Jan Komorowski
Professor at Institutionen för cell- och molekylärbiologi; Beräkningsbiologi och bioinformatik
- Telephone:
- +46 18 471 66 92
- Mobile phone:
- +46 70 425 07 75
- E-mail:
- Jan.Komorowski@icm.uu.se
- Visiting address:
- Husargatan 3
752 37 Uppsala - Postal address:
- Box 596
751 24 UPPSALA
- ORCID:
- 0000-0002-0766-8789
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Short presentation
Dr. Jan Komorowski is an international leader in the area of Artificial Intelligence for Life Sciences. His research focuses on modelling biological systems from big genomic data with machine learning and statistical methods. At the center of his work are models of complex regulatory mechanisms as they change in response to genetic and environmental factors. Dr. Komorowski has spearheaded applications of rule-based modelling using rough sets and introduced the concept of rule networks.
Keywords
- aiv
- cancer
- hiv
- machine learning
- mcfs
- metabolomics
- rosetta
- transcriptomics
- type 2 diabetes
Biography
Dr. Komorowski received an MSc in Computer Science at the Department of Computer Science at University of Warsaw, Poland, and a PhD in Computer Science at Linköping University, Sweden. Dr. Komorowski was Assistant Professor at Harvard University, Adjunct Professor at MIT, and Full Professor of Computer Science at the Norwegian Institute of Technology in Trondheim, Norway. He was Visiting Professor at Åbo Akademi University in Turku, Finland.
In 2002 he was appointed Full Professor and Chair of Bioinformatics at Uppsala University and Director of the Linnaeus Centre for Bioinformatics that he lead until 2010. In 2018 he received the honorary title of Kurt Mothes Visiting Professorship of Martin Luther University in Halle, Germany. Dr. Komorowski is also a Visiting Professor at the Institute of Computer Science, Polish Academy of Sciences, Warszawa. Currently, Dr. Komorowski is Senior Professor of Bioinformatics and Fellow at the Swedish Collegium for Advanced Study. He also holds an affiliate faculty position Division of Infectious Disease & Translational Medicine Division, University of Washington, Seattle.
Dr. Komorowski has published extensively, among others, in Nature Genetics, Genome Research, Nature, Nucleic Acid Research, Nature Communications and Bioinformatics. He is a well-cited bioinformatician with 7,405 citations at Web of Science and 14,592 at Google Scholar. As of August 2019 his h-indices were: 29 - Web of Science, and 43 - Google Scholar. 20 PhD’s graduated under his advisorship. He contributed to the ENCODE project and is currently a member of the PanCancer consortium. Dr. Komorowski currently holds a prestigious NIH award to develop computational models of immune protection by SIV/HIV vaccines, is a Senior Program Committee Member of the IJCAI 2019 and chaired the 2019 Science for Life Laboratory Summit AI for Life Sciences.
Publications
Recent publications
- MindReader (2023)
- Organ-specific metabolic pathways distinguish prediabetes, type 2 diabetes, and normal tissues (2022)
- Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment (2022)
- Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression (2022)
- Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data (2022)
All publications
Articles
- MindReader (2023)
- Organ-specific metabolic pathways distinguish prediabetes, type 2 diabetes, and normal tissues (2022)
- Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment (2022)
- Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression (2022)
- Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data (2022)
- Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy (2021)
- R.ROSETTA (2021)
- Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder (2021)
- Nucleolar rDNA folds into condensed foci with a specific combination of epigenetic marks (2021)
- Multifaceted regulation of hepatic lipid metabolism by YY1 (2021)
- Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas (2021)
- Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets (2021)
- Functional annotation of noncoding mutations in cancer (2021)
- MetaFetcheR (2021)
- Pan-cancer analysis of whole genomes (2020)
- Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis (2020)
- A Multi-Omics Approach to Liver Diseases (2020)
- 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 (2020)
- Analyses of non-coding somatic drivers in 2,658 cancer whole genomes (2020)
- Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control (2019)
- Studies of liver tissue identify functional gene regulatory elements associated to gene expression, type 2 diabetes, and other metabolic diseases (2019)
- Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases (2019)
- Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes (2019)
- Analyzing DNA methylation patterns in subjects diagnosed with schizophrenia using machine learning methods (2019)
- Unveiling new interdependencies between significant DNA methylation sites, gene expression profiles and glioma patients survival (2018)
- Special Issue Introduction (2018)
- Risk stratification in cervical cancer screening by complete screening history (2017)
- PiiL: visualization of DNA methylation and gene expression data in gene pathways (2017)
- Maps of context-dependent putative regulatory regions and genomic signal interactions (2016)
- Identification of combinatorial host-specific signatures with a potential to affect host adaptation in influenza A H1N1 and H3N2 subtypes (2016)
- Combinatorial identification of DNA methylation patterns over age in the human brain (2016)
- A Significant Regulatory Mutation Burden at a High-Affinity Position of the CTCF Motif in Gastrointestinal Cancers (2016)
- Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription (2015)
- 'True' null allele detection in microsatellite loci (2015)
- A complete map of potential pathogenicity markers of avian influenza virus subtype H5 predicted from 11 expressed proteins (2015)
- Ciruvis (2014)
- Nucleosome regulatory dynamics in response to TGF-beta treatment in HepG2 cells (2014)
- Nucleosome regulatory dynamics in response to TGF beta (2014)
- Integration of genome-wide of Stat3 binding and epigenetic modification mapping with transcriptome reveals novel Stat3 target genes in glioma cells (2014)
- The signal transducers Stat1 and Stat3 and their novel target Jmjd3 drive the expression of inflammatory genes in microglia (2014)
- Rule-Based Models of the Interplay between Genetic and Environmental Factors in Childhood Allergy (2013)
- ChIP-seq in steatohepatitis and normal liver tissue identifies candidate disease mechanisms related to progression to cancer (2013)
- Random Reducts (2013)
- Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data (2013)
- A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements (2012)
- Combinations of histone modifications mark exon inclusion levels (2012)
- Monte Carlo feature selection and rule-based models to predict Alzheimer's disease in mild cognitive impairment (2012)
- Gis1 and Rph1 Regulate Glycerol and Acetate Metabolism in Glucose Depleted Yeast Cells (2012)
- Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa (2011)
- SICTIN (2010)
- Nitrogen depletion in the fission yeast Schizosaccharomyces pombe causes nucleosome loss in both promoters and coding regions of activated genes (2010)
- Focal amplifications are associated with high grade and recurrences in stage Ta bladder carcinoma (2010)
- Integrative epigenomic and genomic analysis of malignant pheochromocytoma (2010)
- Recurrent genomic alterations in benign and malignant pheochromocytomas and paragangliomas revealed by whole-genome array comparative genomic hybridization analysis (2010)
- Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP (2009)
- Nucleosomes are well positioned in exons and carry characteristic histone modifications (2009)
- A comprehensive analysis of the structure-function relationship in proteins based on local structure similarity (2009)
- A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome (2009)
- Proteochemometrics mapping of the interaction space for retroviral proteases and their substrates (2009)
- Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq (2009)
- Novel genes in cell cycle control and lipid metabolism with dynamically regulated binding sites for sterol regulatory element-binding protein 1 and RNA polymerase II in HepG2 cells detected by chromatin immunoprecipitation with microarray detection (2009)
- Characterization of novel and complex genomic aberrations in glioblastoma using a 32K BAC array (2009)
- Histone H3 lysine 27 trimethylation in adult differentiated colon associated to cancer DNA hypermethylation (2009)
- Gene expression trends and protein features effectively complement each other in gene function prediction (2009)
- Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing (2009)
- Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing (2009)
- A Segmental Maximum A Posteriori Approach to Genome-wide Copy Number Profiling (2008)
- Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles (2008)
- Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array (2008)
- Monte Carlo feature selection for supervised classification (2008)
- Generalized proteochemometric model of multiple cytochrome P450 enzymes and their inhibitors (2008)
- Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3 (2008)
- Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation (2008)
- Somatic mosaicism for copy number variation in differentiated human tissues (2008)
- Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders (2008)
- Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation. (2008)
- Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors (2007)
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project (2007)
- Rough sets in bioinformatics (2007)
- Proteochemometric analysis of small cyclic peptides' interaction with wild-type and chimeric melanocortin receptors (2007)
- A look inside HIV resistance through retroviral protease interaction maps (2007)
- Computational proteomics analysis of HIV-1 protease interactome (2007)
- A previously unrecognized microdeletion syndrome on chromosome 22 band q11.2 encompassing the BCR gene (2007)
- Overlapping phenotype of wolf-hirschhorn and beckwith-wiedemann syndromes in a girl with der(4)t(4; 1 1)(pter;pter) (2007)
- Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes (2007)
- Endocan is a VEGF-A and PI3K regulated gene with increased expression in human renal cancer (2007)
- Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays (2005)
- Gene expression based classification of gastric carcinoma. (2004)
- Feature synthesis and extraction for the construction of generalized properties of amino acids (2004)
- Liver gene expression in rats in response to the peroxisome proliferator-activated (2003)
- Learning rough set classifiers from gene expressions and clinical data (2002)
- ||-ROSETTA
- Risk Stratification in Cervical Cancer Screening – Validation and Generalization of a Data-driven Screening Recall Model
- ChIP-seq in steatohepatitis and normal liver tissue identifies candidate disease mechanisms related to progression to cancer
- Single Nuclei Transcriptome Analysis of Human Liver with Integration of Proteomics and Capture Hi-C Bulk Tissue Data
- Integration of whole-body PET/MRI with non-targeted metabolomics provides new insights into insulin sensitivity of various tissues
- VisuNet: an interactive tool for rule network visualization of rule-based learning models
- funMotifs: Tissue-specific transcription factor motifs
Chapters
- Discovering Networks of Interdependent Features in High-Dimensional Problems (2016)
- Learning Rule-Based Models - The Rough Set Approach (2014)
- Monte Carlo feature selection and interdependency discovery in supervised classification (2010)
Conferences
- Visualization of Rules in Rule-Based Classifiers (2012)
- Construction of Rough Set-Based Classifiers for Predicting HIV Resistance to Nucleoside Reverse Transcriptase Inhibitors (2008)
- RoSy: A Rough Knowledge Base System (2005)
- Altered gene expression in the olfactory bulb following exposure to 2,6-dichlorophenyl methylsulfone (2005)
Data sets
- SUPPLEMENTARY MATERIAL: Machine learning-based analysis of glioma grades reveals co-enrichment (2021)
- SUPPLEMENTARY MATERIAL: VisuNet: an interactive tool for rule network visualization of rule-based learning models (2021)
- SUPPLEMENTARY MATERIAL: funMotifs: Tissue-specific transcription factor motifs (2021)
- SUPPLEMENTARY MATERIAL: Transcriptomic analysis reveals pro-inflammatory signatures associated with acute myeloid leukemia progression (2021)
- Supplementary material: Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data (2021)
- Supplementary tables:MetaFetcheR: An R package for complete mapping of small compound data (2021)
- SUPPLEMENTAL INFORMATION FOR: Transcriptomic analysis reveals pro-inflammatory signatures associated with acute myeloid leukemia progression (2020)
