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  1. Book ; Online ; E-Book: Gene regulatory networks

    Peter, Isabelle S.

    (Current Topics in Developmental Biology ; Volume 139)

    2020  

    Author's details edited by Isabelle S. Peter, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
    Series title Current Topics in Developmental Biology ; Volume 139
    Keywords Gene regulatory networks
    Subject code 572.865
    Language English
    Size 1 online resource (xv, 431 pages) :, illustrations.
    Publisher Academic Press
    Publishing place Cambridge, MA, United States
    Document type Book ; Online ; E-Book
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    ISBN 0-12-813180-2 ; 978-0-12-813180-0
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: Preface.

    Peter, Isabelle S

    Current topics in developmental biology

    2020  Volume 139, Page(s) xiii–xv

    MeSH term(s) Animals ; Developmental Biology/methods ; Developmental Biology/trends ; Gene Expression Regulation, Developmental ; Gene Regulatory Networks ; Humans
    Language English
    Publishing date 2020-03-09
    Publishing country United States
    Document type Editorial ; Introductory Journal Article
    ISSN 1557-8933 ; 0070-2153
    ISSN (online) 1557-8933
    ISSN 0070-2153
    DOI 10.1016/S0070-2153(20)30074-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The function of architecture and logic in developmental gene regulatory networks.

    Peter, Isabelle S

    Current topics in developmental biology

    2020  Volume 139, Page(s) 267–295

    Abstract: An important contribution of systems biology is the insight that biological systems depend on the function of molecular interactions and not just on individual molecules. System level mechanisms are particularly important in the development of animals ... ...

    Abstract An important contribution of systems biology is the insight that biological systems depend on the function of molecular interactions and not just on individual molecules. System level mechanisms are particularly important in the development of animals and plants which depends not just on transcription factors and signaling molecules, but also on regulatory circuits and gene regulatory networks (GRNs). However, since GRNs consist of transcription factors, it can be challenging to assess the function of regulatory circuits independently of the function of regulatory factors. The comparison of different GRNs offers a way to do so and leads to several observations. First, similar regulatory circuits operate in various developmental contexts and in different species, and frequently, these circuits are associated with similar developmental functions. Second, given regulatory circuits are often used at particular positions within the GRN hierarchy. Third, in some GRNs, regulatory circuits are organized in a particular order in respect to each other. And fourth, the evolution of GRNs occurs not just by co-option of regulatory genes but also by rewiring of regulatory linkages between conserved regulatory genes, indicating that the organization of interactions is important. Thus, even though in most instances the function of regulatory circuits remains to be discovered, it becomes evident that the architecture and logic of GRNs are functionally important for the control of genome activity and for the specification of the body plan.
    MeSH term(s) Animals ; Embryo, Nonmammalian/embryology ; Embryo, Nonmammalian/metabolism ; Gene Expression Regulation, Developmental ; Gene Regulatory Networks ; Genes, Regulator/genetics ; Mesoderm/embryology ; Mesoderm/metabolism ; Models, Genetic ; Sea Urchins/embryology ; Sea Urchins/genetics ; Signal Transduction/genetics ; Systems Biology/methods
    Language English
    Publishing date 2020-05-19
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1557-8933 ; 0070-2153
    ISSN (online) 1557-8933
    ISSN 0070-2153
    DOI 10.1016/bs.ctdb.2020.04.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Homologous gene regulatory networks control development of apical organs and brains in Bilateria.

    Feuda, Roberto / Peter, Isabelle S

    Science advances

    2022  Volume 8, Issue 44, Page(s) eabo2416

    Abstract: Apical organs are relatively simple larval nervous systems. The extent to which apical organs are evolutionarily related to the more complex nervous systems of other animals remains unclear. To identify common developmental mechanisms, we analyzed the ... ...

    Abstract Apical organs are relatively simple larval nervous systems. The extent to which apical organs are evolutionarily related to the more complex nervous systems of other animals remains unclear. To identify common developmental mechanisms, we analyzed the gene regulatory network (GRN) controlling the development of the apical organ in sea urchins. We characterized the developmental expression of 30 transcription factors and identified key regulatory functions for FoxQ2, Hbn, Delta/Notch signaling, and SoxC in the patterning of the apical organ and the specification of neurons. Almost the entire set of apical transcription factors is expressed in the nervous system of worms, flies, zebrafish, frogs, and mice. Furthermore, a regulatory module controlling the axial patterning of the vertebrate brain is expressed in the ectoderm of sea urchin embryos. We conclude that GRNs controlling the formation of bilaterian nervous systems share a common origin and that the apical GRN likely resembles an ancestral regulatory program.
    Language English
    Publishing date 2022-11-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.abo2416
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Methods for the experimental and computational analysis of gene regulatory networks in sea urchins.

    Peter, Isabelle S

    Methods in cell biology

    2018  Volume 151, Page(s) 89–113

    Abstract: The discovery of gene regulatory networks (GRNs) has opened a gate to access the genomic mechanisms controlling development. GRNs are systems of transcriptional regulatory circuits that control the differential specification of cell fates during ... ...

    Abstract The discovery of gene regulatory networks (GRNs) has opened a gate to access the genomic mechanisms controlling development. GRNs are systems of transcriptional regulatory circuits that control the differential specification of cell fates during development by regulating gene expression. The experimental analysis of GRNs involves a collection of methods, each revealing aspects of the overall control process. This review provides an overview of experimental and computational methods that have been successfully applied for solving developmental GRNs in the sea urchin embryo. The key in this approach is to obtain experimental evidence for functional interactions between transcription factors and regulatory DNA. In the second part of this review, a more generally applicable strategy is discussed that shows a path from experimental evidence to annotation of regulatory linkages to the generation of GRN models.
    MeSH term(s) Animals ; Computational Biology/methods ; Embryo, Nonmammalian ; Gene Expression Regulation, Developmental ; Gene Regulatory Networks/genetics ; Genome/genetics ; Models, Biological ; Sea Urchins/genetics ; Sea Urchins/growth & development
    Language English
    Publishing date 2018-12-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ISSN 0091-679X
    ISSN 0091-679X
    DOI 10.1016/bs.mcb.2018.10.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: How Does the Regulatory Genome Work?

    Istrail, Sorin / Peter, Isabelle S

    Journal of computational biology : a journal of computational molecular cell biology

    2019  Volume 26, Issue 7, Page(s) 685–695

    MeSH term(s) Animals ; Endoderm/embryology ; Endoderm/metabolism ; Gene Expression Regulation, Developmental ; Gene Regulatory Networks ; Genome ; Mesoderm/embryology ; Mesoderm/metabolism
    Language English
    Publishing date 2019-06-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2030900-4
    ISSN 1557-8666 ; 1066-5277
    ISSN (online) 1557-8666
    ISSN 1066-5277
    DOI 10.1089/cmb.2019.0097
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Eric Davidson. A genomic control odyssey.

    Peter, Isabelle S

    Developmental biology

    2016  Volume 412, Issue 2 Suppl, Page(s) S41–4

    MeSH term(s) Animals ; Developmental Biology/history ; Gene Regulatory Networks ; Genome ; History, 20th Century ; History, 21st Century ; Sea Urchins/embryology
    Language English
    Publishing date 2016-04-15
    Publishing country United States
    Document type Biography ; Editorial ; Historical Article
    ZDB-ID 1114-9
    ISSN 1095-564X ; 0012-1606
    ISSN (online) 1095-564X
    ISSN 0012-1606
    DOI 10.1016/j.ydbio.2016.01.027
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Regulatory states in the developmental control of gene expression.

    Peter, Isabelle S

    Briefings in functional genomics

    2017  Volume 16, Issue 5, Page(s) 281–287

    Abstract: A growing body of evidence shows that gene expression in multicellular organisms is controlled by the combinatorial function of multiple transcription factors. This indicates that not the individual transcription factors or signaling molecules, but the ... ...

    Abstract A growing body of evidence shows that gene expression in multicellular organisms is controlled by the combinatorial function of multiple transcription factors. This indicates that not the individual transcription factors or signaling molecules, but the combination of expressed regulatory molecules, the regulatory state, should be viewed as the functional unit in gene regulation. Here, I discuss the concept of the regulatory state and its proposed role in the genome-wide control of gene expression. Recent analyses of regulatory gene expression in sea urchin embryos have been instrumental for solving the genomic control of cell fate specification in this system. Some of the approaches that were used to determine the expression of regulatory states during sea urchin embryogenesis are reviewed. Significant developmental changes in regulatory state expression leading to the distinct specification of cell fates are regulated by gene regulatory network circuits. How these regulatory state transitions are encoded in the genome is illuminated using the sea urchin endoderm-mesoderms cell fate decision circuit as an example. These observations highlight the importance of considering developmental gene regulation, and the function of individual transcription factors, in the context of regulatory states.
    MeSH term(s) Animals ; Cell Lineage/genetics ; Gene Expression Regulation, Developmental ; Gene Regulatory Networks ; Models, Biological
    Language English
    Publishing date 2017-04-22
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2540916-5
    ISSN 2041-2657 ; 2041-2649 ; 2041-2647
    ISSN (online) 2041-2657
    ISSN 2041-2649 ; 2041-2647
    DOI 10.1093/bfgp/elx009
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  9. Article ; Online: Re: "Associations Between Thyroid Eye Disease and Glaucoma Among Those Enrolled in the National Institutes of Health All of Us Research Program".

    Sidhu, Amitouj S / Walker, Charles E L / Al Yassin, Ahmed / Xiradis, Nicholas / Tweedie, Peter J / Kim, Duri / Wong, Elizabeth L S / Lee, Matthew K / Tsoi, Amy T / Fu, Michele Y / Ouyang, Ming Hong / Gunasegaram, James / Fatima, Aleeza / Borchert, Grace / Nguyen, Isabelle / Agar, Ash / Francis, Ian C

    Ophthalmic plastic and reconstructive surgery

    2024  Volume 40, Issue 3, Page(s) 356

    MeSH term(s) Humans ; United States ; Graves Ophthalmopathy/diagnosis ; National Institutes of Health (U.S.) ; Glaucoma ; Biomedical Research
    Language English
    Publishing date 2024-01-12
    Publishing country United States
    Document type Letter ; Journal Article
    ZDB-ID 632830-1
    ISSN 1537-2677 ; 0740-9303
    ISSN (online) 1537-2677
    ISSN 0740-9303
    DOI 10.1097/IOP.0000000000002580
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Prophylactic Radiation Therapy for High-Risk Asymptomatic Bone Metastases: A New Standard of Care or Need for More Data?

    Chan, Adrian Wai / Simone, Charles B / van der Linden, Yvette / Hoskin, Peter / Detsky, Jay / Choi, J Isabelle / Lee, S F / Wong, Henry Cy / Martin, Emily J / Raman, Srinivas / Rades, Dirk / Rembielak, Agata / Kazmierska, Joanna / Vassiliou, Vassilios / Alcorn, Sara / Bonomo, Pierluigi / Oldenburger, Eva

    Journal of clinical oncology : official journal of the American Society of Clinical Oncology

    2024  Volume 42, Issue 11, Page(s) 1326–1327

    MeSH term(s) Humans ; Standard of Care ; Bone Neoplasms/radiotherapy ; Palliative Care
    Language English
    Publishing date 2024-02-06
    Publishing country United States
    Document type Letter
    ZDB-ID 604914-x
    ISSN 1527-7755 ; 0732-183X
    ISSN (online) 1527-7755
    ISSN 0732-183X
    DOI 10.1200/JCO.23.02391
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