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ORCIDMehmet Koyutürk
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- affiliation: Case Western Reserve University, USA
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2020 – today
- 2024
[j51]Sean Maxwell, Mehmet Koyutürk:
Random walks with variable restarts for negative-example-informed label propagation. Data Min. Knowl. Discov. 38(6): 4024-4039 (2024)- [i4]Mustafa Coskun, Ananth Grama, Mehmet Koyutürk:
Generalized Learning of Coefficients in Spectral Graph Convolutional Networks. CoRR abs/2409.04813 (2024) - 2023
- [c42]Mengzhen Li
, Mustafa Coskun, Mehmet Koyutürk:
Canonical Representation of Biological Networks Using Graph Convolution. BCB 2023: 5:1-5:9 - [c41]Mengzhen Li, Mehmet Koyutürk:
Generalized Gromov Wasserstein Distance for Seed-Informed Network Alignment. COMPLEX NETWORKS (3) 2023: 258-270 - 2022
- [j50]Serhan Yilmaz, Mohamad Fakhouri, Mehmet Koyutürk, A. Ercüment Çiçek, Öznur Tastan:
Uncovering complementary sets of variants for predicting quantitative phenotypes. Bioinform. 38(4): 908-917 (2022) - [j49]Marzieh Ayati, Serhan Yilmaz, Mark R. Chance, Mehmet Koyutürk:
Functional characterization of co-phosphorylation networks. Bioinform. 38(15): 3785-3793 (2022) - [j48]Phan Trinh Ha, Rhea D'silva, Ethan Chen, Mehmet Koyutürk, Gunnur Karakurt:
Identification of intimate partner violence from free text descriptions in social media. J. Comput. Soc. Sci. 5(2): 1207-1233 (2022) - [j47]Mengzhen Li, Mustafa Coskun, Mehmet Koyutürk:
Consensus embedding for multiple networks: Computation and applications. Netw. Sci. 10(2): 190-206 (2022) - 2021
- [j46]Marzieh Ayati, Mark R. Chance, Mehmet Koyutürk:
Co-phosphorylation networks reveal subtype-specific signaling modules in breast cancer. Bioinform. 37(2): 221-228 (2021) - [j45]Mustafa Coskun, Mehmet Koyutürk:
Node similarity-based graph convolution for link prediction in biological networks. Bioinform. 37(23): 4501-4508 (2021) - [j44]Mustafa Coskun, Abdelkader Baggag, Mehmet Koyutürk:
Fast computation of Katz index for efficient processing of link prediction queries. Data Min. Knowl. Discov. 35(4): 1342-1368 (2021) - [c40]Ahmad Maroof Karimi, Yinghui Wu, Mehmet Koyutürk, Roger H. French:
Spatiotemporal Graph Neural Network for Performance Prediction of Photovoltaic Power Systems. AAAI 2021: 15323-15330 - [c39]Ahmet Mert Hacialiefendioglu, Serhan Yilmaz, Mehmet Koyutürk, Gunnur Karakurt:
Co-occurrence Patterns of Intimate Partner Violence. PSB 2021 - [i3]Sean Maxwell, Mehmet Koyutürk:
Random Walks with Variable Restarts for Negative-Example-Informed Label Propagation. CoRR abs/2110.07011 (2021) - 2020
- [j43]Tyler Cowman, Mustafa Coskun, Ananth Grama, Mehmet Koyutürk:
Integrated querying and version control of context-specific biological networks. Database J. Biol. Databases Curation 2020 (2020) - [j42]Iman Deznabi, Busra Arabaci, Mehmet Koyutürk, Öznur Tastan:
DeepKinZero: zero-shot learning for predicting kinase-phosphosite associations involving understudied kinases. Bioinform. 36(12): 3652-3661 (2020) - [j41]Serhan Yilmaz, Bushra Alghamdi, Srinidhi Singuri, Ahmet Mert Hacialiefendioglu, Tülin Özcan, Mehmet Koyutürk, Gunnur Karakurt:
Identifying health correlates of intimate partner violence against pregnant women. Health Inf. Sci. Syst. 8(1): 36 (2020) - [c38]Mengzhen Li, Mehmet Koyutürk:
Consensus Embeddings for Networks with Multiple Versions. COMPLEX NETWORKS (2) 2020: 39-52
2010 – 2019
- 2019
- [j40]Daniel M. Savel, Mehmet Koyutürk:
Characterizing human genomic coevolution in locus-gene regulatory interactions. BioData Min. 12(1): 8:1-8:15 (2019) - [j39]Dalia Elmansy, Mehmet Koyutürk:
Cross-population analysis for functional characterization of type II diabetes variants. BMC Bioinform. 20-S(12): 320:1-320:17 (2019) - [j38]Marzieh Ayati, Danica Wiredja, Daniela Schlatzer, Sean Maxwell, Ming Li, Mehmet Koyutürk, Mark R. Chance:
CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis. PLoS Comput. Biol. 15(2) (2019) - [c37]Marzieh Ayati, Danica Wiredja, Daniela Schlatzer, Sean Maxwell, Ming Li, Mehmet Koyutürk, Mark R. Chance:
CoPhosK: A Method for Comprehensive Kinase Substrate Annotation using Co-phosphorylation Analysis. BCB 2019: 550 - [i2]Mustafa Coskun, Abdelkader Baggag, Mehmet Koyutürk:
Fast Computation of Katz Index for Efficient Processing of Link Prediction Queries. CoRR abs/1912.06525 (2019) - [i1]Mustafa Coskun, Burcu Bakir-Gungor, Mehmet Koyutürk:
Expanding Label Sets for Graph Convolutional Networks. CoRR abs/1912.09575 (2019) - 2018
- [j37]Mustafa Coskun, Ananth Grama, Mehmet Koyutürk:
Indexed Fast Network Proximity Querying. Proc. VLDB Endow. 11(8): 840-852 (2018) - [j36]Shi Qiao, Mehmet Koyutürk, Z. Meral Özsoyoglu:
Querying of Disparate Association and Interaction Data in Biomedical Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 15(4): 1052-1065 (2018) - [c36]Dalia Elmansy, Mehmet Koyutürk:
Cross-Population Analysis for Functional Characterization of Type II Diabetes Variants. BCB 2018: 595 - 2017
- [j35]Sean Maxwell, Mark R. Chance, Mehmet Koyutürk:
Linearity of network proximity measures: implications for set-based queries and significance testing. Bioinform. 33(9): 1354-1361 (2017) - [j34]Danica Wiredja, Mehmet Koyutürk, Mark R. Chance:
The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics. Bioinform. 33(21): 3489-3491 (2017) - [j33]Kamil Topal, Mehmet Koyutürk, Gultekin Özsoyoglu:
Effects of emotion and topic area on topic shifts in social media discussions. Soc. Netw. Anal. Min. 7(1): 46:1-46:17 (2017) - [j32]Daniel M. Savel, Thomas LaFramboise, Ananth Grama, Mehmet Koyutürk:
Pluribus - Exploring the Limits of Error Correction Using a Suffix Tree. IEEE ACM Trans. Comput. Biol. Bioinform. 14(6): 1378-1388 (2017) - [j31]M. Khalid Khan Niazi, Keluo Yao, Debra L. Zynger, Steven K. Clinton, James Chen, Mehmet Koyutürk, Thomas LaFramboise, Metin N. Gurcan:
Visually Meaningful Histopathological Features for Automatic Grading of Prostate Cancer. IEEE J. Biomed. Health Informatics 21(4): 1027-1038 (2017) - [c35]Zachary Stanfield, Mustafa Coskun, Mehmet Koyutürk:
Drug Response Prediction as a Link Prediction Problem. BCB 2017: 638 - [c34]Kathleen Whiting, Larry Y. Liu, Mehmet Koyutürk, Gunnur Karakurt:
Network Map of Adverse Health Effects Among Victims of Intimate Partner Violence. PSB 2017: 324-335 - 2016
- [j30]Jingchao Ni, Mehmet Koyutürk, Hanghang Tong, Jonathan L. Haines, Rong Xu, Xiang Zhang:
Disease gene prioritization by integrating tissue-specific molecular networks using a robust multi-network model. BMC Bioinform. 17: 453:1-453:13 (2016) - [j29]Marzieh Ayati, Mehmet Koyutürk:
PoCos: Population Covering Locus Sets for Risk Assessment in Complex Diseases. PLoS Comput. Biol. 12(11) (2016) - [c33]Kamil Topal, Mehmet Koyutürk, Gultekin Özsoyoglu:
Emotion -and area-driven topic shift analysis in social media discussions. ASONAM 2016: 510-518 - [c32]Marzieh Ayati, Danica Wiredja, Daniela Schlatzer, Goutham Narla, Mark R. Chance, Mehmet Koyutürk:
MoBaS on Phosphorylation Data. BCB 2016: 521 - [c31]Mustafa Coskun, Ananth Grama, Mehmet Koyutürk:
Efficient Processing of Network Proximity Queries via Chebyshev Acceleration. KDD 2016: 1515-1524 - 2015
- [j28]Marzieh Ayati, Sinan Erten, Mark R. Chance, Mehmet Koyutürk:
MOBAS: identification of disease-associated protein subnetworks using modularity-based scoring. EURASIP J. Bioinform. Syst. Biol. 2015: 7 (2015) - [j27]Matthew Ruffalo, Holleh Husseinzadeh, Hideki Makishima, Bartlomiej Przychodzen, Mohamed Ashkar, Mehmet Koyutürk, Jaroslaw P. Maciejewski, Thomas LaFramboise:
Whole-exome sequencing enhances prognostic classification of myeloid malignancies. J. Biomed. Informatics 58: 104-113 (2015) - [j26]Matthew Ruffalo, Mehmet Koyutürk, Roded Sharan:
Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer. PLoS Comput. Biol. 11(12) (2015) - [c30]Shi Qiao, Mehmet Koyutürk, Z. Meral Özsoyoglu:
Integrated querying of disparate association and interaction data in biomedical applications. BCB 2015: 146-155 - [c29]Marzieh Ayati, Mehmet Koyutürk:
Assessing the collective disease association of multiple genomic loci. BCB 2015: 376-385 - [c28]Mustafa Coskun, Mehmet Koyutürk:
Link Prediction in Large Networks by Comparing the Global View of Nodes in the Network. ICDM Workshops 2015: 485-492 - [e2]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
- [c27]Sean Maxwell, Mark R. Chance, Mehmet Koyutürk:
Efficiently Enumerating All Connected Induced Subgraphs of a Large Molecular Network. AlCoB 2014: 171-182 - [c26]Marzieh Ayati, Mehmet Koyutürk:
Prioritization of genomic locus pairs for testing epistasis. BCB 2014: 240-248 - [c25]Marzieh Ayati, Sinan Erten, Mehmet Koyutürk:
What Do We Learn from Network-Based Analysis of Genome-Wide Association Data? EvoApplications 2014: 865-876 - 2013
- [j25]Vishal N. Patel, Giridharan Gokulrangan, Salim A. Chowdhury, Yanwen Chen, Andrew E. Sloan, Mehmet Koyutürk, Jill S. Barnholtz-Sloan, Mark R. Chance:
Network Signatures of Survival in Glioblastoma Multiforme. PLoS Comput. Biol. 9(9) (2013) - [c24]Daniel M. Savel, Thomas LaFramboise, Ananth Grama, Mehmet Koyutürk:
Suffix-Tree Based Error Correction of NGS Reads Using Multiple Manifestations of an Error. BCB 2013: 351 - [c23]Gürkan Bebek, Mehmet Koyutürk, Thomas LaFramboise, Benjamin J. Raphael, Mark R. Chance:
Session introduction. Pacific Symposium on Biocomputing 2013: 307-309 - 2012
- [j24]Gürkan Bebek, Mehmet Koyutürk, Nathan D. Price, Mark R. Chance:
Network biology methods integrating biological data for translational science. Briefings Bioinform. 13(4): 446-459 (2012) - [j23]Matthew Ruffalo, Mehmet Koyutürk, Soumya Ray, Thomas LaFramboise:
Accurate estimation of short read mapping quality for next-generation genome sequencing. Bioinform. 28(18): 349-355 (2012) - [j22]Yu Liu, Mehmet Koyutürk, Jill S. Barnholtz-Sloan, Mark R. Chance:
Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases. BMC Syst. Biol. 6: 65 (2012) - [j21]Yu Liu, Sean Maxwell, Tao Feng, Xiaofeng Zhu, Robert C. Elston, Mehmet Koyutürk, Mark R. Chance:
Gene, pathway and network frameworks to identify epistatic interactions of single nucleotide polymorphisms derived from GWAS data. BMC Syst. Biol. 6(S-3): S15 (2012) - [j20]Mehmet Koyutürk:
Using Protein Interaction Networks to Understand Complex Diseases. Computer 45(3): 31-38 (2012) - [j19]Sudipto Saha, Theodore Roman, Alex Galante, Mehmet Koyutürk, Rob M. Ewing:
Network-based approaches for extending the Wnt signalling pathway and identifying context-specific sub-networks. Int. J. Comput. Biol. Drug Des. 5(3/4): 185-205 (2012) - [c22]Sinan Erten, Marzieh Ayati, Yu Liu, Mark R. Chance, Mehmet Koyutürk:
Algorithms for detecting complementary SNPs within a region of interest that are associated with diseases. BCB 2012: 194-201 - [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
- [j18]Sinan Erten, Gürkan Bebek, Rob M. Ewing, Mehmet Koyutürk:
DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization. BioData Min. 4: 19 (2011) - [j17]Matthew Ruffalo, Thomas LaFramboise, Mehmet Koyutürk:
Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinform. 27(20): 2790-2796 (2011) - [j16]Salim A. Chowdhury, Rod K. Nibbe, Mark R. Chance, Mehmet Koyutürk:
Subnetwork State Functions Define Dysregulated Subnetworks in Cancer. J. Comput. Biol. 18(3): 263-281 (2011) - [j15]Sinan Erten, Gürkan Bebek, Mehmet Koyutürk:
Vavien: An Algorithm for Prioritizing Candidate Disease Genes Based on Topological Similarity of Proteins in Interaction Networks. J. Comput. Biol. 18(11): 1561-1574 (2011) - [c21]Gürkan Bebek, Mehmet Koyutürk, Mark R. Chance, Nathan D. Price:
Session Introduction. Pacific Symposium on Biocomputing 2011: 1-3 - [c20]Yu Liu, Sanjay R. Patel, Rod K. Nibbe, Sean Maxwell, Salim A. Chowdhury, Mehmet Koyutürk, Xiaofeng Zhu, Emma Larkin, Sarah Buxbaum, Naresh Punjabi, Sina Gharib, Susan Redline, Mark R. Chance:
Systems Biology Analyses of Gene Expression and Genome Wide Association Study Data in Obstructive Sleep Apnea. Pacific Symposium on Biocomputing 2011: 14-25 - [c19]Sinan Erten, Gürkan Bebek, Mehmet Koyutürk:
Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks. RECOMB 2011: 54-68 - 2010
- [j14]Jayesh Pandey, Mehmet Koyutürk, Ananth Grama:
Functional characterization and topological modularity of molecular interaction networks. BMC Bioinform. 11(S-1): 35 (2010) - [j13]Rod K. Nibbe, Mehmet Koyutürk, Mark R. Chance:
An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer. PLoS Comput. Biol. 6(1) (2010) - [j12]Murat Manguoglu, Mehmet Koyutürk, Ahmed H. Sameh, Ananth Grama:
Weighted Matrix Ordering and Parallel Banded Preconditioners for Iterative Linear System Solvers. SIAM J. Sci. Comput. 32(3): 1201-1216 (2010) - [c18]Sinan Erten, Mehmet Koyutürk:
Role of Centrality in Network-Based Prioritization of Disease Genes. EvoBIO 2010: 13-25 - [c17]Gökhan Yavas, Mehmet Koyutürk, Thomas LaFramboise:
Optimization Algorithms for Identification and Genotyping of Copy Number Polymorphisms in Human Populations. PRIB 2010: 74-85 - [c16]Salim A. Chowdhury, Mehmet Koyutürk:
Identification of Coordinately Dysregulated Subnetworks in Complex Phenotypes. Pacific Symposium on Biocomputing 2010: 133-144 - [c15]Gökhan Yavas, Mehmet Koyutürk, Z. Meral Özsoyoglu, Meetha P. Gould, Thomas LaFramboise:
COKGEN: A Software for the Identification of Rare Copy Number Variation from SNP Microarrays. Pacific Symposium on Biocomputing 2010: 371-382 - [c14]Salim A. Chowdhury, Rod K. Nibbe, Mark R. Chance, Mehmet Koyutürk:
Subnetwork State Functions Define Dysregulated Subnetworks in Cancer. RECOMB 2010: 80-95
2000 – 2009
- 2009
- [j11]Sinan Erten, Xin Li, Gürkan Bebek, Jing Li, Mehmet Koyutürk:
Phylogenetic analysis of modularity in protein interaction networks. BMC Bioinform. 10: 333 (2009) - [j10]Bogdan Carbunar, Murali Krishna Ramanathan, Mehmet Koyutürk, Suresh Jagannathan, Ananth Grama:
Efficient tag detection in RFID systems. J. Parallel Distributed Comput. 69(2): 180-196 (2009) - 2008
- [j9]Ronaldo A. Ferreira, Mehmet Koyutürk, Suresh Jagannathan, Ananth Grama:
Semantic indexing in structured peer-to-peer networks. J. Parallel Distributed Comput. 68(1): 64-77 (2008) - [c13]Jayesh Pandey, Mehmet Koyutürk, Shankar Subramaniam, Ananth Grama:
Functional coherence in domain interaction networks. ECCB 2008: 28-34 - [c12]Jayesh Pandey, Mehmet Koyutürk, Wojciech Szpankowski, Ananth Grama:
Annotating Pathways of Interaction Networks. Pacific Symposium on Biocomputing 2008: 153-165 - [c11]Murali Krishna Ramanathan, Mehmet Koyutürk, Ananth Grama, Suresh Jagannathan:
PHALANX: a graph-theoretic framework for test case prioritization. SAC 2008: 667-673 - 2007
- [j8]Mehmet Koyutürk, Wojciech Szpankowski, Ananth Grama:
Assessing Significance of Connectivity and Conservation in Protein Interaction Networks. J. Comput. Biol. 14(6): 747-764 (2007) - [c10]Jayesh Pandey, Mehmet Koyutürk, Yohan Kim, Wojciech Szpankowski, Shankar Subramaniam, Ananth Grama:
Functional annotation of regulatory pathways. ISMB/ECCB (Supplement of Bioinformatics) 2007: 377-386 - 2006
- [j7]Jie Chi, Mehmet Koyutürk, Ananth Grama:
CONQUEST: A Coarse-Grained Algorithm for Constructing Summaries of Distributed Discrete Datasets. Algorithmica 45(3): 377-401 (2006) - [j6]Yohan Kim, Mehmet Koyutürk, Umut Topkara, Ananth Grama, Shankar Subramaniam:
Inferring functional information from domain co-evolution. Bioinform. 22(1): 40-49 (2006) - [j5]Mehmet Koyutürk, Yohan Kim, Umut Topkara, Shankar Subramaniam, Wojciech Szpankowski, Ananth Grama:
Pairwise Alignment of Protein Interaction Networks. J. Comput. Biol. 13(2): 182-199 (2006) - [j4]Mehmet Koyutürk, Yohan Kim, Shankar Subramaniam, Wojciech Szpankowski, Ananth Grama:
Detecting Conserved Interaction Patterns in Biological Networks. J. Comput. Biol. 13(7): 1299-1322 (2006) - [j3]Mehmet Koyutürk, Ananth Grama, Naren Ramakrishnan:
Nonorthogonal decomposition of binary matrices for bounded-error data compression and analysis. ACM Trans. Math. Softw. 32(1): 33-69 (2006) - [c9]Mehmet Koyutürk, Ananth Grama, Wojciech Szpankowski:
Assessing Significance of Connectivity and Conservation in Protein Interaction Networks. RECOMB 2006: 45-59 - 2005
- [j2]Mehmet Koyutürk, Cevdet Aykanat:
Iterative-improvement-based declustering heuristics for multi-disk databases. Inf. Syst. 30(1): 47-70 (2005) - [j1]Mehmet Koyutürk, Ananth Grama, Naren Ramakrishnan:
Compression, Clustering, and Pattern Discovery in Very High-Dimensional Discrete-Attribute Data Sets. IEEE Trans. Knowl. Data Eng. 17(4): 447-461 (2005) - [c8]Mehmet Koyutürk, Ananth Grama, Wojciech Szpankowski:
Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution. RECOMB 2005: 48-65 - [c7]Bogdan Carbunar, Murali Krishna Ramanathan, Mehmet Koyutürk, Christoph Hoffmann, Ananth Grama:
Redundant reader elimination in RFID systems. SECON 2005: 176-184 - 2004
- [c6]Mehmet Koyutürk, Wojciech Szpankowski, Ananth Grama:
Biclustering Gene-Feature Matrices for Statistically Significant Dense Patterns. CSB 2004: 480-484 - [c5]Mehmet Koyutürk, Ananth Grama, Wojciech Szpankowski:
An efficient algorithm for detecting frequent subgraphs in biological networks. ISMB/ECCB (Supplement of Bioinformatics) 2004: 200-207 - [c4]Jie Chi, Mehmet Koyutürk, Ananth Grama:
Conquest: A Distributed Tool for Constructing Summaries of High-Dimensional Discrete Attribute Data Sets. SDM 2004: 154-165 - 2003
- [c3]Mehmet Koyutürk, Ananth Grama, Wojciech Szpankowski:
Algorithms for Bounded-Error Correlation of High Dimensional Data in Microarray Experiments. CSB 2003: 575-580 - [c2]Mehmet Koyutürk, Ananth Grama:
PROXIMUS: a framework for analyzing very high dimensional discrete-attributed datasets. KDD 2003: 147-156 - 2002
- [c1]Mehmet Koyutürk, Ananth Grama, Naren Ramakrishnan:
Algebraic Techniques for Analysis of Large Discrete-Valued Datasets. PKDD 2002: 311-324
Coauthor Index
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