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Marinka Zitnik, Ph.D.

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Ying R, Bourgeois D, You J, Zitnik M, Leskovec J. GNNExplainer: Generating Explanations for Graph Neural Networks. Adv Neural Inf Process Syst. 2019 Dec; 32:9240-9251. PMID: 32265580.
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  2. Copar A, Zupan B, Zitnik M. Fast optimization of non-negative matrix tri-factorization. PLoS One. 2019; 14(6):e0217994. PMID: 31185054.
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  3. Wang X, Zhang Y, Ren X, Zhang Y, Zitnik M, Shang J, Langlotz C, Han J. Cross-type biomedical named entity recognition with deep multi-task learning. Bioinformatics. 2019 05 15; 35(10):1745-1752. PMID: 30307536.
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  4. Nelson W, Zitnik M, Wang B, Leskovec J, Goldenberg A, Sharan R. To Embed or Not: Network Embedding as a Paradigm in Computational Biology. Front Genet. 2019; 10:381. PMID: 31118945.
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  5. Zitnik M, Sosic R, Feldman MW, Leskovec J. Evolution of resilience in protein interactomes across the tree of life. Proc Natl Acad Sci U S A. 2019 03 05; 116(10):4426-4433. PMID: 30765515.
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  6. Zitnik M, Nguyen F, Wang B, Leskovec J, Goldenberg A, Hoffman MM. Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities. Inf Fusion. 2019 Oct; 50:71-91. PMID: 30467459.
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  7. Wang B, Pourshafeie A, Zitnik M, Zhu J, Bustamante CD, Batzoglou S, Leskovec J. Network enhancement as a general method to denoise weighted biological networks. Nat Commun. 2018 08 06; 9(1):3108. PMID: 30082777.
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  8. Zitnik M, Agrawal M, Leskovec J. Modeling polypharmacy side effects with graph convolutional networks. Bioinformatics. 2018 07 01; 34(13):i457-i466. PMID: 29949996.
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  9. Zitnik M, Sosic R, Leskovec J. Prioritizing network communities. Nat Commun. 2018 06 29; 9(1):2544. PMID: 29959323.
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  10. Agrawal M, Zitnik M, Leskovec J. Large-scale analysis of disease pathways in the human interactome. Pac Symp Biocomput. 2018; 23:111-122. PMID: 29218874.
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  11. Carreras-Puigvert J, Zitnik M, Jemth AS, Carter M, Unterlass JE, Hallström B, Loseva O, Karem Z, Calderón-Montaño JM, Lindskog C, Edqvist PH, Matuszewski DJ, Ait Blal H, Berntsson RPA, Häggblad M, Martens U, Studham M, Lundgren B, Wählby C, Sonnhammer ELL, Lundberg E, Stenmark P, Zupan B, Helleday T. A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family. Nat Commun. 2017 11 16; 8(1):1541. PMID: 29142246.
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  12. Zitnik M, Leskovec J. Predicting multicellular function through multi-layer tissue networks. Bioinformatics. 2017 Jul 15; 33(14):i190-i198. PMID: 28881986.
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  13. Zitnik M, Zupan B. Jumping across biomedical contexts using compressive data fusion. Bioinformatics. 2016 06 15; 32(12):i90-i100. PMID: 27307649.
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  14. Zitnik M, Zupan B. COLLECTIVE PAIRWISE CLASSIFICATION FOR MULTI-WAY ANALYSIS OF DISEASE AND DRUG DATA. Pac Symp Biocomput. 2016; 21:81-92. PMID: 26776175.
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  15. Zitnik M, Zupan B. Gene network inference by probabilistic scoring of relationships from a factorized model of interactions. Bioinformatics. 2014 Jun 15; 30(12):i246-i254. PMID: 24931990.
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  16. Zitnik M, Zupan B. Matrix factorization-based data fusion for gene function prediction in baker's yeast and slime mold. Pac Symp Biocomput. 2014; 400-11. PMID: 24297565.
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  17. Kavcic M, Zitnik M, Bucar K, Mihelic A, Stuhec M, Szlachetko J, Cao W, Alonso Mori R, Glatzel P. Separation of two-electron photoexcited atomic processes near the inner-shell threshold. Phys Rev Lett. 2009 Apr 10; 102(14):143001. PMID: 19392433.
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.