🧑‍🔬 Marinka Žitnik

🏛️ Affiliations

🎓Harvard UniversityCambridge · United States2019–2026 · 162 papersEmployment · Associate Professor, Department of Biomedical Informaticscurrent🔬Broad InstituteCambridge · United States2021–2026 · 56 paperscurrent🎓University of LjubljanaLjubljana · Slovenia2008–2019 · 28 papersEducation 2008–2012Education 2012–2015Employment🎓Stanford UniversityStanford · United States2016–2024 · 26 papersEducation 2016–2019Employment🎓Massachusetts Institute of TechnologyCambridge · United States2021–2024 · 8 papers🔬Harvard University PressCambridge · United States2020–2023 · 3 papers🎓Princeton UniversityPrinceton · United States2023–2024 · 2 papers🎓Baylor College of MedicineHouston · United States2014–2015 · 2 papersEmployment

From the bylines of their papers (OpenAlex, 2026-10-14), ORCID and Wikidata; institutions on papers are matched by machine. 3 more institutions on single bylines are not listed.

🧭 Fields, topics and concepts

Of its works in our library, with the number of works on each.

📅 Works by year

2020s

📄 Papers

The most cited first (OpenAlex and our library).

1. Building a knowledge graph to enable precision medicine (2023 · 555 citations)
   Knowledge about diseases is fragmented across publications, databases and ontologies that encode diseases in different and often conflicting ways.
2. Autonomous Knowledge Graph Exploration with Adaptive Breadth-Depth Retrieval (2026)
   Retrieving evidence from knowledge graphs (KGs) for language model queries requires two things at once. The retriever must search widely enough to land in the right part of the graph, and it must follow relational links over several hops. Similarity-based retrievers cover the graph but rarely reason over its…

All works

26 works of theirs in our library, the most cited first; 2 with a page here, the others link their original until we summarise them.

1. Scientific discovery in the age of artificial intelligence ↗Nature 620, 47-60 (2023) · no summary yetHanchen Wang et al.2023 · 1,860 citations
2. Modeling polypharmacy side effects with graph convolutional networks ↗Bioinformatics · no summary yetMarinka Žitnik, Monica Agrawal, Jure Leskovec2018 · 1,517 citations
3. Open Graph Benchmark: Datasets for Machine Learning on Graphs ↗arXiv:2005.00687 · no summary yetWeihua Hu et al.2020 · 712 citations
4. GNNExplainer: Generating Explanations for Graph Neural Networks ↗arXiv (Cornell University) · no summary yetRex Ying et al.2019 · 685 citations
5. Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities ↗Information Fusion · no summary yetMarinka Žitnik et al.2018 · 663 citations
6. Building a knowledge graph to enable precision medicineScientific DataPayal Chandak, Kexin Huang, Marinka Žitnik2023 · 555 citations
7. Predicting multicellular function through multi-layer tissue networks ↗Bioinformatics · no summary yetMarinka Žitnik, Jure Leskovec2017 · 542 citations
8. Learning Structural Node Embeddings via Diffusion Wavelets ↗ACM SIGKDD International Conference on Knowledge Discovery & Data Mining (KDD) · no summary yetClaire Donnat et al.2018 · 366 citations
9. Empowering Biomedical Discovery with AI Agents ↗arXiv:2404.02831 · no summary yetShanghua Gao et al.2024 · 333 citations
10. A foundation model for clinician-centered drug repurposing ↗Nature Medicine · no summary yetKexin Huang et al.2024 · 249 citations
11. Strategies for Pre-training Graph Neural Networks ↗arXiv (Cornell University) · no summary yetWeihua Hu et al.2019 · 228 citations
12. Self-Supervised Contrastive Pre-Training for Time Series Via Time-Frequency Consistency ↗neural information processing systems · no summary yetXiang Zhang et al.2022 · 210 citations
13. Artificial intelligence foundation for therapeutic science ↗Nature Chemical Biology · no summary yetKexin Huang et al.2022 · 201 citations
14. Identification of disease treatment mechanisms through the multiscale interactome ↗Nature Communications · no summary yetCamilo Ruiz, Marinka Žitnik, Jure Leskovec2021 · 168 citations
15. To Embed or Not: Network Embedding as a Paradigm in Computational Biology ↗Frontiers in Genetics · no summary yetWalter Nelson et al.2019 · 167 citations
16. Network enhancement as a general method to denoise weighted biological networks ↗Nature Communications · no summary yetBo Wang et al.2018 · 157 citations
17. Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development ↗arXiv (Cornell University) · no summary yetKexin Huang et al.2021 · 156 citations
18. Evolution of resilience in protein interactomes across the tree of life ↗Proceedings of the National Academy of Sciences · no summary yetMarinka Žitnik et al.2019 · 133 citations
19. Embedding Logical Queries on Knowledge Graphs ↗arXiv:1806.01445 · no summary yetWilliam L. Hamilton et al.2018 · 108 citations
20. Large-scale analysis of disease pathways in the human interactome ↗Pacific Symposium on Biocomputing (PSB) · no summary yetMonica Agrawal, Marinka Žitnik, Jure Leskovec2017 · 106 citations
21. Leveraging the Cell Ontology to classify unseen cell types ↗Nature Communications · no summary yetSheng Wang et al.2021 · 65 citations
22. Prioritizing network communities ↗Nature Communications · no summary yetMarinka Žitnik, Rok Sosič, Jure Leskovec2018 · 57 citations
23. TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools ↗arXiv:2503.10970 · no summary yetShanghua Gao et al.2025 · 17 citations
24. Identification of disease treatment mechanisms through the multiscale interactome ↗RePEc: Research Papers in Economics · no summary yetCamilo Ruiz, Marinka Žitnik, Jure Leskovec7 citations
25. Mutual interactors as a principle for phenotype discovery in molecular interaction networks ↗Pacific Symposium on Biocomputing (PSB) · no summary yetSabri Eyuboglu, Marinka Žitnik, Jure Leskovec2022 · 2 citations

See all 26 works by Marinka Žitnik →

🤝 Co-authors here

2 co-authors with a page, the most papers together first.

• Kexin Huang
• Luciano Del Corro

Venues

Where their works here were published, the most works first, with the editions of those that have a page.

• Nature Communications ×4
• Bioinformatics ×2
• Pacific Symposium on Biocomputing (PSB) ×2
• Annual Meeting of the Association for Computational Linguistics (ACL): ACL 2026
• Scientific Data: Scientific Data 2023
• ACM SIGKDD International Conference on Knowledge Discovery & Data Mining (KDD)
• Frontiers in Genetics
• Information Fusion
• Nature 620, 47-60 (2023)
• Nature Chemical Biology
• Nature Medicine
• Proceedings of the National Academy of Sciences

🔗 Cited by

Papers of our library cite their works 851 times (of the 149,439 papers whose bibliographies we read); 82 citing papers with a page here →.

Updated 1 November 2026

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