Mehmet Koyutürk

104 papers A* 3A 1B 7C 1Misc 9Journal 58Unranked 23

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	ArnoldiGCL: Graph Contrastive Learning via Learnable Arnoldi-Based Guided Spectral Chebyshev Polynomial Filters. KDD (2) Mustafa Coskun, Abdelkader Baggag, Mehmet Koyutürk
2025	J	`jnl`	Guest Editorial for Special Section on ACM BCB 2023. IEEE Trans. Comput. Biol. Bioinform. Jianlin Cheng, Jing He, Mehmet Koyutürk
2025	J	`jnl`	Multiplex Embedding of Biological Networks Using Cross-Network Node Similarities. IEEE Trans. Comput. Biol. Bioinform. Mustafa Coskun, Mehmet Koyutürk
2025	J	`jnl`	Topological-Similarity Based Canonical Representations for Biological Link Prediction. IEEE Trans. Comput. Biol. Bioinform. Mengzhen Li, Mustafa Coskun, Mehmet Koyutürk
2024	—	`conf`	Generalized Learning of Coefficients in Spectral Graph Convolutional Networks. ICKG Mustafa Coskun, Ananth Grama, Mehmet Koyutürk
2024	J	`jnl`	Generalized Learning of Coefficients in Spectral Graph Convolutional Networks. CoRR Mustafa Coskun, Ananth Grama, Mehmet Koyutürk
2024	J	`jnl`	Random walks with variable restarts for negative-example-informed label propagation. Data Min. Knowl. Discov. Sean Maxwell, Mehmet Koyutürk
2023	—	`conf`	Canonical Representation of Biological Networks Using Graph Convolution. BCB Mengzhen Li, Mustafa Coskun, Mehmet Koyutürk
2023	—	`conf`	Generalized Gromov Wasserstein Distance for Seed-Informed Network Alignment. COMPLEX NETWORKS (3) Mengzhen Li, Mehmet Koyutürk
2022	J	`jnl`	Consensus embedding for multiple networks: Computation and applications. Netw. Sci. Mengzhen Li, Mustafa Coskun, Mehmet Koyutürk
2022	J	`jnl`	Functional characterization of co-phosphorylation networks. Bioinform. Marzieh Ayati, Serhan Yilmaz, Mark R. Chance, Mehmet Koyutürk
2022	J	`jnl`	Identification of intimate partner violence from free text descriptions in social media. J. Comput. Soc. Sci. Phan Trinh Ha, Rhea D'silva, Ethan Chen, Mehmet Koyutürk, Gunnur Karakurt
2022	J	`jnl`	Uncovering complementary sets of variants for predicting quantitative phenotypes. Bioinform. Serhan Yilmaz, Mohamad Fakhouri, Mehmet Koyutürk, A. Ercüment Çiçek, Öznur Tastan
2021	Misc	`conf`	Co-occurrence Patterns of Intimate Partner Violence. PSB Ahmet Mert Hacialiefendioglu, Serhan Yilmaz, Mehmet Koyutürk, Gunnur Karakurt
2021	J	`jnl`	Co-phosphorylation networks reveal subtype-specific signaling modules in breast cancer. Bioinform. Marzieh Ayati, Mark R. Chance, Mehmet Koyutürk
2021	J	`jnl`	Fast computation of Katz index for efficient processing of link prediction queries. Data Min. Knowl. Discov. Mustafa Coskun, Abdelkader Baggag, Mehmet Koyutürk
2021	J	`jnl`	Node similarity-based graph convolution for link prediction in biological networks. Bioinform. Mustafa Coskun, Mehmet Koyutürk
2021	J	`jnl`	Random Walks with Variable Restarts for Negative-Example-Informed Label Propagation. CoRR Sean Maxwell, Mehmet Koyutürk
2021	A*	`conf`	Spatiotemporal Graph Neural Network for Performance Prediction of Photovoltaic Power Systems. AAAI Ahmad Maroof Karimi, Yinghui Wu, Mehmet Koyutürk, Roger H. French
2020	—	`conf`	Consensus Embeddings for Networks with Multiple Versions. COMPLEX NETWORKS (2) Mengzhen Li, Mehmet Koyutürk
2020	J	`jnl`	DeepKinZero: zero-shot learning for predicting kinase-phosphosite associations involving understudied kinases. Bioinform. Iman Deznabi, Busra Arabaci, Mehmet Koyutürk, Öznur Tastan
2020	J	`jnl`	Identifying health correlates of intimate partner violence against pregnant women. Health Inf. Sci. Syst. Serhan Yilmaz, Bushra Alghamdi, Srinidhi Singuri, Ahmet Mert Hacialiefendioglu, Tülin Özcan, Mehmet Koyutürk, Gunnur Karakurt
2020	J	`jnl`	Integrated querying and version control of context-specific biological networks. Database J. Biol. Databases Curation Tyler Cowman, Mustafa Coskun, Ananth Grama, Mehmet Koyutürk
2019	J	`jnl`	Characterizing human genomic coevolution in locus-gene regulatory interactions. BioData Min. Daniel M. Savel, Mehmet Koyutürk
2019	—	`conf`	CoPhosK: A Method for Comprehensive Kinase Substrate Annotation using Co-phosphorylation Analysis. BCB Marzieh Ayati, Danica Wiredja, Daniela Schlatzer, Sean Maxwell, Ming Li, Mehmet Koyutürk, Mark R. Chance
2019	J	`jnl`	CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis. PLoS Comput. Biol. Marzieh Ayati, Danica Wiredja, Daniela Schlatzer, Sean Maxwell, Ming Li, Mehmet Koyutürk, Mark R. Chance
2019	J	`jnl`	Cross-population analysis for functional characterization of type II diabetes variants. BMC Bioinform. Dalia Elmansy, Mehmet Koyutürk
2019	J	`jnl`	Expanding Label Sets for Graph Convolutional Networks. CoRR Mustafa Coskun, Burcu Bakir-Gungor, Mehmet Koyutürk
2019	J	`jnl`	Fast Computation of Katz Index for Efficient Processing of Link Prediction Queries. CoRR Mustafa Coskun, Abdelkader Baggag, Mehmet Koyutürk
2018	—	`conf`	Cross-Population Analysis for Functional Characterization of Type II Diabetes Variants. BCB Dalia Elmansy, Mehmet Koyutürk
2018	J	`jnl`	Indexed Fast Network Proximity Querying. Proc. VLDB Endow. Mustafa Coskun, Ananth Grama, Mehmet Koyutürk
2018	J	`jnl`	Querying of Disparate Association and Interaction Data in Biomedical Applications. IEEE ACM Trans. Comput. Biol. Bioinform. Shi Qiao, Mehmet Koyutürk, Z. Meral Özsoyoglu
2017	—	`conf`	Drug Response Prediction as a Link Prediction Problem. BCB Zachary Stanfield, Mustafa Coskun, Mehmet Koyutürk
2017	J	`jnl`	Effects of emotion and topic area on topic shifts in social media discussions. Soc. Netw. Anal. Min. Kamil Topal, Mehmet Koyutürk, Gultekin Özsoyoglu
2017	J	`jnl`	Linearity of network proximity measures: implications for set-based queries and significance testing. Bioinform. Sean Maxwell, Mark R. Chance, Mehmet Koyutürk
2017	Misc	`conf`	Network Map of Adverse Health Effects Among Victims of Intimate Partner Violence. PSB Kathleen Whiting, Larry Y. Liu, Mehmet Koyutürk, Gunnur Karakurt
2017	J	`jnl`	Pluribus - Exploring the Limits of Error Correction Using a Suffix Tree. IEEE ACM Trans. Comput. Biol. Bioinform. Daniel M. Savel, Thomas LaFramboise, Ananth Grama, Mehmet Koyutürk
2017	J	`jnl`	The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics. Bioinform. Danica Wiredja, Mehmet Koyutürk, Mark R. Chance
2017	J	`jnl`	Visually Meaningful Histopathological Features for Automatic Grading of Prostate Cancer. IEEE J. Biomed. Health Informatics M. Khalid Khan Niazi, Keluo Yao, Debra L. Zynger, Steven K. Clinton, James Chen, Mehmet Koyutürk, Thomas LaFramboise, Metin N. Gurcan
2016	J	`jnl`	Disease gene prioritization by integrating tissue-specific molecular networks using a robust multi-network model. BMC Bioinform. Jingchao Ni, Mehmet Koyutürk, Hanghang Tong, Jonathan L. Haines, Rong Xu, Xiang Zhang
2016	A*	`conf`	Efficient Processing of Network Proximity Queries via Chebyshev Acceleration. KDD Mustafa Coskun, Ananth Grama, Mehmet Koyutürk
2016	B	`conf`	Emotion -and area-driven topic shift analysis in social media discussions. ASONAM Kamil Topal, Mehmet Koyutürk, Gultekin Özsoyoglu
2016	—	`conf`	MoBaS on Phosphorylation Data. BCB Marzieh Ayati, Danica Wiredja, Daniela Schlatzer, Goutham Narla, Mark R. Chance, Mehmet Koyutürk
2016	J	`jnl`	PoCos: Population Covering Locus Sets for Risk Assessment in Complex Diseases. PLoS Comput. Biol. Marzieh Ayati, Mehmet Koyutürk
2015	—	`conf`	Assessing the collective disease association of multiple genomic loci. BCB Marzieh Ayati, Mehmet Koyutürk
2015	—	`conf`	Integrated querying of disparate association and interaction data in biomedical applications. BCB Shi Qiao, Mehmet Koyutürk, Z. Meral Özsoyoglu
2015	—	`conf`	Link Prediction in Large Networks by Comparing the Global View of Nodes in the Network. ICDM Workshops Mustafa Coskun, Mehmet Koyutürk
2015	J	`jnl`	MOBAS: identification of disease-associated protein subnetworks using modularity-based scoring. EURASIP J. Bioinform. Syst. Biol. Marzieh Ayati, Sinan Erten, Mark R. Chance, Mehmet Koyutürk
2015	J	`jnl`	Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer. PLoS Comput. Biol. Matthew Ruffalo, Mehmet Koyutürk, Roded Sharan
2015	—	`ed.`	Proceedings of the Eighth International C* Conference on Computer Science & Software Engineering, Yokohama, Japan, July 13-15, 2015 C3S2E Jake Yue Chen, Mohammed J. Zaki, Tamer Kahveci, Saeed Salem, Mehmet Koyutürk
2015	J	`jnl`	Whole-exome sequencing enhances prognostic classification of myeloid malignancies. J. Biomed. Informatics Matthew Ruffalo, Holleh Husseinzadeh, Hideki Makishima, Bartlomiej Przychodzen, Mohamed Ashkar, Mehmet Koyutürk, Jaroslaw P. Maciejewski, Thomas LaFramboise
2014	—	`conf`	Efficiently Enumerating All Connected Induced Subgraphs of a Large Molecular Network. AlCoB Sean Maxwell, Mark R. Chance, Mehmet Koyutürk
2014	—	`conf`	Prioritization of genomic locus pairs for testing epistasis. BCB Marzieh Ayati, Mehmet Koyutürk
2014	B	`conf`	What Do We Learn from Network-Based Analysis of Genome-Wide Association Data? EvoApplications Marzieh Ayati, Sinan Erten, Mehmet Koyutürk
2013	J	`jnl`	Network Signatures of Survival in Glioblastoma Multiforme. PLoS Comput. Biol. Vishal N. Patel, Giridharan Gokulrangan, Salim A. Chowdhury, Yanwen Chen, Andrew E. Sloan, Mehmet Koyutürk, Jill S. Barnholtz-Sloan, Mark R. Chance
2013	Misc	`conf`	Session introduction. Pacific Symposium on Biocomputing Gürkan Bebek, Mehmet Koyutürk, Thomas LaFramboise, Benjamin J. Raphael, Mark R. Chance
2013	—	`conf`	Suffix-Tree Based Error Correction of NGS Reads Using Multiple Manifestations of an Error. BCB Daniel M. Savel, Thomas LaFramboise, Ananth Grama, Mehmet Koyutürk
2012	J	`jnl`	Accurate estimation of short read mapping quality for next-generation genome sequencing. Bioinform. Matthew Ruffalo, Mehmet Koyutürk, Soumya Ray, Thomas LaFramboise
2012	—	`conf`	Algorithms for detecting complementary SNPs within a region of interest that are associated with diseases. BCB Sinan Erten, Marzieh Ayati, Yu Liu, Mark R. Chance, Mehmet Koyutürk
2012	J	`jnl`	Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases. BMC Syst. Biol. Yu Liu, Mehmet Koyutürk, Jill S. Barnholtz-Sloan, Mark R. Chance
2012	J	`jnl`	Gene, pathway and network frameworks to identify epistatic interactions of single nucleotide polymorphisms derived from GWAS data. BMC Syst. Biol. Yu Liu, Sean Maxwell, Tao Feng, Xiaofeng Zhu, Robert C. Elston, Mehmet Koyutürk, Mark R. Chance
2012	J	`jnl`	Network biology methods integrating biological data for translational science. Briefings Bioinform. Gürkan Bebek, Mehmet Koyutürk, Nathan D. Price, Mark R. Chance
2012	J	`jnl`	Network-based approaches for extending the Wnt signalling pathway and identifying context-specific sub-networks. Int. J. Comput. Biol. Drug Des. Sudipto Saha, Theodore Roman, Alex Galante, Mehmet Koyutürk, Rob M. Ewing
2012	—	`ed.`	Proceedings of the 11th International Workshop on Data Mining in Bioinformatics, BIOKDD 2012, Beijing, China, August 12, 2012 BIOKDD Tamer Kahveci, Saeed Salem, Mehmet Koyutürk, Jake Yue Chen, Mohammed J. Zaki
2012	J	`jnl`	Using Protein Interaction Networks to Understand Complex Diseases. Computer Mehmet Koyutürk
2011	J	`jnl`	Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinform. Matthew Ruffalo, Thomas LaFramboise, Mehmet Koyutürk
2011	J	`jnl`	DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization. BioData Min. Sinan Erten, Gürkan Bebek, Rob M. Ewing, Mehmet Koyutürk
2011	B	`conf`	Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks. RECOMB Sinan Erten, Gürkan Bebek, Mehmet Koyutürk
2011	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Gürkan Bebek, Mehmet Koyutürk, Mark R. Chance, Nathan D. Price
2011	J	`jnl`	Subnetwork State Functions Define Dysregulated Subnetworks in Cancer. J. Comput. Biol. Salim A. Chowdhury, Rod K. Nibbe, Mark R. Chance, Mehmet Koyutürk
2011	Misc	`conf`	Systems Biology Analyses of Gene Expression and Genome Wide Association Study Data in Obstructive Sleep Apnea. Pacific Symposium on Biocomputing 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
2011	J	`jnl`	Vavien: An Algorithm for Prioritizing Candidate Disease Genes Based on Topological Similarity of Proteins in Interaction Networks. J. Comput. Biol. Sinan Erten, Gürkan Bebek, Mehmet Koyutürk
2010	J	`jnl`	An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer. PLoS Comput. Biol. Rod K. Nibbe, Mehmet Koyutürk, Mark R. Chance
2010	Misc	`conf`	COKGEN: A Software for the Identification of Rare Copy Number Variation from SNP Microarrays. Pacific Symposium on Biocomputing Gökhan Yavas, Mehmet Koyutürk, Z. Meral Özsoyoglu, Meetha P. Gould, Thomas LaFramboise
2010	J	`jnl`	Functional characterization and topological modularity of molecular interaction networks. BMC Bioinform. Jayesh Pandey, Mehmet Koyutürk, Ananth Grama
2010	Misc	`conf`	Identification of Coordinately Dysregulated Subnetworks in Complex Phenotypes. Pacific Symposium on Biocomputing Salim A. Chowdhury, Mehmet Koyutürk
2010	—	`conf`	Optimization Algorithms for Identification and Genotyping of Copy Number Polymorphisms in Human Populations. PRIB Gökhan Yavas, Mehmet Koyutürk, Thomas LaFramboise
2010	—	`conf`	Role of Centrality in Network-Based Prioritization of Disease Genes. EvoBIO Sinan Erten, Mehmet Koyutürk
2010	B	`conf`	Subnetwork State Functions Define Dysregulated Subnetworks in Cancer. RECOMB Salim A. Chowdhury, Rod K. Nibbe, Mark R. Chance, Mehmet Koyutürk
2010	J	`jnl`	Weighted Matrix Ordering and Parallel Banded Preconditioners for Iterative Linear System Solvers. SIAM J. Sci. Comput. Murat Manguoglu, Mehmet Koyutürk, Ahmed H. Sameh, Ananth Grama
2009	J	`jnl`	Efficient tag detection in RFID systems. J. Parallel Distributed Comput. Bogdan Carbunar, Murali Krishna Ramanathan, Mehmet Koyutürk, Suresh Jagannathan, Ananth Grama
2009	J	`jnl`	Phylogenetic analysis of modularity in protein interaction networks. BMC Bioinform. Sinan Erten, Xin Li, Gürkan Bebek, Jing Li, Mehmet Koyutürk
2008	Misc	`conf`	Annotating Pathways of Interaction Networks. Pacific Symposium on Biocomputing Jayesh Pandey, Mehmet Koyutürk, Wojciech Szpankowski, Ananth Grama
2008	C	`conf`	Functional coherence in domain interaction networks. ECCB Jayesh Pandey, Mehmet Koyutürk, Shankar Subramaniam, Ananth Grama
2008	Misc	`conf`	PHALANX: a graph-theoretic framework for test case prioritization. SAC Murali Krishna Ramanathan, Mehmet Koyutürk, Ananth Grama, Suresh Jagannathan
2008	J	`jnl`	Semantic indexing in structured peer-to-peer networks. J. Parallel Distributed Comput. Ronaldo A. Ferreira, Mehmet Koyutürk, Suresh Jagannathan, Ananth Grama
2007	J	`jnl`	Assessing Significance of Connectivity and Conservation in Protein Interaction Networks. J. Comput. Biol. Mehmet Koyutürk, Wojciech Szpankowski, Ananth Grama
2007	—	`conf`	Functional annotation of regulatory pathways. ISMB/ECCB (Supplement of Bioinformatics) Jayesh Pandey, Mehmet Koyutürk, Yohan Kim, Wojciech Szpankowski, Shankar Subramaniam, Ananth Grama
2006	B	`conf`	Assessing Significance of Connectivity and Conservation in Protein Interaction Networks. RECOMB Mehmet Koyutürk, Ananth Grama, Wojciech Szpankowski
2006	J	`jnl`	CONQUEST: A Coarse-Grained Algorithm for Constructing Summaries of Distributed Discrete Datasets. Algorithmica Jie Chi, Mehmet Koyutürk, Ananth Grama
2006	J	`jnl`	Detecting Conserved Interaction Patterns in Biological Networks. J. Comput. Biol. Mehmet Koyutürk, Yohan Kim, Shankar Subramaniam, Wojciech Szpankowski, Ananth Grama
2006	J	`jnl`	Inferring functional information from domain co-evolution. Bioinform. Yohan Kim, Mehmet Koyutürk, Umut Topkara, Ananth Grama, Shankar Subramaniam
2006	J	`jnl`	Nonorthogonal decomposition of binary matrices for bounded-error data compression and analysis. ACM Trans. Math. Softw. Mehmet Koyutürk, Ananth Grama, Naren Ramakrishnan
2006	J	`jnl`	Pairwise Alignment of Protein Interaction Networks. J. Comput. Biol. Mehmet Koyutürk, Yohan Kim, Umut Topkara, Shankar Subramaniam, Wojciech Szpankowski, Ananth Grama
2005	J	`jnl`	Compression, Clustering, and Pattern Discovery in Very High-Dimensional Discrete-Attribute Data Sets. IEEE Trans. Knowl. Data Eng. Mehmet Koyutürk, Ananth Grama, Naren Ramakrishnan
2005	J	`jnl`	Iterative-improvement-based declustering heuristics for multi-disk databases. Inf. Syst. Mehmet Koyutürk, Cevdet Aykanat
2005	B	`conf`	Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution. RECOMB Mehmet Koyutürk, Ananth Grama, Wojciech Szpankowski
2005	B	`conf`	Redundant reader elimination in RFID systems. SECON Bogdan Carbunar, Murali Krishna Ramanathan, Mehmet Koyutürk, Christoph Hoffmann, Ananth Grama
2004	—	`conf`	An efficient algorithm for detecting frequent subgraphs in biological networks. ISMB/ECCB (Supplement of Bioinformatics) Mehmet Koyutürk, Ananth Grama, Wojciech Szpankowski
2004	—	`conf`	Biclustering Gene-Feature Matrices for Statistically Significant Dense Patterns. CSB Mehmet Koyutürk, Wojciech Szpankowski, Ananth Grama
2004	A	`conf`	Conquest: A Distributed Tool for Constructing Summaries of High-Dimensional Discrete Attribute Data Sets. SDM Jie Chi, Mehmet Koyutürk, Ananth Grama
2003	—	`conf`	Algorithms for Bounded-Error Correlation of High Dimensional Data in Microarray Experiments. CSB Mehmet Koyutürk, Ananth Grama, Wojciech Szpankowski
2003	A*	`conf`	PROXIMUS: a framework for analyzing very high dimensional discrete-attributed datasets. KDD Mehmet Koyutürk, Ananth Grama
2002	—	`conf`	Algebraic Techniques for Analysis of Large Discrete-Valued Datasets. PKDD Mehmet Koyutürk, Ananth Grama, Naren Ramakrishnan