Marinka Zitnik

Fusing bits and DNA

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Home Selected Publications

Selected Publications

Full List / Google Scholar

* indicates equal contribution.

Journal Papers

  1. Marinka Zitnik, Russ Altman, Jure Leskovec. Network-Based Discovery of Drug Indications. In Review, 2019.
  2. Marinka Zitnik, Rok Sosic, Marcus W. Feldman, Jure Leskovec. Evolution of Resilience in Protein Interactomes Across the Tree of Life. Proceedings of the National Academy of Sciences (PNAS), 116, 10:4426-4433, 2019. [bioRxiv] [Website] [Stanford News] [Poster] [Slides ISMB 2019] [Slides CEHG 2019]
  3. Walter Nelson, Marinka Zitnik, Bo Wang, Jure Leskovec, Anna Goldenberg, Roded Sharan. To Embed or Not: Network Embedding as a Paradigm in Computational Biology. Frontiers in Genetics, 10, 381, 2019.
  4. Marinka Zitnik, Francis Nguyen, Bo Wang, Jure Leskovec, Anna Goldenberg, Michael M. Hoffman. Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities. Information Fusion, 50, 71-91, 2019. [arXiv] [Technology Feature in Nature Methods]
  5. Andrej Copar, Blaz Zupan, Marinka Zitnik. Fast Optimization of Non-negative Matrix Tri-factorization. PLoS One, 14, 6, e0217994, 2019. [Code]
  6. Bo Wang*, Armin Pourshafeie*, Marinka Zitnik*, Junjie Zhu, Carlos Bustamante, Serafim Batzoglou, Jure Leskovec. Network Enhancement as a General Method to Denoise Weighted Biological NetworksNature Communications, 9, 3108, 2018 (* First co-authors). [Website] [arXiv] [bioRxiv]
  7. Marinka Zitnik, Rok Sosic, Jure Leskovec. Prioritizing Network Communities. Nature Communications, 9, 2544, 2018. [Website] [Invited talk at JMM 2018 Graph Clustering Session] [arXiv] [bioRxiv]
  8. Xuan Wang, Yu Zhang, Xiang Ren, Yuhao Zhang, Marinka Zitnik, Jingbo Shang, Curtis Langlotz, Jiawei Han. Cross-type Biomedical Named Entity Recognition with Deep Multi-Task LearningBioinformatics, 35, 10:1745-1752, 2018. [arXiv] [bioRxiv] [Code and Data]
  9. Marinka Zitnik, Monica Agrawal, Jure Leskovec. Modeling Polypharmacy Side Effects with Graph Convolutional Networks. Bioinformatics, 34, 13:457-466, 2018. Oral presentation at ISMB'18. [arXiv] [bioRxiv] [Website] [Code] [Slides] [Poster] [Conference Talk] [Stanford News][ScienceDaily] [Phys.org] [Other news stories]
  10. Andrej Copar, Marinka Zitnik, Blaz Zupan. Scalable Non-Negative Matrix Tri-Factorization. BioData Mining, 10, 41, 2017. [Code]
  11. J.C. Puigvert, Marinka Zitnik, A.-S. Jemth, M. Carter, J. Unterlass, B. Hallstrom, O. Loseva, Z. Karem, J.M. Calderon-Montano, C. Lindskog, P.H. Edqvist, D. Matuszewski, H.A. Blal, R. Berntsson, M. Haggblad, U. Martens, M. Studham, M. Uhlen, B. Lundgren, C. Wahlby, E. Sonnhammer, E. Lundberg, P. Stenmark, B. Zupan, T. Helleday. A Comprehensive Structural, Biochemical and Biological Profiling of the Human NUDIX Hydrolase Family. Nature Communications, 8, 1541, 2017. [Karolinska Institutet News] [SciLifeLab News] [Phys.org News]
  12. Marinka Zitnik, Jure Leskovec. Predicting Multicellular Function Through Multi-Layer Tissue Networks. Bioinformatics, 33, 14:190-198, 2017. [Website] [Code] [Slides NetSci17 Network Medicine invited talk] [Video] Oral presentation at ISMB'17.
  13. A. Keller, R.C. Gerkin, Y. Guan, A. Dhurandhar, G. Turu, B. Szalai, J.D. Mainland, Y. Ihara, C.W. Yu, R. Wolfinger, C. Vens, L. Schietgat, K. De Grave, R. Norel, DREAM Olfaction Consortium, G. Stolovitzky, G. Cecchi, L.B. Vosshall, P. Meyer. Predicting Human Olfactory Perception from Chemical Features of Odor Molecules. Science, 355, 6327:820-826, 2017. [Press]
  14. Marinka Zitnik, Blaz Zupan. Jumping Across Biomedical Contexts Using Compressive Data Fusion. Bioinformatics, 32, 12:90-100, 2016. Oral presentation at ISMB'16. [Slides] [Video] [Code]
  15. Martin Strazar, Marinka Zitnik, Blaz Zupan, Jernej Ule, Tomaz Curk. Orthogonal Matrix Factorization Enables Integrative Analysis of Multiple RNA Binding Proteins. Bioinformatics, 32, 10:1527-1535, 2016.
  16. Slavko Zitnik, Marinka Zitnik, Blaz Zupan, Marko Bajec. Sieve-Based Relation Extraction of Gene Regulatory Networks from Biological Literature.BMC Bioinformatics, 16, Suppl 16:S1, 2015. [ACL BioNLP-13]
  17. Marinka Zitnik, Edward A Nam, Christopher Dinh, Adam Kuspa, Gad Shaulsky, Blaz Zupan. Gene Prioritization by Compressive Data Fusion and Chaining. PLoS Computational Biology, 11, 10:e1004552, 2015. Department award for graduate student research. [Code]
  18. Marinka Zitnik, Blaz Zupan. Gene Network Inference by Fusing Data from Diverse Distributions. Bioinformatics, 31, 12:230-239, 2015. Oral presentation at ISMB'15. [Slides] [Video] [Code]
  19. M. Mattiazzi Usaj*, M. Brloznik*, P. Kaferle*, M. Zitnik, H. Wolinski, F. Leitner, S. D. Kohlwein, B. Zupan, U. Petrovic. Genome-Wide Localization Study of Yeast Pex11 Identifies Peroxisome-Mitochondria Interactions Through the ERMES ComplexJournal of Molecular Biology, 427, 11:2072 2087, 2015. (* First co-authors).
  20. Marinka Zitnik, Blaz Zupan. Survival Regression by Data Fusion. Systems Biomedicine, 2, 3:47-53, 2015.
  21. Marinka Zitnik, Blaz Zupan. Data Imputation in Epistatic MAPs by Network-Guided Matrix CompletionJournal of Computational Biology, 22, 6:595-608, 2015. Oral presentation at RECOMB'14. [Slides] [Code]
  22. Marinka Zitnik, Blaz Zupan. Data Fusion by Matrix Factorization. IEEE Transactions on Pattern Analysis and Machine Intelligence, 37, 1:41-53, 2015. [Code]
  23. Marinka Zitnik, Blaz Zupan. Gene Network Inference by Probabilistic Scoring of Relationships from a Factorized Model of Interactions. Bioinformatics, 30, 12:246-254, 2014. Oral presentation at ISMB'14. Department award for graduate student research. [Slides] [Video] [Code]
  24. Marinka Zitnik, Blaz Zupan. Matrix Factorization-Based Data Fusion for Drug-Induced Liver Injury Prediction. Systems Biomedicine, 2, 1:16-22, 2014.
  25. Marinka Zitnik, Vuk Janjic, Chris Larminie, Blaz Zupan, Natasa Przulj. Discovering Disease-Disease Associations by Fusing Systems-Level Molecular Data. Scientific Reports, 3, e3202, 2013. Department award for graduate student research. [Press]
  26. Janez Demsar, ..., Marinka Zitnik, et al. Orange: Data Mining Toolbox in Python. Journal of Machine Learning Research, 14:2349-2353, 2013.
  27. Marinka Zitnik, Blaz Zupan. Nimfa: A Python Library for Nonnegative Matrix FactorizationJournal of Machine Learning Research, 13:849-853, 2012. [Website] [Code]

Conference Papers

  1. Rex Ying, Dylan Bourgeois, Jiaxuan You, Marinka Zitnik, Jure Leskovec. GNN Explainer: Generating Explanations for Graph Neural Networks. In Review, 2019. [arXiv]
  2. Weihua Hu, Bowen Liu, Joseph Gomes, Marinka Zitnik, Percy Liang, Vijay Pande, Jure Leskovec. Pre-training Graph Neural Networks. In Review, 2019. [arXiv]
  3. Sarah Kunz, Marinka Zitnik, John Zupancic, Jure Leskovec, Joseph Rigdon, Jochen Profit. Variation in Neonatal Referral Networks across Patient Groups. In Pediatric Academic Societies Meeting, PAS, 2019.
  4. William Hamilton, Payal Bajaj, Marinka Zitnik, Dan Jurafsky, Jure Leskovec. Embedding Logical Queries on Knowledge Graphs. In Proceedings of Neural Information Processing Systems, NIPS, 32, 2018. [arXiv]
  5. Claire Donnat, Marinka Zitnik, David Hallac, Jure Leskovec. Learning Structural Node Embeddings via Diffusion Wavelets. In International ACM Conference on Knowledge Discovery and Data Mining, KDD, 24, 2018. [Website] [arXiv] [Video]
  6. Monica Agrawal*, Marinka Zitnik*, Jure Leskovec. Large-Scale Analysis of Disease Pathways in the Human Interactome. In Pacific Symposium on Biocomputing, 23:111-122, Hawaii, HI, USA, 2018. [Website] [bioRxiv] (* First co-authors).
  7. Marinka Zitnik, Blaz Zupan. Collective Pairwise Classification for Multi-Way Analysis of Disease and Drug Data. In Pacific Symposium on Biocomputing, 21:81-92, Hawaii, HI, USA, 2016. [Slides] [Code]
  8. Marinka Zitnik, Blaz Zupan. Large-Scale Data Fusion. In Minisymposia at 37th Annnual International Conference of the IEEE Engineering in Medicine and Biology, EMBC, Milan, Italy, 2015. [Slides]
  9. Marinka Zitnik, Blaz Zupan. Survival Regression by Data Fusion. In ISMB 2014CAMDA, Boston, MA, USA, 2014. First prize winner for excellent research at ISMB/CAMDA'14. [Slides]
  10. Marinka Zitnik, Blaz Zupan. Imputation of Quantitative Genetic Interactions in Epistatic MAPs by Interaction Propagation Matrix Completion. In Proceedings of 18th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2014, 8394:448-462, Pittsburgh, PA, USA, 2014. [Slides] [Code]
  11. Marinka Zitnik, Blaz Zupan. Matrix Factorization-Based Data Fusion For Gene Function Prediction in Baker's Yeast and Slime Mold. In Pacific Symposium on Biocomputing, 19:400-411, Hawaii, HI, USA, 2014.
  12. Marinka Zitnik, Blaz Zupan. Matrix Factorization-Based Data Fusion for Drug-Induced Liver Injury Prediction. In ISMB/ECCB 2013, CAMDA, Berlin, Germany, 2013. First prize winner for excellent research at ISMB/CAMDA'13. [Slides]
  13. Slavko Zitnik, Marinka Zitnik, Blaz Zupan, Marko Bajec. Extracting Gene Regulation Networks Using Linear-Chain Conditional Random Fields and Rules. In Association for Computational Linguistics, ACL, BioNLP Shared Task Workshop, Sofia, Bulgaria, 2013. First place winner in extracting gene regulatory networks from text at ACL BioNLP-13.
  14. Jure Zbontar, Marinka Zitnik, Miha Zidar, Gregor Majcen, Matic Potocnik, Blaz Zupan. Team ULjubljana's Solution to the JRS 2012 Data Mining Competition. In Rough Sets and Current Trends in Computing, 7413/2012, 471-478, Chengdu, China, 2012.
Poster Sessions
  1. Marinka Zitnik, Monica Agrawal, Jure Leskovec. Modeling Polypharmacy Side Effects with Graph Convolutional Networks. Poster session presented at International Conference on Intelligent Systems for Molecular Biology, ISMB/ECCB, 6-10 Jul 2018, Chicago, IL, USA. [Poster]
  2. Monica Agrawal*, Marinka Zitnik*, Jure Leskovec. Large-Scale Analysis of Disease Pathways in the Human Interactome. Poster session presented at Pacific Symposium on Biocomputing, 3-7 Jan 2018, Hawaii, HI, USA. [Poster]
  3. Marinka Zitnik, Jure Leskovec. Predicting Multicellular Function Through Multi-Layer Tissue Networks. Poster session presented at International Conference on Intelligent Systems for Molecular Biology, ISMB/ECCB, 21-25 Jul 2017, Prague, Czech Republic. [Poster]
  4. Marinka Zitnik, Blaz Zupan. Jumping Across Gene-Disease Contexts Using Compressive Data Fusion. Poster session presented at International Conference on Intelligent Systems for Molecular Biology, ISMB, 8-12 Jul 2016, Orlando, FL, USA. [Poster]
  5. Marinka Zitnik, Blaz Zupan. Jumping Across Biomedical Contexts Using Compressive Data Fusion. Poster session presented at Pacific Symposium on Biocomputing, 4-8 Jan 2016, Hawaii, HI, USA. [Poster]
  6. Marinka Zitnik, Blaz Zupan. Integrate Everything but the Kitchen Sink: Data Set Selection and Sensitivity Estimation in Collective Factor Models.Poster session presented at International Conference on Intelligent Systems for Molecular Biology, ISMB, 10-14 Jul 2015, Dublin, Ireland. [Poster]
  7. Marinka Zitnik, Edward Nam, Christopher Dinh, Adam Kuspa, Gad Shaulsky, Blaz Zupan. Gene Prioritization by Compressive Data Fusion and Chaining. Poster session presented at Basel Computational Biology Conference, [BC]^2, 7-10 Jun 2015, Basel, Switzerland. Best poster award. [Poster]
  8. Mojca Mattiazzi Usaj, Matej Usaj, Marinka Zitnik, Dana Kablawi, Blaz Zupan, Brenda J. Andrews, Charles Boone. Exploring the Yeast Endocytic Pathway by Combining High-Throughput Genetics and High-Content Microscopy. Poster session presented at International Specialised Symposium on Yeast, 9-12 Oct 2014, Vipava, Slovenia.
  9. Marinka Zitnik, Blaz Zupan. Learning by Fusing Heterogeneous Data. Poster session presented at Heidelberg Laureate Forum, 21-26 Sept 2014, Heidelberg, Germany. [Press]
  10. Marinka Zitnik, Edward Nam, Christopher Dinh, Adam Kuspa, Gad Shaulsky, Blaz Zupan. Data Fusion for Gene Prioritization. Poster session presented at International Conference on Intelligent Systems for Molecular Biology, ISMB, 11-15 Jul 2014, Boston, MA, USA. [Poster]
  11. Marinka ZitnikBlaz Zupan. Biomedical Data Fusion by Simultaneous Matrix Tri-factorization. Poster session presented at Research in Computational Molecular Biology, RECOMB, 2-5 Apr 2014, Pittsburgh, PA, USA. Best poster award. [Poster]
  12. Marinka Zitnik, Blaz Zupan. Matrix Factorization-Based Data Fusion For Gene Function Prediction in Baker's Yeast and Slime Mold. Poster session presented at Pacific Symposium on Biocomputing, 3-7 Jan 2014, Hawaii, HI, USA. [Poster]
  13. Marinka Zitnik, Blaz Zupan. Data Fusion by Matrix Factorization. Poster session presented at Machine Learning Summer School, 2013, 25-26 Sept 2013, Max Planck Institute for Intelligent Systems, Tuebingen, Germany.
  14. Mojca Mattiazzi Usaj, Matej Usaj, Marinka Zitnik, Blaz Zupan, David G. Drubin, Brenda J. Andrews, Charles Boone. Studying yeast endocytosis with high-throughput multi-channel fluorescence microscopy: a tale of cortical actin patches, endosomes and vacuoles. Poster session presented at 13th International Conference on Systems Biology, ICSB, 19-23 Aug 2012, Toronto, Canada.

Research Columns

  1. Marinka ZitnikThe Infinite Mixtures of Food Products. ACM Crossroads, 23, 1:66-67, 2016.
  2. Marinka ZitnikThe Brownian Wanderlust of Things. ACM Crossroads, 22, 3:81-83, 2016.
  3. Lara Zupan, Marinka ZitnikAccording to Sensor 22 Benny is Preparing Dinner. ACM Crossroads, 22, 2:72-74, 2015.
  4. Lara Zupan, Marinka ZitnikSorry Kids, Iron Man's Superpowers aren't Unique. ACM Crossroads, 22, 1:66-67, 2015.
  5. Marinka ZitnikHidden Genes: Understanding Cancer Data with Matrix Factorization. ACM Crossroads, 21, 4:72-74, 2015.
  6. Marinka ZitnikThe Anatomy of a Human Disease NetworkACM Crossroads, 21, 2:58-60, 2014.
  7. Marinka ZitnikDynamics of News from The New York Times. ACM Crossroads, 21, 1:64-66, 2014.
  8. Marinka ZitnikExploring Data with Topological Tools. ACM Crossroads, 20, 4:65-66, 2014.
  9. Marinka ZitnikEfficient Sensor Placement for Environmental MonitoringACM Crossroads, 20, 3:73-75, 2014.
  10. Marinka ZitnikOn Constructing the Tree of Life. ACM Crossroads, 20, 2:65-67, 2013.
  11. Marinka ZitnikZero-Knowledge Proofs. ACM Crossroads, 20, 1: 65-67, 2013.
  12. Marinka ZitnikMatrix Function: A "VIP" in Linear Algebra and its Applications. ACM Crossroads, 19, 3: 66-67, 2013.
  13. Marinka ZitnikIterative Numerical Methods for Nonlinear Systems.ACM Crossroads, 19, 2:64-66, 2012.
  14. Marinka ZitnikUsing Sentiment Analysis to Improve Business OperationsACM Crossroads, 18, 4: 42-43, 2012.
Theses
  1. Marinka ZitnikA Matrix Factorization Approach for Inference from Heterogeneous Data. B.Sc. Thesis, University of Ljubljana, 2012. Summa cum laude. University Preseren's award for best thesis.

  2. Marinka ZitnikLearning by Fusing Heterogeneous Data. Ph.D. Thesis, University of Ljubljana, 2015. Summa cum laude. Jozef Stefan Golden Emblem Prize. [Slides]

Organization of Tutorials and Workshops