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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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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Wen J, Zhang X, Rush E, Panickan VA, Li X, Cai T, Zhou D, Ho YL, Costa L, Begoli E, Hong C, Gaziano JM, Cho K, Lu J, Liao KP, Zitnik M, Cai T. Multimodal representation learning for predicting molecule-disease relations. Bioinformatics. 2023 02 03; 39(2). PMID: 36805623; PMCID: PMC9940625.
    Citations:    Fields:    Translation:Humans
  2. Chandak P, Huang K, Zitnik M. Building a knowledge graph to enable precision medicine. Sci Data. 2023 02 02; 10(1):67. PMID: 36732524; PMCID: PMC9893183.
    Citations: 2     Fields:    Translation:Humans
  3. Chrisman B, Varma M, Maleki S, Brbic M, Joslyn C, Zitnik M. Session Introduction: Graph Representations and Algorithms in Biomedicine. Pac Symp Biocomput. 2023; 28:55-60. PMID: 36540964.
    Citations:    Fields:    Translation:Humans
  4. Eyuboglu S, Zitnik M, Leskovec J. Mutual interactors as a principle for phenotype discovery in molecular interaction networks. Pac Symp Biocomput. 2023; 28:61-72. PMID: 36540965.
    Citations:    Fields:    
  5. Li MM, Huang K, Zitnik M. Graph representation learning in biomedicine and healthcare. Nat Biomed Eng. 2022 12; 6(12):1353-1369. PMID: 36316368.
    Citations: 2     Fields:    Translation:Humans
  6. Wang Q, Huang K, Chandak P, Zitnik M, Gehlenborg N. Extending the Nested Model for User-Centric XAI: A Design Study on GNN-based Drug Repurposing. IEEE Trans Vis Comput Graph. 2022 Oct 12; PP. PMID: 36223348.
    Citations:    Fields:    
  7. Combi C, Amico B, Bellazzi R, Holzinger A, Moore JH, Zitnik M, Holmes JH. A manifesto on explainability for artificial intelligence in medicine. Artif Intell Med. 2022 11; 133:102423. PMID: 36328669.
    Citations: 1     Fields:    Translation:Humans
  8. Huang K, Fu T, Gao W, Zhao Y, Roohani Y, Leskovec J, Coley CW, Xiao C, Sun J, Zitnik M. Artificial intelligence foundation for therapeutic science. Nat Chem Biol. 2022 Oct; 18(10):1033-1036. PMID: 36131149; PMCID: PMC9529840.
    Citations: 3     Fields:    
  9. Patten JJ, Keiser PT, Morselli-Gysi D, Menichetti G, Mori H, Donahue CJ, Gan X, Valle ID, Geoghegan-Barek K, Anantpadma M, Boytz R, Berrigan JL, Stubbs SH, Ayazika T, O'Leary C, Jalloh S, Wagner F, Ayehunie S, Elledge SJ, Anderson D, Loscalzo J, Zitnik M, Gummuluru S, Namchuk MN, Barabási AL, Davey RA. Identification of potent inhibitors of SARS-CoV-2 infection by combined pharmacological evaluation and cellular network prioritization. iScience. 2022 Sep 16; 25(9):104925. PMID: 35992305; PMCID: PMC9374494.
    Citations: 3     
  10. Honarvar H, Agarwal C, Somani S, Vaid A, Lampert J, Wanyan T, Reddy VY, Nadkarni GN, Miotto R, Zitnik M, Wang F, Glicksberg BS. Enhancing convolutional neural network predictions of electrocardiograms with left ventricular dysfunction using a novel sub-waveform representation. Cardiovasc Digit Health J. 2022 Oct; 3(5):220-231. PMID: 36310683; PMCID: PMC9596304.
    Citations:    
  11. Patten JJ, Keiser PT, Gysi D, Menichetti G, Mori H, Donahue CJ, Gan X, do Valle I, Geoghegan-Barek K, Anantpadma M, Boytz R, Berrigan JL, Hulsey-Stubbs S, Ayazika T, O'Leary C, Jalloh S, Wagner F, Ayehunie S, Elledge SJ, Anderson D, Loscalzo J, Zitnik M, Gummuluru S, Namchuk MN, Barabási AL, Davey RA. Identification of druggable host targets needed for SARS-CoV-2 infection by combined pharmacological evaluation and cellular network directed prioritization both in vitro and in vivo. bioRxiv. 2022 Feb 01. PMID: 33907750; PMCID: PMC8077576.
    Citations:    
  12. Pan J, Kwon JJ, Talamas JA, Borah AA, Vazquez F, Boehm JS, Tsherniak A, Zitnik M, McFarland JM, Hahn WC. Sparse dictionary learning recovers pleiotropy from human cell fitness screens. Cell Syst. 2022 04 20; 13(4):286-303.e10. PMID: 35085500; PMCID: PMC9035054.
    Citations: 4     Fields:    Translation:Humans
  13. Stupp D, Sharon E, Bloch I, Zitnik M, Zuk O, Tabach Y. Co-evolution based machine-learning for predicting functional interactions between human genes. Nat Commun. 2021 11 09; 12(1):6454. PMID: 34753957.
    Citations: 6     Fields:    Translation:HumansCells
  14. Wanyan T, Honarvar H, Jaladanki SK, Zang C, Naik N, Somani S, De Freitas JK, Paranjpe I, Vaid A, Zhang J, Miotto R, Wang Z, Nadkarni GN, Zitnik M, Azad A, Wang F, Ding Y, Glicksberg BS. Contrastive learning improves critical event prediction in COVID-19 patients. Patterns (N Y). 2021 Dec 10; 2(12):100389. PMID: 34723227; PMCID: PMC8542449.
    Citations: 8     
  15. Wang S, Pisco AO, McGeever A, Brbic M, Zitnik M, Darmanis S, Leskovec J, Karkanias J, Altman RB. Leveraging the Cell Ontology to classify unseen cell types. Nat Commun. 2021 09 21; 12(1):5556. PMID: 34548483.
    Citations: 8     Fields:    Translation:HumansAnimalsCells
  16. Kunz SN, Helkey D, Zitnik M, Phibbs CS, Rigdon J, Zupancic JAF, Profit J. Quantifying the variation in neonatal transport referral patterns using network analysis. J Perinatol. 2021 12; 41(12):2795-2803. PMID: 34035453; PMCID: PMC8613294.
    Citations: 1     Fields:    Translation:Humans
  17. Morselli Gysi D, do Valle Í, Zitnik M, Ameli A, Gan X, Varol O, Ghiassian SD, Patten JJ, Davey RA, Loscalzo J, Barabási AL. Network medicine framework for identifying drug-repurposing opportunities for COVID-19. Proc Natl Acad Sci U S A. 2021 05 11; 118(19). PMID: 33906951; PMCID: PMC8126852.
    Citations: 106     Fields:    Translation:HumansAnimalsCells
  18. Huang K, Fu T, Glass LM, Zitnik M, Xiao C, Sun J. DeepPurpose: a deep learning library for drug-target interaction prediction. Bioinformatics. 2021 04 01; 36(22-23):5545-5547. PMID: 33275143.
    Citations: 44     Fields:    
  19. Ruiz C, Zitnik M, Leskovec J. Identification of disease treatment mechanisms through the multiscale interactome. Nat Commun. 2021 03 19; 12(1):1796. PMID: 33741907.
    Citations: 19     Fields:    Translation:HumansAnimalsCells
  20. Wanyan T, Honarvar H, Jaladanki SK, Zang C, Naik N, Somani S, Freitas JK, Paranjpe I, Vaid A, Miotto R, Nadkarni GN, Zitnik M, Wang F, Ding Y, Glicksberg BS. Contrastive Learning Improves Critical Event Prediction in COVID-19 Patients. ArXiv. 2021 Jan 11. PMID: 33442560; PMCID: PMC7805456.
    Citations:    
  21. Huang K, Xiao C, Glass LM, Zitnik M, Sun J. SkipGNN: predicting molecular interactions with skip-graph networks. Sci Rep. 2020 12 03; 10(1):21092. PMID: 33273494; PMCID: PMC7713130.
    Citations: 8     Fields:    
  22. Brbic M, Zitnik M, Wang S, Pisco AO, Altman RB, Darmanis S, Leskovec J. MARS: discovering novel cell types across heterogeneous single-cell experiments. Nat Methods. 2020 12; 17(12):1200-1206. PMID: 33077966.
    Citations: 28     Fields:    Translation:AnimalsCells
  23. Gysi DM, Valle ÍD, Zitnik M, Ameli A, Gan X, Varol O, Ghiassian SD, Patten JJ, Davey R, Loscalzo J, Barabási AL. Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19. ArXiv. 2020 Apr 15. PMID: 32550253; PMCID: PMC7280907.
    Citations:    
  24. 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; PMCID: PMC7138248.
    Citations: 45     
  25. Copar A, Zupan B, Zitnik M. Fast optimization of non-negative matrix tri-factorization. PLoS One. 2019; 14(6):e0217994. PMID: 31185054; PMCID: PMC6559648.
    Citations:    Fields:    
  26. 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.
    Citations: 35     Fields:    
  27. 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; PMCID: PMC6504708.
    Citations: 37     
  28. 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; PMCID: PMC6410798.
    Citations: 18     Fields:    
  29. 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; PMCID: PMC6242341.
    Citations: 113     
  30. 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.
    Citations: 20     Fields:    Translation:HumansCells
  31. Zitnik M, Agrawal M, Leskovec J. Modeling polypharmacy side effects with graph convolutional networks. Bioinformatics. 2018 07 01; 34(13):i457-i466. PMID: 29949996.
    Citations: 166     Fields:    Translation:Humans
  32. Zitnik M, Sosic R, Leskovec J. Prioritizing network communities. Nat Commun. 2018 06 29; 9(1):2544. PMID: 29959323.
    Citations: 13     Fields:    Translation:HumansAnimals
  33. 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.
    Citations: 21     Fields:    Translation:HumansCells
  34. 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.
    Citations: 45     Fields:    Translation:HumansCells
  35. Zitnik M, Leskovec J. Predicting multicellular function through multi-layer tissue networks. Bioinformatics. 2017 Jul 15; 33(14):i190-i198. PMID: 28881986; PMCID: PMC5870717.
    Citations: 46     Fields:    Translation:Humans
  36. Zitnik M, Zupan B. Jumping across biomedical contexts using compressive data fusion. Bioinformatics. 2016 06 15; 32(12):i90-i100. PMID: 27307649.
    Citations: 6     Fields:    Translation:Humans
  37. 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; PMCID: PMC4719585.
    Citations: 9     Fields:    Translation:Humans
  38. 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.
    Citations: 3     Fields:    Translation:Cells
  39. 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.
    Citations: 14     Fields:    Translation:Animals
  40. 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.
    Citations: 3     Fields:    
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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.