Publications

MindReader: Unsupervised Classification of Electroencephalographic Data

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

Part of Sensors, 2023.

DOI for MindReader: Unsupervised Classification of Electroencephalographic Data Download full text (pdf) of MindReader: Unsupervised Classification of Electroencephalographic Data

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

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

Part of Cancers, 2022.

DOI for Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment Download full text (pdf) of Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment

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.

Part of Scientific Reports, 2022.

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

Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression

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

Part of Blood Advances SUPPLEMENTAL INFORMATION FOR: Transcriptomic analysis reveals pro-inflammatory signatures associated with acute myeloid leukemia progression SUPPLEMENTARY MATERIAL: Transcriptomic analysis reveals pro-inflammatory signatures associated with acute myeloid leukemia progression, p. 152-164, 2022.

DOI for Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression Download full text (pdf) of 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.

Part of Cell Reports Medicine, 2022.

DOI for Organ-specific metabolic pathways distinguish prediabetes, type 2 diabetes, and normal tissues Download full text (pdf) of Organ-specific metabolic pathways distinguish prediabetes, type 2 diabetes, and normal tissues

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

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

Part of The Plant Journal, p. 1534-1548, 2021.

DOI for 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.

Part of PLoS Pathogens, 2021.

DOI for Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy Download full text (pdf) of Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy

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

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

Part of Blood Advances SUPPLEMENTAL INFORMATION FOR: Genomic characterization of adult and pediatric relapsed acute myeloid leukemia reveals novel therapeutic targets, p. 900-912, 2021.

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

Multifaceted regulation of hepatic lipid metabolism by YY1

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

Part of Life Science Alliance, 2021.

DOI for Multifaceted regulation of hepatic lipid metabolism by YY1 Download full text (pdf) of Multifaceted regulation of hepatic lipid metabolism by YY1

Functional annotation of noncoding mutations in cancer

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

Part of Life Science Alliance, 2021.

DOI for Functional annotation of noncoding mutations in cancer Download full text (pdf) of Functional annotation of noncoding mutations in cancer

Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

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

Part of Nature Communications, 2021.

DOI for Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas Download full text (pdf) of Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data

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

Part of Metabolites, 2021.

DOI for MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data Download full text (pdf) of MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data

R.ROSETTA: an interpretable machine learning framework

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

Part of BMC Bioinformatics, 2021.

DOI for R.ROSETTA: an interpretable machine learning framework Download full text (pdf) of R.ROSETTA: an interpretable machine learning framework

Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder

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

Part of Frontiers in Genetics, 2021.

DOI for Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder Download full text (pdf) of Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder

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.

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 Download full text (pdf) of A Multi-Omics Approach to Liver Diseases: Integration of Single Nuclei Transcriptomics with Proteomics and HiCap Bulk Data in Human Liver

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.

Part of Communications Biology, 2020.

DOI for Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis Download full text (pdf) of Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis

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.

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 Download full text (pdf) of 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

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

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

Part of Nature, p. 102-111, 2020.

DOI for Analyses of non-coding somatic drivers in 2,658 cancer whole genomes Download full text (pdf) of Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

Pan-cancer analysis of whole genomes

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

Part of Nature, p. 82-93, 2020.

DOI for Pan-cancer analysis of whole genomes Download full text (pdf) of Pan-cancer analysis of whole genomes

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

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

Part of Journal of Psychiatric Research, p. 41-47, 2019.

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

Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control

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

Part of Nature Communications, 2019.

DOI for Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control Download full text (pdf) of Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control

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.

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 Download full text (pdf) of Studies of liver tissue identify functional gene regulatory elements associated to gene expression, type 2 diabetes, and other metabolic diseases

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.

Part of Scientific Reports, 2019.

DOI for Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases Download full text (pdf) of Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases

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.

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 Download full text (pdf) of Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes

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

Grabherr, Manfred; Kaminska, Bozena; Komorowski, Jan

Part of Genes, 2018.

DOI for Special Issue Introduction: The Wonders and Mysteries Next Generation Sequencing Technologies Help Reveal Download full text (pdf) of Special Issue Introduction: The Wonders and Mysteries Next Generation Sequencing Technologies Help Reveal

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.

Part of Scientific Reports, 2018.

DOI for Unveiling new interdependencies between significant DNA methylation sites, gene expression profiles and glioma patients survival Download full text (pdf) of Unveiling new interdependencies between significant DNA methylation sites, gene expression profiles and glioma patients survival

PiiL: visualization of DNA methylation and gene expression data in gene pathways

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

Part of BMC Genomics, 2017.

DOI for PiiL: visualization of DNA methylation and gene expression data in gene pathways Download full text (pdf) of PiiL: visualization of DNA methylation and gene expression data in gene pathways

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.

Part of International Journal of Cancer, p. 200-209, 2017.

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

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

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

Part of BMC Bioinformatics, 2016.

DOI for Combinatorial identification of DNA methylation patterns over age in the human brain Download full text (pdf) of Combinatorial identification of DNA methylation patterns over age in the human brain

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

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 Download full text (pdf) of Identification of combinatorial host-specific signatures with a potential to affect host adaptation in influenza A H1N1 and H3N2 subtypes

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.

Part of Human Mutation, p. 904-913, 2016.

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

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

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

Part of Nucleic Acids Research, p. 9110-9120, 2016.

DOI for Maps of context-dependent putative regulatory regions and genomic signal interactions Download full text (pdf) of Maps of context-dependent putative regulatory regions and genomic signal interactions

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

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 Download full text (pdf) of A complete map of potential pathogenicity markers of avian influenza virus subtype H5 predicted from 11 expressed proteins

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

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 Download full text (pdf) of Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription

'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.

Part of Molecular Ecology Resources, p. 477-488, 2015.

DOI for '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

Part of BMC Bioinformatics, p. 139-, 2014.

DOI for Ciruvis: a web-based tool for rule networks and interaction detection using rule-based classifiers Download full text (pdf) of Ciruvis: a web-based tool for rule networks and interaction detection using rule-based classifiers

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.

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 Download full text (pdf) of The signal transducers Stat1 and Stat3 and their novel target Jmjd3 drive the expression of inflammatory genes in microglia

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.

Part of Biochimica et Biophysica Acta, p. 1341-1350, 2014.

DOI for 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 treatment in HepG2 cells

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

Part of Nucleic Acids Research, p. 6921-6934, 2014.

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

Nucleosome regulatory dynamics in response to TGF beta

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

Part of Nucleic Acids Research, p. 6921-6934, 2014.

DOI for Nucleosome regulatory dynamics in response to TGF beta

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.

Part of BMC Medical Genomics, p. 50-, 2013.

DOI for 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

Part of BMC Bioinformatics, p. 280-, 2013.

DOI for Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data Download full text (pdf) of Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data

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.

Part of Fundamenta Informaticae, p. 273-288, 2013.

DOI for 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.

Part of PLOS ONE, p. e80080-, 2013.

DOI for Rule-Based Models of the Interplay between Genetic and Environmental Factors in Childhood Allergy Download full text (pdf) of Rule-Based Models of the Interplay between Genetic and Environmental Factors in Childhood Allergy

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.

Part of Journal of neural transmission, p. 821-831, 2012.

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

Combinations of histone modifications mark exon inclusion levels

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

Part of PLOS ONE, 2012.

DOI for Combinations of histone modifications mark exon inclusion levels Download full text (pdf) of Combinations of histone modifications mark exon inclusion levels

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.

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 Download full text (pdf) of 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.

Part of PLOS ONE, p. e31577-, 2012.

DOI for Gis1 and Rph1 Regulate Glycerol and Acetate Metabolism in Glucose Depleted Yeast Cells Download full text (pdf) of Gis1 and Rph1 Regulate Glycerol and Acetate Metabolism in Glucose Depleted Yeast Cells

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.

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

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.

Part of Genome Research, p. 361-371, 2010.

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

SICTIN: Rapid footprinting of massively parallel sequencing data

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

Part of BioData Mining, 2010.

DOI for SICTIN: Rapid footprinting of massively parallel sequencing data Download full text (pdf) of SICTIN: Rapid footprinting of massively parallel sequencing data

Integrative epigenomic and genomic analysis of malignant pheochromocytoma

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

Part of Experimental and Molecular Medicine, p. 484-502, 2010.

DOI for 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.

Part of Endocrine-Related Cancer, p. 561-579, 2010.

DOI for 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.

Part of International Journal of Cancer, p. 1390-1402, 2010.

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

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

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

Part of Bioinformatics and Biology Insights, p. 109-127, 2009.

Download full text (pdf) of A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome

Nucleosomes are well positioned in exons and carry characteristic histone modifications

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

Part of Genome Research, p. 1732-1741, 2009.

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

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.

Part of Nucleic Acids Research, p. 7498-7508, 2009.

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

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

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

Part of Neuro-Oncology, p. 803-818, 2009.

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

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.

Part of Genome Biology, p. R129-, 2009.

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

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

Part of Nucleic Acids Research, p. e85-, 2009.

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

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.

Part of Nucleic Acids Research, p. 7498-7508, 2009.

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

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

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

Part of Bioorganic & Medicinal Chemistry, p. 5229-5237, 2009.

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

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.

Part of PLoS ONE, p. e6266-, 2009.

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

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.

Part of Bioinformatics, p. 322-330, 2009.

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

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.

Part of The FEBS Journal, p. 1878-1890, 2009.

DOI for 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

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.

Part of Epigenetics, p. 107-113, 2009.

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.

Part of Genome Research, p. 380-392, 2008.

DOI for 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

Generalized proteochemometric model of multiple cytochrome P450 enzymes and their inhibitors

Kontijevskis, Aleksejs; Komorowski, Jan; Wikberg, Jarl

Part of Journal of chemical information and modeling, p. 1840-1850, 2008.

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

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

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

Part of Molecular Cell, p. 232-46, 2008.

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

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.

Part of BMC Genomics, p. 601-, 2008.

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

Monte Carlo feature selection for supervised classification

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

Part of Bioinformatics, p. 110-117, 2008.

DOI for Monte Carlo feature selection for supervised classification

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

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

Part of Bioinformatics, p. 751-758, 2008.

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

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

Part of BMC Bioinformatics, p. 484-, 2008.

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

Somatic mosaicism for copy number variation in differentiated human tissues

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

Part of Human Mutation, p. 1118-24, 2008.

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

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.

Part of American Journal of Human Genetics, p. 763-71, 2008.

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

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.

Part of Human Mutation, p. 398-408, 2008.

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

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.

Part of American Journal of Medical Genetics, Part A, p. 1760-1766, 2007.

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

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

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