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1. Full Text Selective Glucocorticoid Receptor Modulation Prevents and Reverses Nonalcoholic Fatty Liver Disease in Male Mice
by Koorneef, Lisa L and Heuvel, J.K. van den and Kroon, J and Boon, M.R and Hoen, P.A.C. 't and Hettne, K.M and Rensen, P.C and Meijer, Onno C
Endocrinology, ISSN 0013-7227, 2018, Volume 159, Issue 12, pp. 3925 - 3936
Medication for nonalcoholic fatty liver disease (NAFLD) is an unmet need. Glucocorticoid (GC) stress hormones drive fat metabolism in the liver, but both full... 
DENSITY | PLATFORM | PROJECT | CHOLESTEROL | METABOLISM | EFFICACY | PATHWAY | ENDOCRINOLOGY & METABOLISM | WEIGHT-GAIN | HEPATIC STEATOSIS | EXPRESSION | Fat metabolism | Glucocorticoids | Liver | Genes | Menopause | Lipids | Stimulation | Genomes | Lipoprotein lipase | Hormones | Lipase | Accumulation | Mimicry | High fat diet | Fatty liver | Modulation | Efflux | Nutrient deficiency | Liver diseases | Gene expression | Fatty acids | Cholesterol | Lipoproteins (very low density) | Gas chromatography | Diet | Low fat diet | Metabolic disorders
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2. Full Text Large-scale plasma metabolome analysis reveals alterations in HDL metabolism in migraine
by Onderwater, G.L.J and Ligthart, L and Bot, M and Demirkan, Ayşe and Fu, Jingyuan and van der Kallen, CJH and Vijfhuizen, LS and Pool, R and Liu, J and Vanmolkot, F.H.M and Beekman, Marian and Wen, K.X and Amin, Najaf and Thesing, C.S and Pijpers, J.A and Kies, D.A and Zielman, Ronald and den Boer, I and van Greevenbroek, MMJ and Arts, I.C.W and Milaneschi, Yuri and Schram, Miranda and Dagnelie, P.C and Franke, Lude and Ikram, Arfan and Ferrari, Michel and Goeman, Jelle and Lagboom, P Eline and Wijmenga, Cisca and Stehouwer, Coen and Boomsma, Dorret and Duijn, C.M and Penninx, Brenda and t Hoen, PAC and Terwindt, Gisela and BBMRI Metabolomics Consortium and on behalf of the BBMRI Metabolomics Consortium
Neurology, ISSN 0028-3878, 01/2019, Volume 92, Issue 16, pp. E1899 - E1911
markdownabstractObjective To identify a plasma metabolomic biomarker signature for migraine. Methods Plasma samples from 8 Dutch cohorts (n = 10,153: 2,800... 
BIOMARKERS | RISK-FACTORS | CARDIOVASCULAR-DISEASE | GLOBAL TEST | LIPOPROTEINS | ASSOCIATION | EPIDEMIOLOGY | CLINICAL NEUROLOGY | 101 | 223
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3. Full Text Computational approaches for the analysis of RNA-protein interactions: A primer for biologists
by Moore, K.S and Hoen, P.A.C. 't
Journal of Biological Chemistry, ISSN 0021-9258, 2019, Volume 294, Issue 1, pp. 1 - 9
RNA-binding proteins (RBPs) play important roles in the control of gene expression and the coordination of different layers of post-transcriptional regulation.... 
computational biology | next generation sequencing | BIOCHEMISTRY & MOLECULAR BIOLOGY | translation control | RNA-protein interaction | HIDDEN MARKOV-MODELS | BINDING PROTEIN | PREDICTION | CLIP | RNA-binding protein | RNA-seq | SEQUENCE | SITES | SELECTION | statistics
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4. Full Text Whole Transcriptome RNA Sequencing As a Comprehensive Diagnostic Tool for Acute Myeloid Leukemia
by Griffioen, Marieke and Arindrarto, Wibowo and Borras, Daniel M and Locher, Irene J and van Diessen, Saskia A.M.E and van der Holst, Rosalie and van der Meijden, Edith D and Honders, M. Willy and de Leeuw, Rick H and Jedema, Inge and Kroes, Wilma G.M and Knijnenburg, Jeroen and Vermaat, Joost and Valk, Peter and Janssen, Bart and de Knijff, Peter and van Bergen, Cornelis A.M and van den Akker, Erik B and 't Hoen, Peter A.C and Kielbasa, Szymon M and Laros, Jeroen F.J and Veelken, Hendrik
Blood, ISSN 0006-4971, 11/2018, Volume 132, Issue Supplement 1, pp. 2762 - 2762
Abstract Introduction Acute myeloid leukemia (AML) is characterized by uncontrolled proliferation of malignant myeloid progenitor cells in the bone marrow that... 
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5. Full Text Comparative transcriptomics of shear stress treated Pkd1−/− cells and pre-cystic kidneys reveals pathways involved in early polycystic kidney disease
by Kunnen, Steven J and Malas, Tareq B and Formica, Chiara and Leonhard, Wouter N and ’t Hoen, Peter A.C and Peters, Dorien J.M
Biomedicine & Pharmacotherapy, ISSN 0753-3322, 12/2018, Volume 108, pp. 1123 - 1134
Mutations in the or genes are the cause of autosomal dominant polycystic kidney disease (ADPKD). The encoded proteins localize within the cell membrane and... 
Shear stress | Renal epithelial cell | Mechanotransduction | RNA-seq | Next generation sequencing | Polycystic kidney disease | MEDICINE, RESEARCH & EXPERIMENTAL | RENAL EPITHELIAL-CELLS | ACCELERATES CYSTOGENESIS | INJURY | ENDOCYTOSIS | WNT SIGNALING PATHWAYS | THERAPY | MODELS | GENE | CALCIUM | PHARMACOLOGY & PHARMACY | PRIMARY CILIA | Polycystic Kidney Diseases - genetics | Kidney Tubules, Proximal - pathology | Epithelial Cells - metabolism | Organ Size | Stress, Mechanical | TRPP Cation Channels - deficiency | Male | Gene Expression Profiling | Signal Transduction - genetics | Cilia - metabolism | Animals | Polycystic Kidney Diseases - pathology | Gene Deletion | Transcription, Genetic | Mice | TRPP Cation Channels - metabolism
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6. Full Text Comparative transcriptomics of shear stress treated Pkd1 .sup.-/- cells and pre-cystic kidneys reveals pathways involved in early polycystic kidney disease
by Kunnen, Steven J and Malas, Tareq B and Formica, Chiara and Leonhard, Wouter N and t Hoen, Peter A.C and Peters, Dorien J.M
Biomedicine & Pharmacotherapy, ISSN 0753-3322, 12/2018, Volume 108, p. 1123
Mutations in the PKD1 or PKD2 genes are the cause of autosomal dominant polycystic kidney disease (ADPKD). The encoded proteins localize within the cell... 
RNA sequencing | Anopheles | RNA | Genes | Genetic research | Bone morphogenetic proteins | Comparative analysis | Transforming growth factors | Gene expression | Polycystic kidney disease
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7. Full Text Alternative mRNA transcription, processing, and translation: insights from RNA sequencing
by de Klerk, Eleonora and t Hoen, Peter A.C
Trends in Genetics, ISSN 0168-9525, 2015, Volume 31, Issue 3, pp. 128 - 139
Highlights • RNA sequencing uncovers mechanisms regulating gene expression. • Use of alternative TSSs, PASs, and exons is the rule. • Alternative translation... 
Medical Education | RNA sequencing | translation | alternative splicing | transcriptome | gene expression | alternative polyadenylation | Alternative polyadenylation | Alternative splicing | Translation | Gene expression | Transcriptome | HUMAN TISSUES | MAMMALIAN-CELLS | BREAST-CANCER | 3' UNTRANSLATED REGIONS | OPEN READING FRAMES | IN-VIVO | GENETICS & HEREDITY | SECONDARY STRUCTURE | POLYMERASE-II | ANALYSIS GENE-EXPRESSION | GENOME-WIDE IDENTIFICATION | Protein Biosynthesis | Sequence Analysis, RNA | Alternative Splicing | Humans | RNA, Messenger - genetics | Polyadenylation | Transcription, Genetic | Gene Expression Profiling | High-Throughput Nucleotide Sequencing - methods | Promoter Regions, Genetic - genetics | Genetic translation | Messenger RNA | Genetic transcription
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8. Full Text Whole Transcriptome Sequencing (RNAseq) As a Comprehensive, Cost-Efficient Diagnostic Tool for Acute Myeloid Leukemia
by Griffioen, Marieke and Arindrarto, Wibowo and Borràs, Daniel and van Diessen, Saskia A.M.E and van der Meijden, Edith D and Honders, M. Willy and Alloul, Mariam and Jedema, Inge and Kroes, Wilma G.M and Valk, Peter J.M and Janssen, Bart and van Bergen, Cornelis A.M and Kiełbasa, Szymon M and Laros, Jeroen F.J and 't Hoen, Peter A.C and Veelken, Hendrik
Blood, ISSN 0006-4971, 12/2016, Volume 128, Issue 22, pp. 1701 - 1701
Abstract Background Acute myeloid leukemia (AML) is caused by cooperating oncogenic driver mutations that induce uncontrolled proliferation in combination with... 
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9. Full Text Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions
by Nolte-'t Hoen, E.N.M and Buermans, H.P and Waasdorp, M and Stoorvogel, W and Wauben, M.H.M and t Hoen, P.A.C
Nucleic Acids Research, ISSN 0305-1048, 2012, Volume 40, Issue 18, pp. 9272 - 9285
Cells release RNA-carrying vesicles and membrane-free RNA/protein complexes into the extracellular milieu. Horizontal vesicle-mediated transfer of such shuttle... 
International (English) | PROTEIN | PARTICLE | MEMBRANE-VESICLES | BIOCHEMISTRY & MOLECULAR BIOLOGY | TRANSCRIPTION | COMPLEXES | EXOSOMES | MICROVESICLES | MICRORNAS | IDENTIFICATION | LYMPHOCYTES | Coculture Techniques | Dendritic Cells - immunology | Cells, Cultured | RNA, Small Untranslated - physiology | RNA, Transfer - analysis | Sequence Analysis, RNA | MicroRNAs - analysis | RNA, Small Untranslated - analysis | T-Lymphocytes - chemistry | RNA, Small Untranslated - chemistry | Repetitive Sequences, Nucleic Acid | T-Lymphocytes - immunology | Transport Vesicles - chemistry | High-Throughput Nucleotide Sequencing | RNA, Transfer - chemistry | MicroRNAs - chemistry | Dendritic Cells - chemistry | Biotypes | Vesicles | non-coding RNA | tRNA | Data processing | Evolution | miRNA | RNA
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10. Full Text Ribosome Profiling Uncovers the Role of uORFs in Translational Control of Gene Expression during Erythroblast Differentiation
by Thiadens, Klaske A.M.H and de Klerk, Eleonora and Fokkema, Ivo F.A.C and ‘t Hoen, Peter A.C and von Lindern, Marieke
Blood, ISSN 0006-4971, 12/2014, Volume 124, Issue 21, pp. 2658 - 2658
Abstract The erythroid progenitor compartment possesses a large expansion capacity, both in vivo and in vitro, which enables a rapid restoration of peripheral... 
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11. Full Text Systematic identification of trans eQTLs as putative drivers of known disease associations
by Westra, Harm-Jan and Peters, Marjolein J and Esko, Tonu and Yaghootkar, Hanieh and Schurmann, Claudia and Kettunen, Johannes and Christiansen, Mark W and Fairfax, Benjamin P and Schramm, Katharina and Powell, Joseph E and Zhernakova, Alexana and Zhernakova, Daria V and Veldink, Jan H and Van den Berg, Leonard H and Karjalainen, Juha and Withoff, Sebo and Uitterlinden, Ane G and Hofman, Albert and Rivadeneira, Fernando and t Hoen, Peter A. C and Reinmaa, Eva and Fischer, Krista and Nelis, Mari and Milani, Lili and Melzer, David and Ferrucci, Luigi and Singleton, Anew B and Hernandez, Dena G and Nalls, Michael A and Homuth, Georg and Nauck, Matthias and Radke, Doerte and Voelker, Uwe and Perola, Markus and Salomaa, Veikko and Brody, Jennifer and Suchy-Dicey, Astrid and Gharib, Sina A and Enquobahrie, Daniel A and Lumley, Thomas and Montgomery, Grant W and Makino, Seiko and Prokisch, Holger and Herder, Christian and Roden, Michael and Grallert, Harald and Meitinger, Thomas and Strauch, Konstantin and Li, Yang and Jansen, Ritsert C and Visscher, Peter M and Knight, Julian C and Psaty, Bruce M and Ripatti, Samuli and Teumer, Alexander and Frayling, Timothy M and Metspalu, Anes and van Meurs, Joyce B. J and Franke, Lude and Hoen, Peter A.C. ’t
Nature Genetics, ISSN 1061-4036, 10/2013, Volume 45, Issue 10, pp. 1238 - 1243
Identifying the downstream effects of disease-associated SNPs is challenging. To help overcome this problem, we performed expression quantitative trait locus... 
POPULATION | INTERFERON | MYOCARDIAL-INFARCTION | VARIANTS | GENE-EXPRESSION | SUSCEPTIBILITY LOCI | LUPUS-ERYTHEMATOSUS | RISK | GENOME-WIDE ASSOCIATION | BLOOD | CELLS | C1Q | POLYMORPHISMS | GENETICS & HEREDITY | CIS | Diabetes Mellitus, Type 1 - genetics | Genetic Predisposition to Disease | Polymorphism, Single Nucleotide | Quantitative Trait Loci | Humans | Lupus Erythematosus, Systemic - genetics | Quantitative trait loci | Genetic aspects | Systemic lupus erythematosus | Single nucleotide polymorphisms | Research | Identification and classification | Studies | Genomes | Disease | Gene expression | Binding sites | Meta-analysis
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12. Full Text A putative role for genome-wide epigenetic regulatory mechanisms in Huntington’s disease: A computational assessment
by Mina, Eleni and van Roon-Mom, Willeke and Verschure, Pernette and 't Hoen, Peter A.C and Thompson, Mark and Kaliyaperumal, Rajaram and Hettne, Kristina and Schultes, Erik and Mons, Barend and Roos, Marco
F1000Research, ISSN 2046-1402, 2017, Volume 6, p. 1888
Background: Huntington's Disease (HD) is an incurable disease of the adult brain. Massive changes in gene expression are a prominent feature. Epigenetic... 
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13. Full Text The FAIR Guiding Principles for scientific data management and stewardship
by Wilkinson, Mark D and Dumontier, Michel and Aalbersberg, Ijsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-willem and Da Silva Santos, Luiz Bonino and Bourne, Philip E and Bouwman, Jildau and Brookes, Anthony J and Clark, Tim and Crosas, Mercè and Dillo, Ingrid and Dumon, Olivier and Edmunds, Scott and <