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Tamer Kahveci - Publications

Affiliations: 
University of Florida, Gainesville, Gainesville, FL, United States 
Area:
Computer Science
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Year Citation  Score
2021 Ren Y, Sarkar A, Veltri P, Ay A, Dobra A, Kahveci T. Pattern discovery in multilayer networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34398763 DOI: 10.1109/TCBB.2021.3105001  0.431
2020 Yoon BJ, Qian X, Kahveci T, Pal R. Selected Research Articles from the 2019 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). Bmc Genomics. 21: 584. PMID 32900374 DOI: 10.1186/S12864-020-06934-Y  0.384
2019 Rivera-Mulia JC, Kim S, Gabr H, Chakraborty A, Ay F, Kahveci T, Gilbert DM. Replication timing networks reveal a link between transcription regulatory circuits and replication timing control. Genome Research. PMID 31434679 DOI: 10.1101/Gr.247049.118  0.681
2019 Chow K, Sarkar A, Elhesha R, Cinaglia P, Ay A, Kahveci T. ANCA: Alignment-based Network Construction Algorithm. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 31226082 DOI: 10.1109/Tcbb.2019.2923620  0.516
2019 Yoon BJ, Qian X, Kahveci T, Pal R. Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). Bmc Bioinformatics. 20: 316. PMID 31217001 DOI: 10.1186/S12859-019-2830-5  0.384
2019 Ren Y, Ay A, Dobra A, Kahveci T. Characterizing building blocks of resource constrained biological networks. Bmc Bioinformatics. 20: 318. PMID 31216986 DOI: 10.1186/S12859-019-2838-X  0.439
2019 Elhesha R, Sarkar A, Boucher C, Kahveci T. Identification of co-evolving temporal networks. Bmc Genomics. 20: 434. PMID 31189471 DOI: 10.1186/S12864-019-5719-9  0.494
2019 Sarkar A, Atay Y, Erickson AL, Arisi I, Saltini C, Kahveci T. An efficient algorithm for identifying mutated subnetworks associated with survival in cancer. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 30990435 DOI: 10.1109/Tcbb.2019.2911069  0.428
2018 Ren Y, Ay A, Kahveci T. Shortest path counting in probabilistic biological networks. Bmc Bioinformatics. 19: 465. PMID 30514202 DOI: 10.1186/S12859-018-2480-Z  0.503
2018 Altuntas V, Gok M, Kahveci T. Stability Analysis of Biological Networks' Diffusion State. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 30452376 DOI: 10.1109/Tcbb.2018.2881887  0.48
2018 Ren Y, Ay A, Gerke TA, Kahveci T. Identification of jointly correlated gene sets. Journal of Bioinformatics and Computational Biology. 16: 1840019. PMID 30419787 DOI: 10.1142/S021972001840019X  0.319
2018 Alim MA, Ay A, Hasan MM, Thai MT, Kahveci T. Construction of Signaling Pathways with RNAi Data and Multiple Reference Networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics. 15: 1079-1091. PMID 30102599 DOI: 10.1109/Tcbb.2017.2710129  0.51
2018 Sarkar A, Ren Y, Elhesha R, Kahveci T. A new algorithm for counting independent motifs in probabilistic networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 29994098 DOI: 10.1109/Tcbb.2018.2821666  0.525
2018 Ren Y, Sarkar A, Kahveci T. ProMotE: an efficient algorithm for counting independent motifs in uncertain network topologies. Bmc Bioinformatics. 19: 242. PMID 29940838 DOI: 10.1186/S12859-018-2236-9  0.494
2018 Mukherjee K, Hasan MM, Boucher C, Kahveci T. Counting motifs in dynamic networks. Bmc Systems Biology. 12: 6. PMID 29671392 DOI: 10.1186/S12918-018-0533-6  0.483
2018 Yoon BJ, Qian X, Kahveci T, Pal R. Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). Bmc Bioinformatics. 19: 69. PMID 29589557 DOI: 10.1186/S12859-018-2058-9  0.384
2017 Yoon BJ, Qian X, Kahveci T. Selected research articles from the 2016 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). Bmc Bioinformatics. 18: 159. PMID 28361697 DOI: 10.1186/S12859-017-1521-3  0.384
2017 Elhesha R, Kahveci T, Baiser B. Motif centrality in food web networks Journal of Complex Networks. 5: 641-664. DOI: 10.1093/Comnet/Cnw032  0.366
2016 Elhesha R, Kahveci T. Identification of large disjoint motifs in biological networks. Bmc Bioinformatics. 17: 408. PMID 27716036 DOI: 10.1186/S12859-016-1271-7  0.496
2016 Kim S, Sundaresan V, Zhou L, Kahveci T. Integrating Domain Specific Knowledge and Network Analysis to Predict Drug Sensitivity of Cancer Cell Lines. Plos One. 11: e0162173. PMID 27607242 DOI: 10.1371/Journal.Pone.0162173  0.31
2016 Ren Y, Wang Q, Hasan MM, Ay A, Kahveci T. Identifying the topology of signaling networks from partial RNAi data. Bmc Systems Biology. 10: 53. PMID 27490106 DOI: 10.1186/S12918-016-0301-4  0.433
2016 Baiser B, Elhesha R, Kahveci T. Motifs in the assembly of food web networks Oikos. 125: 480-491. DOI: 10.1111/Oik.02532  0.442
2015 Gabr H, Kahveci T. Signal reachability facilitates characterization of probabilistic signaling networks. Bmc Bioinformatics. 16: S6. PMID 26679404 DOI: 10.1186/1471-2105-16-S17-S6  0.471
2015 Gabr H, Rivera-Mulia JC, Gilbert DM, Kahveci T. Computing interaction probabilities in signaling networks. Eurasip Journal On Bioinformatics & Systems Biology. 2015: 10. PMID 26587014 DOI: 10.1186/S13637-015-0031-8  0.442
2015 Hasan MM, Kahveci T. Indexing a protein-protein interaction network expedites network alignment. Bmc Bioinformatics. 16: 326. PMID 26453444 DOI: 10.1186/S12859-015-0756-0  0.512
2015 Gabr H, Todor A, Dobra A, Kahveci T. Reachability Analysis in Probabilistic Biological Networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 12: 53-66. PMID 26357078 DOI: 10.1109/Tcbb.2014.2343967  0.383
2015 Rivera-Mulia JC, Buckley Q, Sasaki T, Zimmerman J, Didier RA, Nazor K, Loring JF, Lian Z, Weissman SM, Robins AJ, Schulz TC, Menendez L, Kulik MJ, Dalton S, Gabr H, ... Kahveci T, et al. Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells. Genome Research. PMID 26055160 DOI: 10.1101/Gr.187989.114  0.31
2015 Ay A, Gong D, Kahveci T. Hierarchical decomposition of dynamically evolving regulatory networks. Bmc Bioinformatics. 16: 161. PMID 25976669 DOI: 10.1186/S12859-015-0529-9  0.483
2015 Hasan MM, Kahveci T. Indexing a protein-protein interaction network expedites network alignment Bmc Bioinformatics. 16. DOI: 10.1186/s12859-015-0756-0  0.34
2015 Alim MA, Ay A, Hasan MM, Thai MT, Kahveci T. Multiple reference networks improve accuracy of signaling network construction Bcb 2015 - 6th Acm Conference On Bioinformatics, Computational Biology, and Health Informatics. 176-185. DOI: 10.1145/2808719.2808737  0.44
2015 Todor A, Dobra A, Kahveci T. Counting motifs in probabilistic biological networks Bcb 2015 - 6th Acm Conference On Bioinformatics, Computational Biology, and Health Informatics. 116-125. DOI: 10.1145/2808719.2808731  0.414
2015 Gabr H, Dobra A, Kahveci T. Estimating reachability in dense biological networks Bcb 2015 - 6th Acm Conference On Bioinformatics, Computational Biology, and Health Informatics. 86-95. DOI: 10.1145/2808719.2808728  0.392
2015 Wang Q, Ren Y, Hasan MM, Ay A, Kahveci T. Construction of signaling networks with incomplete RNAi data Proceedings - 2015 Ieee International Conference On Bioinformatics and Biomedicine, Bibm 2015. 157-162. DOI: 10.1109/BIBM.2015.7359674  0.4
2014 Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, ... ... Kahveci T, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515: 355-64. PMID 25409824 DOI: 10.1038/Nature13992  0.518
2014 Ay A, Gong D, Kahveci T. Network-based Prediction of Cancer under Genetic Storm. Cancer Informatics. 13: 15-31. PMID 25368507 DOI: 10.4137/Cin.S14025  0.409
2014 Todor A, Gabr H, Dobra A, Kahveci T. Large scale analysis of signal reachability Bioinformatics. 30: I96-I104. PMID 24932011 DOI: 10.1093/Bioinformatics/Btu262  0.479
2014 Hasan MM, Kahveci T. Incremental network querying in biological networks Acm Bcb 2014 - 5th Acm Conference On Bioinformatics, Computational Biology, and Health Informatics. 752-759. DOI: 10.1145/2649387.2660845  0.422
2014 Gabr H, Kahveci T. Characterization of probabilistic signaling networks through signal propagation 2014 Ieee 4th International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2014. DOI: 10.1109/ICCABS.2014.6863909  0.358
2013 Hasan MM, Kavurucu Y, Kahveci T. A scalable method for discovering significant subnetworks. Bmc Systems Biology. 7: S3. PMID 24565174 DOI: 10.1186/1752-0509-7-S4-S3  0.499
2013 Todor A, Dobra A, Kahveci T. Characterizing the topology of probabilistic biological networks Ieee/Acm Transactions On Computational Biology and Bioinformatics. 10: 970-983. PMID 24334390 DOI: 10.1109/Tcbb.2013.108  0.473
2013 Todor A, Dobra A, Kahveci T. Characterizing Topology of Probabilistic Biological Networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. PMID 24018700  0.334
2013 Todor A, Dobra A, Kahveci T. Probabilistic biological network alignment Ieee/Acm Transactions On Computational Biology and Bioinformatics. 10: 109-121. PMID 23702548 DOI: 10.1109/Tcbb.2012.142  0.469
2013 Gabr H, Dobra A, Kahveci T. From uncertain protein interaction networks to signaling pathways through intensive color coding 18th Pacific Symposium On Biocomputing, Psb 2013. 111-122. PMID 23424117  0.344
2013 Sheikh SI, Kahveci T, Ranka S, Gordon Burleigh J. Stability analysis of phylogenetic trees. Bioinformatics (Oxford, England). 29: 166-74. PMID 23162082 DOI: 10.1093/Bioinformatics/Bts657  0.309
2013 Hasan MM, Kahveci T. Color distribution can accelerate network alignment 2013 Acm Conference On Bioinformatics, Computational Biology and Biomedical Informatics, Acm-Bcb 2013. 52-61. DOI: 10.1145/2506583.2506594  0.427
2012 Hashemikhabir S, Ayaz ES, Kavurucu Y, Can T, Kahveci T. Large-scale signaling network reconstruction. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 9: 1696-708. PMID 23221085 DOI: 10.1109/Tcbb.2012.128  0.511
2012 Ramu A, Kahveci T, Burleigh JG. A scalable method for identifying frequent subtrees in sets of large phylogenetic trees. Bmc Bioinformatics. 13: 256. PMID 23033843 DOI: 10.1186/1471-2105-13-256  0.338
2012 Gülsoy G, Bandhyopadhyay N, Kahveci T. HIDEN: Hierarchical decomposition of regulatory networks. Bmc Bioinformatics. 13: 250. PMID 23016513 DOI: 10.1186/1471-2105-13-250  0.77
2012 Gülsoy G, Gandhi B, Kahveci T. Topac: alignment of gene regulatory networks using topology-aware coloring. Journal of Bioinformatics and Computational Biology. 10: 1240001. PMID 22809302 DOI: 10.1142/S021972001240001X  0.782
2012 Ay F, Dang M, Kahveci T. Metabolic network alignment in large scale by network compression. Bmc Bioinformatics. 13: S2. PMID 22536900 DOI: 10.1186/1471-2105-13-S3-S2  0.724
2012 Marbach D, Roy S, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M. Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks. Genome Research. 22: 1334-49. PMID 22456606 DOI: 10.1101/Gr.127191.111  0.741
2012 Gülsoy G, Kahveci T. Inferring gene functions from metabolic reactions Proceedings - Ieee International Workshop On Genomic Signal Processing and Statistics. 159-163. DOI: 10.1109/GENSIPS.2012.6507753  0.325
2012 Todor A, Dobra A, Kahveci T. Uncertain interactions affect degree distribution of biological networks Proceedings - 2012 Ieee International Conference On Bioinformatics and Biomedicine, Bibm 2012. 457-461. DOI: 10.1109/BIBM.2012.6392723  0.342
2012 Hasan MM, Kavurucu Y, Kahveci T. SiS: Significant subnetworks in massive number of network topologies Proceedings - 2012 Ieee International Conference On Bioinformatics and Biomedicine, Bibm 2012. 107-112. DOI: 10.1109/BIBM.2012.6392653  0.421
2012 Ay F, Gülsoy G, Kahveci T. Mining Biological Networks for Similar Patterns Intelligent Systems Reference Library. 25: 63-99. DOI: 10.1007/978-3-642-23151-3_5  0.71
2011 Gülsoy G, Kahveci T. RINQ: Reference-based Indexing for Network Queries. Bioinformatics (Oxford, England). 27: i149-58. PMID 21685064 DOI: 10.1093/bioinformatics/btr203  0.795
2011 Venkateswaran JG, Song B, Kahveci T, Jermaine C. TRIAL: A tool for finding distant structural similarities Ieee/Acm Transactions On Computational Biology and Bioinformatics. 8: 819-831. PMID 21393655 DOI: 10.1109/Tcbb.2009.28  0.726
2011 Ay F, Kellis M, Kahveci T. SubMAP: aligning metabolic pathways with subnetwork mappings. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 219-35. PMID 21385030 DOI: 10.1089/Cmb.2010.0280  0.71
2011 Song B, Büyüktahtakin IE, Ranka S, Kahveci T. Manipulating the steady state of metabolic pathways. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 8: 732-47. PMID 20479507 DOI: 10.1109/Tcbb.2010.41  0.378
2011 Gülsoy G, Gandhi B, Kahveci T. Topology aware coloring of gene regulatory networks 2011 Acm Conference On Bioinformatics, Computational Biology and Biomedicine, Bcb 2011. 435-440. DOI: 10.1145/2147805.2147865  0.399
2011 Dang M, Ay F, Kahveci T. A novel framework for large scale metabolic network alignments by compression 2011 Acm Conference On Bioinformatics, Computational Biology and Biomedicine, Bcb 2011. 274-283. DOI: 10.1145/2147805.2147835  0.696
2010 Bandyopadhyay N, Kahveci T. GBA manager: an online tool for querying low-complexity regions in proteins. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 73-7. PMID 20078398 DOI: 10.1089/Cmb.2009.0006  0.313
2010 Ay F, Kahveci T. Functional similarities of reaction sets in metabolic pathways 2010 Acm International Conference On Bioinformatics and Computational Biology, Acm-Bcb 2010. 102-111. DOI: 10.1145/1854776.1854795  0.591
2010 Ay F, Gulsoy G, Kahveci T. Finding steady states of large scale regulatory networks through partitioning 2010 Ieee International Workshop On Genomic Signal Processing and Statistics, Gensips 2010. DOI: 10.1109/GENSIPS.2010.5719669  0.662
2010 Ay F, Dinh TN, Thai MT, Kahveci T. Finding dynamic modules of biological regulatory networks 10th Ieee International Conference On Bioinformatics and Bioengineering 2010, Bibe 2010. 136-143. DOI: 10.1109/BIBE.2010.31  0.662
2009 Bandyopadhyay N, Kahveci T, Goodison S, Sun Y, Ranka S. Pathway-BasedFeature Selection Algorithm for Cancer Microarray Data. Advances in Bioinformatics. 532989. PMID 20204186 DOI: 10.1155/2009/532989  0.337
2009 Ay F, Xu F, Kahveci T. Scalable steady state analysis of Boolean biological regulatory networks. Plos One. 4: e7992. PMID 19956604 DOI: 10.1371/Journal.Pone.0007992  0.683
2009 Ay F, Kahveci T, DE Crécy-Lagard V. A fast and accurate algorithm for comparative analysis of metabolic pathways. Journal of Bioinformatics and Computational Biology. 7: 389-428. PMID 19507283 DOI: 10.1142/S0219720009004163  0.657
2008 Ay F, Kahveci T, de Crécy-Lagard V. Consistent alignment of metabolic pathways without abstraction. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 7: 237-48. PMID 19642284  0.619
2008 Sridhar P, Song B, Kahveci T, Ranka S. Mining metabolic networks for optimal drug targets. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 291-302. PMID 18229694  0.323
2008 Venkateswaran J, Kahveci T, Jermaine C, Lachwani D. Reference-based indexing for metric spaces with costly distance measures Vldb Journal. 17: 1231-1251. DOI: 10.1007/s00778-007-0062-1  0.734
2007 Zhang X, Kahveci T. QOMA: quasi-optimal multiple alignment of protein sequences. Bioinformatics (Oxford, England). 23: 162-8. PMID 17121778 DOI: 10.1093/Bioinformatics/Btl590  0.307
2006 Venkateswaran J, Kahveci T, Camoglu O. Finding data broadness via generalized nearest neighbors Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3896: 645-663. DOI: 10.1007/11687238_39  0.73
2004 Camoglu O, Kahveci T, Singh AK. Index-based similarity search for protein structure databases. Journal of Bioinformatics and Computational Biology. 2: 99-126. PMID 15272435 DOI: 10.1142/S0219720004000491  0.331
2004 Kahveci T, Ljosa V, Singh AK. Speeding up whole-genome alignment by indexing frequency vectors. Bioinformatics (Oxford, England). 20: 2122-34. PMID 15073002 DOI: 10.1093/Bioinformatics/Bth212  0.302
2004 Kahveci T, Singh AK. Optimizing Similarity Search for Arbitrary Length Time Series Queries Ieee Transactions On Knowledge and Data Engineering. 16: 418-433. DOI: 10.1109/Tkde.2004.1269667  0.331
2003 Camoglu O, Kahveci T, Singh AK. PSI: indexing protein structures for fast similarity search. Bioinformatics (Oxford, England). 19: i81-3. PMID 12855441 DOI: 10.1093/Bioinformatics/Btg1009  0.322
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