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  1. Article: Artificial intelligence, molecular subtyping, biomarkers, and precision oncology.

    Shen, John Paul

    Emerging topics in life sciences

    2021  Volume 5, Issue 6, Page(s) 747–756

    Abstract: A targeted cancer therapy is only useful if there is a way to accurately identify the tumors that are susceptible to that therapy. Thus rapid expansion in the number of available targeted cancer treatments has been accompanied by a robust effort to ... ...

    Abstract A targeted cancer therapy is only useful if there is a way to accurately identify the tumors that are susceptible to that therapy. Thus rapid expansion in the number of available targeted cancer treatments has been accompanied by a robust effort to subdivide the traditional histological and anatomical tumor classifications into molecularly defined subtypes. This review highlights the history of the paired evolution of targeted therapies and biomarkers, reviews currently used methods for subtype identification, and discusses challenges to the implementation of precision oncology as well as possible solutions.
    MeSH term(s) Artificial Intelligence ; Biomarkers ; Humans ; Medical Oncology/methods ; Neoplasms/diagnosis ; Neoplasms/pathology ; Neoplasms/therapy ; Precision Medicine/methods
    Chemical Substances Biomarkers
    Language English
    Publishing date 2021-12-09
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 2882721-1
    ISSN 2397-8554 ; 2397-8554 ; 2397-8562
    ISSN (online) 2397-8554
    ISSN 2397-8554 ; 2397-8562
    DOI 10.1042/ETLS20210212
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Regarding Blood-Based Next-Generation Sequencing Analysis of Appendiceal Cancers.

    Shen, John Paul

    The oncologist

    2020  Volume 25, Issue 12, Page(s) e2019–e2020

    MeSH term(s) Appendiceal Neoplasms/genetics ; High-Throughput Nucleotide Sequencing ; Humans
    Language English
    Publishing date 2020-10-21
    Publishing country England
    Document type Letter ; Comment
    ZDB-ID 1409038-7
    ISSN 1549-490X ; 1083-7159
    ISSN (online) 1549-490X
    ISSN 1083-7159
    DOI 10.1002/onco.13559
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4845: Show issues Location:
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    Zs.MO 494: Show issues

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  3. Book ; Online: Towards a Design Framework for TNN-Based Neuromorphic Sensory Processing Units

    Vellaisamy, Prabhu / Shen, John Paul

    2022  

    Abstract: Temporal Neural Networks (TNNs) are spiking neural networks that exhibit brain-like sensory processing with high energy efficiency. This work presents the ongoing research towards developing a custom design framework for designing efficient application- ... ...

    Abstract Temporal Neural Networks (TNNs) are spiking neural networks that exhibit brain-like sensory processing with high energy efficiency. This work presents the ongoing research towards developing a custom design framework for designing efficient application-specific TNN-based Neuromorphic Sensory Processing Units (NSPUs). This paper examines previous works on NSPU designs for UCR time-series clustering and MNIST image classification applications. Current ideas for a custom design framework and tools that enable efficient software-to-hardware design flow for rapid design space exploration of application-specific NSPUs while leveraging EDA tools to obtain post-layout netlist and power-performance-area (PPA) metrics are described. Future research directions are also outlined.
    Keywords Computer Science - Emerging Technologies ; Computer Science - Hardware Architecture ; Computer Science - Neural and Evolutionary Computing
    Publishing date 2022-05-27
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Corrigendum: SemNet: Learning semantic attributes for human activity recognition with deep belief networks.

    Venkatachalam, Shanmuga / Nair, Harideep / Zeng, Ming / Tan, Cathy Shunwen / Mengshoel, Ole J / Shen, John Paul

    Frontiers in big data

    2023  Volume 6, Page(s) 1170820

    Abstract: This corrects the article DOI: 10.3389/fdata.2022.879389.]. ...

    Abstract [This corrects the article DOI: 10.3389/fdata.2022.879389.].
    Language English
    Publishing date 2023-03-10
    Publishing country Switzerland
    Document type Published Erratum
    ISSN 2624-909X
    ISSN (online) 2624-909X
    DOI 10.3389/fdata.2023.1170820
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls.

    Shen, John Paul / Ideker, Trey

    Journal of molecular biology

    2018  Volume 430, Issue 18 Pt A, Page(s) 2900–2912

    Abstract: Synthetic lethal interactions, in which the simultaneous loss of function of two genes produces a lethal phenotype, are being explored as a means to therapeutically exploit cancer-specific vulnerabilities and expand the scope of precision oncology. ... ...

    Abstract Synthetic lethal interactions, in which the simultaneous loss of function of two genes produces a lethal phenotype, are being explored as a means to therapeutically exploit cancer-specific vulnerabilities and expand the scope of precision oncology. Currently, three Food and Drug Administration-approved drugs work by targeting the synthetic lethal interaction between BRCA1/2 and PARP. This review examines additional efforts to discover networks of synthetic lethal interactions and discusses both challenges and opportunities regarding the translation of new synthetic lethal interactions into the clinic.
    MeSH term(s) Animals ; Biomarkers, Tumor ; Computational Biology/methods ; Disease Susceptibility ; Epistasis, Genetic ; Genomics/methods ; Humans ; Neoplasms/diagnosis ; Neoplasms/etiology ; Neoplasms/metabolism ; Neoplasms/therapy ; Precision Medicine/methods ; Synthetic Lethal Mutations ; Translational Research, Biomedical
    Chemical Substances Biomarkers, Tumor
    Language English
    Publishing date 2018-06-20
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2018.06.026
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 867: Show issues Location:
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  6. Article: Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls

    Shen, John Paul / Ideker, Trey

    Journal of molecular biology. 2018 Sept. 14, v. 430, no. 18

    2018  

    Abstract: Synthetic lethal interactions, in which the simultaneous loss of function of two genes produces a lethal phenotype, are being explored as a means to therapeutically exploit cancer-specific vulnerabilities and expand the scope of precision oncology. ... ...

    Abstract Synthetic lethal interactions, in which the simultaneous loss of function of two genes produces a lethal phenotype, are being explored as a means to therapeutically exploit cancer-specific vulnerabilities and expand the scope of precision oncology. Currently, three Food and Drug Administration-approved drugs work by targeting the synthetic lethal interaction between BRCA1/2 and PARP. This review examines additional efforts to discover networks of synthetic lethal interactions and discusses both challenges and opportunities regarding the translation of new synthetic lethal interactions into the clinic.
    Keywords drugs ; genes ; phenotype ; tumor suppressor proteins
    Language English
    Dates of publication 2018-0914
    Size p. 2900-2912.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2018.06.026
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 4' 63/108: Show issues

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  7. Article ; Online: SemNet: Learning semantic attributes for human activity recognition with deep belief networks.

    Venkatachalam, Shanmuga / Nair, Harideep / Zeng, Ming / Tan, Cathy Shunwen / Mengshoel, Ole J / Shen, John Paul

    Frontiers in big data

    2022  Volume 5, Page(s) 879389

    Abstract: Human Activity Recognition (HAR) is a prominent application in mobile computing and Internet of Things (IoT) that aims to detect human activities based on multimodal sensor signals generated as a result of diverse body movements. Human physical ... ...

    Abstract Human Activity Recognition (HAR) is a prominent application in mobile computing and Internet of Things (IoT) that aims to detect human activities based on multimodal sensor signals generated as a result of diverse body movements. Human physical activities are typically composed of simple actions (such as "arm up", "arm down", "arm curl", etc.), referred to as
    Language English
    Publishing date 2022-08-30
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2624-909X
    ISSN (online) 2624-909X
    DOI 10.3389/fdata.2022.879389
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  8. Article: Taxane-based Chemotherapy is Effective in Metastatic Appendiceal Adenocarcinoma.

    Dansby, Julia / More, Aditya / Zeineddine, Mohammad / Yousef, Abdelrahman / Bent, Alisha / Dayyani, Farshid / Wolff, Robert / Overman, Michael / Shen, John Paul

    medRxiv : the preprint server for health sciences

    2023  

    Abstract: Appendiceal cancer is a rare, orphan disease with no therapies currently approved by the FDA for its treatment. Given the limited data regarding drug efficacy, these tumors have historically been treated with chemotherapy designed for colon cancer. ... ...

    Abstract Appendiceal cancer is a rare, orphan disease with no therapies currently approved by the FDA for its treatment. Given the limited data regarding drug efficacy, these tumors have historically been treated with chemotherapy designed for colon cancer. However, an overwhelming body of molecular data has demonstrated that appendiceal adenocarcinoma is a distinct entity with key molecular differences from colon cancer, notably rare
    Language English
    Publishing date 2023-07-13
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.07.11.23292522
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  9. Article ; Online: Correcting CRISPR for copy number.

    Shen, John Paul / Ideker, Trey

    Nature genetics

    2017  Volume 49, Issue 12, Page(s) 1674–1675

    Abstract: The CRISPR-Cas9 system enables global screens of gene function with high sensitivity and specificity, but off-target effects have been reported for CRISPR guide RNAs targeting genes that are amplified at high copy number. A new study describes a ... ...

    Abstract The CRISPR-Cas9 system enables global screens of gene function with high sensitivity and specificity, but off-target effects have been reported for CRISPR guide RNAs targeting genes that are amplified at high copy number. A new study describes a computational approach to correct for this copy number effect, increasing the specificity of CRIPSR screens to identify essential genes.
    MeSH term(s) CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA Copy Number Variations ; Genes, Essential ; RNA, Guide, CRISPR-Cas Systems ; Sensitivity and Specificity
    Chemical Substances RNA, Guide, CRISPR-Cas Systems
    Language English
    Publishing date 2017-11-17
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/ng.3994
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3613: Show issues Location:
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    Zs.MG 46: Show issues

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  10. Article ; Online: Taxane-Based Chemotherapy Is Effective in Metastatic Appendiceal Adenocarcinoma.

    Dansby, Julia / More, Aditya / Zeineddine, Mohammad / Yousef, Abdelrahman / Bent, Alisha / Dayyani, Farshid / Wolff, Robert / Overman, Michael / Shen, John Paul

    The oncologist

    2023  Volume 28, Issue 12, Page(s) e1303–e1305

    Abstract: Appendiceal cancer is a rare, orphan disease with no therapies currently approved by the FDA for its treatment. Given the limited data regarding drug efficacy, these tumors have historically been treated with chemotherapy designed for colon cancer. ... ...

    Abstract Appendiceal cancer is a rare, orphan disease with no therapies currently approved by the FDA for its treatment. Given the limited data regarding drug efficacy, these tumors have historically been treated with chemotherapy designed for colon cancer. However, an overwhelming body of molecular data has demonstrated that appendiceal adenocarcinoma is a distinct entity with key molecular differences from colon cancer, notably rare APC mutation. Recognizing that APC loss-of-function is thought to contribute to taxane resistance and that taxanes are effective in the treatment of other gastrointestinal tumors, including gastric, esophageal, and small bowel adenocarcinoma, we completed a single-center retrospective study to assess efficacy. In a cohort of 13 patients with metastatic appendiceal adenocarcinoma, treated with taxane chemotherapy the median overall survival was 8.8 months. Of 10 evaluable patients, we observed 3 responses, 4 patients with stable disease, and 3 with progression (30% response rate, 70% disease control rate). The results of this study showing activity of taxane-based chemotherapy in appendiceal adenocarcinoma support further clinical investigation of taxane therapy in this orphan disease.
    MeSH term(s) Humans ; Retrospective Studies ; Rare Diseases ; Taxoids/therapeutic use ; Appendiceal Neoplasms/drug therapy ; Appendiceal Neoplasms/genetics ; Adenocarcinoma/drug therapy ; Adenocarcinoma/genetics ; Adenocarcinoma/pathology ; Colonic Neoplasms/drug therapy ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use
    Chemical Substances taxane (1605-68-1) ; Taxoids
    Language English
    Publishing date 2023-09-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 1409038-7
    ISSN 1549-490X ; 1083-7159
    ISSN (online) 1549-490X
    ISSN 1083-7159
    DOI 10.1093/oncolo/oyad263
    Database MEDical Literature Analysis and Retrieval System OnLINE

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