We use machine learning and data mining techniques and apply them to data from systems biology. We are interested in how data from many different data sources can contribute to accuracy of prediction, and how they together reveal interesting and testable new relations in biology.
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: it is over 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.
- Overcoming the curse of dimensionality with the use of background knowledge, Basic Research and Application Project, J2-5480, 2013−2016
- Post-transcriptional regulatory networks in neurodegenerative diseases, Basic Research and Application Project, J7-5460, 2013−2016
- Epidemiology and Biodiversity Studies of Plant Pathogens, Basic Research and Application Project, L4-5525, 2013−2016
- 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
- Assessment of machine learning reliability methods for quantifying the applicability domain of QSAR regression models
J Chem Inf Model, 54(2):431-441, 2014.
- Imputation of quantitative genetic interactions in epistatic MAPs by interaction propagation matrix completion
In: RECOMB, Pittsburgh, 2014.
- Matrix factorization-based data fusion for gene function prediction in baker's yeast and slime mold
In: PSB, Jan 2014, The Big Island of Hawaii.
- 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.
- New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data
BMC Bioinformatics, 11:163, 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.
- Polymorphic members of the lag gene family mediate kin discrimination in Dictyostelium
Current Biology, 19(7):567-572, 2009.
- Computational approaches for the genetic and phenotypic characterization of a Saccharomyces cerevisiae wine yeast collection
Yeast, 26(12):675-692, 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.