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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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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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
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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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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

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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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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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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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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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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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

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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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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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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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
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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
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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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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

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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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
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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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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

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

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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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
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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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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
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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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'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

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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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

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

Nucleosome regulatory dynamics in response to TGF-beta treatment in HepG2 cells

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 treatment in HepG2 cells

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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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

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
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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

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
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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
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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
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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
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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
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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