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The value of data

Barend Mons, Herman van Haagen, Christine Chichester, Peter-Bram 't Hoen, Johan T den Dunnen, Gertjan van Ommen, Erik van Mulligen, Bharat Singh, Rob Hooft, Marco Roos, Joel Hammond, Bruce Kiesel (+4 others)
2011 Nature Genetics  
1,4 , Johan T den Dunnen 1 , Gertjan van Ommen 1,4 , Erik van Mulligen 3,4 , Bharat Singh 2,3 , Rob Hooft 2,4 , Marco Roos 1,2,4 , Joel Hammond 5 , Bruce Kiesel 5 , Belinda Giardine 6 , Jan Velterop 4,7  ...  , Paul Groth 4,8 & Erik Schultes 1,4 Figure 2 2 A proposal for the future of scholarly communication.  ... 
doi:10.1038/ng0411-281 pmid:21445068 fatcat:ffxifjtm4vcr3jw3mcjxaclqq4

Huntington's disease biomarker progression profile identified by transcriptome sequencing in peripheral blood

Anastasios Mastrokolias, Yavuz Ariyurek, Jelle J Goeman, Erik van Duijn, Raymund AC Roos, Roos C van der Mast, GertJan B van Ommen, Johan T den Dunnen, Peter AC 't Hoen, Willeke MC van Roon-Mom
2015 European Journal of Human Genetics  
Asterisks represent statistical significance from a Student's t-test (*Po0.05, **Po0.01). Error bars represent SEM values.  ...  Canonical pathway analysis using IPA further confirmed our initial Global test results, as common pathways reported were those of diabetes mellitus, Toll-like receptor and T-cell receptor signaling.  ... 
doi:10.1038/ejhg.2014.281 pmid:25626709 pmcid:PMC4592077 fatcat:lp6prx7ynjhnjay77jud46mv3m

Promoter DNA Methylation Pattern Identifies Prognostic Subgroups in Childhood T-Cell Acute Lymphoblastic Leukemia

Magnus Borssén, Lars Palmqvist, Kristina Karrman, Jonas Abrahamsson, Mikael Behrendtz, Jesper Heldrup, Erik Forestier, Göran Roos, Sofie Degerman, Carmen J. Marsit
2013 PLoS ONE  
Treatment of pediatric T-cell acute lymphoblastic leukemia (T-ALL) has improved, but there is a considerable fraction of patients experiencing a poor outcome.  ...  CIMP2 T-ALL patients had significantly worse overall and event free survival (p = 0.02 and p = 0.001, respectively) compared to CIMP+ cases.  ...  However, about 15% derive from the T-cell lineage (T-ALL).  ... 
doi:10.1371/journal.pone.0065373 pmid:23762353 pmcid:PMC3675104 fatcat:n3cytc5cezfk3kfldbecju2e3e

Acute stress impairs inhibitory control based on individual differences in parasympathetic nervous system activity

Leslie E. Roos, Erik L. Knight, Kathryn G. Beauchamp, Elliot T. Berkman, Kelsie Faraday, Katie Hyslop, Philip A. Fisher
2017 Biological Psychology  
Roos received support from HHS-2014-ACF-ACYF-CA-0803. Elliot Berkman received support from NIH grants R01 AG048840, R21 CA175241 and P50 DA035763. Philip A.  ... 
doi:10.1016/j.biopsycho.2017.03.004 pmid:28268165 pmcid:PMC5448703 fatcat:jwwj3tasljdx5crf6ora6kopc4

Immortalization of T-Cells Is Accompanied by Gradual Changes in CpG Methylation Resulting in a Profile Resembling a Subset of T-Cell Leukemias

Sofie Degerman, Mattias Landfors, Jan Konrad Siwicki, John Revie, Magnus Borssén, Emma Evelönn, Erik Forestier, Krystyna H. Chrzanowska, Patrik Rydén, W. Nicol Keith, Göran Roos
2014 Neoplasia: An International Journal for Oncology Research  
Interestingly, the pattern of CpG site methylation observed in immortal T-cell cultures was similar to clinical T-cell acute lymphoblastic leukemia (T-ALL) samples classified as CpG island methylator phenotype  ...  The presence of non-random methylation events in in vitro immortalized T-cell cultures and diagnostic T-ALL samples indicates altered methylation of CpG sites with a possible role in malignant hematopoiesis  ...  cultures and in relation to diagnostic T-cell acute lymphoblastic leukemia (T-ALL) samples.  ... 
doi:10.1016/j.neo.2014.07.001 pmid:25065939 pmcid:PMC4198827 fatcat:lhbcvy7grfhu3bcoax2lrdh2hi

Conceptual precision is key in acute stress research: A commentary on Shields, Sazma, & Yonelinas, 2016

Leslie E. Roos, Erik L. Knight, Kathryn G. Beauchamp, Ryan J. Giuliano, Philip A. Fisher, Elliot T. Berkman
2017 Neuroscience and Biobehavioral Reviews  
., 2008) , so acute stressors might have greater effects on Stop Signal (consistent with a recent finding by our research group; Roos et al., 2017) , compared with Go/No-Go inhibition performance.  ...  Similarly, our own research examining the effects of acute stress on stop-signal inhibition found that parasympathetic augmentation to the TSST predicted individual differences in EF impairment (Roos  ... 
doi:10.1016/j.neubiorev.2017.10.005 pmid:28988779 pmcid:PMC5840802 fatcat:qm557bpumnatbl2jetfetznhyy

A putative role for genome-wide epigenetic regulatory mechanisms in Huntington's disease: A computational assessment

Eleni Mina, Willeke van Roon-Mom, Pernette Verschure, Peter A.C. 't Hoen, Mark Thompson, Rajaram Kaliyaperumal, Kristina Hettne, Erik Schultes, Barend Mons, Marco Roos
2017 F1000Research  
Differential expression was computed using moderated t statistics with the package limma 35 (version 3.14.1), which is provided by the bioconductor project 36 , R version https://www.bioconductor. org/  ... 
doi:10.12688/f1000research.9703.1 fatcat:cn4drsedardsdgk6fxwqjb2yh4

DNA Methylation Adds Prognostic Value to Minimal Residual Disease Status in Pediatric T-Cell Acute Lymphoblastic Leukemia

Magnus Borssén, Zahra Haider, Mattias Landfors, Ulrika Norén-Nyström, Kjeld Schmiegelow, Ann E. Åsberg, Jukka Kanerva, Hans O. Madsen, Hanne Marquart, Mats Heyman, Magnus Hultdin, Göran Roos (+2 others)
2016 Pediatric Blood & Cancer  
INTRODUCTION T-cell acute lymphoblastic leukemia (T-ALL) accounts for 10-15% of childhood ALL, but is more common among adolescents and adults.  ...  [8, 22, 23] The prognostic relevance of CIMP classification in pediatric T-ALL shown in this paper confirms our previous finding in a separate T-ALL cohort.  ... 
doi:10.1002/pbc.25958 pmid:26928953 fatcat:dzn7majbwrb5lkk74veqyeprhm

T helper 17.1 cells associate with multiple sclerosis disease activity: perspectives for early intervention

Jamie van Langelaar, Roos M van der Vuurst de Vries, Malou Janssen, Annet F Wierenga-Wolf, Isis M Spilt, Theodora A Siepman, Wendy Dankers, Georges M G M Verjans, Helga E de Vries, Erik Lubberts, Rogier Q Hintzen, Marvin M van Luijn
2018 Brain  
Across all pro-inflammatory T helper cells analysed in relapsing-remitting multiple sclerosis blood, Th1-like Th17 subpopulation T helper 17.1 (Th17.1; CCR6 + CXCR3 + CCR4 À ) expressed the highest very  ...  Interleukin-17-expressing CD4 + T helper 17 (Th17) cells are considered as critical regulators of multiple sclerosis disease activity.  ...  staining of the T helper subsets of interest.  ... 
doi:10.1093/brain/awy069 pmid:29659729 fatcat:4oblt2djnvdf7c2rluca3g3lm4

Common disease signatures from gene expression analysis in Huntington's disease human blood and brain

Eleni Mina, Willeke van Roon-Mom, Kristina Hettne, Erik van Zwet, Jelle Goeman, Christian Neri, Peter A.C. 't Hoen, Barend Mons, Marco Roos
2016 Orphanet Journal of Rare Diseases  
Common annotations included major histocompatibility complex location, lymphocyte activation, cytokine activity, T cell activation and adaptive immune response.  ... 
doi:10.1186/s13023-016-0475-2 pmid:27476530 pmcid:PMC4968014 fatcat:kietohcjxvfixdv2sc7qxjdmge

Drug prioritization using the semantic properties of a knowledge graph

Tareq B. Malas, Wytze J. Vlietstra, Roman Kudrin, Sergey Starikov, Mohammed Charrout, Marco Roos, Dorien J. M. Peters, Jan A. Kors, Rein Vos, Peter A. C. 't Hoen, Erik M. van Mulligen, Kristina M. Hettne
2019 Scientific Reports  
Based on the extracted features, the classifier is trained/cross-validated to classify the status of each drug-disease combination as "Approved" (A) or "Terminated" (T). www.nature.com/scientificreports  ... 
doi:10.1038/s41598-019-42806-6 pmid:31000794 pmcid:PMC6472420 fatcat:oytdymtcqjgxxel2h7f45rf3oy

The Implicitome: A Resource for Rationalizing Gene-Disease Associations

Kristina M. Hettne, Mark Thompson, Herman H. H. B. M. van Haagen, Eelke van der Horst, Rajaram Kaliyaperumal, Eleni Mina, Zuotian Tatum, Jeroen F. J. Laros, Erik M. van Mulligen, Martijn Schuemie, Emmelien Aten, Tong Shu Li (+11 others)
2016 PLoS ONE  
High-throughput experimental methods such as medical sequencing and genome-wide association studies (GWAS) identify increasingly large numbers of potential relations between genetic variants and diseases. Both biological complexity (millions of potential gene-disease associations) and the accelerating rate of data production necessitate computational approaches to prioritize and rationalize potential gene-disease relations.
doi:10.1371/journal.pone.0149621 pmid:26919047 pmcid:PMC4769089 fatcat:dru6ynlspfaf7dsrfj6ojiqg74

Supplemental material for Clinical prediction of thrombectomy eligibility: A systematic review and 4-item decision tree

Gaia T Koster, T Truc My Nguyen, Erik W Van Zwet, Bjarty L Garcia, Hannah R Rowling, J Bosch, Wouter J Schonewille, Birgitta K Velthuis, Ido R Van Der Wijngaard, Heleen M Den Hertog, Yvo BWEM Roos, Marianne AA Van Walderveen (+2 others)
2018 Figshare  
Supplemental material for Clinical prediction of thrombectomy eligibility: A systematic review and 4-item decision tree by Gaia T Koster, T Truc My Nguyen, Erik W van Zwet, Bjarty L Garcia, Hannah R Rowling  ...  , J Bosch, Wouter J Schonewille, Birgitta K Velthuis, Ido R van der Wijngaard, Heleen M den Hertog, Yvo BWEM Roos, Marianne AA van Walderveen, Marieke JH Wermer and Nyika D Kruyt in International Journal  ... 
doi:10.25384/sage.7087637.v1 fatcat:eoo5nf2zzrbflp2clx7kzfscsm

Clinical prediction of thrombectomy eligibility: A systematic review and 4-item decision tree

Gaia T Koster, T Truc My Nguyen, Erik W van Zwet, Bjarty L Garcia, Hannah R Rowling, J Bosch, Wouter J Schonewille, Birgitta K Velthuis, Ido R van der Wijngaard, Heleen M den Hertog, Yvo BWEM Roos, Marianne AA van Walderveen (+2 others)
2018 International Journal of Stroke  
Continuous variables are compared using the t test or Mann-Whitney U test, and are presented as mean AE standard deviation or median (interquartile range, IQR) if appropriate.  ...  Koster http://orcid.org/0000-0001-7138-5313 T Truc My Nguyen http://orcid.org/0000-0003-3545-3053  ...  Funding The author(s) disclosed receipt of the following financial support for the research, authorship and/or publication of this article: This work was supported by The Netherlands Brain ORCID iD Gaia T  ... 
doi:10.1177/1747493018801225 pmid:30209989 fatcat:3mtkjtuznjgotinowlpnddtqbe

Integration of targeted metabolomics and transcriptomics identifies deregulation of phosphatidylcholine metabolism in Huntington's disease peripheral blood samples

Anastasios Mastrokolias, Rene Pool, Eleni Mina, Kristina M. Hettne, Erik van Duijn, Roos C. van der Mast, GertJan van Ommen, Peter A. C. 't Hoen, Cornelia Prehn, Jerzy Adamski, Willeke van Roon-Mom
2016 Metabolomics  
Introduction Metabolic changes have been frequently associated with Huntington's disease (HD). At the same time peripheral blood represents a minimally invasive sampling avenue with little distress to Huntington's disease patients especially when brain or other tissue samples are difficult to collect. Objectives We investigated the levels of 163 metabolites in HD patient and control serum samples in order to identify disease related changes. Additionally, we integrated the metabolomics data
more » ... our previously published next generation sequencing-based gene expression data from the same patients in order to interconnect the metabolomics changes with transcriptional alterations. Methods This analysis was performed using targeted metabolomics and flow injection electrospray ionization tandem mass spectrometry in 133 serum samples from 97 Huntington's disease patients (29 pre-symptomatic and 68 symptomatic) and 36 controls. Results By comparing HD mutation carriers with controls we identified 3 metabolites significantly changed in HD (serine and threonine and one phosphatidylcholine-PC ae C36:0) and an additional 8 phosphatidylcholines (PC aa C38:6, PC aa C36:0, PC ae C38:0, PC aa C38:0, PC ae C38:6, PC ae C42:0, PC aa C36:5 and PC ae C36:0) that exhibited a significant association with disease severity. Using workflow based exploitation of pathway databases and by integrating our metabolomics data with our gene expression data from the same patients we identified 4 deregulated phosphatidylcholine metabolism related genes (ALDH1B1, MBOAT1, MTRR and PLB1) that showed significant association with the changes in metabolite concentrations. Conclusion Our results support the notion that phosphatidylcholine metabolism is deregulated in HD blood and that these metabolite alterations are associated with specific gene expression changes.
doi:10.1007/s11306-016-1084-8 pmid:27524956 pmcid:PMC4963448 fatcat:2iog33cdyncsldoaustht5xfm4
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