--- title: "Marinka Žitnik · Broad Institute — author profile and papers" description: "Marinka Žitnik, Broad Institute: 2 papers on Elamur Research (2023–2026), h-index 53 — affiliations, topics, co-authors and who cites them in…" canonical: "https://research.elamur.ai/free/en/authors/marinka-zitnik/" --- [Elamur Research](https://md.research.elamur.ai/free/en/) · [this page in HTML](https://research.elamur.ai/free/en/authors/marinka-zitnik/) [home](https://md.research.elamur.ai/free/en/) / [authors](https://md.research.elamur.ai/free/en/authors/) / Marinka Žitnik # Marinka Žitnik Marinka Žitnik has 2 papers in our library, in 2023–2026, most of them on [Knowledge graphs & ontologies](https://md.research.elamur.ai/free/en/topics/knowledge-graphs/), [Information retrieval & search](https://md.research.elamur.ai/free/en/topics/information-retrieval/); often with [Kexin Huang](https://md.research.elamur.ai/free/en/authors/kexin-huang/), [Luciano Del Corro](https://md.research.elamur.ai/free/en/authors/luciano-del-corro/). 2 papers in our library · 2023–2026 [OpenAlex](https://openalex.org/A5086052373) · [ORCID](https://orcid.org/0000-0001-8530-7228) · [Wikidata](https://www.wikidata.org/wiki/Q59753151) · [**h-index 53**](https://openalex.org/authors/A5086052373) · [308 works](https://openalex.org/works?filter=author.id:A5086052373) · [16,500 citations](https://openalex.org/works?filter=author.id:A5086052373&sort=cited_by_count:desc) OpenAlex, 2026-10-14 [📄 2 works in our library](https://md.research.elamur.ai/free/en/authors/marinka-zitnik/#papers) · [🔗 Cited 851 times in our library](https://md.research.elamur.ai/free/en/authors/marinka-zitnik/cited-by/) · [24 more in our library without a page yet](#also) · [⭐ Paper Stars ranking: #3636](https://md.research.elamur.ai/free/en/paper-stars/page/37/#star-3636) The profile is the library's match of the name; two people with one name are not always told apart. Elsewhere: [Google Scholar](https://scholar.google.com/citations?view_op=search_authors&mauthors=Marinka+%C5%BDitnik) · [Semantic Scholar](https://www.semanticscholar.org/search?q=Marinka+%C5%BDitnik) · [dblp](https://dblp.org/search?q=Marinka+%C5%BDitnik) · [ACL Anthology](https://aclanthology.org/search/?q=Marinka+%C5%BDitnik) ## Affiliations [🎓**Harvard University** Cambridge · United States 2019–2026 · 162 papersEmployment · Associate Professor, Department of Biomedical Informatics*current*](https://md.research.elamur.ai/free/en/universities/harvard-university/) · [🔬**Broad Institute** Cambridge · United States 2021–2026 · 56 papers*current*](https://md.research.elamur.ai/free/en/labs/broad-institute/) · [🎓**University of Ljubljana** Ljubljana · Slovenia 2008–2019 · 28 papersEducation 2008–2012Education 2012–2015Employment](https://md.research.elamur.ai/free/en/universities/university-of-ljubljana/) · [🎓**Stanford University** Stanford · United States 2016–2024 · 26 papersEducation 2016–2019Employment](https://md.research.elamur.ai/free/en/universities/stanford-university/) · [🎓**Massachusetts Institute of Technology** Cambridge · United States 2021–2024 · 8 papers](https://md.research.elamur.ai/free/en/universities/massachusetts-institute-of-technology/) · [🔬**Harvard University Press** Cambridge · United States 2020–2023 · 3 papers](https://ror.org/006v7bf86) · [🎓**Princeton University** Princeton · United States 2023–2024 · 2 papers](https://md.research.elamur.ai/free/en/universities/princeton-university/) · [🎓**Baylor College of Medicine** Houston · United States 2014–2015 · 2 papersEmployment](https://ror.org/02pttbw34) 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. 📚 Shelves 7 The field of science this work belongs to (OpenAlex fields).[Computer Science · 2 works](https://md.research.elamur.ai/free/en/shelves/computer-science/) · [Biochemistry, Genetics and Molecular Biology · 1 work](https://md.research.elamur.ai/free/en/shelves/biochemistry-genetics-and-molecular-biology/) · [Computational Theory and Mathematics · 1 work](https://md.research.elamur.ai/free/en/shelves/computer-science/computational-theory-and-mathematics/) · [Molecular Biology · 1 work](https://md.research.elamur.ai/free/en/shelves/biochemistry-genetics-and-molecular-biology/molecular-biology/) · [Artificial Intelligence · 1 work](https://md.research.elamur.ai/free/en/shelves/computer-science/artificial-intelligence/) · [Arts and Humanities · 1 work](https://md.research.elamur.ai/free/en/shelves/arts-and-humanities/) · [Language and Linguistics · 1 work](https://md.research.elamur.ai/free/en/shelves/arts-and-humanities/language-and-linguistics/) 🧭 Topics 2 Research subjects and languages the work is about.[Knowledge graphs & ontologies · 2 works](https://md.research.elamur.ai/free/en/topics/knowledge-graphs/) · [Information retrieval & search · 1 work](https://md.research.elamur.ai/free/en/topics/information-retrieval/) 💡 Concepts 1 Key ideas and methods explained on our concept pages.[Knowledge graph · 1 work](https://md.research.elamur.ai/free/en/concepts/knowledge-graph/) ## Works by year ### 2020s [**2026** 1 paper](https://md.research.elamur.ai/free/en/authors/marinka-zitnik/year/2026/) · [**2023** 1 paper](https://md.research.elamur.ai/free/en/authors/marinka-zitnik/year/2023/) ## Papers The most cited first (OpenAlex and our library). 1. **[Building a knowledge graph to enable precision medicine](https://md.research.elamur.ai/free/en/papers/chandak-2023-building-knowledge-graph-enable-precision/)** *(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](https://md.research.elamur.ai/free/en/papers/polonuer-2026-autonomous-knowledge-graph-exploration-adaptive/)** *(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 ↗](https://doi.org/10.1038/s41586-023-06221-2) Nature 620, 47-60 (2023) · no summary yet**Hanchen Wang et al.*2023 · 1,860 citations* 2. **[Modeling polypharmacy side effects with graph convolutional networks ↗](https://doi.org/10.1093/bioinformatics/bty294) Bioinformatics · no summary yet**Marinka Žitnik, Monica Agrawal, Jure Leskovec*2018 · 1,517 citations* 3. **[Open Graph Benchmark: Datasets for Machine Learning on Graphs ↗](https://arxiv.org/abs/2005.00687) arXiv:2005.00687 · no summary yet**Weihua Hu et al.*2020 · 712 citations* 4. **[GNNExplainer: Generating Explanations for Graph Neural Networks ↗](https://arxiv.org/abs/1903.03894) arXiv (Cornell University) · no summary yet**Rex Ying et al.*2019 · 685 citations* 5. **[Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities ↗](https://doi.org/10.1016/j.inffus.2018.09.012) Information Fusion · no summary yet**Marinka Žitnik et al.*2018 · 663 citations* 6. **[Building a knowledge graph to enable precision medicine](https://md.research.elamur.ai/free/en/papers/chandak-2023-building-knowledge-graph-enable-precision/) [Scientific Data](https://md.research.elamur.ai/free/en/venues/scientific-data/)**Payal Chandak, Kexin Huang, Marinka Žitnik*2023 · 555 citations* 7. **[Predicting multicellular function through multi-layer tissue networks ↗](https://doi.org/10.1093/bioinformatics/btx252) Bioinformatics · no summary yet**Marinka Žitnik, Jure Leskovec*2017 · 542 citations* 8. **[Learning Structural Node Embeddings via Diffusion Wavelets ↗](https://doi.org/10.1145/3219819.3220025) ACM SIGKDD International Conference on Knowledge Discovery & Data Mining (KDD) · no summary yet**Claire Donnat et al.*2018 · 366 citations* 9. **[Empowering Biomedical Discovery with AI Agents ↗](https://arxiv.org/abs/2404.02831) arXiv:2404.02831 · no summary yet**Shanghua Gao et al.*2024 · 333 citations* 10. **[A foundation model for clinician-centered drug repurposing ↗](https://doi.org/10.1038/s41591-024-03233-x) Nature Medicine · no summary yet**Kexin Huang et al.*2024 · 249 citations* 11. **[Strategies for Pre-training Graph Neural Networks ↗](https://arxiv.org/abs/1905.12265) arXiv (Cornell University) · no summary yet**Weihua Hu et al.*2019 · 228 citations* 12. **[Self-Supervised Contrastive Pre-Training for Time Series Via Time-Frequency Consistency ↗](https://doi.org/10.52202/068431-0288) neural information processing systems · no summary yet**Xiang Zhang et al.*2022 · 210 citations* 13. **[Artificial intelligence foundation for therapeutic science ↗](https://doi.org/10.1038/s41589-022-01131-2) Nature Chemical Biology · no summary yet**Kexin Huang et al.*2022 · 201 citations* 14. **[Identification of disease treatment mechanisms through the multiscale interactome ↗](https://doi.org/10.1038/s41467-021-21770-8) Nature Communications · no summary yet**Camilo Ruiz, Marinka Žitnik, Jure Leskovec*2021 · 168 citations* 15. **[To Embed or Not: Network Embedding as a Paradigm in Computational Biology ↗](https://doi.org/10.3389/fgene.2019.00381) Frontiers in Genetics · no summary yet**Walter Nelson et al.*2019 · 167 citations* 16. **[Network enhancement as a general method to denoise weighted biological networks ↗](https://doi.org/10.1038/s41467-018-05469-x) Nature Communications · no summary yet**Bo Wang et al.*2018 · 157 citations* 17. **[Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development ↗](https://arxiv.org/abs/2102.09548) arXiv (Cornell University) · no summary yet**Kexin Huang et al.*2021 · 156 citations* 18. **[Evolution of resilience in protein interactomes across the tree of life ↗](https://doi.org/10.1073/pnas.1818013116) Proceedings of the National Academy of Sciences · no summary yet**Marinka Žitnik et al.*2019 · 133 citations* 19. **[Embedding Logical Queries on Knowledge Graphs ↗](https://arxiv.org/abs/1806.01445) arXiv:1806.01445 · no summary yet**William L. Hamilton et al.*2018 · 108 citations* 20. **[Large-scale analysis of disease pathways in the human interactome ↗](https://doi.org/10.1142/9789813235533_0011) Pacific Symposium on Biocomputing (PSB) · no summary yet**Monica Agrawal, Marinka Žitnik, Jure Leskovec*2017 · 106 citations* 21. **[Leveraging the Cell Ontology to classify unseen cell types ↗](https://doi.org/10.1038/s41467-021-25725-x) Nature Communications · no summary yet**Sheng Wang et al.*2021 · 65 citations* 22. **[Prioritizing network communities ↗](https://doi.org/10.1038/s41467-018-04948-5) Nature Communications · no summary yet**Marinka Žitnik, Rok Sosič, Jure Leskovec*2018 · 57 citations* 23. **[TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools ↗](https://arxiv.org/abs/2503.10970) arXiv:2503.10970 · no summary yet**Shanghua Gao et al.*2025 · 17 citations* 24. **[Identification of disease treatment mechanisms through the multiscale interactome ↗](https://doi.org/10.1101/2020.04.30.069690) RePEc: Research Papers in Economics · no summary yet**Camilo Ruiz, Marinka Žitnik, Jure Leskovec*7 citations* 25. **[Mutual interactors as a principle for phenotype discovery in molecular interaction networks ↗](https://doi.org/10.1142/9789811270611_0007) Pacific Symposium on Biocomputing (PSB) · no summary yet**Sabri Eyuboglu, Marinka Žitnik, Jure Leskovec*2022 · 2 citations* [See all 26 works by Marinka Žitnik →](https://md.research.elamur.ai/free/en/authors/marinka-zitnik/works/) ## Co-authors here 2 co-authors with a page, the most papers together first. - [Kexin Huang](https://md.research.elamur.ai/free/en/authors/kexin-huang/) - [Luciano Del Corro](https://md.research.elamur.ai/free/en/authors/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)](https://md.research.elamur.ai/free/en/venues/acl/): [ACL 2026](https://md.research.elamur.ai/free/en/venues/acl/2026/) - [Scientific Data](https://md.research.elamur.ai/free/en/venues/scientific-data/): [Scientific Data 2023](https://md.research.elamur.ai/free/en/venues/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 →](https://md.research.elamur.ai/free/en/authors/marinka-zitnik/cited-by/). Updated 1 November 2026