DNA microarrays for comparison of gene expression profiles between diagnosis and relapse in precursor-B acute lymphoblastic leukemia: choice of technique and purification influence the identification of potential diagnostic markers

Autor: C Van Huffel, L F A Wessels, Anthonie Willem Langerak, M.E.L. van der Burg, Mjt Reinders, C M M van den Burg, F J T Staal, J. J. M. Van Dongen, Miranda R. M. Baert, Barbara H. Barendregt, V H J van der Velden

Publikováno v: Leukemia, 17, 1324-1332. Nature Publishing Group

Microarrays for gene expression profiling are rapidly becoming important research tools for the identification of novel markers, for example, for novel classification of leukemias and lymphomas. Here, we review the considerations and infrastructure f

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::68d4cf0dbe8f7bec2b0a9d536f9831cd
https://pure.eur.nl/en/publications/a2083d4c-2e37-4a2e-8722-709d43ee9a54

Combined plasma protein and memory T cell profiling discern IBD-patient-immunotypes related to intestinal disease and treatment outcomes.

Autor: Heredia M; Laboratory of Pediatrics, Division Gastroenterology and Nutrition, Erasmus University Medical Center, Rotterdam, The Netherlands., Charrout M; Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands., Klomberg RCW; Department of Pediatric Gastroenterology, Erasmus University Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands., Aardoom MA; Department of Pediatric Gastroenterology, Erasmus University Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands., Jongsma MME; Department of Pediatric Gastroenterology, Erasmus University Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands., Kemos P; Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK., Hulleman-van Haaften DH; Laboratory of Pediatrics, Division Gastroenterology and Nutrition, Erasmus University Medical Center, Rotterdam, The Netherlands., Tuk B; Laboratory of Pediatrics, Division Gastroenterology and Nutrition, Erasmus University Medical Center, Rotterdam, The Netherlands., van Berkel LA; Laboratory of Pediatrics, Division Gastroenterology and Nutrition, Erasmus University Medical Center, Rotterdam, The Netherlands., Bley Folly B; Laboratory of Pediatrics, Division Gastroenterology and Nutrition, Erasmus University Medical Center, Rotterdam, The Netherlands., Calado B; Laboratory of Pediatrics, Division Gastroenterology and Nutrition, Erasmus University Medical Center, Rotterdam, The Netherlands., Nugteren S; Laboratory of Pediatrics, Division Gastroenterology and Nutrition, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands., Simons-Oosterhuis Y; Laboratory of Pediatrics, Division Gastroenterology and Nutrition, Erasmus University Medical Center, Rotterdam, The Netherlands., Doukas M; Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands., Sanders MA; Department of Hematology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands., van Beek G; Department of Hematology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands., Ruemmele FM; Department of Pediatric Gastroenterology, Necker-Enfants Malades University Hospital, Institut Imagine, AP-HP, Université Paris Cité, Paris, France., Croft NM; Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK., Mahfouz A; Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands., Reinders MJT; Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands., Escher JC; Department of Pediatric Gastroenterology, Erasmus University Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands., de Ridder L; Department of Pediatric Gastroenterology, Erasmus University Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands., Samsom JN; Laboratory of Pediatrics, Division Gastroenterology and Nutrition, Erasmus University Medical Center, Rotterdam, The Netherlands. Electronic address: j.samsom@erasmusmc.nl.

Publikováno v: Mucosal immunology [Mucosal Immunol] 2024 Sep 26. Date of Electronic Publication: 2024 Sep 26.

NMR metabolomics-guided DNA methylation mortality predictors.

Autor: Bizzarri D; Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands; Leiden Computational Biology Center, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands; Delft Bioinformatics Lab, TU Delft, Delft, the Netherlands., Reinders MJT; Leiden Computational Biology Center, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands; Delft Bioinformatics Lab, TU Delft, Delft, the Netherlands., Kuiper L; Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands; Center for Nutrition, Prevention and Health Services, National Institute for Public Health and Environment (RIVM), Bilthoven, the Netherlands., Beekman M; Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands., Deelen J; Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands; Max Planck Institute for the Biology of Ageing, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne, Germany., van Meurs JBJ; Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands; Department of Orthopaedics & Sports, Erasmus Medical Center, Rotterdam, the Netherlands., van Dongen J; Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, the Netherlands; Amsterdam Public Health Research Institute, Amsterdam, the Netherlands., Pool R; Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Amsterdam Public Health Research Institute, Amsterdam, the Netherlands., Boomsma DI; Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, the Netherlands; Amsterdam Public Health Research Institute, Amsterdam, the Netherlands., Ghanbari M; Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands., Franke L; Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands., Slagboom PE; Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands; Max Planck Institute for the Biology of Ageing, Cologne, Germany., van den Akker EB; Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands; Leiden Computational Biology Center, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands; Delft Bioinformatics Lab, TU Delft, Delft, the Netherlands. Electronic address: e.b.van_den_akker@lumc.nl.

Publikováno v: EBioMedicine [EBioMedicine] 2024 Sep; Vol. 107, pp. 105279. Date of Electronic Publication: 2024 Aug 17.

SIRV: spatial inference of RNA velocity at the single-cell resolution.

Autor: Abdelaal T; Department of Radiology, Leiden University Medical Center, 2333ZC Leiden, The Netherlands.; Systems and Biomedical Engineering Department, Faculty of Engineering Cairo University, 12613 Giza, Egypt.; Delft Bioinformatics Lab, Delft University of Technology, 2628 XEDelft, The Netherlands., Grossouw LM; Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, 3584 CX Utrecht, The Netherlands., Pasterkamp RJ; Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, 3584 CX Utrecht, The Netherlands., Lelieveldt BPF; Department of Radiology, Leiden University Medical Center, 2333ZC Leiden, The Netherlands.; Delft Bioinformatics Lab, Delft University of Technology, 2628 XEDelft, The Netherlands., Reinders MJT; Delft Bioinformatics Lab, Delft University of Technology, 2628 XEDelft, The Netherlands.; Department of Human Genetics, Leiden University Medical Center, 2333ZC Leiden, The Netherlands.; Leiden Computational Biology Center, Leiden University Medical Center, 2333ZC Leiden, The Netherlands., Mahfouz A; Delft Bioinformatics Lab, Delft University of Technology, 2628 XEDelft, The Netherlands.; Department of Human Genetics, Leiden University Medical Center, 2333ZC Leiden, The Netherlands.; Leiden Computational Biology Center, Leiden University Medical Center, 2333ZC Leiden, The Netherlands.

Publikováno v: NAR genomics and bioinformatics [NAR Genom Bioinform] 2024 Aug 06; Vol. 6 (3), pp. lqae100. Date of Electronic Publication: 2024 Aug 06 (Print Publication: 2024).

A transcriptomic based deconvolution framework for assessing differentiation stages and drug responses of AML.

Autor: Karakaslar EO; Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands.; Pattern Recognition & Bioinformatics, Delft University of Technology, Delft, The Netherlands.; Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands., Severens JF; Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands.; Pattern Recognition & Bioinformatics, Delft University of Technology, Delft, The Netherlands.; Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands., Sánchez-López E; Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands.; Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands., van Veelen PA; Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands., Zlei M; Department of Flow Cytometry, Medical Laboratory, Regional Institute of Oncology, Iasi, Romania.; Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands., van Dongen JJM; Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands.; Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC, USAL-CSIC-FICUS) and Department of Medicine, University of Salamanca, Salamanca, Spain., Otte AM; Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands., Halkes CJM; Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands., van Balen P; Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands., Veelken H; Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands.; Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands., Reinders MJT; Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands.; Pattern Recognition & Bioinformatics, Delft University of Technology, Delft, The Netherlands.; Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands., Griffioen M; Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands., van den Akker EB; Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands. e.b.van_den_akker@lumc.nl.; Pattern Recognition & Bioinformatics, Delft University of Technology, Delft, The Netherlands. e.b.van_den_akker@lumc.nl.; Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands. e.b.van_den_akker@lumc.nl.

Publikováno v: NPJ precision oncology [NPJ Precis Oncol] 2024 May 18; Vol. 8 (1), pp. 105. Date of Electronic Publication: 2024 May 18.