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  1. Book ; Online ; E-Book: Data Driven Science for Clinically Actionable Knowledge in Diseases

    Catchpoole, Daniel R.

    (Analytics and AI for Healthcare Series)

    2024  

    Author's details edited by Daniel R. Catchpoole [and three others]
    Series title Analytics and AI for Healthcare Series
    Keywords Diseases ; Medicine/Data processing
    Subject code 616
    Language English
    Size 1 online resource (255 pages)
    Edition First edition.
    Publisher CRC Press
    Publishing place Boca Raton, FL
    Document type Book ; Online ; E-Book
    Note Includes index.
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    ISBN 1-003-29235-6 ; 1-003-80168-4 ; 9781032273518 ; 978-1-003-29235-7 ; 978-1-003-80168-9 ; 1032273518
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

    Full text online

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  2. Article ; Online: An Approach to Evaluate the Costs and Outputs of Academic Biobanks.

    Rush, Amanda / Catchpoole, Daniel R / Watson, Peter H / Byrne, Jennifer A

    Biopreservation and biobanking

    2024  

    Abstract: Academic biobanks commonly report sustainability challenges, which may be exacerbated by a lack of information on biobank value. To better understand the costs and supported outputs that contribute to biobank value, we developed a systematic, ... ...

    Abstract Academic biobanks commonly report sustainability challenges, which may be exacerbated by a lack of information on biobank value. To better understand the costs and supported outputs that contribute to biobank value, we developed a systematic, generalizable methodology to determine biobank inputs and publications arising from biobank-supported research. We then tested this in a small cohort (
    Language English
    Publishing date 2024-04-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2593993-2
    ISSN 1947-5543 ; 1947-5535
    ISSN (online) 1947-5543
    ISSN 1947-5535
    DOI 10.1089/bio.2023.0112
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Identification of differentially distributed gene expression and distinct sets of cancer-related genes identified by changes in mean and variability.

    Roberts, Aedan G K / Catchpoole, Daniel R / Kennedy, Paul J

    NAR genomics and bioinformatics

    2022  Volume 4, Issue 1, Page(s) lqab124

    Abstract: There is increasing evidence that changes in the variability or overall distribution of gene expression are important both in normal biology and in diseases, particularly cancer. Genes whose expression differs in variability or distribution without a ... ...

    Abstract There is increasing evidence that changes in the variability or overall distribution of gene expression are important both in normal biology and in diseases, particularly cancer. Genes whose expression differs in variability or distribution without a difference in mean are ignored by traditional differential expression-based analyses. Using a Bayesian hierarchical model that provides tests for both differential variability and differential distribution for bulk RNA-seq data, we report here an investigation into differential variability and distribution in cancer. Analysis of eight paired tumour-normal datasets from The Cancer Genome Atlas confirms that differential variability and distribution analyses are able to identify cancer-related genes. We further demonstrate that differential variability identifies cancer-related genes that are missed by differential expression analysis, and that differential expression and differential variability identify functionally distinct sets of potentially cancer-related genes. These results suggest that differential variability analysis may provide insights into genetic aspects of cancer that would not be revealed by differential expression, and that differential distribution analysis may allow for more comprehensive identification of cancer-related genes than analyses based on changes in mean or variability alone.
    Language English
    Publishing date 2022-01-14
    Publishing country England
    Document type Journal Article
    ISSN 2631-9268
    ISSN (online) 2631-9268
    DOI 10.1093/nargab/lqab124
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Toward Deploying a Deep Learning Model for Diagnosis of Rhabdomyosarcoma.

    Ho, David Joon / Agaram, Narasimhan P / Frankel, Arthur O / Lathara, Melvin / Catchpoole, Daniel / Keller, Charles / Hameed, Meera R

    Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc

    2024  Volume 37, Issue 3, Page(s) 100421

    MeSH term(s) Humans ; Deep Learning ; Rhabdomyosarcoma/diagnosis ; Rhabdomyosarcoma/pathology ; Diagnosis, Differential
    Language English
    Publishing date 2024-02-08
    Publishing country United States
    Document type Letter
    ZDB-ID 645073-8
    ISSN 1530-0285 ; 0893-3952
    ISSN (online) 1530-0285
    ISSN 0893-3952
    DOI 10.1016/j.modpat.2024.100421
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2450: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: Withdrawn: Variations in Altered Global Gene Expression caused by Topoisomerase II Poisons Assessed with Reference to Differences in DNA Binding

    Zihlif, Malek / Catchpoole, Daniel R / Stewart, Bernard W / Wakelin, Laurence P G

    Current molecular pharmacology

    2022  

    Language English
    Publishing date 2022-03-01
    Publishing country United Arab Emirates
    Document type Journal Article
    ISSN 1874-4702
    ISSN (online) 1874-4702
    DOI 10.2174/1874467215666220301115946
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The "Federated Pediatric BioCloud" Model: State of the Art and Future Prospects in Pediatric Biospecimen Science.

    Schleif, William S / Goldenberg, Neil A / Catchpoole, Daniel R

    The Journal of pediatrics

    2020  Volume 221S, Page(s) S43–S48

    MeSH term(s) Biomedical Research ; Child ; Cloud Computing ; Humans ; Pediatrics ; Tissue Banks
    Language English
    Publishing date 2020-06-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 3102-1
    ISSN 1097-6833 ; 0022-3476
    ISSN (online) 1097-6833
    ISSN 0022-3476
    DOI 10.1016/j.jpeds.2020.02.068
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Um IV Zs.116: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  7. Article ; Online: ISBER's Global Outlook: A Summary of Recent International Activities.

    Catchpoole, Daniel R / Parry-Jones, Alison / Kozlakidis, Zisis

    Biopreservation and biobanking

    2019  Volume 17, Issue 1, Page(s) 91–92

    MeSH term(s) Biological Specimen Banks/organization & administration ; Biological Specimen Banks/standards ; Biomedical Research ; Global Health ; Humans ; International Cooperation ; Quality Control ; Specimen Handling/standards
    Language English
    Publishing date 2019-01-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2593993-2
    ISSN 1947-5543 ; 1947-5535
    ISSN (online) 1947-5543
    ISSN 1947-5535
    DOI 10.1089/bio.2019.29047.drc
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: DROSHA regulates mesenchymal gene expression in Wilms tumor.

    Tiburcio, Patricia D B / Desai, Kavita / Kim, Jiwoong / Zhou, Qinbo / Guo, Lei / Xiao, Xue / Zhou, Li / Yuksel, Aysen / Catchpoole, Daniel R / Amatruda, James F / Xu, Lin / Chen, Kenneth S

    Molecular cancer research : MCR

    2024  

    Abstract: Wilms tumor, the most common pediatric kidney cancer, resembles embryonic renal progenitors. Currently, there are no ways to therapeutically target Wilms tumor driver mutations, such as in the microRNA processing gene DROSHA. Here we used a "multi-omics" ...

    Abstract Wilms tumor, the most common pediatric kidney cancer, resembles embryonic renal progenitors. Currently, there are no ways to therapeutically target Wilms tumor driver mutations, such as in the microRNA processing gene DROSHA. Here we used a "multi-omics" approach to define the effects of DROSHA mutation in Wilms tumor. We categorized Wilms tumor mutations into four mutational subclasses with unique transcriptional effects: microRNA processing, MYCN activation, chromatin remodeling, and kidney developmental factors. In particular, we find that DROSHA mutations are correlated with de-repressing microRNA target genes that regulate differentiation and proliferation and a self-renewing, mesenchymal state. We model these findings by inhibiting DROSHA expression in a Wilms tumor cell line, which led to upregulation of the cell cycle regulator cyclin D2 (CCND2). Furthermore, we observed that DROSHA mutations in Wilms tumor and DROSHA silencing in vitro were associated with a mesenchymal state with aberrations in redox metabolism. Accordingly, we demonstrate that Wilms tumor cells lacking microRNAs are sensitized to ferroptotic cell death through inhibition of glutathione peroxidase 4 (GPX4), the enzyme that detoxifies lipid peroxides. Implications: This study reveals genotype-transcriptome relationships in Wilms tumor and points to ferroptosis as a potentially therapeutic vulnerability in one subset of Wilms tumor.
    Language English
    Publishing date 2024-04-22
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2098788-2
    ISSN 1557-3125 ; 1541-7786
    ISSN (online) 1557-3125
    ISSN 1541-7786
    DOI 10.1158/1541-7786.MCR-23-0930
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5744: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  9. Article ; Online: Biobank: What's in a Name?

    Watson, Peter H / Hewitt, Robert E / Catchpoole, Daniel R / Grizzle, William E

    Biopreservation and biobanking

    2019  Volume 17, Issue 3, Page(s) 204–208

    MeSH term(s) Biological Specimen Banks ; Biomedical Research ; Specimen Handling ; Terminology as Topic
    Language English
    Publishing date 2019-06-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2593993-2
    ISSN 1947-5543 ; 1947-5535
    ISSN (online) 1947-5543
    ISSN 1947-5535
    DOI 10.1089/bio.2019.29053.mjb
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: WILMS TUMOR MUTATIONAL SUBCLASSES CONVERGE TO DRIVE

    Xu, Lin / Desai, Kavita / Kim, Jiwoong / Zhou, Qinbo / Guo, Lei / Xiao, Xue / Zhang, Yanfeng / Zhou, Li / Yuksel, Aysen / Catchpoole, Daniel R / Amatruda, James F / Chen, Kenneth S

    medRxiv : the preprint server for health sciences

    2023  

    Abstract: Wilms tumor, the most common kidney cancer in pediatrics, arises from embryonic renal progenitors. Although many patients are cured with multimodal therapy, outcomes remain poor for those with high-risk features. Recent sequencing efforts have provided ... ...

    Abstract Wilms tumor, the most common kidney cancer in pediatrics, arises from embryonic renal progenitors. Although many patients are cured with multimodal therapy, outcomes remain poor for those with high-risk features. Recent sequencing efforts have provided few biological or clinically actionable insights. Here, we performed DNA and RNA sequencing on 94 Wilms tumors to understand how Wilms tumor mutations transform the transcriptome to arrest differentiation and drive proliferation. We show that most Wilms tumor mutations fall into four classes, each with unique transcriptional signatures: microRNA processing, MYCN activation, chromatin remodeling, and kidney development. In particular, the microRNA processing enzyme
    Language English
    Publishing date 2023-02-02
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.01.30.23285117
    Database MEDical Literature Analysis and Retrieval System OnLINE

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