Tamer Kahveci - Publications

Affiliations: 
University of Florida, Gainesville, Gainesville, FL, United States 
Area:
Computer Science

93 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.92
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  0.4
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  0.92
2016 Baiser B, Elhesha R, Kahveci T. Motifs in the assembly of food web networks Oikos. 125: 480-491. DOI: 10.1111/oik.02532  0.92
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  0.92
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  0.92
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  0.92
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  0.92
2015 Hasan MM, Kahveci T. Indexing a protein-protein interaction network expedites network alignment Bmc Bioinformatics. 16. DOI: 10.1186/s12859-015-0756-0  0.92
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  0.92
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  0.92
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  0.92
2015 Gabr H, Todor A, Dobra A, Kahveci T. Reachability analysis in probabilistic biological networks Ieee/Acm Transactions On Computational Biology and Bioinformatics. 12: 53-66. DOI: 10.1109/TCBB.2014.2343967  0.92
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  0.92
2014 Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, ... ... Kahveci T, et al. Topologically associating domains are stable units of replication-timing regulation. Nature. 515: 402-5. PMID 25409831 DOI: 10.1038/nature13986  0.92
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  0.92
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  0.92
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  0.92
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  0.92
2014 Cobb R, Elhesha R, Burleigh JG, Kahveci T. Extracting phylogenetic signals from multi-labeled gene trees and its significance for species tree construction Acm Bcb 2014 - 5th Acm Conference On Bioinformatics, Computational Biology, and Health Informatics. 3-12. DOI: 10.1145/2649387.2649389  0.92
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  0.92
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  0.92
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  0.92
2013 Gregory JF, Park Y, Lamers Y, Bandyopadhyay N, Chi YY, Lee K, Kim S, da Silva V, Hove N, Ranka S, Kahveci T, Muller KE, Stevens RD, Newgard CB, Stacpoole PW, et al. Metabolomic analysis reveals extended metabolic consequences of marginal vitamin B-6 deficiency in healthy human subjects. Plos One. 8: e63544. PMID 23776431 DOI: 10.1371/journal.pone.0063544  0.92
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  0.92
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  0.92
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  0.92
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  0.92
2013 Gabr H, Todor A, Zandi H, Dobra A, Kahveci T. PReach: Reachability in probabilistic signaling networks 2013 Acm Conference On Bioinformatics, Computational Biology and Biomedical Informatics, Acm-Bcb 2013. 3-12. DOI: 10.1145/2506583.2506586  0.92
2013 Kahveci T, Salem S, Koyuturk M. Guest editorial for special section on BIOKDD Ieee/Acm Transactions On Computational Biology and Bioinformatics. 10: 1199-1200. DOI: 10.1109/TCBB.2013.184  0.92
2013 Kahveci T, Singh M. Guest editorial for ACM BCB Ieee/Acm Transactions On Computational Biology and Bioinformatics. 10: 1089-1090. DOI: 10.1109/TCBB.2013.182  0.92
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  0.92
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  0.92
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  0.92
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  0.92
2012 Bandyopadhyay N, Somaiya M, Ranka S, Kahveci T. CMRF: analyzing differential gene regulation in two group perturbation experiments. Bmc Genomics. 13: S2. PMID 22537297 DOI: 10.1186/1471-2164-13-S2-S2  0.92
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  0.92
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  0.92
2012 Bandyopadhyay N, Ranka S, Kahveci T. SSLPred: predicting synthetic sickness lethality. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 7-18. PMID 22174258  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
2011 El Yacoubi B, Hatin I, Deutsch C, Kahveci T, Rousset JP, Iwata-Reuyl D, Murzin AG, de Crécy-Lagard V. A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification. The Embo Journal. 30: 882-93. PMID 21285948 DOI: 10.1038/emboj.2010.363  0.92
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  0.92
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  0.92
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  0.92
2011 Bandyopadhyay N, Somaiya M, Ranka S, Kahveci T. Identifying differentially regulated genes 2011 Ieee 1st International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2011. 19-25. DOI: 10.1109/ICCABS.2011.5729877  0.92
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  0.92
2010 Song B, Ranka S, Kahveci T. Enzymatic target identification with dynamic states 2010 Acm International Conference On Bioinformatics and Computational Biology, Acm-Bcb 2010. 180-187. DOI: 10.1145/1854776.1854804  0.92
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  0.92
2010 Bandyopadhyay N, Settles AM, Kahveci T. RepFrag: A graph based method for finding repeats and transposons from fragmented genomes 2010 Acm International Conference On Bioinformatics and Computational Biology, Acm-Bcb 2010. 92-101. DOI: 10.1145/1854776.1854794  0.92
2010 Xu F, Jampani R, Wu M, Jermaine C, Kahveci T. Surrogate ranking for very expensive similarity queries Proceedings - International Conference On Data Engineering. 848-859. DOI: 10.1109/ICDE.2010.5447888  0.92
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  0.92
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  0.92
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  0.92
2009 Liu J, Bandyopadhyay N, Ranka S, Baudis M, Kahveci T. Inferring progression models for CGH data. Bioinformatics (Oxford, England). 25: 2208-15. PMID 19528087 DOI: 10.1093/bioinformatics/btp365  0.92
2009 Song B, Sridhar P, Kahveci T, Ranka S. Double iterative optimisation for metabolic network-based drug target identification. International Journal of Data Mining and Bioinformatics. 3: 124-44. PMID 19517985 DOI: 10.1504/IJDMB.2009.024847  0.92
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  0.92
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  0.92
2008 Liu J, Ranka S, Kahveci T. Classification and feature selection algorithms for multi-class CGH data. Bioinformatics (Oxford, England). 24: i86-95. PMID 18586749 DOI: 10.1093/bioinformatics/btn145  0.92
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  0.92
2008 Li X, Kahveci T, Settles AM. A novel genome-scale repeat finder geared towards transposons. Bioinformatics (Oxford, England). 24: 468-76. PMID 18089620 DOI: 10.1093/bioinformatics/btm613  0.92
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  0.92
2007 Sridhar P, Kahveci T, Ranka S. An iterative algorithm for metabolic network-based drug target identification. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 88-99. PMID 17992747  0.92
2007 Liu J, Ranka S, Kahveci T. Markers improve clustering of CGH data. Bioinformatics (Oxford, England). 23: 450-7. PMID 17150994 DOI: 10.1093/bioinformatics/btl624  0.92
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  0.92
2007 Zhang X, Kahveci T. QOMA2: Optimizing the alignment of many sequences Proceedings of the 7th Ieee International Conference On Bioinformatics and Bioengineering, Bibe. 780-787. DOI: 10.1109/BIBE.2007.4375649  0.92
2007 Liu J, Ranka S, Kahveci T. A web server for mining Comparative Genomic Hybridization (CGH) data Aip Conference Proceedings. 953: 144-161. DOI: 10.1063/1.2817337  0.92
2006 Zhang X, Kahveci T. A new approach for alignment of multiple proteins. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 339-50. PMID 17094251  0.92
2006 Li X, Kahveci T. A Novel algorithm for identifying low-complexity regions in a protein sequence. Bioinformatics (Oxford, England). 22: 2980-7. PMID 17018537 DOI: 10.1093/bioinformatics/btl495  0.92
2006 Liu J, Mohammed J, Carter J, Ranka S, Kahveci T, Baudis M. Distance-based clustering of CGH data. Bioinformatics (Oxford, England). 22: 1971-8. PMID 16705014 DOI: 10.1093/bioinformatics/btl185  0.92
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  0.92
2005 Li Y, Li T, Kahveci T, Fortes J. Workload characterization of bioinformatics applications Proceedings - Ieee Computer Society's Annual International Symposium On Modeling, Analysis, and Simulation of Computer and Telecommunications Systems, Mascots. 2005: 15-22. DOI: 10.1109/MASCOTS.2005.77  0.92
2005 Pol A, Kahveci T. Highly scalable and accurate seeds for subsequence alignment Proceedings - Bibe 2005: 5th Ieee Symposium On Bioinformatics and Bioengineering. 2005: 27-31. DOI: 10.1109/BIBE.2005.37  0.92
2005 Kahveci T, Ramaswamy V, Tao H, Li T. Approximate global alignment of sequences Proceedings - Bibe 2005: 5th Ieee Symposium On Bioinformatics and Bioengineering. 2005: 81-88. DOI: 10.1109/BIBE.2005.13  0.92
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  0.92
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  0.92
2004 Bhattacharya A, Can T, Kahveci T, Singh AK, Wang YF. Progress: simultaneous searching of protein databases by sequence and structure. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 264-75. PMID 14992509  0.92
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  0.92
2003 Camoğlu O, Kahveci T, Singh AK. Towards index-based similarity search for protein structure databases. Proceedings / Ieee Computer Society Bioinformatics Conference. Ieee Computer Society Bioinformatics Conference. 2: 148-58. PMID 16452789 DOI: 10.1109/CSB.2003.1227314  0.92
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  0.92
2003 Kahveci T, Singh A. MAP: searching large genome databases Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 303-314. PMID 12603037  0.92
2003 Kahveci T, Singh AK. Fast alignment of large genome databases: A demonstration Proceedings - International Conference On Data Engineering. 768-770. DOI: 10.1109/ICDE.2003.1260862  0.92
2003 Kahveci T, Lang CA, Singh AK. Joining massive high-dimensional datasets Proceedings - International Conference On Data Engineering. 265-276. DOI: 10.1109/ICDE.2003.1260798  0.92
2003 Kahveci T, Singh AK. Genome on demand: Interactive substring searching Proceedings of the 2003 Ieee Bioinformatics Conference, Csb 2003. 551-552. DOI: 10.1109/CSB.2003.1227405  0.92
2002 Kahveci T, Singh A, Gürel A. Similarity searching for multi-attribute sequences Proceedings of the International Conference On Scientific and Statistical Database Management, Ssdbm. 2002: 175-184. DOI: 10.1109/SSDM.2002.1029718  0.92
2002 Kahveci T, Singh A, Gürel A. An efficient index structure for shift and scale invariant search of multi-attribute time sequences Proceedings - International Conference On Data Engineering. 266.  0.92
2001 Kahveci T, Singh A. Variable length queries for time series data Proceedings - International Conference On Data Engineering. 273-282.  0.92
2001 Kahveci T, Singh AK. An efficient index structure for string databases Vldb 2001 - Proceedings of 27th International Conference On Very Large Data Bases. 351-360.  0.92
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