Komorowski lab
![21-9](/images/200.49dda2ce187eb0652cd1b959/1684931807804/21-9.jpg)
Our laboratory is dedicated to machine learning for life sciences. Our research focuses on developing models of biological systems from big genomic data by developing machine learning, statistical methods and algorithms. Our aims are twofold: to contribute to automation of the modeling process and to make discoveries in life sciences.
Research projects
Our laboratory is dedicated to machine learning for life sciences. Our research focuses on developing models of biological systems from big genomic data by developing machine learning, statistical methods and algorithms. Our aims are twofold: to contribute to automation of the modeling process and to make discoveries in life sciences. At the center of our work are models of complex regulatory mechanisms as they change in response to genetic and environmental factors. Our researchers and students pursue studies of, among others, transcriptome data, mutation and DNA modification data, metabolomics, screening and clinical data in the context of cancer, diabetes and viral diseases.
The lab collaborates with researchers in life sciences both in Uppsala and worldwide. We contributed to the ENCODE project and are members of the PCAWG - PanCancer Analysis of WHOLE GENOMES - initiative. We participate in a highly interdisciplinary project on diabetes type 2 funded by AstraZeneca. We work together with Professor Bozena Kaminska, Nencki Institute of Experimental Biology and other Polish scientists on developing an atlas for regulatory regions in the human brain. Most recently, we have established collaboration with the US Center for Innate Immunity and Immune Disease (CIIID) in Seattle, directed by Professor Michael Gale.
We host aspiring exchange students, including high school students, who wish to learn about advanced and emerging methods of analyzing and interpreting computational models built from big genomic data.
Laboratory director, Dr. Komorowski, is Chaired Professor of Bioinformatics. Previously, he was faculty member at Harvard University, Norwegian Institute of Technology in Trondheim, Norway, and Åbo Akademi University in Turku, Finland. He is also Visiting Professor at the Institute of Computer Science of Polish Academy of Sciences. He has published extensively, among others, in Nature Genetics, Genome Research, Nature, Nucleic Acid Research, and Bioinformatics.
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Group members
Publications
MindReader: Unsupervised Classification of Electroencephalographic Data
Part of Sensors, 2023
- DOI for MindReader: Unsupervised Classification of Electroencephalographic Data
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Part of Scientific Reports, 2022
Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment
Part of Cancers, 2022
- DOI for Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment
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Organ-specific metabolic pathways distinguish prediabetes, type 2 diabetes, and normal tissues
Part of Cell Reports Medicine, 2022
- DOI for Organ-specific metabolic pathways distinguish prediabetes, type 2 diabetes, and normal tissues
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Part of Blood Advances, p. 152-164, 2022
- DOI for Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression
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Functional annotation of noncoding mutations in cancer
Part of Life Science Alliance, 2021
- DOI for Functional annotation of noncoding mutations in cancer
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Part of Blood Advances, p. 900-912, 2021
Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy
Part of PLoS Pathogens, 2021
- DOI for Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy
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Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder
Part of Frontiers in Genetics, 2021
- DOI for Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder
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Part of Nature Communications, 2021
- DOI for Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas
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MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data
Part of Metabolites, 2021
- DOI for MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data
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Multifaceted regulation of hepatic lipid metabolism by YY1
Part of Life Science Alliance, 2021
- DOI for Multifaceted regulation of hepatic lipid metabolism by YY1
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Nucleolar rDNA folds into condensed foci with a specific combination of epigenetic marks
Part of The Plant Journal, p. 1534-1548, 2021
R.ROSETTA: an interpretable machine learning framework
Part of BMC Bioinformatics, 2021
- DOI for R.ROSETTA: an interpretable machine learning framework
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Part of Omics, p. 180-194, 2020
- DOI for A Multi-Omics Approach to Liver Diseases: Integration of Single Nuclei Transcriptomics with Proteomics and HiCap Bulk Data in Human Liver
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Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
Part of Nature, p. 102-111, 2020
- DOI for Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
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Part of Communications Biology, 2020
- DOI for Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
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Part of Scientific Reports, 2020
- DOI for Integration of whole-body [18F]FDG PET/MRI with non-targeted metabolomics can provide new insights on tissue-specific insulin resistance in type 2 diabetes
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Pan-cancer analysis of whole genomes
Part of Nature, p. 82-93, 2020
- DOI for Pan-cancer analysis of whole genomes
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Part of Scientific Reports, 2019
- DOI for Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases
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Part of Journal of Psychiatric Research, p. 41-47, 2019
Part of Scientific Reports, 2019
- DOI for Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes
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Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control
Part of Nature Communications, 2019
- DOI for Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control
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Part of Human Genomics, 2019
- DOI for Studies of liver tissue identify functional gene regulatory elements associated to gene expression, type 2 diabetes, and other metabolic diseases
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Part of Genes, 2018
- DOI for Special Issue Introduction: The Wonders and Mysteries Next Generation Sequencing Technologies Help Reveal
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Part of Scientific Reports, 2018
- DOI for Unveiling new interdependencies between significant DNA methylation sites, gene expression profiles and glioma patients survival
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PiiL: visualization of DNA methylation and gene expression data in gene pathways
Part of BMC Genomics, 2017
- DOI for PiiL: visualization of DNA methylation and gene expression data in gene pathways
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Part of International Journal of Cancer, p. 200-209, 2017
Part of Human Mutation, p. 904-913, 2016
Combinatorial identification of DNA methylation patterns over age in the human brain
Part of BMC Bioinformatics, 2016
- DOI for Combinatorial identification of DNA methylation patterns over age in the human brain
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Part of BMC Genomics, 2016
- DOI for Identification of combinatorial host-specific signatures with a potential to affect host adaptation in influenza A H1N1 and H3N2 subtypes
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Maps of context-dependent putative regulatory regions and genomic signal interactions
Part of Nucleic Acids Research, p. 9110-9120, 2016
- DOI for Maps of context-dependent putative regulatory regions and genomic signal interactions
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Part of BMC Microbiology, 2015
- DOI for A complete map of potential pathogenicity markers of avian influenza virus subtype H5 predicted from 11 expressed proteins
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Part of BMC Genomics, 2015
- DOI for Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription
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Part of Molecular Ecology Resources, p. 477-488, 2015
Ciruvis: a web-based tool for rule networks and interaction detection using rule-based classifiers
Part of BMC Bioinformatics, p. 139, 2014
- DOI for Ciruvis: a web-based tool for rule networks and interaction detection using rule-based classifiers
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Part of Biochimica et Biophysica Acta, p. 1341-1350, 2014
Nucleosome regulatory dynamics in response to TGF beta
Part of Nucleic Acids Research, p. 6921-6934, 2014
Nucleosome regulatory dynamics in response to TGF-beta treatment in HepG2 cells
Part of Nucleic Acids Research, p. 6921-6934, 2014
Part of Journal of Molecular Medicine, p. 239-254, 2014
- DOI for The signal transducers Stat1 and Stat3 and their novel target Jmjd3 drive the expression of inflammatory genes in microglia
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Part of BMC Medical Genomics, p. 50, 2013
Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data
Part of BMC Bioinformatics, p. 280, 2013
- DOI for Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data
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Random Reducts: A Monte Carlo Rough Set-based Method for Feature Selection in Large Datasets
Part of Fundamenta Informaticae, p. 273-288, 2013
Rule-Based Models of the Interplay between Genetic and Environmental Factors in Childhood Allergy
Part of PLOS ONE, 2013
- DOI for Rule-Based Models of the Interplay between Genetic and Environmental Factors in Childhood Allergy
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Part of Algorithms for Molecular Biology, p. 2, 2012
- DOI for A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements
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Combinations of histone modifications mark exon inclusion levels
Part of PLOS ONE, 2012
- DOI for Combinations of histone modifications mark exon inclusion levels
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Gis1 and Rph1 Regulate Glycerol and Acetate Metabolism in Glucose Depleted Yeast Cells
Part of PLOS ONE, 2012
- DOI for Gis1 and Rph1 Regulate Glycerol and Acetate Metabolism in Glucose Depleted Yeast Cells
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Part of Journal of neural transmission, p. 821-831, 2012
Part of BMC Cancer, p. 450, 2011
- DOI for Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa
- Download full text (pdf) of Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa
Focal amplifications are associated with high grade and recurrences in stage Ta bladder carcinoma
Part of International Journal of Cancer, p. 1390-1402, 2010
People
Jan Komorowski, Professor
Carl Fredrik Barrenäs
Nicholas Baltzer
Karolina Smolinska Garbulowska
Sara Alaa Yones