Marinka Zitnik

Fusing bits and DNA

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Bioinformatics

Article: ISMB/ECCB 2017: Feature Learning in Multi-layer Tissue Networks

I'm giving a talk on feature learning in multi-layer tissue networks and tissue-specific protein function prediction at ISMB/ECCB. Check out the slides, the poster and the recorded talk!

Article: Understanding Protein Functions in Different Biological Contexts

Our paper on predicting multicellular function through multi-layer tissue networks is published in Bioinformatics and is included in the proceedings of ISMB/ECCB 2017, a premier conference in bioinformatics and computational biology. Understanding...

Article: Invited Talk on Uncovering Cellular Functions Through Multi-Layer Tissue Networks

I'm giving an invited talk on discovering gene functions through multi-layer tissue networks at the Network Medicine meeting at NetSci 2017. Check out the slides!

Article: Invited Talk on Boosting Biomedical Discovery Through Network Data Analytics

I'm giving an invited talk on speeding-up scientific discovery in biomedicine through computational network analytics at the International Conference for Big Data and AI in Medicine.

Article: Jozef Stefan Golden Emblem Prize

Last month, I was honored to receive Jozef Stefan Golden Emblem for winning PhD dissertation in the fields of natural sciences, medicine and biotechnology. The prize is awarded by Jozef Stefan Institute. I look forward to making further progress on...

Article: Submit to AIME 2017 Workshop on Advanced Healthcare Analytics

You are cordially invited to submit a paper to the Workshop on Advanced Predictive Models in Healthcare that will take place during the AIME 2017 conference. This workshop will focus on topics related to advanced predictive models, capable of ...

Article: ISMB 2016: Connecting Gene-Disease Contexts

We presented our recent approach for disease module detection at the ISMB 2016. Slides are available. The method is capable of making inference over heterogeneous data collections in new interesting ways! One of them, an approach we call jumping ac...

Article: Bioinformatics: Jumping Across Contexts Using Compressive Fusion

Our paper on Jumping across biomedical contexts using compressive data fusion has just appeared in Bioinformatics. We will present the paper at ISMB 2016 in July 2016. The rapid growth of diverse biological data allows us to consider interactions...

Article: Bioinformatics: Orthogonal Factorization of RNA-Binding Proteins

Our paper on integrative analysis of multiple RNA-binding proteins has just appeared in Bioinformatics. RNA binding proteins (RBPs) are important for many cellular processes, including post-transcriptional control of gene expression, splicing,...

Also labeled: Data Fusion, Factorized Models

Article: PSB 2016: Collective Pairwise Classification for Multi-Way Analysis

Our paper on Collective Pairwise Classification for Multi-Way Analysis has been published in the Proceedings of the 21st Pacific Symposium on Biocomputing. We will present the work at the PSB conference in January 2016. In the paper, we develop a...

Article: BMC Bioinformatics: Extracting Gene Regulatory Networks from Text

Our paper on Sieve-based relation extraction of gene regulatory networks from biological literature has been published in BMC Bioinformatics. In the paper, we describe a network extraction algorithm, which is an improvement on our winning submission...

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: Gene Network Inference via Data Fusion

Our paper at ISMB 2015 addresses a challenging task of inferring gene networks by taking into consideration potentially many data sets. Importantly, these data sets might be nonidentically distributed and can follow any combination of exponential...

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: Compressive Data Fusion and Persistent Homology

My talk at the Summer School on Computational Topology in Ljubljana, Slovenia was about coupling compressive data fusion methods with algebraic topology, in particular persistent homology. There, I discussed how the latent data space obtained by f...

Article: Bioinformatics: Gene Network Inference by Fusing Diverse Distributions

Our paper on Gene network inference by fusing data from diverse distributions has been published in Bioinformatics. We will present it at ISMB 2015 in Dublin. In the paper we describe FuseNet, a Markov network formulation that infers networks from a...

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...

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