Tamer Kahveci

ORCID

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 41

Top Venues

BCB

BMC Bioinform.

IEEE ACM Trans. Comput. Biol. Bioinform.

CoRR

Publications

Hoang M. Ngo, Nguyen Hoang Khoi Do, Minh N. Vu, Tamer Kahveci, My T. Thai
CHARME: A chain-based reinforcement learning approach for the minor embedding problem. CoRR (2024)
Qiaosi Tang, Ranjala Ratnayake, Gustavo de M. Seabra, Zhe Jiang, Ruogu Fang, Lina Cui, Yousong Ding, Tamer Kahveci, Jiang Bian, Chenglong Li, Hendrik Luesch, Yanjun Li
Morphological profiling for drug discovery in the era of deep learning. Briefings Bioinform. 25 (4) (2024)
Hoang M. Ngo, Tamim Khatib, My T. Thai, Tamer Kahveci
QOMIC: Quantum optimization for motif identification. CoRR (2023)
Hoang M. Ngo, Tamer Kahveci, My T. Thai
ATOM: An Efficient Topology Adaptive Algorithm for Minor Embedding in Quantum Computing. ICC (2023)
Aysegul Bumin, Megan Shah, Kejun Huang, Tamer Kahveci
Vulture: VULnerabilities in impuTing drUg REsistance. BCB (2023)
Qiaosi Tang, Ranjala Ratnayake, Gustavo de M. Seabra, Zhe Jiang, Ruogu Fang, Lina Cui, Yousong Ding, Tamer Kahveci, Jiang Bian, Chenglong Li, Hendrik Luesch, Yanjun Li
Morphological Profiling for Drug Discovery in the Era of Deep Learning. CoRR (2023)
Richard Bailey, Aisharjya Sarkar, Aaditya Singh, Alin Dobra, Tamer Kahveci
Optimal Supervised Reduction of High Dimensional Transcription Data. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (5) (2023)
Aysegul Bumin, Anna M. Ritz, Donna K. Slonim, Tamer Kahveci, Kejun Huang
FiT: fiber-based tensor completion for drug repurposing. BCB (2022)
Aisharjya Sarkar, Aaditya Singh, Richard Bailey, Alin Dobra, Tamer Kahveci
Optimal separation of high dimensional transcriptome for complex multigenic traits. BCB (2022)
Aisharjya Sarkar, Prabhat Mishra, Tamer Kahveci
Data Perturbation and Recovery of Time Series Gene Expression Data. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (2) (2022)
Yuanfang Ren, Aisharjya Sarkar, Pierangelo Veltri, Ahmet Ay, Alin Dobra, Tamer Kahveci
Pattern Discovery in Multilayer Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (2) (2022)
Yuanfang Ren, Aisharjya Sarkar, Aysegul Bumin, Kejun Huang, Pierangelo Veltri, Alin Dobra, Tamer Kahveci
Identification of co-existing embeddings of a motif in multilayer networks. BCB (2022)
Kevin Chow, Aisharjya Sarkar, Rasha Elhesha, Pietro Cinaglia, Ahmet Ay, Tamer Kahveci
ANCA: Alignment-Based Network Construction Algorithm. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (2) (2021)
Marco Oliva, Massimiliano Rossi, Jouni Sirén, Giovanni Manzini, Tamer Kahveci, Travis Gagie, Christina Boucher
Efficiently Merging r-indexes. DCC (2021)
Giuseppe Tradigo, Pietro Hiram Guzzi, Tamer Kahveci, Pierangelo Veltri
A method to assess COVID-19 infected numbers in Italy during peak pandemic period. BIBM (2020)
Aisharjya Sarkar, Yilmaz Atay, Alana Lorraine Erickson, Ivan Arisi, Cesare Saltini, Tamer Kahveci
An Efficient Algorithm for Identifying Mutated Subnetworks Associated with Survival in Cancer. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (5) (2020)
Volkan Altuntas, Murat Gök, Tamer Kahveci
Stability Analysis of Biological Networks' Diffusion State. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (4) (2020)
Kingshuk Mukherjee, Bahar Alipanahi, Tamer Kahveci, Leena Salmela, Christina Boucher
Aligning optical maps to de Bruijn graphs. Bioinform. 35 (18) (2019)
Rasha Elhesha, Aisharjya Sarkar, Pietro Cinaglia, Christina Boucher, Tamer Kahveci
Co-evolving Patterns in Temporal Networks of Varying Evolution. BCB (2019)
Yuanfang Ren, Ahmet Ay, Alin Dobra, Tamer Kahveci
Characterizing building blocks of resource constrained biological networks. BMC Bioinform. (12) (2019)
Aisharjya Sarkar, Yuanfang Ren, Rasha Elhesha, Tamer Kahveci
A New Algorithm for Counting Independent Motifs in Probabilistic Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (4) (2019)
Tamer Kahveci, Giuseppe Pozzi, Amarda Shehu, May Dongmei Wang
Guest Editorial on the Special Issue on Informatics on Biomedical Data Learning, Reasoning, and Representation. IEEE J. Biomed. Health Informatics 23 (1) (2019)
Yuanfang Ren, Aisharjya Sarkar, Ahmet Ay, Alin Dobra, Tamer Kahveci
Finding Conserved Patterns in Multilayer Networks. BCB (2019)
Amarda Shehu, Giuseppe Pozzi, Tamer Kahveci
Guest Editorial for the ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (5) (2019)
Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci, Ranadip Pal
Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). BMC Bioinform. (12) (2019)
Yuanfang Ren, Ahmet Ay, Alin Dobra, Tamer Kahveci
Characterizing Building Blocks of Resource Constrained Biological Networks. BCB (2018)
Kingshuk Mukherjee, Md Mahmudul Hasan, Christina Boucher, Tamer Kahveci
Counting motifs in dynamic networks. BMC Syst. Biol. 12 (1) (2018)
Kevin Chow, Ahmet Ay, Rasha Elhesha, Tamer Kahveci
ANCA: Alignment-based Network Construction Algorithm. BCB (2018)
Yuanfang Ren, Ahmet Ay, Travis A. Gerke, Tamer Kahveci
Identification of jointly correlated gene sets. J. Bioinform. Comput. Biol. 16 (5) (2018)
Rasha Elhesha, Aisharjya Sarkar, Christina Boucher, Tamer Kahveci
Identification of Co-evolving Temporal Networks. BCB (2018)
Yuanfang Ren, Aisharjya Sarkar, Tamer Kahveci
ProMotE: an efficient algorithm for counting independent motifs in uncertain network topologies. BMC Bioinform. 19 (1) (2018)
Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci, Ranadip Pal
Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). BMC Bioinform. (3) (2018)
Md Abdul Alim, Ahmet Ay, Md Mahmudul Hasan, My T. Thai, Tamer Kahveci
Construction of Signaling Pathways with RNAi Data and Multiple Reference Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (4) (2018)
Yuanfang Ren, Ahmet Ay, Tamer Kahveci
Shortest path counting in probabilistic biological networks. BMC Bioinform. 19 (1) (2018)
Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci
Selected research articles from the 2016 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). BMC Bioinform. 18 (S-4) (2017)
Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci
CNB-MAC'17: The Fourth International Workshop on Computational Network Biology: Modeling, Analysis, and Control. BCB (2017)
Amarda Shehu, Tamer Kahveci, Giuseppe Pozzi
Highlights Talks at ACM BCB 2017. BCB (2017)
Rasha Elhesha, Tamer Kahveci, Benjamin Baiser
Motif centrality in food web networks. J. Complex Networks 5 (4) (2017)
Rasha Elhesha, Tamer Kahveci
Identification of large disjoint motifs in biological networks. BMC Bioinform. 17 (2016)
Yuanfang Ren, Qiyao Wang, Md Mahmudul Hasan, Ahmet Ay, Tamer Kahveci
Identifying the topology of signaling networks from partial RNAi data. BMC Syst. Biol. 10 (S-2) (2016)
Aisharjya Sarkar, Yuanfang Ren, Rasha Elhesha, Tamer Kahveci
Counting independent motifs in probabilistic networks. BCB (2016)
Qiyao Wang, Yuanfang Ren, Md Mahmudul Hasan, Ahmet Ay, Tamer Kahveci
Construction of signaling networks with incomplete RNAi data. BIBM (2015)
Md Abdul Alim, Ahmet Ay, Md Mahmudul Hasan, My T. Thai, Tamer Kahveci
Multiple reference networks improve accuracy of signaling network construction. BCB (2015)
Haitham Gabr, Andrei Todor, Alin Dobra, Tamer Kahveci
Reachability Analysis in Probabilistic Biological Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (1) (2015)
Haitham Gabr, Juan Carlos Rivera-Mulia, David M. Gilbert, Tamer Kahveci
Computing interaction probabilities in signaling networks. EURASIP J. Bioinform. Syst. Biol. 2015 (2015)
Andrei Todor, Alin Dobra, Tamer Kahveci
Counting motifs in probabilistic biological networks. BCB (2015)
Haitham Gabr, Juan Carlos Rivera-Mulia, David M. Gilbert, Tamer Kahveci
Computing interaction probabilities in signaling networks. BCB (2015)
Md Mahmudul Hasan, Tamer Kahveci
Indexing a protein-protein interaction network expedites network alignment. BMC Bioinform. 16 (2015)
Haitham Gabr, Alin Dobra, Tamer Kahveci
Estimating reachability in dense biological networks. BCB (2015)
Ahmet Ay, Dihong Gong, Tamer Kahveci
Hierarchical decomposition of dynamically evolving regulatory networks. BMC Bioinform. 16 (2015)
Haitham Gabr, Tamer Kahveci
Signal reachability facilitates characterization of probabilistic signaling networks. BMC Bioinform. 16 (S17) (2015)
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, Günhan Gülsoy, Jonathan H. Dennis, Michael P. Snyder, John A. Stamatoyannopoulos, James Taylor, Ross C. Hardison, Tamer Kahveci, Bing Ren, David M. Gilbert
Topologically associating domains are stable units of replication-timing regulation Open. Nat. 515 (7527) (2014)
Md Mahmudul Hasan, Tamer Kahveci
Incremental network querying in biological networks. BCB (2014)
Haitham Gabr, Tamer Kahveci
Characterization of probabilistic signaling networks through signal propagation. ICCABS (2014)
Ryan Cobb, Rasha Elhesha, J. Gordon Burleigh, Tamer Kahveci
Extracting phylogenetic signals from multi-labeled gene trees and its significance for species tree construction. BCB (2014)
Andrei Todor, Haitham Gabr, Alin Dobra, Tamer Kahveci
Large scale analysis of signal reachability. Bioinform. 30 (12) (2014)
Saad I. Sheikh, Tamer Kahveci, Sanjay Ranka, J. Gordon Burleigh
Stability analysis of phylogenetic trees. Bioinform. 29 (2) (2013)
Andrei Todor, Alin Dobra, Tamer Kahveci
Characterizing the Topology of Probabilistic Biological Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (4) (2013)
Tamer Kahveci, Mona Singh
Guest Editorial for ACM BCB. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (5) (2013)
Md Mahmudul Hasan, Yusuf Kavurucu, Tamer Kahveci
A scalable method for discovering significant subnetworks. BMC Syst. Biol. 7 (S-4) (2013)
Andrei Todor, Alin Dobra, Tamer Kahveci, Christopher Dudley
Making massive probabilistic databases practical. CoRR (2013)
Md Mahmudul Hasan, Tamer Kahveci
Color distribution can accelerate network alignment. BCB (2013)
Haitham Gabr, Andrei Todor, Helia Zandi, Alin Dobra, Tamer Kahveci
PReach: Reachability in Probabilistic Signaling Networks. BCB (2013)
Andrei Todor, Haitham Gabr, Alin Dobra, Tamer Kahveci
Reachability analysis in large probabilistic biological networks. BCB (2013)
Haitham Gabr, Alin Dobra, Tamer Kahveci
From Uncertain Protein Interaction Networks to Signaling Pathways Through Intensive Color Coding. Pacific Symposium on Biocomputing (2013)
Andrei Todor, Alin Dobra, Tamer Kahveci
Probabilistic Biological Network Alignment. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (1) (2013)
Md Mahmudul Hasan, Yusuf Kavurucu, Tamer Kahveci
SiS: Significant subnetworks in massive number of network topologies. BIBM (2012)
Andrei Todor, Alin Dobra, Tamer Kahveci
Uncertain interactions affect degree distribution of biological networks. BIBM (2012)
Günhan Gülsoy, Tamer Kahveci
Inferring gene functions from metabolic reactions. GENSiPS (2012)
Günhan Gülsoy, Nirmalya Bandyopadhyay, Tamer Kahveci
HIDEN: Hierarchical decomposition of regulatory networks. BMC Bioinform. 13 (2012)
Avinash Ramu, Tamer Kahveci, J. Gordon Burleigh
A scalable method for identifying frequent subtrees in sets of large phylogenetic trees. BMC Bioinform. 13 (2012)
Seyedsasan Hashemikhabir, Eyüp Serdar Ayaz, Yusuf Kavurucu, Tolga Can, Tamer Kahveci
Large-Scale Signaling Network Reconstruction. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (6) (2012)
Ferhat Ay, Michael Dang, Tamer Kahveci
Metabolic network alignment in large scale by network compression. BMC Bioinform. 13 (S-3) (2012)
Nirmalya Bandyopadhyay, Sanjay Ranka, Tamer Kahveci
SSLPred : Predicting Synthetic Sickness Lethality. Pacific Symposium on Biocomputing (2012)
Günhan Gülsoy, Bhavik Gandhi, Tamer Kahveci
Topac: Alignment of gene Regulatory Networks Using Topology-Aware Coloring. J. Bioinform. Comput. Biol. 10 (1) (2012)
Günhan Gülsoy, Bhavik Gandhi, Tamer Kahveci
Topology aware coloring of gene regulatory networks. BCB (2011)
Günhan Gülsoy, Tamer Kahveci
RINQ: Reference-based Indexing for Network Queries. Bioinform. 27 (13) (2011)
Michael Dang, Ferhat Ay, Tamer Kahveci
A novel framework for large scale metabolic network alignments by compression. BCB (2011)
Ferhat Ay, Manolis Kellis, Tamer Kahveci
SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings. J. Comput. Biol. 18 (3) (2011)
Jayendra Venkateswaran, Bin Song, Tamer Kahveci, Chris Jermaine
TRIAL: A Tool for Finding Distant Structural Similarities. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (3) (2011)
Nirmalya Bandyopadhyay, Manas Somaiya, Sanjay Ranka, Tamer Kahveci
Identifying differentially regulated genes. ICCABS (2011)
Bin Song, I. Esra Büyüktahtakin, Sanjay Ranka, Tamer Kahveci
Manipulating the Steady State of Metabolic Pathways. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (3) (2011)
Ferhat Ay, Tamer Kahveci
SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings. RECOMB (2010)
Ferhat Ay, Günhan Gülsoy, Tamer Kahveci
Finding steady states of large scale regulatory networks through partitioning. GENSiPS (2010)
Nirmalya Bandyopadhyay, A. Mark Settles, Tamer Kahveci
RepFrag: a graph based method for finding repeats and transposons from fragmented genomes. BCB (2010)
Bin Song, Sanjay Ranka, Tamer Kahveci
Enzymatic target identification with dynamic states. BCB (2010)
Ferhat Ay, Tamer Kahveci
Functional similarities of reaction sets in metabolic pathways. BCB (2010)
Fei Xu, Ravi Jampani, Mingxi Wu, Chris Jermaine, Tamer Kahveci
Surrogate ranking for very expensive similarity queries. ICDE (2010)
Nirmalya Bandyopadhyay, Tamer Kahveci
GBA Manager: An Online Tool for Querying Low-Complexity Regions in Proteins. J. Comput. Biol. 17 (1) (2010)
Ferhat Ay, Thang N. Dinh, My T. Thai, Tamer Kahveci
Finding Dynamic Modules of Biological Regulatory Networks. BIBE (2010)
Bin Song, Padmavati Sridhar, Tamer Kahveci, Sanjay Ranka
Double iterative optimisation for metabolic network-based drug target identification. Int. J. Data Min. Bioinform. 3 (2) (2009)
Nirmalya Bandyopadhyay, Tamer Kahveci, Steve Goodison, Yijun Sun, Sanjay Ranka
Pathway-Based Feature Selection Algorithm for Cancer Microarray Data. Adv. Bioinformatics 2009 (2009)
Ferhat Ay, Tamer Kahveci, Valérie de Crécy-Lagard
A Fast and Accurate Algorithm for Comparative Analysis of metabolic Pathways. J. Bioinform. Comput. Biol. 7 (3) (2009)
Jun Liu, Nirmalya Bandyopadhyay, Sanjay Ranka, Michael Baudis, Tamer Kahveci
Inferring progression models for CGH data. Bioinform. 25 (17) (2009)
Xuehui Li, Tamer Kahveci, A. Mark Settles
A novel genome-scale repeat finder geared towards transposons. Bioinform. 24 (4) (2008)
Jun Liu, Sanjay Ranka, Tamer Kahveci
Classification and feature selection algorithms for multi-class CGH data. ISMB (2008)
Padmavati Sridhar, Bin Song, Tamer Kahveci, Sanjay Ranka
Mining Metabolic Networks for Optimal Drug Targets. Pacific Symposium on Biocomputing (2008)
Jayendra Venkateswaran, Tamer Kahveci, Christopher M. Jermaine, Deepak Lachwani
Reference-based indexing for metric spaces with costly distance measures. VLDB J. 17 (5) (2008)
Xuehui Li, Tamer Kahveci
Quality-Based Similarity Search for Biological Sequence Databases. BIOCOMP (2007)
Jun Liu, Sanjay Ranka, Tamer Kahveci
Markers improve clustering of CGH data. Bioinform. 23 (4) (2007)

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Publication Activity (10 Years)

Top Topics

Top Venues

Tamer Kahveci