Trecode: a FAIR eco-system for the analysis and archiving of omics data in a combined diagnostic and research setting

Autor: Kerstens Hh, Verwiel Et, Jayne Y. Hehir-Kwa, Tops Bb, van de Geer E, Patrick Kemmeren, van der Leest D, van Run C

MotivationThe increase in speed, reliability and cost-effectiveness of high-throughput sequencing has led to the widespread clinical application of genome (WGS), exome (WXS) and transcriptome analysis. WXS and RNA sequencing is now being implemented

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::8e0efbe959e4fbb857e1482d086b497c
https://doi.org/10.1101/2020.11.13.363689

Erratum to: Dynamics of gene silencing during X inactivation using allele-specific RNA-seq.

Autor: Marks H; Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, 6500HB, The Netherlands. H.Marks@ncmls.ru.nl., Kerstens HH; Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, 6500HB, The Netherlands., Barakat TS; Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, The Netherlands., Splinter E; Hubrecht Institute, University Medical Center Utrecht, Uppsalalaan 8, Utrecht, 3584CT, The Netherlands., Dirks RA; Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, 6500HB, The Netherlands., van Mierlo G; Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, 6500HB, The Netherlands., Joshi O; Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, 6500HB, The Netherlands., Wang SY; Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, 6500HB, The Netherlands., Babak T; Biology Department, Queen's University, Kingston, ON, Canada., Albers CA; Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, 6500HB, The Netherlands., Kalkan T; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK., Smith A; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK., Jouneau A; INRA, UMR1198 Biologie du Développement et Reproduction, Jouy-en-Josas, F-78350, France., de Laat W; Hubrecht Institute, University Medical Center Utrecht, Uppsalalaan 8, Utrecht, 3584CT, The Netherlands., Gribnau J; Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, The Netherlands., Stunnenberg HG; Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, 6500HB, The Netherlands. H.Stunnenberg@ncmls.ru.nl.

Publikováno v: Genome biology [Genome Biol] 2016 Feb 05; Vol. 17, pp. 22. Date of Electronic Publication: 2016 Feb 05.

Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity.

Autor: Saeed S; Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands., Quintin J; Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, Netherlands., Kerstens HH; Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands., Rao NA; Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands., Aghajanirefah A; Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands., Matarese F; Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands., Cheng SC; Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, Netherlands., Ratter J; Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, Netherlands., Berentsen K; Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands., van der Ent MA; Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands., Sharifi N; Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands., Janssen-Megens EM; Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands., Ter Huurne M; Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands., Mandoli A; Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands., van Schaik T; Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands., Ng A; Center for Computational and Integrative Biology and Gastrointestinal Unit, Massachusetts General Hospital, Harvard School of Medicine, Boston, MA 02114, USA. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA., Burden F; Department of Haematology, University of Cambridge, Cambridge, UK. National Health Service, Blood and Transplant Cambridge Centre, Cambridge Biomedical Campus, Cambridge CB0 2PT, UK., Downes K; Department of Haematology, University of Cambridge, Cambridge, UK. National Health Service, Blood and Transplant Cambridge Centre, Cambridge Biomedical Campus, Cambridge CB0 2PT, UK., Frontini M; Department of Haematology, University of Cambridge, Cambridge, UK. National Health Service, Blood and Transplant Cambridge Centre, Cambridge Biomedical Campus, Cambridge CB0 2PT, UK., Kumar V; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands., Giamarellos-Bourboulis EJ; Fourth Department of Internal Medicine, University of Athens, Medical School, 1 Rimini Street, 12462 Athens, Greece., Ouwehand WH; Department of Haematology, University of Cambridge, Cambridge, UK. National Health Service, Blood and Transplant Cambridge Centre, Cambridge Biomedical Campus, Cambridge CB0 2PT, UK., van der Meer JW; Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, Netherlands., Joosten LA; Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, Netherlands., Wijmenga C; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands., Martens JH; Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands., Xavier RJ; Center for Computational and Integrative Biology and Gastrointestinal Unit, Massachusetts General Hospital, Harvard School of Medicine, Boston, MA 02114, USA. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA., Logie C; Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands. h.stunnenberg@ncmls.ru.nl mihai.netea@radboudumc.nl c.logie@ncmls.ru.nl., Netea MG; Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, Netherlands. h.stunnenberg@ncmls.ru.nl mihai.netea@radboudumc.nl c.logie@ncmls.ru.nl., Stunnenberg HG; Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands. h.stunnenberg@ncmls.ru.nl mihai.netea@radboudumc.nl c.logie@ncmls.ru.nl.

Publikováno v: Science (New York, N.Y.) [Science] 2014 Sep 26; Vol. 345 (6204), pp. 1251086.

SMIM1 underlies the Vel blood group and influences red blood cell traits.

Autor: Cvejic A; Department of Haematology, University of Cambridge, CB2 0PT, United Kingdom.; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, United Kingdom., Haer-Wigman L; Department of Experimental Immunohaematology, Sanquin Research, 1066 CX, Amsterdam, The Netherlands.; Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, 1066 CX, The Netherlands., Stephens JC; Department of Haematology, University of Cambridge, CB2 0PT, United Kingdom.; NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, United Kingdom.; NHS Blood and Transplant, Cambridge, CB2 0PT, United Kingdom., Kostadima M; EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom., Smethurst PA; Department of Haematology, University of Cambridge, CB2 0PT, United Kingdom.; NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, United Kingdom.; NHS Blood and Transplant, Cambridge, CB2 0PT, United Kingdom., Frontini M; Department of Haematology, University of Cambridge, CB2 0PT, United Kingdom.; NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, United Kingdom.; NHS Blood and Transplant, Cambridge, CB2 0PT, United Kingdom., van den Akker E; Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, 1066 CX, The Netherlands.; Department of Hematopoiesis, Sanquin Research, Amsterdam, 1066 CX, The Netherlands., Bertone P; EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom., Bielczyk-Maczyńska E; Department of Haematology, University of Cambridge, CB2 0PT, United Kingdom.; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, United Kingdom.; NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, United Kingdom.; NHS Blood and Transplant, Cambridge, CB2 0PT, United Kingdom., Farrow S; Department of Haematology, University of Cambridge, CB2 0PT, United Kingdom.; NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, United Kingdom.; NHS Blood and Transplant, Cambridge, CB2 0PT, United Kingdom., Fehrmann RS; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, 9700 RB, The Netherlands., Gray A; NHS Blood and Transplant, Tooting, London, SW17 0RB, United Kingdom., de Haas M; Department of Experimental Immunohaematology, Sanquin Research, 1066 CX, Amsterdam, The Netherlands.; Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, 1066 CX, The Netherlands., Haver VG; University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, 9700 RB, The Netherlands., Jordan G; Somerville, Massachusetts, USA., Karjalainen J; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, 9700 RB, The Netherlands., Kerstens HH; Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, 6525 GA, The Netherlands., Kiddle G; Department of Haematology, University of Cambridge, CB2 0PT, United Kingdom.; NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, United Kingdom.; NHS Blood and Transplant, Cambridge, CB2 0PT, United Kingdom., Lloyd-Jones H; Department of Haematology, University of Cambridge, CB2 0PT, United Kingdom.; NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, United Kingdom.; NHS Blood and Transplant, Cambridge, CB2 0PT, United Kingdom., Needs M; NHS Blood and Transplant, Tooting, London, SW17 0RB, United Kingdom., Poole J; International Blood Group Reference Laboratory, NHS Blood and Transplant, North Bristol Park, Northway, Filton, Bristol, BS34 7QH, United Kingdom., Soussan AA; Department of Experimental Immunohaematology, Sanquin Research, 1066 CX, Amsterdam, The Netherlands.; Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, 1066 CX, The Netherlands., Rendon A; Department of Haematology, University of Cambridge, CB2 0PT, United Kingdom.; NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, United Kingdom.; NHS Blood and Transplant, Cambridge, CB2 0PT, United Kingdom.; MRC Biostatistics Unit, Institute of Public Health, Cambridge, CB2 0SR, United Kingdom., Rieneck K; Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, Copenhagen, DK-2100, Denmark., Sambrook JG; Department of Haematology, University of Cambridge, CB2 0PT, United Kingdom.; NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, United Kingdom.; NHS Blood and Transplant, Cambridge, CB2 0PT, United Kingdom., Schepers H; University of Groningen, University Medical Center Groningen, Department of Experimental Hematology, Groningen, 9700 RB, The Netherlands.; University of Groningen, University Medical Center Groningen, Department of Stem Cell Biology, Groningen, 9700 RB, The Netherlands., Silljé HHW; University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, 9700 RB, The Netherlands., Sipos B; EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom., Swinkels D; Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic diseases, Radboud University Medical Centre, Nijmegen, 6500 HB, The Netherlands., Tamuri AU; EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom., Verweij N; University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, 9700 RB, The Netherlands., Watkins NA; NHS Blood and Transplant, Cambridge, CB2 0PT, United Kingdom., Westra HJ; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, 9700 RB, The Netherlands., Stemple D; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, United Kingdom., Franke L; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, 9700 RB, The Netherlands., Soranzo N; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, United Kingdom., Stunnenberg HG; Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, 6525 GA, The Netherlands., Goldman N; EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom., van der Harst P; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, 9700 RB, The Netherlands.; University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, 9700 RB, The Netherlands., van der Schoot CE; Department of Experimental Immunohaematology, Sanquin Research, 1066 CX, Amsterdam, The Netherlands.; Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, 1066 CX, The Netherlands., Ouwehand WH; Department of Haematology, University of Cambridge, CB2 0PT, United Kingdom.; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, United Kingdom.; NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, United Kingdom.; NHS Blood and Transplant, Cambridge, CB2 0PT, United Kingdom., Albers CA; Department of Haematology, University of Cambridge, CB2 0PT, United Kingdom.; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, United Kingdom.; NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, United Kingdom.; NHS Blood and Transplant, Cambridge, CB2 0PT, United Kingdom.; Department of Human Genetics, Radboud University Medical Centre, Nijmegen, 6500 HB, The Netherlands.

Publikováno v: Nature genetics [Nat Genet] 2013 May; Vol. 45 (5), pp. 542-545. Date of Electronic Publication: 2013 Apr 07.

Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos).

Autor: Kraus RH; Resource Ecology Group, Wageningen University, PO Box 47, 6700 AA Wageningen, The Netherlands. Robert.Kraus@wur.nl, Kerstens HH, Van Hooft P, Crooijmans RP, Van Der Poel JJ, Elmberg J, Vignal A, Huang Y, Li N, Prins HH, Groenen MA

Publikováno v: BMC genomics [BMC Genomics] 2011 Mar 16; Vol. 12, pp. 150. Date of Electronic Publication: 2011 Mar 16.