Marinka Zitnik
Marinka Zitnik, PhD
Assistant Professor of Biomedical Informatics, Harvard Medical School

Marinka Zitnik investigates machine learning for science and medicine. Her methods leverage biomedical data at the scale of billions of interactions among millions of entities, blend machine learning with statistics and data science, and infuse biomedical knowledge into deep learning. Problems she investigates are motivated by network biology and medicine, genomics, drug discovery, and health.

Dr. Zitnik's research vision is that in the future data science and artificial intelligence will be routinely used to give clinicians diagnostic recommendations; give scientists testable hypotheses they can confirm experimentally and offer them insights into safe and precise treatments; and give patients guidance on self-care, e.g., how to lead a healthy lifestyle and recognize disease early. To realize this vision, Dr. Zitnik develops methods to reason over rich interconnected data and translates the methods into solutions for biomedical problems.

Before joining Harvard, Dr. Zitnik was a postdoctoral fellow in Computer Science at Stanford University and was involved in projects at Chan Zuckerberg Biohub. She received her Ph.D. in Computer Science from University of Ljubljana while also researching at Imperial College London, University of Toronto, Baylor College of Medicine, and Stanford University. 

DBMI Research Areas
Current Postdoctoral Fellowship Opportunities
Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities.
Authors: Zitnik M, Nguyen F, Wang B, Leskovec J, Goldenberg A, Hoffman MM.
Inf Fusion
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Cross-type biomedical named entity recognition with deep multi-task learning.
Authors: Wang X, Zhang Y, Ren X, Zhang Y, Zitnik M, Shang J, Langlotz C, Han J.
Bioinformatics
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Evolution of resilience in protein interactomes across the tree of life.
Authors: Zitnik M, Sosic R, Feldman MW, Leskovec J.
Proc Natl Acad Sci U S A
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To Embed or Not: Network Embedding as a Paradigm in Computational Biology.
Authors: Nelson W, Zitnik M, Wang B, Leskovec J, Goldenberg A, Sharan R.
Front Genet
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Fast optimization of non-negative matrix tri-factorization.
Authors: Copar A, Zupan B, Zitnik M.
PLoS One
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Network enhancement as a general method to denoise weighted biological networks.
Authors: Wang B, Pourshafeie A, Zitnik M, Zhu J, Bustamante CD, Batzoglou S, Leskovec J.
Nat Commun
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Modeling polypharmacy side effects with graph convolutional networks.
Authors: Zitnik M, Agrawal M, Leskovec J.
Bioinformatics
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Prioritizing network communities.
Authors: Zitnik M, Sosic R, Leskovec J.
Nat Commun
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Large-scale analysis of disease pathways in the human interactome.
Authors: Agrawal M, Zitnik M, Leskovec J.
Pac Symp Biocomput
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A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family.
Authors: 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.
Nat Commun
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