A. Stubbs

Most-cited papers

1. Abstract 808: Intrinsic gene expression profiles of gliomas are a better predictor of survival than histology

   L. Gravendeel, M. Kouwenhoven, O. Gevaert, J. D. de Rooi +13 more

   2010500 citations

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2. Integrated transcript and genome analyses reveal NKX2-1 and MEF2C as potential oncogenes in T cell acute lymphoblastic leukemia.

   I. Homminga, R. Pieters, A. Langerak, J. D. de Rooi +20 more

   2011Cancer Cell381 citations Open access

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3. The recurrent SET-NUP214 fusion as a new HOXA activation mechanism in pediatric T-cell acute lymphoblastic leukemia.

   P. Van Vlierberghe, M. van Grotel, J. Tchinda, Charles Lee +12 more

   2007Blood234 citations Open access

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4. CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy

   S. Hiltemann, Hailiang Mei, M. de Hollander, Ivo Palli +3 more

   2014GigaScience127 citations Open access

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5. Antibiotic misuse in respiratory tract infections in children and adults—a prospective, multicentre study (TAILORED Treatment)

   C. V. van Houten, A. Cohen, D. Engelhard, J. Hays +40 more

   2019European Journal of Clinical Microbiology and Infectious Diseases117 citations Open access

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6. A European Spectrum of Pharmacogenomic Biomarkers: Implications for Clinical Pharmacogenomics

   C. Mizzi, Eleni Dalabira, Judit Kumuthini, N. Dzimiri +46 more

   2016PLoS ONE117 citations Open access

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7. IL-7 Receptor Mutations and Steroid Resistance in Pediatric T cell Acute Lymphoblastic Leukemia: A Genome Sequencing Study

   Yun-Lei Li, J. Buijs-Gladdines, K. Canté-Barrett, A. Stubbs +11 more

   2016PLoS Medicine100 citations Open access

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8. Identification of Patients with Recurrent Glioblastoma Who May Benefit from Combined Bevacizumab and CCNU Therapy: A Report from the BELOB Trial.

   L. Erdem-Eraslan, M. J. van den Bent, Y. Hoogstrate, Hina Naz-Khan +17 more

   2016Cancer Research97 citations Open access

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9. Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota

   A. Heikema, D. Horst-Kreft, S. A. Boers, Rick J Jansen +8 more

   2020Genes95 citations Open access

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10. An International Ki67 Reproducibility Study in Adrenal Cortical Carcinoma

    T. Papathomas, E. Pucci, T. Giordano, Hao Lu +24 more

    2016American Journal of Surgical Pathology80 citations Open access

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11. Discriminating somatic and germline mutations in tumor DNA samples without matching normals

    S. Hiltemann, G. Jenster, J. Trapman, P. J. van der Spek +1 more

    2015Genome Research80 citations Open access

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12. Consensus molecular subtype classification of colorectal adenomas

    Malgorzata A. Komor, L. Bosch, G. Bounova, A. Bolijn +27 more

    2018Journal of Pathology77 citations Open access

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13. Early- and late-onset preeclampsia and the tissue-specific epigenome of the placenta and newborn.

    E. Herzog, A. Eggink, S. Willemsen, R. Slieker +7 more

    2017Placenta67 citations Open access

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14. Similar recombination-activating gene (RAG) mutations result in similar immunobiological effects but in different clinical phenotypes

    Hanna IJspeert, G. Driessen, M. Moorhouse, N. Hartwig +12 more

    2014Journal of Allergy and Clinical Immunology67 citations Open access

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15. Transcriptome Analysis of Infected and Bystander Type 2 Alveolar Epithelial Cells during Influenza A Virus Infection Reveals In Vivo Wnt Pathway Downregulation

    Aidan S. Hancock, Christopher J. Stairiker, Alina C. Boesteanu, Elisa Monzón-Casanova +6 more

    2018Journal of Virology61 citations Open access

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16. Correlation of Protein and Gene Expression Profiles of Inflammatory Proteins After Endotoxin Challenge in Human Subjects

    U. Prabhakar, T. M. Conway, P. Murdock, J. Mooney +18 more

    2005DNA and Cell Biology55 citations

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17. Evaluation of the Antigen-Experienced B-Cell Receptor Repertoire in Healthy Children and Adults

    Hanna IJspeert, P. V. van Schouwenburg, David van Zessen, Ingrid Pico-Knijnenburg +3 more

    2016Frontiers in Immunology54 citations Open access

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18. Antigen Receptor Galaxy: A User-Friendly, Web-Based Tool for Analysis and Visualization of T and B Cell Receptor Repertoire Data

    Hanna IJspeert, P. V. van Schouwenburg, David van Zessen, Ingrid Pico-Knijnenburg +2 more

    2017Journal of Immunology49 citations Open access

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19. Folic acid supplementation normalizes the endothelial progenitor cell transcriptome of patients with type 1 diabetes: a case-control pilot study

    O. van Oostrom, D. D. de Kleijn, J. Fledderus, M. Pescatori +4 more

    2009Cardiovascular Diabetology46 citations Open access

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20. NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy

    W. de Koning, Milad Miladi, S. Hiltemann, A. Heikema +7 more

    2020GigaScience45 citations Open access

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21. Gene fusions by chromothripsis of chromosome 5q in the VCaP prostate cancer cell line

    Inês Teles Alves, S. Hiltemann, T. Hartjes, P. J. van der Spek +3 more

    2013Human Genetics41 citations

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22. Automated Selection of Hotspots (ASH): enhanced automated segmentation and adaptive step finding for Ki67 hotspot detection in adrenal cortical cancer

    Hao Lu, T. Papathomas, David van Zessen, Ivo Palli +4 more

    2014Diagnostic Pathology39 citations Open access

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23. XLF deficiency results in reduced N-nucleotide addition during V(D)J recombination.

    Hanna IJspeert, J. Rozmus, K. Schwarz, R. Warren +15 more

    2016Blood38 citations Open access

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24. Guide-free Cas9 from pathogenic Campylobacter jejuni bacteria causes severe damage to DNA

    Chinmoy Saha, Prarthana Mohanraju, A. Stubbs, Gaurav Dugar +18 more

    2020Science Advances37 citations Open access

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25. Sialin, an anion transporter defective in sialic acid storage diseases, shows highly variable expression in adult mouse brain, and is developmentally regulated.

    N. Yarovaya, R. Schot, L. Fodero, Michelle McMahon +11 more

    2005Neurobiology of Disease36 citations Open access

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26. ImmunoGlobulin galaxy (IGGalaxy) for simple determination and quantitation of immunoglobulin heavy chain rearrangements from NGS

    M. Moorhouse, David van Zessen, Hanna IJspeert, S. Hiltemann +4 more

    2014BMC Immunology34 citations Open access

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27. Galaxy for accessible, reproducible, and collaborative data analyses: 2026 update

    Enis Najat Rafael Andrade Mihail Christophe Patrick Ahm Afgan Amoukou Buono Anton Antoniewski Austin Awan , E. Afgan, Najat Amoukou, R. Buono +168 more

    2026Nucleic Acids Research32 citations Open access

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28. Next-generation antigen receptor sequencing of paired diagnosis and relapse samples of B-cell acute lymphoblastic leukemia: Clonal evolution and implications for minimal residual disease target selection.

    P. Theunissen, Maaike de Bie, David van Zessen, V. de Haas +2 more

    2019Leukemia research : a Forum for Studies on Leukemia and Normal Hemopoiesis26 citations Open access

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29. FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research

    K. Joeri van der Velde, Gurnoor Singh, Rajaram Kaliyaperumal, X. Liao +20 more

    2022Scientific Data24 citations Open access

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30. OralDisk: A Chair-Side Compatible Molecular Platform Using Whole Saliva for Monitoring Oral Health at the Dental Practice

    Desirée Baumgartner, Benita Johannsen, M. Specht, Jane Luddecke +26 more

    2021Biosensors24 citations Open access

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31. Cellular, mitochondrial and molecular alterations associate with early left ventricular diastolic dysfunction in a porcine model of diabetic metabolic derangement

    I. Heinonen, O. Sorop, B. M. van Dalen, R. Wüst +12 more

    2020Scientific Reports23 citations Open access

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32. Identification of CVID Patients With Defects in Immune Repertoire Formation or Specification

    P. V. van Schouwenburg, Hanna IJspeert, Ingrid Pico-Knijnenburg, V. Dalm +5 more

    2018Frontiers in Immunology22 citations Open access

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33. Identification of cancer predisposition variants in apparently healthy individuals using a next-generation sequencing-based family genomics approach

    I. Karageorgos, C. Mizzi, E. Giannopoulou, C. Pavlidis +12 more

    2015Human Genomics22 citations Open access

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34. Next-generation sequencing reveals novel rare fusion events with functional implication in prostate cancer

    I. T. Alves, T. Hartjes, E. Mcclellan, S. Hiltemann +11 more

    2014Oncogene22 citations

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35. Application of Whole Genome Sequencing Technology in the Investigation of Genetic Causes of Fetal, Perinatal, and Early Infant Death

    J. Armes, Mark G. Williams, G. Price, T. Wallis +12 more

    2018Pediatric and Developmental Pathology20 citations

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36. Mining the human genome using virtual reality

    Bram Stolk, Faizal Abdoelrahman, A. H. Koning, Paul Wielinga +5 more

    2002Eurographics Symposium on Parallel Graphics and Visualization20 citations

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37. Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur

    S. Hiltemann, S. A. Boers, P. J. van der Spek, R. Jansen +2 more

    2018GigaScience19 citations Open access

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38. Chair/bedside diagnosis of oral and respiratory tract infections, and identification of antibiotic resistances for personalised monitoring and treatment

    K. Mitsakakis, F. Stumpf, O. Strohmeier, V. Klein +29 more

    2016International Conference on Wearable Micro and Nano Technologies for Personalised Health19 citations Open access

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39. The recurrent SET-NUP 214 fusion as a new HOXA activation mechanism in pediatric T-cell acute lymphoblastic leukemia

    P. Van Vlierberghe, M. van Grotel, J. Tchinda, Charles Lee +12 more

    200819 citations

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40. Antigen receptor sequencing of paired bone marrow samples shows homogeneous distribution of acute lymphoblastic leukemia subclones

    P. Theunissen, David van Zessen, A. Stubbs, M. Faham +3 more

    2017Haematologica18 citations Open access

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41. Huvariome: a web server resource of whole genome next-generation sequencing allelic frequencies to aid in pathological candidate gene selection

    A. Stubbs, E. Mcclellan, Sebastiaan Horsman, S. Hiltemann +11 more

    2012Journal of Clinical Bioinformatics18 citations Open access

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42. The tissue-specific aspect of genome-wide DNA methylation in newborn and placental tissues: implications for epigenetic epidemiologic studies

    E. Herzog, A. Eggink, S. Willemsen, R. Slieker +6 more

    2020Journal of Developmental Origins of Health and Disease17 citations Open access

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43. Strategies for B-Cell Receptor Repertoire Analysis in Primary Immunodeficiencies: From Severe Combined Immunodeficiency to Common Variable Immunodeficiency

    Hanna IJspeert, M. Wentink, David van Zessen, G. Driessen +7 more

    2015Frontiers in Immunology17 citations Open access

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44. Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics

    S. A. Boers, S. Hiltemann, A. Stubbs, R. Jansen +1 more

    2018European Journal of Clinical Microbiology and Infectious Diseases16 citations Open access

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45. Comprehensive Investigation of Parameter Choice in Viral Integration Site Analysis and Its Effects on the Gene Annotations Produced

    M. Huston, M. Brugman, Sebastiaan Horsman, A. Stubbs +2 more

    2012Human Gene Therapy14 citations Open access

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46. Absence of Common Somatic Alterations in Genes on 1p and 19q in Oligodendrogliomas

    L. Bralten, Stephan Nouwens, C. Kockx, L. Erdem +8 more

    2011PLoS ONE14 citations Open access

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47. Whole genome sequencing of a dizygotic twin suggests a role for the serotonin receptor HTR7 in autism spectrum disorder

    C. Helsmoortel, Sigrid M. A. Swagemakers, G. Vandeweyer, A. Stubbs +4 more

    2016American Journal of Medical Genetics Part B: Neuropsychiatric Genetics12 citations

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48. Identification, Validation, and Utilization of Immune Cells in Pancreatic Ductal Adenocarcinoma Based on Marker Genes

    W. de Koning, D. Latifi, Yun-Lei Li, C. V. van Eijck +2 more

    2021Frontiers in Immunology10 citations Open access

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49. Identification of Associated Genes and Diseases in Patients With Congenital Upper-Limb Anomalies: A Novel Application of the OMT Classification.

    Martijn Baas, A. Stubbs, David van Zessen, R. Galjaard +3 more

    2017Journal of Hand Surgery-American Volume10 citations

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50. Deciphering imprints of impaired memory B-cell maturation in germinal centers of three patients with common variable immunodeficiency

    P. V. van Schouwenburg, S. Unger, Kathryn J. Payne, Fabian M. P. Kaiser +10 more

    2022Frontiers in Immunology9 citations Open access

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