I lecture and perform research in machine learning, data mining and decision support, and apply these to problems in bioinformatics and systems biology. My current major interests are data fusion and reconstruction of gene networks.
I run Bioinformatics Lab and enjoy participating in its software projects that include a data mining suite Orange, a web-based gene expression analytics dictyExpress, and next generation sequencing pipeline PIPA. Our first popular web application was GenePath: check it out, it is almost ten years old but still runs!
From August 2013 I am visiting Gad Shaulsky and Adam Kuspa Labs at the Department of Molecular and Human Genetics at Baylor College of Medicine in Houston. Thanks to Fullbright Scholarship, University of Ljubljana, and Baylor College of Medicine.
Activities and Events
- CARE-MI - Cardio repair european multidisciplinary initiative, European Project (Framework Programmes), 242038, 2010−2015
- Computational approaches for identification of bacterial resistance pathways in Dictyostelium, Bilateral Collaboration Project, BI-US/13-14-016, 2013−2014
- Artificial intelligence and inteligent systems, Research Programme, P2-0209, 2009−2014
- Growth and defense trade-offs in multitrophic interaction between potato and its two major pests, Basic Research and Application Project, J4-4165, 2011−2014
- Functional genomics of potato-PVY interactions, Basic Research and Application Project, J1-4268, 2011−2014
- Functional genomics of cholesterol homeostasis: the role of lanosterol 14alpha-demethylase in development of metabolic disorders, Basic Research and Application Project, J7-4053, 2011−2014
- Combination of next generation sequencing and metagenomic analysis in the diagnostics of severe hop stunting, Basic Research and Application Project, J4-4153, 2011−2014
- FightingDrugFailure, European Project (Framework Programmes), PITN-GA-2009-238132, 2010−2013
- CLIP - Mapping functional protein-RNA interactions to identify new targets for oligonucleotide-based therapy , International Project, ERC (2010) A/203738, 2010−2013
- A next-generation analytics toolbox for integrated high-throughput genomic data analysis, Bilateral Collaboration Project, BI-US/11-12-020, 2011−2012
- Qualitative modeling from data, Basic Research and Application Project, J2-2194 (B), 2009−2012
- Data and knowledge integration methods for network systems biology, Basic Research and Application Project, J2-2197, 2009−2012
- Knowledge technology approaches in drug discovery: analysis and experiment planning in high-throughput genetics, Basic Research and Application Project, L2-1112, 2008−2010
- X-MEDIA: Large Scale Knowledge Sharing and Reuse Across Media, European Project (Framework Programmes), FP6-26978, 2006−2010
- Discovering disease-disease associations by fusing systems-level molecular data
Scientific Reports, 13:3202, 2013.
- Orange: data mining toolbox in Python
Journal of Machine Learning Research, 14:2349-2353, 2013.
- Bacterial discrimination by dictyostelid amoebae reveals the complexity of ancient interspecies interactions
Current Biology, 23(10):862-872, 2013.
- ABC transporters in Dictyostelium discoideum development
PLoS One, 8 (8). e70040, 2013.
- Computational models for prediction of yeast strain potential for winemaking from phenotypic profiles
PLoS One, 8 (7). e66523, 2013.
- Knowledge-based bioinformatics for the study of mammalian oocytes
International Journal of Developmental Biology, 56 (10-12): 859-866, 2012.
- NIMFA: A Python Library for Nonnegative Matrix Factorization
Journal of Machine Learning Research, 13:849-853, 2012.
- Stage prediction of embryonic stem cell differentiation from genome-wide expression data
Bioinformatics, 27(18):2546-2553, 2011.
- Subgroup discovery in data sets with multi-dimensional responses
Intelligent Data Analysis, 15(4):533-549, 2011.
- Characterizing the RNA targets and position-dependent splicing regulation by TDP-43
Nature Neuroscience, 14(4):452-458, 2011.
- SNPsyn: detection and exploration of SNP-SNP interactions
Nucleic Acids Res, 39 (Suppl ). W444-9, 2011.
- miR669a and miR669q prevent skeletal muscle differentiation in postnatal cardiac progenitors
J Cell Biol, 193:1197-1212, 2011.
- New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data
BMC Bioinformatics, 11:163, 2010.
- iCLIP predicts the dual splicing effects of TIA-RNA interactions
PLoS Biology, 8 (10). e1000530, 2010.
- FragViz: visualization of fragmented networks
BMC Bioinformatics, 11 (457), 2010.
- Inference of the Molecular Mechanism of Action from Genetic Interaction and Gene Expression Data
OMICS A journal of Integrative Biology, 14(4):357-367, 2010.
- iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
Nature Structural & Molecular Biology, 17:909-915, 2010.
- Conserved developmental transcriptomes in evolutionarily divergent species
Genome Biology, 11:R35, 2010.
- Does replication groups scoring reduce false positive rate in SNP interaction discovery?
BMC Genomics, 11:58, 2010.
- Polymorphic members of the lag gene family mediate kin discrimination in Dictyostelium
Current Biology, 19(7):567-572, 2009.
- dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface
BMC Bioinformatics, 10:265, 2009.
- Predictive data mining in clinical medicine: Current issues and guidelines
Internation Journal of Medical Informatics, 77(2):81-97, 2008.
- Open-source tools for data mining
Clinics in Laboratory Medicine, 28(1):37-54, 2008.
- Towards knowledge-based gene expression data mining
Journal of Biomedical Informatics, 40(6):787-802, 2007.
- Visualization-based cancer microarray data classification analysis
Bioinformatics, 23(16):2147-2154, 2007.
- VizRank: Data Visualization Guided by Machine Learning
Data Mining and Knowledge Discovery, 13(2):119-136, 2006.
- Epistasis analysis with global transcriptional phenotypes
Nature Genetics, 37(5):471-477, 2005.
- Microarray data mining with visual programming
Bioinformatics, 21(3):396-398, 2005.
- Attribute Interactions in Medical Data Analysis
In: 9th Conference on Artificial Intelligence in Medicine in Europe (AIME 2003), October 18-22, 2003, Protaras, Cyprus.
- GenePath: a System for Automated Construction of Genetic Networks from Mutant Data
Bioinformatics, 19(3):383, 2003.
- Machine learning for survival analysis: a case study on recurrence of prostate cancer
Artificial Intelligence in Medicine, 20(1):59-75, 2000.