Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes
Himmelstein, Daniel S., Baranzini, Sergio E.·2015·PLOS Computational Biology
Cited by (176)
Items 101–176 of 176
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- Molecular cartooning with knowledge graphsBrook E. Santangelo, Lucas A. Gillenwater, Nourah M. Salem, Lawrence Hunter · 2022 · Frontiers in Bioinformatics
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- Final response to reviewsErik Quaeghebeur · 2019 · Wind energy science
- Learning graph representations for disease gene predictionSezin Kircali Ata · 2019
- Knowledge graph analytics platform with LINCS and IDG for Parkinson’s disease target illuminationJeremy J. Yang, Christopher R. Gessner, Joel L. Duerksen, Daniel Biber, Jessica Binder, Murat Ozturk, Brian Foote, Robin McEntire, Kyle Stirling, Ying Ding et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
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- Tensor Methods for Signal Reconstruction and Network EmbeddingCharilaos I. Kanatsoulis · 2020 · University of Minnesota Digital Conservancy (University of Minnesota)
- Point-of-interest recommendation in location-based social networksAlireza Pourali · 2021
- Point-of-interest recommendation in location-based social networksAlireza Pourali · 2021
- Creation of Networks for the Analysis of Disease SimilaritiesEduardo P. García del Valle · 2022
- Estudo da atividade de células citotóxicas em portadores de esclerose múltipla em uso de diferentes tratamentosVinicius de Oliveira Boldrini · 2020
- Regulação da expressão de Runx3 em linfócitos T CD4+ maduros durante a evolução da encefalomielite autoimune experimentalAna Maria Marques · 2022
- Navigating the Multiverse: A Hitchhiker's Guide to Selecting Harmonisation Methods for Multimodal Biomedical DataMurali Aadhitya Magateshvaren Saras, Mithun Kumar Mitra, Sonika Tyagi · 2024 · Research Square
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- Multi-Agent On-Device Language Models and Graph-Enhanced Image Generation for Forensic Scene ReconstructionAkilesh S, Tulasi Raman R, A. Sasithradevi, S Kanimozhi, P. Prakash · 2025 · IEEE Madhya Pradesh Section Conference (MPCON)
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- HetNetEX: Exact Asymptotic Inference in Heterogeneous Biomedical Knowledge GraphsTusharkanti Ghosh, Lucas A. Gillenwater, Casey S. Greene, James C. Costello · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
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