Genome-wide profiling of DNA repair proteins in single cells.

Autor: de Luca KL; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) & University Medical Center Utrecht, Utrecht, the Netherlands. science@kimdeluca.com.; Oncode Institute, Utrecht, the Netherlands. science@kimdeluca.com., Rullens PMJ; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) & University Medical Center Utrecht, Utrecht, the Netherlands.; Oncode Institute, Utrecht, the Netherlands.; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands., Karpinska MA; Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany., de Vries SS; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) & University Medical Center Utrecht, Utrecht, the Netherlands.; Oncode Institute, Utrecht, the Netherlands., Gacek-Matthews A; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria., Pongor LS; Cancer Genomics and Epigenetics Core Group, Hungarian Center of Excellence for Molecular Medicine (HCEMM), Szeged, Hungary., Legube G; MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France., Jachowicz JW; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria., Oudelaar AM; Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany., Kind J; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) & University Medical Center Utrecht, Utrecht, the Netherlands. j.kind@hubrecht.eu.; Oncode Institute, Utrecht, the Netherlands. j.kind@hubrecht.eu.; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands. j.kind@hubrecht.eu.

Publikováno v: Nature communications [Nat Commun] 2024 Nov 21; Vol. 15 (1), pp. 9918. Date of Electronic Publication: 2024 Nov 21.

Nuclear chromosome locations dictate segregation error frequencies.

Autor: Klaasen SJ; Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands., Truong MA; Oncode Institute, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands., van Jaarsveld RH; Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands., Koprivec I; Ruđer Bošković Institute, Zagreb, Croatia., Štimac V; Ruđer Bošković Institute, Zagreb, Croatia., de Vries SG; Oncode Institute, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands., Risteski P; Ruđer Bošković Institute, Zagreb, Croatia., Kodba S; Ruđer Bošković Institute, Zagreb, Croatia., Vukušić K; Ruđer Bošković Institute, Zagreb, Croatia., de Luca KL; Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands., Marques JF; Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands., Gerrits EM; Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands., Bakker B; Department of Ageing Biology/ERIBA, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands., Foijer F; Department of Ageing Biology/ERIBA, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands., Kind J; Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands.; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands., Tolić IM; Ruđer Bošković Institute, Zagreb, Croatia., Lens SMA; Oncode Institute, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands., Kops GJPL; Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands. g.kops@hubrecht.eu.

Publikováno v: Nature [Nature] 2022 Jul; Vol. 607 (7919), pp. 604-609. Date of Electronic Publication: 2022 Jul 13.

Single-Cell DamID to Capture Contacts Between DNA and the Nuclear Lamina in Individual Mammalian Cells.

Autor: de Luca KL; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht and Oncode Institute, Utrecht, The Netherlands., Kind J; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht and Oncode Institute, Utrecht, The Netherlands. j.kind@hubrecht.eu.

Publikováno v: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2021; Vol. 2157, pp. 159-172.

Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells.

Autor: Rooijers K; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Markodimitraki CM; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Rang FJ; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., de Vries SS; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Chialastri A; Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA.; Center for Bioengineering, University of California Santa Barbara, Santa Barbara, CA, USA., de Luca KL; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Mooijman D; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands.; Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany., Dey SS; Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA. sdey@ucsb.edu.; Center for Bioengineering, University of California Santa Barbara, Santa Barbara, CA, USA. sdey@ucsb.edu., Kind J; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands. j.kind@hubrecht.eu.

Publikováno v: Nature biotechnology [Nat Biotechnol] 2019 Jul; Vol. 37 (7), pp. 766-772. Date of Electronic Publication: 2019 Jun 17.

Genomic and functional overlap between somatic and germline chromosomal rearrangements.

Autor: van Heesch S; Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands., Simonis M; Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands., van Roosmalen MJ; Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands., Pillalamarri V; Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA., Brand H; Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA., Kuijk EW; Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands., de Luca KL; Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands., Lansu N; Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands., Braat AK; Department of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands., Menelaou A; Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands., Hao W; Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands., Korving J; Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands., Snijder S; Department of Clinical Genetics, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands., van der Veken LT; Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands., Hochstenbach R; Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands., Knegt AC; Department of Clinical Genetics, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands., Duran K; Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands., Renkens I; Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands., Alekozai N; Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands., Jager M; Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands., Vergult S; Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium., Menten B; Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium., de Bruijn E; Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands., Boymans S; Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands., Ippel E; Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands., van Binsbergen E; Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands., Talkowski ME; Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA., Lichtenbelt K; Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands., Cuppen E; Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands. Electronic address: e.cuppen@hubrecht.eu., Kloosterman WP; Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands. Electronic address: w.kloosterman@umcutrecht.nl.

Publikováno v: Cell reports [Cell Rep] 2014 Dec 24; Vol. 9 (6), pp. 2001-10. Date of Electronic Publication: 2014 Dec 11.