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ORCIDTamer Kahveci
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- affiliation: University of Florida, Gainesville, USA
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2020 – today
- 2023
[j58]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): 3093-3105 (2023)- [c63]Aysegul Bumin, Megan Shah, Kejun Huang, Tamer Kahveci:
Vulture: VULnerabilities in impuTing drUg REsistance. BCB 2023: 56:1-56:6 - [c62]Hoang M. Ngo, Tamer Kahveci, My T. Thai:
ATOM: An Efficient Topology Adaptive Algorithm for Minor Embedding in Quantum Computing. ICC 2023: 2692-2697 - [i2]Hoang M. Ngo, Tamim Khatib, My T. Thai, Tamer Kahveci:
QOMIC: Quantum optimization for motif identification. CoRR abs/2311.03400 (2023) - 2022
- [j57]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): 741-752 (2022) - [j56]Aisharjya Sarkar, Prabhat Mishra, Tamer Kahveci:
Data Perturbation and Recovery of Time Series Gene Expression Data. IEEE ACM Trans. Comput. Biol. Bioinform. 19(2): 830-842 (2022) - [c61]Aysegul Bumin, Anna M. Ritz, Donna K. Slonim, Tamer Kahveci, Kejun Huang:
FiT: fiber-based tensor completion for drug repurposing. BCB 2022: 31:1-31:10 - [c60]Aisharjya Sarkar, Aaditya Singh, Richard Bailey, Alin Dobra, Tamer Kahveci:
Optimal separation of high dimensional transcriptome for complex multigenic traits. BCB 2022: 32:1-32:5 - [c59]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: 39:1-39:10 - 2021
- [j55]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): 512-524 (2021) - [c58]Marco Oliva, Massimiliano Rossi, Jouni Sirén, Giovanni Manzini, Tamer Kahveci, Travis Gagie, Christina Boucher:
Efficiently Merging r-indexes. DCC 2021: 203-212 - 2020
- [j54]Volkan Altuntas, Murat Gök, Tamer Kahveci:
Stability Analysis of Biological Networks' Diffusion State. IEEE ACM Trans. Comput. Biol. Bioinform. 17(4): 1406-1418 (2020) - [j53]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): 1582-1594 (2020) - [c57]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: 3017-3020
2010 – 2019
- 2019
- [j52]Kingshuk Mukherjee, Bahar Alipanahi, Tamer Kahveci, Leena Salmela, Christina Boucher:
Aligning optical maps to de Bruijn graphs. Bioinform. 35(18): 3250-3256 (2019) - [j51]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. 20-S(12): 316:1-316:3 (2019) - [j50]Yuanfang Ren, Ahmet Ay, Alin Dobra, Tamer Kahveci:
Characterizing building blocks of resource constrained biological networks. BMC Bioinform. 20-S(12): 318:1-318:14 (2019) - [j49]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): 1049-1062 (2019) - [j48]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): 1409 (2019) - [j47]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): 81-82 (2019) - [c56]Yuanfang Ren, Aisharjya Sarkar, Ahmet Ay, Alin Dobra, Tamer Kahveci:
Finding Conserved Patterns in Multilayer Networks. BCB 2019: 97-102 - [c55]Rasha Elhesha, Aisharjya Sarkar, Pietro Cinaglia, Christina Boucher, Tamer Kahveci:
Co-evolving Patterns in Temporal Networks of Varying Evolution. BCB 2019: 494-503 - 2018
- [j46]Yuanfang Ren, Aisharjya Sarkar, Tamer Kahveci:
ProMotE: an efficient algorithm for counting independent motifs in uncertain network topologies. BMC Bioinform. 19(1): 242:1-242:17 (2018) - [j45]Yuanfang Ren, Ahmet Ay, Tamer Kahveci:
Shortest path counting in probabilistic biological networks. BMC Bioinform. 19(1): 465:1-465:19 (2018) - [j44]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. 19-S(3): 69:1-69:4 (2018) - [j43]Kingshuk Mukherjee, Md Mahmudul Hasan, Christina Boucher, Tamer Kahveci:
Counting motifs in dynamic networks. BMC Syst. Biol. 12(1): 1-12 (2018) - [j42]Yuanfang Ren, Ahmet Ay, Travis A. Gerke, Tamer Kahveci:
Identification of jointly correlated gene sets. J. Bioinform. Comput. Biol. 16(5): 1840019:1-1840019:23 (2018) - [j41]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): 1079-1091 (2018) - [c54]Kevin Chow, Ahmet Ay, Rasha Elhesha, Tamer Kahveci:
ANCA: Alignment-based Network Construction Algorithm. BCB 2018: 21-26 - [c53]Yuanfang Ren, Ahmet Ay, Alin Dobra, Tamer Kahveci:
Characterizing Building Blocks of Resource Constrained Biological Networks. BCB 2018: 581-582 - [c52]Rasha Elhesha, Aisharjya Sarkar, Christina Boucher, Tamer Kahveci:
Identification of Co-evolving Temporal Networks. BCB 2018: 591-592 - [r2]Tamer Kahveci:
Index Structures for Biological Sequences. Encyclopedia of Database Systems (2nd ed.) 2018 - 2017
- [j40]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): 1-3 (2017) - [j39]Rasha Elhesha, Tamer Kahveci, Benjamin Baiser:
Motif centrality in food web networks. J. Complex Networks 5(4): 641-664 (2017) - [c51]Amarda Shehu, Tamer Kahveci, Giuseppe Pozzi:
Highlights Talks at ACM BCB 2017. BCB 2017: 635 - [c50]Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci:
CNB-MAC'17: The Fourth International Workshop on Computational Network Biology: Modeling, Analysis, and Control. BCB 2017: 750 - [e4]Nurit Haspel, Lenore J. Cowen, Amarda Shehu, Tamer Kahveci, Giuseppe Pozzi:
Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2017, Boston, MA, USA, August 20-23, 2017. ACM 2017, ISBN 978-1-4503-4722-8 [contents] - 2016
- [j38]Rasha Elhesha, Tamer Kahveci:
Identification of large disjoint motifs in biological networks. BMC Bioinform. 17: 408 (2016) - [j37]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): 53 (2016) - [c49]Aisharjya Sarkar, Yuanfang Ren, Rasha Elhesha, Tamer Kahveci:
Counting independent motifs in probabilistic networks. BCB 2016: 231-240 - 2015
- [j36]Ahmet Ay, Dihong Gong, Tamer Kahveci:
Hierarchical decomposition of dynamically evolving regulatory networks. BMC Bioinform. 16: 161:1-161:19 (2015) - [j35]Md Mahmudul Hasan, Tamer Kahveci:
Indexing a protein-protein interaction network expedites network alignment. BMC Bioinform. 16: 326:1-326:17 (2015) - [j34]Haitham Gabr, Tamer Kahveci:
Signal reachability facilitates characterization of probabilistic signaling networks. BMC Bioinform. 16(S17): S6 (2015) - [j33]Haitham Gabr, Juan Carlos Rivera-Mulia, David M. Gilbert, Tamer Kahveci:
Computing interaction probabilities in signaling networks. EURASIP J. Bioinform. Syst. Biol. 2015: 10 (2015) - [j32]Haitham Gabr, Andrei Todor, Alin Dobra, Tamer Kahveci:
Reachability Analysis in Probabilistic Biological Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 12(1): 53-66 (2015) - [c48]Haitham Gabr, Alin Dobra, Tamer Kahveci:
Estimating reachability in dense biological networks. BCB 2015: 86-95 - [c47]Andrei Todor, Alin Dobra, Tamer Kahveci:
Counting motifs in probabilistic biological networks. BCB 2015: 116-125 - [c46]Md Abdul Alim, Ahmet Ay, Md Mahmudul Hasan, My T. Thai, Tamer Kahveci:
Multiple reference networks improve accuracy of signaling network construction. BCB 2015: 176-185 - [c45]Haitham Gabr, Juan Carlos Rivera-Mulia, David M. Gilbert, Tamer Kahveci:
Computing interaction probabilities in signaling networks. BCB 2015: 646 - [c44]Qiyao Wang, Yuanfang Ren, Md Mahmudul Hasan, Ahmet Ay, Tamer Kahveci:
Construction of signaling networks with incomplete RNAi data. BIBM 2015: 157-162 - [e3]Jake Yue Chen, Mohammed J. Zaki, Tamer Kahveci, Saeed Salem, Mehmet Koyutürk:
Proceedings of the Eighth International C* Conference on Computer Science & Software Engineering, Yokohama, Japan, July 13-15, 2015. ACM 2015, ISBN 978-1-4503-3419-8 [contents] - 2014
- [j31]Andrei Todor, Haitham Gabr, Alin Dobra, Tamer Kahveci:
Large scale analysis of signal reachability. Bioinform. 30(12): 96-104 (2014) - [j30]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): 402-405 (2014) - [c43]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: 3-12 - [c42]Md Mahmudul Hasan, Tamer Kahveci:
Incremental network querying in biological networks. BCB 2014: 752-759 - [c41]Haitham Gabr, Tamer Kahveci:
Characterization of probabilistic signaling networks through signal propagation. ICCABS 2014: 1-2 - 2013
- [j29]Saad I. Sheikh, Tamer Kahveci, Sanjay Ranka, J. Gordon Burleigh:
Stability analysis of phylogenetic trees. Bioinform. 29(2): 166-174 (2013) - [j28]Md Mahmudul Hasan, Yusuf Kavurucu, Tamer Kahveci:
A scalable method for discovering significant subnetworks. BMC Syst. Biol. 7(S-4): S3 (2013) - [j27]Andrei Todor, Alin Dobra, Tamer Kahveci:
Probabilistic Biological Network Alignment. IEEE ACM Trans. Comput. Biol. Bioinform. 10(1): 109-121 (2013) - [j26]Andrei Todor, Alin Dobra, Tamer Kahveci:
Characterizing the Topology of Probabilistic Biological Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 10(4): 970-983 (2013) - [j25]Tamer Kahveci, Mona Singh:
Guest Editorial for ACM BCB. IEEE ACM Trans. Comput. Biol. Bioinform. 10(5): 1089-1090 (2013) - [c40]Haitham Gabr, Andrei Todor, Helia Zandi, Alin Dobra, Tamer Kahveci:
PReach: Reachability in Probabilistic Signaling Networks. BCB 2013: 3 - [c39]Md Mahmudul Hasan, Tamer Kahveci:
Color distribution can accelerate network alignment. BCB 2013: 52 - [c38]Andrei Todor, Haitham Gabr, Alin Dobra, Tamer Kahveci:
Reachability analysis in large probabilistic biological networks. BCB 2013: 691 - [c37]Haitham Gabr, Alin Dobra, Tamer Kahveci:
From Uncertain Protein Interaction Networks to Signaling Pathways Through Intensive Color Coding. Pacific Symposium on Biocomputing 2013: 111-122 - [i1]Andrei Todor, Alin Dobra, Tamer Kahveci, Christopher Dudley:
Making massive probabilistic databases practical. CoRR abs/1307.0844 (2013) - 2012
- [j24]Günhan Gülsoy, Nirmalya Bandyopadhyay, Tamer Kahveci:
HIDEN: Hierarchical decomposition of regulatory networks. BMC Bioinform. 13: 250 (2012) - [j23]Avinash Ramu, Tamer Kahveci, J. Gordon Burleigh:
A scalable method for identifying frequent subtrees in sets of large phylogenetic trees. BMC Bioinform. 13: 256 (2012) - [j22]Ferhat Ay, Michael Dang, Tamer Kahveci:
Metabolic network alignment in large scale by network compression. BMC Bioinform. 13(S-3): S2 (2012) - [j21]Günhan Gülsoy, Bhavik Gandhi, Tamer Kahveci:
Topac: Alignment of gene Regulatory Networks Using Topology-Aware Coloring. J. Bioinform. Comput. Biol. 10(1) (2012) - [j20]Seyedsasan Hashemikhabir, Eyüp Serdar Ayaz, Yusuf Kavurucu, Tolga Can, Tamer Kahveci:
Large-Scale Signaling Network Reconstruction. IEEE ACM Trans. Comput. Biol. Bioinform. 9(6): 1696-1708 (2012) - [c36]Md Mahmudul Hasan, Yusuf Kavurucu, Tamer Kahveci:
SiS: Significant subnetworks in massive number of network topologies. BIBM 2012: 1-6 - [c35]Andrei Todor, Alin Dobra, Tamer Kahveci:
Uncertain interactions affect degree distribution of biological networks. BIBM 2012: 1-5 - [c34]Günhan Gülsoy, Tamer Kahveci:
Inferring gene functions from metabolic reactions. GENSiPS 2012: 159-163 - [c33]Nirmalya Bandyopadhyay, Sanjay Ranka, Tamer Kahveci:
SSLPred : Predicting Synthetic Sickness Lethality. Pacific Symposium on Biocomputing 2012: 7-18 - [e2]Sanjay Ranka, Tamer Kahveci, Mona Singh:
ACM International Conference on Bioinformatics, Computational Biology and Biomedicine, BCB' 12, Orlando, FL, USA - October 08 - 10, 2012. ACM 2012, ISBN 978-1-4503-1670-5 [contents] - [e1]Tamer Kahveci, Saeed Salem, Mehmet Koyutürk, Jake Yue Chen, Mohammed J. Zaki:
Proceedings of the 11th International Workshop on Data Mining in Bioinformatics, BIOKDD 2012, Beijing, China, August 12, 2012. ACM 2012, ISBN 978-1-4503-1552-4 [contents] - 2011
- [j19]Günhan Gülsoy, Tamer Kahveci:
RINQ: Reference-based Indexing for Network Queries. Bioinform. 27(13): 149-158 (2011) - [j18]Ferhat Ay, Manolis Kellis, Tamer Kahveci:
SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings. J. Comput. Biol. 18(3): 219-235 (2011) - [j17]Bin Song, I. Esra Büyüktahtakin, Sanjay Ranka, Tamer Kahveci:
Manipulating the Steady State of Metabolic Pathways. IEEE ACM Trans. Comput. Biol. Bioinform. 8(3): 732-747 (2011) - [j16]Jayendra Venkateswaran, Bin Song, Tamer Kahveci, Chris Jermaine:
TRIAL: A Tool for Finding Distant Structural Similarities. IEEE ACM Trans. Comput. Biol. Bioinform. 8(3): 819-831 (2011) - [c32]Michael Dang, Ferhat Ay, Tamer Kahveci:
A novel framework for large scale metabolic network alignments by compression. BCB 2011: 274-283 - [c31]Günhan Gülsoy, Bhavik Gandhi, Tamer Kahveci:
Topology aware coloring of gene regulatory networks. BCB 2011: 435-440 - [c30]Nirmalya Bandyopadhyay, Manas Somaiya, Sanjay Ranka, Tamer Kahveci:
Identifying differentially regulated genes. ICCABS 2011: 19-25 - 2010
- [j15]Nirmalya Bandyopadhyay, Tamer Kahveci:
GBA Manager: An Online Tool for Querying Low-Complexity Regions in Proteins. J. Comput. Biol. 17(1): 73-77 (2010) - [c29]Nirmalya Bandyopadhyay, A. Mark Settles, Tamer Kahveci:
RepFrag: a graph based method for finding repeats and transposons from fragmented genomes. BCB 2010: 92-101 - [c28]Ferhat Ay, Tamer Kahveci:
Functional similarities of reaction sets in metabolic pathways. BCB 2010: 102-111 - [c27]Bin Song, Sanjay Ranka, Tamer Kahveci:
Enzymatic target identification with dynamic states. BCB 2010: 180-187 - [c26]Ferhat Ay, Thang N. Dinh, My T. Thai, Tamer Kahveci:
Finding Dynamic Modules of Biological Regulatory Networks. BIBE 2010: 136-143 - [c25]Ferhat Ay, Günhan Gülsoy, Tamer Kahveci:
Finding steady states of large scale regulatory networks through partitioning. GENSiPS 2010: 1-4 - [c24]Fei Xu, Ravi Jampani, Mingxi Wu, Chris Jermaine, Tamer Kahveci:
Surrogate ranking for very expensive similarity queries. ICDE 2010: 848-859 - [c23]Ferhat Ay, Tamer Kahveci:
SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings. RECOMB 2010: 15-30
2000 – 2009
- 2009
- [j14]Nirmalya Bandyopadhyay, Tamer Kahveci, Steve Goodison, Yijun Sun, Sanjay Ranka:
Pathway-Based Feature Selection Algorithm for Cancer Microarray Data. Adv. Bioinformatics 2009: 532989:1-532989:16 (2009) - [j13]Jun Liu, Nirmalya Bandyopadhyay, Sanjay Ranka, Michael Baudis, Tamer Kahveci:
Inferring progression models for CGH data. Bioinform. 25(17): 2208-2215 (2009) - [j12]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): 124-144 (2009) - [j11]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): 389-428 (2009) - [r1]Tamer Kahveci:
Index Structures for Biological Sequences. Encyclopedia of Database Systems 2009: 1428-1432 - 2008
- [j10]Xuehui Li, Tamer Kahveci, A. Mark Settles:
A novel genome-scale repeat finder geared towards transposons. Bioinform. 24(4): 468-476 (2008) - [j9]Jayendra Venkateswaran, Tamer Kahveci, Christopher M. Jermaine, Deepak Lachwani:
Reference-based indexing for metric spaces with costly distance measures. VLDB J. 17(5): 1231-1251 (2008) - [c22]Jun Liu, Sanjay Ranka, Tamer Kahveci:
Classification and feature selection algorithms for multi-class CGH data. ISMB 2008: 86-95 - [c21]Padmavati Sridhar, Bin Song, Tamer Kahveci, Sanjay Ranka:
Mining Metabolic Networks for Optimal Drug Targets. Pacific Symposium on Biocomputing 2008: 291-302 - 2007
- [j8]Xu Zhang, Tamer Kahveci:
QOMA: quasi-optimal multiple alignment of protein sequences. Bioinform. 23(2): 162-168 (2007) - [j7]Jun Liu, Sanjay Ranka, Tamer Kahveci:
Markers improve clustering of CGH data. Bioinform. 23(4): 450-457 (2007) - [c20]Xu Zhang, Tamer Kahveci:
QOMA2: Optimizing the alignment of many sequences. BIBE 2007: 780-787 - [c19]Xuehui Li, Tamer Kahveci:
Quality-Based Similarity Search for Biological Sequence Databases. BIOCOMP 2007: 567-573 - [c18]Padmavati Sridhar, Tamer Kahveci, Sanjay Ranka:
An Iterative Algorithm for Metabolic Network-Based Drug Target Identification. Pacific Symposium on Biocomputing 2007: 88-99 - 2006
- [j6]Jun Liu, Jaaved Mohammed, James Carter, Sanjay Ranka, Tamer Kahveci, Michael Baudis:
Distance-based clustering of CGH data. Bioinform. 22(16): 1971-1978 (2006) - [j5]Xuehui Li, Tamer Kahveci:
A Novel algorithm for identifying low-complexity regions in a protein sequence. Bioinform. 22(24): 2980-2987 (2006) - [c17]Jayendra Venkateswaran, Tamer Kahveci, Orhan Çamoglu:
Finding Data Broadness Via Generalized Nearest Neighbors. EDBT 2006: 645-663 - [c16]Xu Zhang, Tamer Kahveci:
A New Approach for Alignment of Multiple Proteins. Pacific Symposium on Biocomputing 2006: 339-350 - [c15]Jayendra Venkateswaran, Deepak Lachwani, Tamer Kahveci, Christopher M. Jermaine:
Reference-based Indexing of Sequence Databases. VLDB 2006: 906-917 - 2005
- [c14]Abhijit Pol, Tamer Kahveci:
Highly Scalable and Accurate Seeds for Subsequence Alignment. BIBE 2005: 27-31 - [c13]