Jan Komorowski

A transparent rule-based framework using k-mer profiles for detection of cryptic infections in tomato whole-genome metagenomic data

Khakvar, Reza; Pulinkala, Girish; Sar, Maya Baghdy; Komorowski, Jan

Ingår i Physiological and molecular plant pathology, 2026

• DOI för A transparent rule-based framework using k-mer profiles for detection of cryptic infections in tomato whole-genome metagenomic data

Combinatorial DNMTs and EZH2 inhibition reprograms the H3K27me3 and DNAme-mediated onco-epigenome to suppress multiple myeloma proliferation

Atienza Párraga, Alba; Nylund, Patrick; Diamanti, Klev; Garrido-Zabala, Berta et al.

Ingår i Scientific Reports, 2025

• DOI för Combinatorial DNMTs and EZH2 inhibition reprograms the H3K27me3 and DNAme-mediated onco-epigenome to suppress multiple myeloma proliferation
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MindReader: Unsupervised Classification of Electroencephalographic Data

Rivas-Carrillo, Salvador Daniel; Akkuratov, Evgeny E.; Valdez Ruvalcaba, Hector; Vargas-Sanchez, Angel et al.

Ingår i Sensors, 2023

• DOI för MindReader: Unsupervised Classification of Electroencephalographic Data
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Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data

Yones, Sara A.; Annett, Alva; Stoll, Patricia; Diamanti, Klev et al.

Ingår i Scientific Reports, 2022

• DOI för Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data

Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment

Garbulowski, Mateusz; Smolinska Garbulowska, Karolina; Cabuk, Ugur; Younes, Sara et al.

Ingår i Cancers, 2022

• DOI för Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment
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A transparent rule-based framework using k-mer profiles for detection of cryptic infections in tomato whole-genome metagenomic data

Khakvar, Reza; Pulinkala, Girish; Sar, Maya Baghdy; Komorowski, Jan

Ingår i Physiological and molecular plant pathology, 2026

• DOI för A transparent rule-based framework using k-mer profiles for detection of cryptic infections in tomato whole-genome metagenomic data

Combinatorial DNMTs and EZH2 inhibition reprograms the H3K27me3 and DNAme-mediated onco-epigenome to suppress multiple myeloma proliferation

Atienza Párraga, Alba; Nylund, Patrick; Diamanti, Klev; Garrido-Zabala, Berta et al.

Ingår i Scientific Reports, 2025

• DOI för Combinatorial DNMTs and EZH2 inhibition reprograms the H3K27me3 and DNAme-mediated onco-epigenome to suppress multiple myeloma proliferation
• Ladda ner fulltext (pdf) av Combinatorial DNMTs and EZH2 inhibition reprograms the H3K27me3 and DNAme-mediated onco-epigenome to suppress multiple myeloma proliferation

MindReader: Unsupervised Classification of Electroencephalographic Data

Rivas-Carrillo, Salvador Daniel; Akkuratov, Evgeny E.; Valdez Ruvalcaba, Hector; Vargas-Sanchez, Angel et al.

Ingår i Sensors, 2023

• DOI för MindReader: Unsupervised Classification of Electroencephalographic Data
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Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data

Yones, Sara A.; Annett, Alva; Stoll, Patricia; Diamanti, Klev et al.

Ingår i Scientific Reports, 2022

• DOI för Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data

Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment

Garbulowski, Mateusz; Smolinska Garbulowska, Karolina; Cabuk, Ugur; Younes, Sara et al.

Ingår i Cancers, 2022

• DOI för Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment
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Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression

Stratmann, Svea; Yones, Sara A.; Garbulowski, Mateusz; Sun, Jitong et al.

Ingår i Blood Advances, s. 152-164, 2022

• DOI för Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression
• Ladda ner fulltext (pdf) av Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression

Organ-specific metabolic pathways distinguish prediabetes, type 2 diabetes, and normal tissues

Diamanti, Klev; Cavalli, Marco; Pereira, Maria J.; Pan, Gang et al.

Ingår i Cell Reports Medicine, 2022

• DOI för Organ-specific metabolic pathways distinguish prediabetes, type 2 diabetes, and normal tissues
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Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

Stepniak, Karolina; Machnicka, Magdalena A.; Mieczkowski, Jakub; Macioszek, Anna et al.

Ingår i Nature Communications, 2021

• DOI för Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas
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Multifaceted regulation of hepatic lipid metabolism by YY1

Pan, Gang; Diamanti, Klev; Cavalli, Marco; Gutierrez, Ariadna Lara et al.

Ingår i Life Science Alliance, 2021

• DOI för Multifaceted regulation of hepatic lipid metabolism by YY1
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MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data

Yones, Sara A.; Csombordi, Rajmund; Komorowski, Jan; Diamanti, Klev

Ingår i Metabolites, 2021

• DOI för MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data
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Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets

Stratmann, Svea; Yones, Sara A.; Mayrhofer, Markus; Norgren, Nina et al.

Ingår i Blood Advances, s. 900-912, 2021

• DOI för Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets

R.ROSETTA: an interpretable machine learning framework

Garbulowski, Mateusz; Diamanti, Klev; Smolinska, Karolina; Baltzer, Nicholas et al.

Ingår i BMC Bioinformatics, 2021

• DOI för R.ROSETTA: an interpretable machine learning framework
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Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder

Garbulowski, Mateusz; Smolinska Garbulowska, Karolina; Diamanti, Klev; Pan, Gang et al.

Ingår i Frontiers in Genetics, 2021

• DOI för Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder
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Nucleolar rDNA folds into condensed foci with a specific combination of epigenetic marks

Kutashev, Konstantin O.; Franek, Michal; Diamanti, Klev; Komorowski, Jan et al.

Ingår i The Plant Journal, s. 1534-1548, 2021

• DOI för Nucleolar rDNA folds into condensed foci with a specific combination of epigenetic marks

Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy

Barrenäs, Fredrik; Hansen, Scott G.; Law, Lynn; Driscoll, Connor et al.

Ingår i PLoS Pathogens, 2021

• DOI för Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy
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Functional annotation of noncoding mutations in cancer

Umer, Husen Muhammad; Smolinska, Karolina; Komorowski, Jan; Wadelius, Claes

Ingår i Life Science Alliance, 2021

• DOI för Functional annotation of noncoding mutations in cancer
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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

Diamanti, Klev; Visvanathar, Robin; Pereira, Maria J.; Cavalli, Marco et al.

Ingår i Scientific Reports, 2020

• DOI för 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
• Ladda ner fulltext (pdf) av 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

Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis

Carlevaro-Fita, Joana; Lanzos, Andres; Feuerbach, Lars; Hong, Chen et al.

Ingår i Communications Biology, 2020

• DOI för Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
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A Multi-Omics Approach to Liver Diseases: Integration of Single Nuclei Transcriptomics with Proteomics and HiCap Bulk Data in Human Liver

Cavalli, Marco; Diamanti, Klev; Pan, Gang; Spalinskas, Rapolas et al.

Ingår i Omics, s. 180-194, 2020

• DOI för 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

Rheinbay, Esther; Nielsen, Morten Muhlig; Abascal, Federico; Wala, Jeremiah A. et al.

Ingår i Nature, s. 102-111, 2020

• DOI för Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
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Pan-cancer analysis of whole genomes

Campbell, Peter J.; Diamanti, Klev; Komorowski, Jan; Umer, Husen Muhammad et al.

Ingår i Nature, s. 82-93, 2020

• DOI för Pan-cancer analysis of whole genomes
• Ladda ner fulltext (pdf) av Pan-cancer analysis of whole genomes

Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases

Cavalli, Marco; Baltzer, Nicholas; Umer, Husen Muhammad; Grau, Jan et al.

Ingår i Scientific Reports, 2019

• DOI för Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases
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Studies of liver tissue identify functional gene regulatory elements associated to gene expression, type 2 diabetes, and other metabolic diseases

Cavalli, Marco; Baltzer, Nicholas; Pan, Gang; Walls, Jose Ramon Barcenas et al.

Ingår i Human Genomics, 2019

• DOI för Studies of liver tissue identify functional gene regulatory elements associated to gene expression, type 2 diabetes, and other metabolic diseases
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Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control

Barrenäs, Fredrik; Raehtz, Kevin; Xu, Cuiling; Law, Lynn et al.

Ingår i Nature Communications, 2019

• DOI för Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control
• Ladda ner fulltext (pdf) av Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control

Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes

Diamanti, Klev; Cavalli, Marco; Pan, Gang; Pereira, Maria J et al.

Ingår i Scientific Reports, 2019

• DOI för Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes
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Analyzing DNA methylation patterns in subjects diagnosed with schizophrenia using machine learning methods

Moghadam, Behrooz Torabi; Etemadikhah, Mitra; Rajkowska, Grazyna; Stocluneier, Craig et al.

Ingår i Journal of Psychiatric Research, s. 41-47, 2019

• DOI för Analyzing DNA methylation patterns in subjects diagnosed with schizophrenia using machine learning methods

Special Issue Introduction: The Wonders and Mysteries Next Generation Sequencing Technologies Help Reveal

Grabherr, Manfred; Kaminska, Bozena; Komorowski, Jan

Ingår i Genes, 2018

• DOI för Special Issue Introduction: The Wonders and Mysteries Next Generation Sequencing Technologies Help Reveal
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Unveiling new interdependencies between significant DNA methylation sites, gene expression profiles and glioma patients survival

Dabrowski, Michal J.; Draminski, Michal; Diamanti, Klev; Stepniak, Karolina et al.

Ingår i Scientific Reports, 2018

• DOI för 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

Torabi Moghadam, Behrooz; Zamani, Neda; Komorowski, Jan; Grabherr, Manfred

Ingår i BMC Genomics, 2017

• DOI för PiiL: visualization of DNA methylation and gene expression data in gene pathways
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Risk stratification in cervical cancer screening by complete screening history: Applying bioinformatics to a general screening population

Baltzer, Nicholas; Sundström, Karin; Nygård, Jan F.; Dillner, Joakim et al.

Ingår i International Journal of Cancer, s. 200-209, 2017

• DOI för Risk stratification in cervical cancer screening by complete screening history: Applying bioinformatics to a general screening population

Maps of context-dependent putative regulatory regions and genomic signal interactions

Diamanti, Klev; Umer, Husen M.; Kruczyk, Marcin; Dabrowski, Michal J. et al.

Ingår i Nucleic Acids Research, s. 9110-9120, 2016

• DOI för Maps of context-dependent putative regulatory regions and genomic signal interactions
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Identification of combinatorial host-specific signatures with a potential to affect host adaptation in influenza A H1N1 and H3N2 subtypes

Khaliq, Zeeshan; Leijon, Mikael; Belak, Sandor; Komorowski, Jan

Ingår i BMC Genomics, 2016

• DOI för Identification of combinatorial host-specific signatures with a potential to affect host adaptation in influenza A H1N1 and H3N2 subtypes
• Ladda ner fulltext (pdf) av Identification of combinatorial host-specific signatures with a potential to affect host adaptation in influenza A H1N1 and H3N2 subtypes

Combinatorial identification of DNA methylation patterns over age in the human brain

Torabi Moghadam, Behrooz; Dabrowski, Michal; Kaminska, Bozena; Grabherr, Manfred G. et al.

Ingår i BMC Bioinformatics, 2016

• DOI för Combinatorial identification of DNA methylation patterns over age in the human brain
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A Significant Regulatory Mutation Burden at a High-Affinity Position of the CTCF Motif in Gastrointestinal Cancers

Umer, Husen M.; Cavalli, Marco; Dabrowski, Michal J.; Diamanti, Klev et al.

Ingår i Human Mutation, s. 904-913, 2016

• DOI för A Significant Regulatory Mutation Burden at a High-Affinity Position of the CTCF Motif in Gastrointestinal Cancers

'True' null allele detection in microsatellite loci: a comparison of methods, assessment of difficulties and survey of possible improvements

Dabrowski, M. J.; Bornelöv, Susanne; Kruczyk, M.; Baltzer, N. et al.

Ingår i Molecular Ecology Resources, s. 477-488, 2015

• DOI för 'True' null allele detection in microsatellite loci: a comparison of methods, assessment of difficulties and survey of possible improvements

Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription

Bornelöv, Susanne; Komorowski, Jan; Wadelius, Claes

Ingår i BMC Genomics, 2015

• DOI för 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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A complete map of potential pathogenicity markers of avian influenza virus subtype H5 predicted from 11 expressed proteins

Khaliq, Zeeshan; Leijon, Mikael; Belak, Sandor; Komorowski, Jan

Ingår i BMC Microbiology, 2015

• DOI för A complete map of potential pathogenicity markers of avian influenza virus subtype H5 predicted from 11 expressed proteins
• Ladda ner fulltext (pdf) av A complete map of potential pathogenicity markers of avian influenza virus subtype H5 predicted from 11 expressed proteins

Nucleosome regulatory dynamics in response to TGF-beta

Enroth, Stefan; Andersson, Robin; Bysani, Madhusudhan Reddy; Wallerman, Ola et al.

Ingår i Nucleic Acids Research, s. 6921-6934, 2014

• DOI för Nucleosome regulatory dynamics in response to TGF-beta

Ciruvis: a web-based tool for rule networks and interaction detection using rule-based classifiers

Bornelöv, Susanne; Marillet, Simon; Komorowski, Jan

Ingår i BMC Bioinformatics, s. 139, 2014

• DOI för Ciruvis: a web-based tool for rule networks and interaction detection using rule-based classifiers
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Nucleosome regulatory dynamics in response to TGF beta

Enroth, Stefan; Andersson, Robin; Bysani, Madhusudhan; Wallerman, Ola et al.

Ingår i Nucleic Acids Research, s. 6921-6934, 2014

• DOI för Nucleosome regulatory dynamics in response to TGF beta

The signal transducers Stat1 and Stat3 and their novel target Jmjd3 drive the expression of inflammatory genes in microglia

Przanowski, Piotr; Dabrowski, Michal; Ellert-Miklaszewska, Aleksandra; Kloss, Michal et al.

Ingår i Journal of Molecular Medicine, s. 239-254, 2014

• DOI för The signal transducers Stat1 and Stat3 and their novel target Jmjd3 drive the expression of inflammatory genes in microglia
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Integration of genome-wide of Stat3 binding and epigenetic modification mapping with transcriptome reveals novel Stat3 target genes in glioma cells

Kruczyk, Marcin; Przanowski, Piotr; Dabrowski, Michal; Swiatek-Machado, Karolina et al.

Ingår i Biochimica et Biophysica Acta, s. 1341-1350, 2014

• DOI för Integration of genome-wide of Stat3 binding and epigenetic modification mapping with transcriptome reveals novel Stat3 target genes in glioma cells

Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data

Kruczyk, Marcin; Umer, Husen Muhammad; Enroth, Stefan; Komorowski, Jan

Ingår i BMC Bioinformatics, s. 280, 2013

• DOI för Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data
• Ladda ner fulltext (pdf) av Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data

ChIP-seq in steatohepatitis and normal liver tissue identifies candidate disease mechanisms related to progression to cancer

Bysani, Madhu Sudhan Reddy; Wallerman, Ola; Bornelöv, Susanne; Zatloukal, Kurt et al.

Ingår i BMC Medical Genomics, s. 50, 2013

• DOI för ChIP-seq in steatohepatitis and normal liver tissue identifies candidate disease mechanisms related to progression to cancer

Rule-Based Models of the Interplay between Genetic and Environmental Factors in Childhood Allergy

Bornelöv, Susanne; Saaf, Annika; Melen, Erik; Bergstrom, Anna et al.

Ingår i PLOS ONE, 2013

• DOI för Rule-Based Models of the Interplay between Genetic and Environmental Factors in Childhood Allergy
• Ladda ner fulltext (pdf) av Rule-Based Models of the Interplay between Genetic and Environmental Factors in Childhood Allergy

Random Reducts: A Monte Carlo Rough Set-based Method for Feature Selection in Large Datasets

Kruczyk, Marcin; Baltzer, Nicholas; Mieczkowski, Jakub; Dramiński, Michał et al.

Ingår i Fundamenta Informaticae, s. 273-288, 2013

• DOI för Random Reducts: A Monte Carlo Rough Set-based Method for Feature Selection in Large Datasets

A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements

Enroth, Stefan; Andersson, Claes R.; Andersson, Robin; Wadelius, Claes et al.

Ingår i Algorithms for Molecular Biology, s. 2, 2012

• DOI för A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements
• Ladda ner fulltext (pdf) av A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements

Gis1 and Rph1 Regulate Glycerol and Acetate Metabolism in Glucose Depleted Yeast Cells

Orzechowski Westholm, Jakub; Tronnersjö, Susanna; Nordberg, Niklas; Olsson, Ida et al.

Ingår i PLOS ONE, 2012

• DOI för Gis1 and Rph1 Regulate Glycerol and Acetate Metabolism in Glucose Depleted Yeast Cells
• Ladda ner fulltext (pdf) av Gis1 and Rph1 Regulate Glycerol and Acetate Metabolism in Glucose Depleted Yeast Cells

Combinations of histone modifications mark exon inclusion levels

Enroth, Stefan; Bornelöv, Susanne; Wadelius, Claes; Komorowski, Jan

Ingår i PLOS ONE, 2012

• DOI för Combinations of histone modifications mark exon inclusion levels
• Ladda ner fulltext (pdf) av Combinations of histone modifications mark exon inclusion levels

Monte Carlo feature selection and rule-based models to predict Alzheimer's disease in mild cognitive impairment

Kruczyk, Marcin; Zetterberg, Henrik; Hansson, Oskar; Rolstad, Sindre et al.

Ingår i Journal of neural transmission, s. 821-831, 2012

• DOI för Monte Carlo feature selection and rule-based models to predict Alzheimer's disease in mild cognitive impairment

Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa

Enroth, Stefan; Rada-Iglesisas, Alvaro; Andersson, Robin; Wallerman, Ola et al.

Ingår i BMC Cancer, s. 450, 2011

• DOI för Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa
• Ladda ner fulltext (pdf) av Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa

SICTIN: Rapid footprinting of massively parallel sequencing data

Enroth, Stefan; Andersson, Robin; Wadelius, Claes; Komorowski, Jan

Ingår i BioData Mining, 2010

• DOI för SICTIN: Rapid footprinting of massively parallel sequencing data
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Integrative epigenomic and genomic analysis of malignant pheochromocytoma

Sandgren, Johanna; Andersson, Robin; Rada-Iglesias, Alvaro; Enroth, Stefan et al.

Ingår i Experimental and Molecular Medicine, s. 484-502, 2010

• DOI för Integrative epigenomic and genomic analysis of malignant pheochromocytoma

Recurrent genomic alterations in benign and malignant pheochromocytomas and paragangliomas revealed by whole-genome array comparative genomic hybridization analysis

Sandgren, Johanna; Diaz de Ståhl, Teresita; Andersson, Robin; Menzel, Uwe et al.

Ingår i Endocrine-Related Cancer, s. 561-579, 2010

• DOI för Recurrent genomic alterations in benign and malignant pheochromocytomas and paragangliomas revealed by whole-genome array comparative genomic hybridization analysis

Focal amplifications are associated with high grade and recurrences in stage Ta bladder carcinoma

Nord, Helena; Segersten, Ulrika; Sandgren, Johanna; Wester, Kenneth et al.

Ingår i International Journal of Cancer, s. 1390-1402, 2010

• DOI för Focal amplifications are associated with high grade and recurrences in stage Ta bladder carcinoma

Nitrogen depletion in the fission yeast Schizosaccharomyces pombe causes nucleosome loss in both promoters and coding regions of activated genes

Kristell, Carolina; Orzechowski Westholm, Jakub; Olsson, Ida; Ronne, Hans et al.

Ingår i Genome Research, s. 361-371, 2010

• DOI för Nitrogen depletion in the fission yeast Schizosaccharomyces pombe causes nucleosome loss in both promoters and coding regions of activated genes

A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome

Kierczak, Marcin; Ginalski, Krzysztof; Dramiński, Michal; Koronacki, Jacek et al.

Ingår i Bioinformatics and Biology Insights, s. 109-127, 2009

• Ladda ner fulltext (pdf) av A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome

A comprehensive analysis of the structure-function relationship in proteins based on local structure similarity

Hvidsten, Torgeir R; Lægreid, Astrid; Kryshtafovych, Andriy; Andersson, Gunnar et al.

Ingår i PLoS ONE, 2009

• DOI för A comprehensive analysis of the structure-function relationship in proteins based on local structure similarity

Nucleosomes are well positioned in exons and carry characteristic histone modifications

Andersson, Robin; Enroth, Stefan; Rada-Iglesias, Alvaro; Wadelius, Claes et al.

Ingår i Genome Research, s. 1732-1741, 2009

• DOI för Nucleosomes are well positioned in exons and carry characteristic histone modifications

Proteochemometrics mapping of the interaction space for retroviral proteases and their substrates

Kontijevskis, Aleksejs; Petrovska, Ramona; Yahorava, Sviatlana; Komorowski, Jan et al.

Ingår i Bioorganic & Medicinal Chemistry, s. 5229-5237, 2009

• DOI för Proteochemometrics mapping of the interaction space for retroviral proteases and their substrates

Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing

Wallerman, Ola; Motallebipour, Mehdi; Enroth, Stefan; Patra, Kalicharan et al.

Ingår i Nucleic Acids Research, s. 7498-7508, 2009

• DOI för Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing

Histone H3 lysine 27 trimethylation in adult differentiated colon associated to cancer DNA hypermethylation

Rada-Iglesias, Alvaro; Enroth, Stefan; Andersson, Robin; Wanders, Alkwin et al.

Ingår i Epigenetics, s. 107-113, 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

Motallebipour, Mehdi; Enroth, Stefan; Punga, Tanel; Ameur, Adam et al.

Ingår i The FEBS Journal, s. 1878-1890, 2009

• DOI för 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

Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP

Ameur, Adam; Rada-Iglesias, Alvaro; Komorowski, Jan; Wadelius, Claes

Ingår i Nucleic Acids Research, 2009

• DOI för Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP

Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq

Motallebipour, Mehdi; Ameur, Adam; Bysani, Madhusudhan Reddy; Patra, Kalicharan et al.

Ingår i Genome Biology, 2009

• DOI för Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq

Gene expression trends and protein features effectively complement each other in gene function prediction

Wabnik, Krzysztof; Hvidsten, Torgeir R; Kedzierska, Anna; Van Leene, Jelle et al.

Ingår i Bioinformatics, s. 322-330, 2009

• DOI för Gene expression trends and protein features effectively complement each other in gene function prediction

Characterization of novel and complex genomic aberrations in glioblastoma using a 32K BAC array

Nord, Helena; Hartmann, Christian; Andersson, Robin; Menzel, Uwe et al.

Ingår i Neuro-Oncology, s. 803-818, 2009

• DOI för Characterization of novel and complex genomic aberrations in glioblastoma using a 32K BAC array

Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing

Wallerman, Ola; Motallebipour, Mehdi; Enroth, Stefan; Patra, Kalicharan et al.

Ingår i Nucleic Acids Research, s. 7498-7508, 2009

• DOI för Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing

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

Rada-Iglesias, Alvaro; Ameur, Adam; Kapranov, Philipp; Enroth, Stefan et al.

Ingår i Genome Research, s. 380-392, 2008

• DOI för 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

Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3

Orzechowski Westholm, Jakub; Nordberg, Niklas; Murén, Eva; Ameur, Adam et al.

Ingår i BMC Genomics, s. 601, 2008

• DOI för Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3

Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation.

Westholm, Jakub Orzechowski; Xu, Feifei; Ronne, Hans; Komorowski, Jan

Ingår i BMC Bioinformatics, s. 484, 2008

• DOI för Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation.

A Segmental Maximum A Posteriori Approach to Genome-wide Copy Number Profiling

Andersson, Robin; Bruder, Carl E G; Piotrowski, Arkadiusz; Menzel, Uwe et al.

Ingår i Bioinformatics, s. 751-758, 2008

• DOI för A Segmental Maximum A Posteriori Approach to Genome-wide Copy Number Profiling

Generalized proteochemometric model of multiple cytochrome P450 enzymes and their inhibitors

Kontijevskis, Aleksejs; Komorowski, Jan; Wikberg, Jarl

Ingår i Journal of chemical information and modeling, s. 1840-1850, 2008

• DOI för Generalized proteochemometric model of multiple cytochrome P450 enzymes and their inhibitors

Monte Carlo feature selection for supervised classification

Draminski, Michal; Rada-Iglesias, Alvaro; Enroth, Stefan; Wadelius, Claes et al.

Ingår i Bioinformatics, s. 110-117, 2008

• DOI för Monte Carlo feature selection for supervised classification

Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation

Pandey, Radha Raman; Mondal, Tanmoy; Mohammad, Faizaan; Enroth, Stefan et al.

Ingår i Molecular Cell, s. 232-46, 2008

• DOI för Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation

Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array

de Ståhl, Teresita Díaz; Sandgren, Johanna; Piotrowski, Arkadiusz; Nord, Helena et al.

Ingår i Human Mutation, s. 398-408, 2008

• DOI för Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array

Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles

Bruder, Carl E G; Piotrowski, Arkadiusz; Gijsbers, Antoinet A C J; Andersson, Robin et al.

Ingår i American Journal of Human Genetics, s. 763-71, 2008

• DOI för Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles

Somatic mosaicism for copy number variation in differentiated human tissues

Piotrowski, Arkadiusz; Bruder, Carl E G; Andersson, Robin; de Ståhl, Teresita Diaz et al.

Ingår i Human Mutation, s. 1118-24, 2008

• DOI för Somatic mosaicism for copy number variation in differentiated human tissues

Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors

Andersson, Claes R.; Hvidsten, Torgeir R.; Isaksson, Anders; Gustafsson, Mats G. et al.

Ingår i BMC Systems Biology, s. 45, 2007

• DOI för Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors

Proteochemometric analysis of small cyclic peptides' interaction with wild-type and chimeric melanocortin receptors

Kontijevskis, Aleksejs; Petrovska, Ramona; Mutule, Ilze; Uhlén, Staffan et al.

Ingår i Proteins, s. 83-96, 2007

• DOI för Proteochemometric analysis of small cyclic peptides' interaction with wild-type and chimeric melanocortin receptors

Computational proteomics analysis of HIV-1 protease interactome

Kontijevskis, Aleksejs; Wikberg, Jarl E. S.; Komorowski, Jan

Ingår i Proteins, s. 305-312, 2007

• DOI för Computational proteomics analysis of HIV-1 protease interactome

A look inside HIV resistance through retroviral protease interaction maps

Kontijevskis, Aleksejs; Prusis, Peteris; Petrovska, Ramona; Yahorava, Sviatlana et al.

Ingår i PloS Computational Biology, s. 424-435, 2007

• DOI för A look inside HIV resistance through retroviral protease interaction maps

A previously unrecognized microdeletion syndrome on chromosome 22 band q11.2 encompassing the BCR gene

Mikhail, Fady M.; Descartes, Maria; Piotrowski, Arkadiusz; Andersson, Robin et al.

Ingår i American journal of medical genetics. Part A, s. 2178-2184, 2007

• DOI för A previously unrecognized microdeletion syndrome on chromosome 22 band q11.2 encompassing the BCR gene

Endocan is a VEGF-A and PI3K regulated gene with increased expression in human renal cancer

Rennel, Emma; Mellberg, Sofie; Dimberg, Anna; Petersson, Ludvig et al.

Ingår i Experimental Cell Research, s. 1285-1294, 2007

• DOI för Endocan is a VEGF-A and PI3K regulated gene with increased expression in human renal cancer

Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes

Rada-Iglesias, Alvaro; Enroth, Stefan; Ameur, Adam; Koch, Christoph M. et al.

Ingår i Genome Research, s. 708-719, 2007

• DOI för Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Birney, Ewan; Stamatoyannopoulos, John A.; Dutta, Anindya; Guigó, Roderic et al.

Ingår i Nature, s. 799-816, 2007

• DOI för Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Overlapping phenotype of wolf-hirschhorn and beckwith-wiedemann syndromes in a girl with der(4)t(4; 1 1)(pter;pter)

Mikhail, Fady M.; Sathienkijkanchai, Achara; Robin, Nathaniel H.; Prucka, Sandra et al.

Ingår i American Journal of Medical Genetics, Part A, s. 1760-1766, 2007

• DOI för Overlapping phenotype of wolf-hirschhorn and beckwith-wiedemann syndromes in a girl with der(4)t(4; 1 1)(pter;pter)

Rough set-based proteochemometrics modeling of G-protein-coupled receptor-ligand

Strömbergsson, Helena; Prusis, Peteris; Midelfart, Herman; Lapinsh, Maris et al.

Ingår i Proteins, s. 24-34, 2006

• DOI för Rough set-based proteochemometrics modeling of G-protein-coupled receptor-ligand

Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays

Rada-Iglesias, Alvaro; Wallerman, Ola; Koch, Christoph; Ameur, Adam et al.

Ingår i Human Molecular Genetics, s. 3435-3447, 2005

• DOI för Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays

Feature synthesis and extraction for the construction of generalized properties of amino acids

Rudnicki, W. R.; Komorowski, J

Ingår i Rough Sets and Current Trends in Computing, s. 786-791, 2004

Gene expression based classification of gastric carcinoma.

Nørsett, Kristin G; Laegreid, Astrid; Midelfart, Herman; Yadetie, Fekadu et al.

Ingår i Cancer Lett, s. 227-37, 2004

Liver gene expression in rats in response to the peroxisome proliferator-activated

Yadetie, Fekadu; Laegreid, Astrid; Bakke, Ingunn; Kusnierczyk, Waclaw et al.

Ingår i Physiol Genomics, s. 9-19, 2003

Learning rough set classifiers from gene expressions and clinical data

Midelfart, H; Komorowski, J; Nørsett, K; Yadetie, F et al.

Ingår i Fundamenta Informaticae, s. 155-183, 2002

Single Nuclei Transcriptome Analysis of Human Liver with Integration of Proteomics and Capture Hi-C Bulk Tissue Data

Cavalli, Marco; Diamanti, Klev; Pan, Gang; Rapolas, Spalinskas et al.

Rough sets in bioinformatics

Hvidsten, Torgeir R.; Komorowski, Jan

Ingår i Transactions on Rough Sets VII: Lecture Notes in Computer Science 4400, s. 225-243, 2007

Supplementary material: Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data

Yones, Sara A.; Annett, Alva; Stoll, Patricia; Diamanti, Klev et al.

2021

• Ladda ner fulltext (pdf) av Supplementary material: Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data

SUPPLEMENTARY MATERIAL: VisuNet: an interactive tool for rule network visualization of rule-based learning models

Smolinska Garbulowska, Karolina; Garbulowski, Mateusz; Diamanti, Klev; Davoy, Xavier et al.

2021

• Ladda ner fulltext (pdf) av SUPPLEMENTARY MATERIAL: VisuNet: an interactive tool for rule network visualization of rule-based learning models

SUPPLEMENTARY MATERIAL: Transcriptomic analysis reveals pro-inflammatory signatures associated with acute myeloid leukemia progression

Stratmann, Svea; Yones, Sara A.; Garbulowski, Mateusz; Sun, Jitong et al.

2021

SUPPLEMENTARY MATERIAL: funMotifs: Tissue-specific transcription factor motifs

Smolinska, Karolina; Umer, Husen Muhammad; Khaliq, Zeeshan; Marzouka, Nour-al-dain et al.

2021

Supplementary tables:MetaFetcheR: An R package for complete mapping of small compound data

Yones, Sara A.; Csombordi, Rajmund; Komorowski, Jan; Diamanti, Klev

2021

• Ladda ner fulltext (pdf) av Supplementary tables:MetaFetcheR: An R package for complete mapping of small compound data

SUPPLEMENTARY MATERIAL: Machine learning-based analysis of glioma grades reveals co-enrichment

Garbulowski, Mateusz; Smolinska Garbulowska, Karolina; Çabuk, Uğur; Yones, Sara A. et al.

2021

SUPPLEMENTAL INFORMATION FOR: Transcriptomic analysis reveals pro-inflammatory signatures associated with acute myeloid leukemia progression

Stratmann, Svea; Yones, Sara A.; Garbulowski, Mateusz; Sun, Jitong et al.

2020

• Ladda ner fulltext (pdf) av SUPPLEMENTAL INFORMATION FOR: Transcriptomic analysis reveals pro-inflammatory signatures associated with acute myeloid leukemia progression

Discovering Networks of Interdependent Features in High-Dimensional Problems

Dramiński, Michał; Da̧browski, Michał J.; Diamanti, Klev; Koronacki, Jacek et al.

Ingår i Big Data Analysis, s. 285-304, Springer, 2016

• DOI för Discovering Networks of Interdependent Features in High-Dimensional Problems

Learning Rule-Based Models - The Rough Set Approach

Komorowski, Jan

Ingår i Comprehensive Biomedical Physics, s. 19-39, Elsevier, 2014

• DOI för Learning Rule-Based Models - The Rough Set Approach

Monte Carlo feature selection and interdependency discovery in supervised classification

Dramiński, Michał; Kierczak, Marcin; Koronacki, Jacek; Komorowski, Jan

Ingår i Advances in Machine Learning, Springer, 2010

• Ladda ner fulltext (pdf) av Monte Carlo feature selection and interdependency discovery in supervised classification

Visualization of Rules in Rule-Based Classifiers

Bornelöv, Susanne; Enroth, Stefan; Komorowski, Jan

Ingår i INTELLIGENT DECISION TECHNOLOGIES (IDT'2012), VOL 1, s. 329-338, 2012

• DOI för Visualization of Rules in Rule-Based Classifiers

Construction of Rough Set-Based Classifiers for Predicting HIV Resistance to Nucleoside Reverse Transcriptase Inhibitors

Kierczak, Marcin; Rudnicki, Witold; Komorowski, Jan

Ingår i GRANULAR COMPUTING, s. 249-258, 2008

• DOI för Construction of Rough Set-Based Classifiers for Predicting HIV Resistance to Nucleoside Reverse Transcriptase Inhibitors

A Statistical Method for Determining Importance of Variables in an Information System

Rudnicki, Witold R.; Kierczak, Marcin M.; Koronacki, Jacek; Komorowski, Jan

Ingår i Rough Sets and Current Trends in Computing, s. 557-566, 2006

• DOI för A Statistical Method for Determining Importance of Variables in an Information System

RoSy: A Rough Knowledge Base System

Andersson, Robin; Vitória, Aida; Maluszynski, Jan; Komorowski, Jan

Ingår i Rough Sets, Fuzzy Sets, Data Mining, and Granular Computing, s. 48-58, 2005

• DOI för RoSy: A Rough Knowledge Base System

Altered gene expression in the olfactory bulb following exposure to 2,6-dichlorophenyl methylsulfone

Bergström, Ulrika; Olsson, Jan A; Hvidsten, Torgeir R; Komorowski, Jan et al.

Ingår i Toxicology Letters 158 Supp 1., s. 61, 2005

Integration of whole-body PET/MRI with non-targeted metabolomics provides new insights into insulin sensitivity of various tissues

Diamanti, Klev; Visvanathar, Robin; Pereira, Maria J; Cavalli, Marco et al.

||-ROSETTA

Baltzer, Nicholas; Komorowski, Jan

VisuNet: an interactive tool for rule network visualization of rule-based learning models

Smolinska, Karolina; Garbulowski, Mateusz; Diamanti, Klev; Davoy, Xavier et al.

Ingår i SUPPLEMENTARY MATERIAL: VisuNet: an interactive tool for rule network visualization of rule-based learning models

funMotifs: Tissue-specific transcription factor motifs

Smolinska, Karolina; Umer, Husen M.; Khaliq, Zeeshan; Marzouka, Nour-al-dain et al.

Ingår i SUPPLEMENTARY MATERIAL: funMotifs: Tissue-specific transcription factor motifs

Risk Stratification in Cervical Cancer Screening – Validation and Generalization of a Data-driven  Screening Recall Model

Baltzer, Nicholas; Komorowski, Jan; Sundström, Karin; Nygård, Jan et al.

ChIP-seq in steatohepatitis and normal liver tissue identifies candidate disease mechanisms related to progression to cancer

Bysani, Madhusudhan Reddy; Wallerman, Ola; Bornelöv, Susanne; Zatloukal, Kurt et al.

Single-cell transcriptomic profiling identifies developmental haematopoietic program enrichment in KMT2A-rearranged infant acute lymphoblastic leukaemia

Garrido-Zabala, Berta; Pushkaran Pulinkala, Girish; Nylund, Patrick; Tziola, Stefania Iliana et al.