The single-cell eQTLGen consortium

Autor: MGP van der Wijst, DH de Vries, HE Groot, G Trynka, CC Hon, MJ Bonder, O Stegle, MC Nawijn, Y Idaghdour, P van der Harst, CJ Ye, J Powell, FJ Theis, A Mahfouz, M Heinig, L Franke

Publikováno v: eLife, Vol 9 (2020)

In recent years, functional genomics approaches combining genetic information with bulk RNA-sequencing data have identified the downstream expression effects of disease-associated genetic risk factors through so-called expression quantitative trait l

Externí odkaz: https://doaj.org/article/cee96dfc8cdd40b3bab880c4b5f4822c

Complex genetic variation in nearly complete human genomes.

Autor: Logsdon GA; Perelman School of Medicine, University of Pennsylvania, Department of Genetics, Epigenetics Institute, Philadelphia, PA, USA.; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Ebert P; Core Unit Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.; Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany., Audano PA; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA., Loftus M; Clemson University, Department of Genetics & Biochemistry, Clemson, SC, USA.; Center for Human Genetics, Clemson University, Greenwood, SC, USA., Porubsky D; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Ebler J; Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.; Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany., Yilmaz F; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA., Hallast P; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA., Prodanov T; Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.; Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany., Yoo D; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Paisie CA; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA., Harvey WT; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Zhao X; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA., Martino GV; Clemson University, Department of Genetics & Biochemistry, Clemson, SC, USA.; Center for Human Genetics, Clemson University, Greenwood, SC, USA.; Medical University of South Carolina, College of Graduate Studies, Charleston, SC, USA., Henglin M; Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.; Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany., Munson KM; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Rabbani K; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA., Chin CS; Foundation of Biological Data Sciences, Belmont, CA, USA., Gu B; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA., Ashraf H; Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.; Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany., Austine-Orimoloye O; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom., Balachandran P; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA., Bonder MJ; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Oncode Institute, Utrecht, The Netherlands.; Division of Computational Genomics and Systems Genetics, German Cancer Research Center, Heidelberg, Germany., Cheng H; Department of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT, USA., Chong Z; Department of Biomedical Informatics and Data Science, Heersink School of Medicine, University of Alabama, Birmingham, AL, USA., Crabtree J; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA., Gerstein M; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA., Guethlein LA; Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA., Hasenfeld P; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany., Hickey G; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA., Hoekzema K; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Hunt SE; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom., Jensen M; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA., Jiang Y; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA., Koren S; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA., Kwon Y; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Li C; Temple University, Department of Computer and Information Sciences, College of Science and Technology, Philadelphia, PA, USA.; Temple University, Institute for Genomics and Evolutionary Medicine, Philadelphia, PA, USA., Li H; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA., Li J; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA., Norman PJ; Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA.; Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA., Oshima KK; Perelman School of Medicine, University of Pennsylvania, Department of Genetics, Epigenetics Institute, Philadelphia, PA, USA., Paten B; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA., Phillippy AM; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA., Pollock NR; Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA., Rausch T; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany., Rautiainen M; Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland., Scholz S; Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany., Song Y; Department of Biomedical Informatics and Data Science, Heersink School of Medicine, University of Alabama, Birmingham, AL, USA., Söylev A; Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.; Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany., Sulovari A; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA., Surapaneni L; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom., Tsapalou V; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany., Zhou W; Department of Computational Medicine & Bioinformatics, University of Michigan, MI, USA., Zhou Y; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA., Zhu Q; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.; Stanford Health Care, Palo Alto, CA, USA., Zody MC; New York Genome Center, New York, NY, USA., Mills RE; Department of Computational Medicine & Bioinformatics, University of Michigan, MI, USA., Devine SE; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA., Shi X; Temple University, Department of Computer and Information Sciences, College of Science and Technology, Philadelphia, PA, USA.; Temple University, Institute for Genomics and Evolutionary Medicine, Philadelphia, PA, USA., Talkowski ME; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.; Department of Neurology, Harvard Medical School, Boston, MA, USA., Chaisson MJP; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA., Dilthey AT; Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany.; Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany., Konkel MK; Clemson University, Department of Genetics & Biochemistry, Clemson, SC, USA.; Center for Human Genetics, Clemson University, Greenwood, SC, USA., Korbel JO; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany., Lee C; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA., Beck CR; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.; The University of Connecticut Health Center, Farmington, CT, USA., Eichler EE; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA., Marschall T; Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.; Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Sep 25. Date of Electronic Publication: 2024 Sep 25.

Epigenome-wide association study on the plasma metabolome suggests self-regulation of the glycine and serine pathway through DNA methylation.

Autor: Wu J; Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands., Palasantzas V; Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.; Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands., Andreu-Sánchez S; Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.; Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands., Plösch T; Department of Obstetrics and Gynecology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.; Perinatal Neurobiology Research Group, Department of Pediatrics, School of Medicine and Health Sciences, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany., Leonard S; Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.; Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands., Li S; Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands., Bonder MJ; Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands., Westra HJ; Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands., van Meurs J; Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.; Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands., Ghanbari M; Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.; Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands., Franke L; Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands., Zhernakova A; Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands., Fu J; Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.; Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands., Hoogerland JA; Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands. j.a.hoogerland@umcg.nl.; Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands. j.a.hoogerland@umcg.nl., Zhernakova DV; Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands. d.pital-zhernakova@umcg.nl.

Publikováno v: Clinical epigenetics [Clin Epigenetics] 2024 Aug 13; Vol. 16 (1), pp. 104. Date of Electronic Publication: 2024 Aug 13.

Expression profiling of cerebrospinal fluid identifies dysregulated antiviral mechanisms in multiple sclerosis.

Autor: Ban M; Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK., Bredikhin D; European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany.; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Huang Y; Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK.; European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK., Bonder MJ; European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany.; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany., Katarzyna K; University of Cambridge, CRUK Cambridge Institute, Cambridge CB2 0RE, UK., Oliver AJ; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK., Wilson NK; Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK.; Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK., Coupland P; University of Cambridge, CRUK Cambridge Institute, Cambridge CB2 0RE, UK., Hadfield J; University of Cambridge, CRUK Cambridge Institute, Cambridge CB2 0RE, UK., Göttgens B; Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK.; Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK., Madissoon E; European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK.; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK., Stegle O; European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany.; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.; European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK., Sawcer S; Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK.

Publikováno v: Brain : a journal of neurology [Brain] 2024 Feb 01; Vol. 147 (2), pp. 554-565.

pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls.

Autor: Snajder R; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany. rene.snajder@gmail.com.; Faculty for Biosciences, Heidelberg University, Heidelberg, Germany. rene.snajder@gmail.com.; HIDSS4Health, Helmholtz Information and Data Science School for Health, Heidelberg, Germany. rene.snajder@gmail.com., Leger A; European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL), Hinxton, Cambridge, UK.; Current affiliation: Oxford Nanopore Technologies, Gosling Building, Oxford Science Park, Oxford, UK., Stegle O; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.; Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.; Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK., Bonder MJ; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.; Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.

Publikováno v: Genome biology [Genome Biol] 2023 Apr 20; Vol. 24 (1), pp. 83. Date of Electronic Publication: 2023 Apr 20.