Marinka Zitnik

Fusing bits and DNA

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Bioinformatics

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: ACM XRDS: On Constructing the Tree of Life

The Winter 2013 issue of XRDS: Crossroads, the ACM magazine for students features the latest in wearable computing, such as wearable brain computer interface, human motion capturing and tracking how we read, the augmented reality and airwriting. 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...

Article: Extracting Gene Regulation Networks Using Linear-Chain Conditional Random Fields and Rules @ACL 2013, BioNLP Workshop

This week Slavko Zitnik will present our paper (he is the first author) at ACL, ACL BioNLP Workshop on extending linear-chain conditional random fields (CRF) with skip-mentions to extract gene regulatory networks from biomedical literature and a...

Article: ISMB/ECCB 2013 - 21st International Conference on Intelligent Systems in Molecular Biology & 12th European Conference on Computational Biology

I participated in CAMDA Satellite Meeting on critical assessment of massive data analysis during 29th and 20th July at ISMB in Berlin, where I presented our matrix factorization-based data fusion approach to predicting drug-induced liver injury from...

Also labeled: Computer Science, Maths, Networking

Article: CAMDA 2013: Matrix Factorization-Based Data Fusion for Drug-Induced Liver Injury Prediction

This work was recognized as first prize winner for excellent research at ISMB/ECCB CAMDA 2013 Conference. I am giving a talk at CAMDA 2013 Conference, which runs as a satellite meeting of ISMB/ECCB 2013 Conference. CAMDA focuses on challenges in the...

Article: BioDay: Trends in Bioinformatics @Hekovnik

In May I participated at the first BioDay meeting organized by Hekovnik in Ljubljana, Slovenia. The aim of the BioDay events is the exchange of ideas, knowledge and fostering collaboration and networking between life scientists, computer scientists,...

Article: Winning BioNLP Challenge 2013: Extracting Gene Regulation Network

I have recently participated in BioNLP Shared Task 2013 Challenge together with Slavko Zitnik and won the first place in the task extracting gene regulation networks. The goal of the challenge was to assess the performance of information extraction...

Article: Preseren Award of U of Ljubljana, 2012

In first week of December U of Ljubljana celebrates traditional "Week of University" (Why?) during which numerous invited lectures, presentations and award ceremonies are organized. This year, I was awarded the faculty award for best students and...

Article: @University of Toronto, Terrence Donnelly Centre for Cellular and Biomolecular Research (Part III)

So what have I been up to in recent weeks here at Toronto? Highlights include my first ride with famous American yellow school bus to a reception at ICSB12 conference, some sightseeing in Toronto city and a trip to Niagara Falls. Besides, I have...

Article: @University of Toronto, The 13th International Conference on Systems Biology (Part II)

The 13th international conference on systems biology was held in Toronto, 19th--23rd August 2012. Here is a list of talks from platform sessions which I found especially interesting: Modeling the regulatory diversity of human cancers (S....

Article: @University of Toronto, Terrence Donnelly Centre for Cellular and Biomolecular Research (Part I)

In the past few days I have settled in Toronto, Canada, where I will stay until October this year. As a graduate student I will be working at the University of Toronto, Terrence Donnelly Centre for Cellular and Biomolecular Research in the Charlie...

Article: Undergraduate Thesis Defense

Yesterday I defended my undergraduate Thesis entitled A Matrix Factorization Approach for Inference of Prediction Models from Heterogeneous Data Sources (slo: Pristop matrične faktorizacije za gradnjo napovednih modelov iz heterogenih podatkovnih v...