Marinka Zitnik

Fusing bits and DNA

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Factorization

Article: Submit to Frontiers in Genetics: Single-Cell Data Analytics

I am thrilled about an opportunity to co-edit a research topic on single-cell data analytics, resources, challenges and perspectives for Frontiers in Genetics! With this research topic, we aim to provide a broad coverage of single-cell data analytic...

Article: Scalable Matrix Tri-Factorization

In our new paper on accelerating matrix tri-factorization we show how to learn factorized representations that scale well on multi-processor and multi-GPU architectures. The new approach speeds up computations by more than two orders of magnitude...

Article: PLoS CompBio: Gene Prioritization by Compressive Data Fusion

Our paper on Gene prioritization by compressive data fusion and chaining has been published in PLoS Computational Biology. In the paper, we present Collage, a new data fusion approach to gene prioritization. Together with collaborators from Baylor...

Article: Data Fusion Tutorial at the IEEE Engineering in Medicine and Biology

Together with Blaz Zupan we organize a tutorial on data fusion at the International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). In the tutorial, we will explore latent factor models, a popular class of approaches that ...

Article: ACM XRDS: Understanding Cancer with Matrix Factorization

The Summer issue of ACM XRDS is here! In this issue we write about computational biology. Our features and interviews present different perspectives about some of the most recent advances of computational biology. You can read about personalized...

Article: ISMB 2015: Integrate Everything but the Kitchen Sink

Our poster at ISMB 2015 is concerned with data set selection and sensitivity estimation in collective factor models. Molecular biology data is rich in volume as well as heterogeneity. We can view individual data sets as relations between objects of...

Article: Invited Talk on Learning Latent Factor Models by Data Fusion

Our invited talk at the Workshop on Matrix Computations for Biomedical Informatics at the 15th Conference on Artificial Intelligence in Medicine, AIME in Pavia, Italy, discussed the use of collective latent factor models for various predictive...

Article: Poster Award at the Basel Computational Biology Conference

Our poster on Gene prioritization by compressive data fusion and chaining got best poster award at the Basel Computational Biology Conference ([BC]^2). The poster highlights our recent computational method that prioritizes genes by fusing ...

Article: Data Fusion Tutorial at the Basel Computational Biology Conference

Together with Blaz Zupan we organize a tutorial on data fusion at the Basel Computational Biology Conference ([BC]^2). The tutorial is targeted at computational scientists, data mining researchers and molecular biologists interested in large-scale...

Article: Syst Biomed: Survival Regression by Data Fusion

Our recent paper in Systems Biomedicine describes a new computational approach that predicts patient’s survival time from a collection of heterogeneous data sets. This is the full paper of our award winning entry at CAMDA meeting at ISMB 2014, Boston,...

Article: J Comp Biol: Network-Guided Matrix Completion

Our recent paper in Journal of Computational Biology introduces an interaction data imputation method called network-guided matrix completion (NG-MC). The core part of NG-MC is low-rank probabilistic matrix completion that incorporates prior knowledge...

Article: IEEE TPAMI: Data Fusion by Matrix Factorization

We recently published a paper on a new data fusion method in IEEE Transactions on Pattern Analysis and Machine Intelligence. For most problems in science and engineering we can obtain data sets that describe the observed system from various ...

Article: CAMDA 2014: Survival Regression by Data Fusion

I have presented at CAMDA 2014 an extension of our recent matrix factorization-based data fusion approach that couples data fusion with survival regression. CAMDA 2014 runs as a satellite meeting at ISMB 2014, Boston, MA, USA. Our presentation got ...

Article: Gene network inference by probabilistic scoring of relationships from a factorized model of interactions

Bioinformatics just published a special issue devoted to ISMB 2014 proceedings papers that will be presented next month at the world's premier conference on computational biology -- ISMB 2014 in Boston, MA, USA. Our paper, Gene network inference by...

Article: @RECOMB 2014, Pittsburgh, PA (Part II)

We are presenting a poster about our recent data fusion methodology (ArXiv preprint) at RECOMB Conference. Thanks to Prof. Blaz Zupan for the storyline and Prof. Richard H. Kessin for valuable comments. xkcd.com served as an inspiration of poster...

Article: @RECOMB 2014, Pittsburgh, PA (Part I)

We got accepted a paper on Imputation of Quantitative Genetic Interactions in Epistatic MAPs by Interaction Propagation Matrix Completion to RECOMB 2014. Epistatic Miniarray Profile (E-MAP) is a popular large-scale gene interaction discovery...

Article: @Pacific Symposium on Biocomputing 2014, Hawaii

I am participating at PSB 2014, Pacific Symposium on Biocomputing, an international conference of current research in the theory and application of computational methods in problems of biological significance, which is held on the Big Island of...

Article: @Baylor College of Medicine, Department of Molecular and Human Genetics

Between December 2013 and August 2014 I am visiting the Department of Molecular and Human Genetics at Baylor College of Medicine, Houston, TX, USA. During my stay we will do research on computational methods for data fusion and their applications in...

Article: Press Coverage of Our Recent Study About Connections Between Human Diseases

BioTechniques, The International Journal of Life Science Methods highlighted our recent paper on Discovering disease-disease associations by fusing systems-level molecular data, which was published by Nature's Scientific Reports. In the paper we ...

Article: Discovering Disease-Disease Associations by Fusing Molecular Data

Nature's Scientific Reports has published our latest paper on data fusion, Discovering disease-disease associations by fusing systems-level molecular data, in which we combine various sources of biological information to discover human disease-disease...

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