas; Murat Gök; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

An Efficient Algorithm for Identifying Mutated Subnetworks Associated with Survival in Cancer. - Aisharjya Sarkar; Yilmaz Atay; Alana Lorraine Erickson; Ivan Arisi; Cesare Saltini; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Efficiently Merging r-indexes. - Marco Oliva; Massimiliano Rossi 001; Jouni Sirén; Giovanni Manzini; Tamer Kahveci; Travis Gagie; Christina Boucher 001 (DCC, 2021)

ANCA: Alignment-Based Network Construction Algorithm. - Kevin Chow; Aisharjya Sarkar; Rasha Elhesha; Pietro Cinaglia; Ahmet Ay; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

FiT: fiber-based tensor completion for drug repurposing. - Aysegul Bumin; Anna M. Ritz; Donna K. Slonim; Tamer Kahveci; Kejun Huang (BCB, 2022)

Identification of co-existing embeddings of a motif in multilayer networks. - Yuanfang Ren; Aisharjya Sarkar; Aysegul Bumin; Kejun Huang; Pierangelo Veltri; Alin Dobra; Tamer Kahveci (BCB, 2022)

Optimal separation of high dimensional transcriptome for complex multigenic traits. - Aisharjya Sarkar; Aaditya Singh; Richard Bailey; Alin Dobra; Tamer Kahveci (BCB, 2022)

Pattern Discovery in Multilayer Networks. - Yuanfang Ren; Aisharjya Sarkar; Pierangelo Veltri; Ahmet Ay; Alin Dobra; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Data Perturbation and Recovery of Time Series Gene Expression Data. - Aisharjya Sarkar; Prabhat Mishra 001; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Vulture: VULnerabilities in impuTing drUg REsistance. - Aysegul Bumin; Megan Shah; Kejun Huang; Tamer Kahveci (BCB, 2023)

ATOM: An Efficient Topology Adaptive Algorithm for Minor Embedding in Quantum Computing. - Hoang M. Ngo; Tamer Kahveci; My T. Thai (ICC, 2023)

PartialFibers: An Efficient Method for Predicting Drug-Drug Interactions. - Aysegul Bumin; Kejun Huang; Tamer Kahveci (ICCABS, 2023)

QOMIC: Quantum optimization for motif identification. - Hoang M. Ngo; Tamim Khatib; My T. Thai; Tamer Kahveci (CoRR, 2023)

Optimal Supervised Reduction of High Dimensional Transcription Data. - Richard Bailey; Aisharjya Sarkar; Aaditya Singh; Alin Dobra; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

DANTE: Determining Adaptation trajectories in biological Networks Through Evolutionary mapping. - Tamim Khatib; Oscar Diaz de la Rua; Kawthar Moria; Tamer Kahveci (BCB, 2024)

Morphological profiling for drug discovery in the era of deep learning. - Qiaosi Tang; Ranjala Ratnayake; Gustavo de M. Seabra; Zhe Jiang 001; Ruogu Fang; Lina Cui; Yousong Ding; Tamer Kahveci; Jiang Bian 001; Chenglong Li; Hendrik Luesch; Yanjun Li 005 (Briefings Bioinform., 2024)

CHARME: A chain-based reinforcement learning approach for the minor embedding problem. - Hoang M. Ngo; Nguyen Hoang Khoi Do; Minh N. Vu; Tamer Kahveci; My T. Thai (CoRR, 2024)

IDEEA: information diffusion model for integrating gene expression and EEG data in identifying Alzheimer's disease markers. - Enes Ozelbas; Tuba Sevimoglu; Tamer Kahveci (Mach. Learn. Sci. Technol., 2024)