Marinka Zitnik

Fusing bits and DNA

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Home Selected Publications

Selected Publications

Journal Papers

  1. Marinka Zitnik, Rok Sosic, Jure Leskovec. Prioritizing Network Communities. In Review, 2017.
  2. Marinka Zitnik, Monica Agrawal, Jure Leskovec. Network-Based Discovery of Drug Indications. In Review, 2017.
  3. Andrej Copar, Marinka Zitnik, Blaz Zupan. Scalable Non-Negative Matrix Tri-Factorization. In Review, 2017.
  4. J.C. Puigvert, M. Zitnik, B. Hallstrom, M. Carter, A.-S. Jemth, O. Loseva, Z. Karem, J.M. Calderon-Montaño, J. Unterlass, C. Lindskog, P.H. Edqvist, D. Matuszewski, H.A. Blal, R. Berntsson, M. Haggblad, U. Martens, M. Studham, M. Uhlen, B. Lundgren, C. Wählby, E. Sonnhammer, E. Lundberg, P. Stenmark, B. Zupan, T. Helleday. A Comprehensive Structural, Biochemical and Biological Profiling of the Human NUDIX Hydrolase Family. In Review, 2017.
  5. 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] Oral presentation at ISMB'17.
  6. 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]
  7. 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]
  8. 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.
  9. 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]
  10. 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]
  11. 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]
  12. 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.
  13. Marinka Zitnik, Blaz Zupan. Survival Regression by Data Fusion. Systems Biomedicine, 2, 3:47-53, 2015.
  14. Marinka Zitnik, Blaz Zupan. Data Imputation in Epistatic MAPs by Network-Guided Matrix Completion. Journal of Computational Biology, 22, 6:595-608, 2015. Oral presentation at RECOMB'14. [Slides] [Code]
  15. Marinka Zitnik, Blaz Zupan. Data Fusion by Matrix Factorization. IEEE Transactions on Pattern Analysis and Machine Intelligence, 37, 1:41-53, 2015. [Code]
  16. 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]
  17. Marinka Zitnik, Blaz Zupan. Matrix Factorization-Based Data Fusion for Drug-Induced Liver Injury Prediction. Systems Biomedicine, 2, 1:16-22, 2014.
  18. 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]
  19. 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. 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]
  2. 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]
  3. Marinka Zitnik, Blaz Zupan. Survival Regression by Data Fusion. In ISMB 2014, CAMDA, Boston, MA, USA, 2014. First prize winner for excellent research at ISMB/CAMDA'14. [Slides]
  4. 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]
  5. 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.
  6. 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]
  7. 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.
  8. Jure Zbontar, Marinka Zitnik, Miha Zidar, Gregor Majcen, Matic Potočnik, 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, Jure Leskovec. Predicting Multicellular Function Through Multi-Layer Tissue Networks. Poster session presented at International Conference on Intelligent Systems for Molecular Biology, ISMB/ECCB, Jul 21-25 2017, Prague, Czech Republic. [Poster]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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.
  7. Marinka Zitnik, Blaz Zupan. Learning by Fusing Heterogeneous Data. Poster session presented at Heidelberg Laureate Forum, 21-26 Sept 2014, Heidelberg, Germany. [Press]
  8. 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]
  9. Marinka Zitnik, Blaz 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]
  10. 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]
  11. 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.
  12. 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.
Invited Talks
  1. Marinka Zitnik. To appear. Jan 10-13 2018. AMS-MAA Joint Mathematics Meetings, Clustering of Graphs: Theory, Practice, and Applications, San Diego, CA, USA.
  2. Marinka Zitnik. Uncovering Cellular Functions Through Multi-Layer Tissue Networks. Jun 19 2017. NetSci 2017, Network Medicine, Indianapolis, IN, USA. [Slides]
  3. Marinka Zitnik. Boosting Biomedical Discovery Through Network Data Analytics. Apr 13 2017. International Conference for Big Data and AI in Medical & FinTech, Taiwan.
  4. Marinka Zitnik. Predictive Network Medicine. Apr 12 2017. Asia University, Taiwan.
  5. Marinka Zitnik. Learning by Fusing Heterogeneous Data. Jan 5 2017. Jozef Stefan Institute, Ljubljana, Slovenia. [Slides]
  6. Marinka Zitnik. Structure, Organization and Dynamics of Complex Networks for Cancer Analytics. Oct 19 2016, DARPA Cancer Analytics Workshop, White House Cancer Moonshot, Washington D.C., USA.
  7. Marinka Zitnik, Blaz Zupan. Learning Latent Factor Models by Data Fusion. Jun 20 2015, 15th Conference on Artificial Intelligence in Medicine, AIMEWorkshop on Matrix Computations in Biomedical Informatics, Pavia, Italy. [Slides]
  8. Marinka Zitnik. Compressive Data Fusion and Persistent Homology. Jun 24 2015, Summer School on Computational Topology and Topological Data Analysis, University of Ljubljana, Slovenia. [Slides]
  9. Marinka Zitnik. If Computer Science is a Science about Computers then Biology is a Science about Microscopes. Oct 15 2014, TEDx, University of Ljubljana, Slovenia.
  10. Marinka Zitnik. Data Fusion by Matrix Factorization. Jan 30 2014, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
  11. Marinka Zitnik. Topological Methods in Machine Learning. Jul 2 2013, Summer School on Computational Topology and Topological Data Analysis, University of Ljubljana, Slovenia. [Slides]
  12. Marinka Zitnik. Data Fusion for Dictyostelium Bacterial Response Gene Prioritization. Jun 12 2013, 8th CFGBC Symposium, Faculty of Medicine, University of Ljubljana, Slovenia.
  13. Marinka Zitnik. Biomedical Data Fusion: The Whole Can be More Than the Sum of its Components. May 24 2013, BioDay: Trends in Bioinformatics, Ljubljana, Slovenia.
  14. Marinka Zitnik. A Matrix Factorization Approach for Inference of Prediction Models from Heterogeneous Data Sources. Sept 9 2012, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.

Research Columns

  1. Marinka Zitnik. The Infinite Mixtures of Food Products. ACM Crossroads, 23, 1:66-67, 2016.
  2. Marinka Zitnik. The 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 Zitnik. Hidden Genes: Understanding Cancer Data with Matrix Factorization. ACM Crossroads, 21, 4:72-74, 2015.
  6. Marinka Zitnik. The Anatomy of a Human Disease NetworkACM Crossroads, 21, 2:58-60, 2014.
  7. Marinka Zitnik. Dynamics of News from The New York Times. ACM Crossroads, 21, 1:64-66, 2014.
  8. Marinka Zitnik. Exploring Data with Topological Tools. ACM Crossroads, 20, 4:65-66, 2014.
  9. Marinka Zitnik. Efficient Sensor Placement for Environmental MonitoringACM Crossroads, 20, 3:73-75, 2014.
  10. Marinka Zitnik. On 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 SystemsACM Crossroads, 19, 2: 64-66, 2012.
  14. Marinka ZitnikUsing Sentiment Analysis to Improve Business OperationsACM Crossroads, 18, 4: 42-43, 2012.
Theses
  1. Marinka Zitnik. A 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 Zitnik. Learning by Fusing Heterogeneous Data. Ph.D. Thesis, University of Ljubljana, 2015. Summa cum laude. Jozef Stefan Golden Emblem Prize.

Organization of Tutorials and Workshops