Single cell multi-omics analysis of chromothriptic medulloblastoma highlights genomic and transcriptomic consequences of genome instability

Autor: Manasi Ratnaparkhe, Thomas Hoefer, Kendra K. Maass, Martin Sill, Anna Jauch, Oliver Stegle, Przybilla Mj, Thorsten Kolb, Marc Zapatka, David R Ghasemi, John Wong, Andrey Korshunov, Aurélie Ernst, Koerber, Kristian W. Pajtler, Rajesh Kumar, Nicola Casiraghi, Stefan M. Pfister, Hana Susak, Parra Rg, Mallm P, Milena Simovic

Chromothripsis is a form of genome instability, whereby a presumably single catastrophic event generates extensive genomic rearrangements of one or few chromosome(s). However, little is known about the heterogeneity of chromothripsis across different

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::8644b355416c8958cbdffe4a3d30166e
https://doi.org/10.1101/2021.06.25.449944

Multi-omic and single-cell profiling of chromothriptic medulloblastoma reveals genomic and transcriptomic consequences of genome instability.

Autor: Smirnov P; Group Genome Instability in Tumors, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany., Przybilla MJ; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.; Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK., Simovic-Lorenz M; Group Genome Instability in Tumors, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany., Parra RG; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.; Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain., Susak H; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany., Ratnaparkhe M; Group Genome Instability in Tumors, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany., Wong JK; Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany., Körber V; Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany., Mallm JP; Single-cell Open Lab, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany., Philippos G; Group Genome Instability in Tumors, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany., Sill M; Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.; Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany., Kolb T; Group Genome Instability in Tumors, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany., Kumar R; Group Genome Instability in Tumors, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany., Casiraghi N; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany., Okonechnikov K; Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.; Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany., Ghasemi DR; Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.; Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany., Maaß KK; Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.; Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany., Pajtler KW; Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.; Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany., Jauch A; Institute of Human Genetics, Heidelberg University, Heidelberg, Germany., Korshunov A; Clinical Cooperation Unit Neuropathology, DKFZ, Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany., Höfer T; Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany., Zapatka M; Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany., Pfister SM; Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.; Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany., Huber W; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany., Stegle O; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. o.stegle@dkfz-heidelberg.de.; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany. o.stegle@dkfz-heidelberg.de., Ernst A; Group Genome Instability in Tumors, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany. a.ernst@dkfz-heidelberg.de.

Publikováno v: Nature communications [Nat Commun] 2024 Nov 23; Vol. 15 (1), pp. 10183. Date of Electronic Publication: 2024 Nov 23.

Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families.

Autor: Parra RG; Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain., Freiberger MI; Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina., Poley-Gil M; Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain., Fernandez-Martin M; Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain., Radusky LG; Manas.tech, 300 Lenora Street 1541, Seattle, WA 98121, USA., Ruiz-Serra V; Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain., Wolynes PG; Center for Theoretical Biological Physics and Department of Chemistry, Rice University, Houston, TX 77005, USA., Ferreiro DU; Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina., Valencia A; Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain.; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2024 Jul 05; Vol. 52 (W1), pp. W233-W237.

1st ASCS: Expanding the ISCB Student Council Symposia to Asia.

Autor: Grover A; Department of Computer Science, ETH Zurich, Zurich, Switzerland.; Swiss Institute of Bioinformatics (SIB), Zurich, Switzerland., Riaz A; CECOS-RMI Precision Medicine Lab, Peshawar, Pakistan., Al Sium SM; Industrial Microbiology Research Division, BCSIR Chattogram Laboratories, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh., Dincaslan FB; Institute for Health Innovation and Technology, 117599, Singapore.; Department of Biomedical Engineering, National University of Singapore, 119077, Singapore., Chowdhury SF; Biological Research Division, BCSIR Dhaka Laboratories, Bangladesh Council of Scientific and Industrial Research (BCSIR), Bangladesh, Dhaka, Bangladesh., Olguin-Orellana GJ; Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Universidad de Talca, 1 Poniente 1141, Talca, Chile.; Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca, Chile., Parra RG; Barcelona Supercomputing Center, Barcelona, Spain., Eranti P; Universite Paris Cite, Inserm, UMRS-1124, Group of Genomic Epidemiology of Multifactorial Diseases, Paris, France.

Publikováno v: F1000Research [F1000Res] 2023 Jun 20; Vol. 12, pp. 703. Date of Electronic Publication: 2023 Jun 20 (Print Publication: 2023).

Resolving the fine structure in the energy landscapes of repeat proteins.

Autor: Sanches MN; Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil., Parra RG; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Viegas RG; Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil.; Federal Institute of Education, Science and Technology of São Paulo (IFSP), Catanduva, SP 15.808-305, Brazil., Oliveira AB Jr; Center for Theoretical Biological Physics, Rice University, Houston, TX, USA., Wolynes PG; Center for Theoretical Biological Physics, Rice University, Houston, TX, USA., Ferreiro DU; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, C1428EGA Buenos Aires, Argentina., Leite VBP; Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil.

Publikováno v: QRB discovery [QRB Discov] 2022 Jun 10; Vol. 3, pp. e7. Date of Electronic Publication: 2022 Jun 10 (Print Publication: 2022).