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  1. AU=Eisen Michael B
  2. AU="Manal S. Selim" AU="Manal S. Selim"
  3. AU="Alturki, Ramadan"
  4. AU="Kluger, Benzi"
  5. AU="Mitchell, Krista"
  6. AU="Oakes, Mary"
  7. AU="Kevill, Dennis N"
  8. AU="Rojas, Almudena"
  9. AU=Dalmau Josep AU=Dalmau Josep
  10. AU="Vaňáčová, Štěpánka"
  11. AU="Hancioglu, Baris"
  12. AU="Scribner, Kim T"
  13. AU="Emanuel Schmassmann"
  14. AU="Patel, Monica"
  15. AU=Passariello Margherita
  16. AU=Saikia Bedangshu
  17. AU="Dion, Dominique"
  18. AU="Magami, Shunsuke"
  19. AU="Wagner, Henrik"

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  1. Artikel ; Online: Intrinsic protein disorder is insufficient to drive subnuclear clustering in embryonic transcription factors.

    Hannon, Colleen E / Eisen, Michael B

    eLife

    2024  Band 12

    Abstract: Modern microscopy has revealed that core nuclear functions, including transcription, replication, and heterochromatin formation, occur in spatially restricted clusters. Previous work from our lab has shown that subnuclear high-concentration clusters of ... ...

    Abstract Modern microscopy has revealed that core nuclear functions, including transcription, replication, and heterochromatin formation, occur in spatially restricted clusters. Previous work from our lab has shown that subnuclear high-concentration clusters of transcription factors may play a role in regulating RNA synthesis in the early
    Mesh-Begriff(e) Animals ; Transcription Factors/genetics ; Protein Conformation ; Proteome ; Amino Acid Sequence ; Drosophila/metabolism ; Intrinsically Disordered Proteins/metabolism
    Chemische Substanzen Transcription Factors ; Proteome ; Intrinsically Disordered Proteins
    Sprache Englisch
    Erscheinungsdatum 2024-01-26
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.88221
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Evolutionary analyses of intrinsically disordered regions reveal widespread signals of conservation.

    Singleton, Marc D / Eisen, Michael B

    PLoS computational biology

    2024  Band 20, Heft 4, Seite(n) e1012028

    Abstract: Intrinsically disordered regions (IDRs) are segments of proteins without stable three-dimensional structures. As this flexibility allows them to interact with diverse binding partners, IDRs play key roles in cell signaling and gene expression. Despite ... ...

    Abstract Intrinsically disordered regions (IDRs) are segments of proteins without stable three-dimensional structures. As this flexibility allows them to interact with diverse binding partners, IDRs play key roles in cell signaling and gene expression. Despite the prevalence and importance of IDRs in eukaryotic proteomes and various biological processes, associating them with specific molecular functions remains a significant challenge due to their high rates of sequence evolution. However, by comparing the observed values of various IDR-associated properties against those generated under a simulated model of evolution, a recent study found most IDRs across the entire yeast proteome contain conserved features. Furthermore, it showed clusters of IDRs with common "evolutionary signatures," i.e. patterns of conserved features, were associated with specific biological functions. To determine if similar patterns of conservation are found in the IDRs of other systems, in this work we applied a series of phylogenetic models to over 7,500 orthologous IDRs identified in the Drosophila genome to dissect the forces driving their evolution. By comparing models of constrained and unconstrained continuous trait evolution using the Brownian motion and Ornstein-Uhlenbeck models, respectively, we identified signals of widespread constraint, indicating conservation of distributed features is mechanism of IDR evolution common to multiple biological systems. In contrast to the previous study in yeast, however, we observed limited evidence of IDR clusters with specific biological functions, which suggests a more complex relationship between evolutionary constraints and function in the IDRs of multicellular organisms.
    Mesh-Begriff(e) Evolution, Molecular ; Animals ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/genetics ; Intrinsically Disordered Proteins/metabolism ; Phylogeny ; Conserved Sequence/genetics ; Computational Biology/methods ; Drosophila/genetics ; Proteome/chemistry ; Proteome/metabolism ; Proteome/genetics ; Drosophila Proteins/genetics ; Drosophila Proteins/chemistry ; Drosophila Proteins/metabolism
    Chemische Substanzen Intrinsically Disordered Proteins ; Proteome ; Drosophila Proteins
    Sprache Englisch
    Erscheinungsdatum 2024-04-25
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1012028
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: We need to act now.

    Eisen, Michael B

    eLife

    2020  Band 9

    Abstract: eLife, like the rest of science, must tackle the many inequalities experienced by Black scientists. ...

    Abstract eLife, like the rest of science, must tackle the many inequalities experienced by Black scientists.
    Mesh-Begriff(e) African Americans ; Human Rights ; Humans ; Leadership ; Models, Organizational ; Publishing/organization & administration ; Publishing/standards ; Racism/prevention & control ; Science/organization & administration ; Science/standards ; Social Justice
    Sprache Englisch
    Erscheinungsdatum 2020-06-05
    Erscheinungsland England
    Dokumenttyp Editorial
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.59636
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: We need to act now

    Michael B Eisen

    eLife, Vol

    2020  Band 9

    Abstract: eLife, like the rest of science, must tackle the many inequalities experienced by Black scientists. ...

    Abstract eLife, like the rest of science, must tackle the many inequalities experienced by Black scientists.
    Schlagwörter racism in science ; equality ; diversity and inclusion ; scientific publishing ; eLife ; careers in science ; discrimination ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Sprache Englisch
    Erscheinungsdatum 2020-06-01T00:00:00Z
    Verlag eLife Sciences Publications Ltd
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  5. Artikel ; Online: Single-nucleus RNA-sequencing in pre-cellularization Drosophila melanogaster embryos.

    Albright, Ashley R / Stadler, Michael R / Eisen, Michael B

    PloS one

    2022  Band 17, Heft 6, Seite(n) e0270471

    Abstract: Our current understanding of the regulation of gene expression in the early Drosophila melanogaster embryo comes from observations of a few genes at a time, as with in situ hybridizations, or observation of gene expression levels without regards to ... ...

    Abstract Our current understanding of the regulation of gene expression in the early Drosophila melanogaster embryo comes from observations of a few genes at a time, as with in situ hybridizations, or observation of gene expression levels without regards to patterning, as with RNA-sequencing. Single-nucleus RNA-sequencing however, has the potential to provide new insights into the regulation of gene expression for many genes at once while simultaneously retaining information regarding the position of each nucleus prior to dissociation based on patterned gene expression. In order to establish the use of single-nucleus RNA sequencing in Drosophila embryos prior to cellularization, here we look at gene expression in control and insulator protein, dCTCF, maternal null embryos during zygotic genome activation at nuclear cycle 14. We find that early embryonic nuclei can be grouped into distinct clusters according to gene expression. From both virtual and published in situ hybridizations, we also find that these clusters correspond to spatial regions of the embryo. Lastly, we provide a resource of candidate differentially expressed genes that might show local changes in gene expression between control and maternal dCTCF null nuclei with no detectable differential expression in bulk. These results highlight the potential for single-nucleus RNA-sequencing to reveal new insights into the regulation of gene expression in the early Drosophila melanogaster embryo.
    Mesh-Begriff(e) Animals ; Drosophila/genetics ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/metabolism ; Embryo, Nonmammalian/metabolism ; Gene Expression Regulation, Developmental ; Morphogenesis/genetics ; RNA/metabolism ; Sequence Analysis, RNA
    Chemische Substanzen Drosophila Proteins ; RNA (63231-63-0)
    Sprache Englisch
    Erscheinungsdatum 2022-06-24
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0270471
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel: Unified bursting strategies in ectopic and endogenous

    Berrocal, Augusto / Lammers, Nicholas C / Garcia, Hernan G / Eisen, Michael B

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Transcription often occurs in bursts as gene promoters switch stochastically between active and inactive states. Enhancers can dictate transcriptional activity in animal development through the modulation of burst frequency, duration, or amplitude. ... ...

    Abstract Transcription often occurs in bursts as gene promoters switch stochastically between active and inactive states. Enhancers can dictate transcriptional activity in animal development through the modulation of burst frequency, duration, or amplitude. Previous studies observed that different enhancers can achieve a wide range of transcriptional outputs through the same strategies of bursting control. For example, despite responding to different transcription factors, all
    Sprache Englisch
    Erscheinungsdatum 2023-02-10
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2023.02.09.527927
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel ; Online: Single-nucleus RNA-sequencing in pre-cellularization Drosophila melanogaster embryos.

    Ashley R Albright / Michael R Stadler / Michael B Eisen

    PLoS ONE, Vol 17, Iss 6, p e

    2022  Band 0270471

    Abstract: Our current understanding of the regulation of gene expression in the early Drosophila melanogaster embryo comes from observations of a few genes at a time, as with in situ hybridizations, or observation of gene expression levels without regards to ... ...

    Abstract Our current understanding of the regulation of gene expression in the early Drosophila melanogaster embryo comes from observations of a few genes at a time, as with in situ hybridizations, or observation of gene expression levels without regards to patterning, as with RNA-sequencing. Single-nucleus RNA-sequencing however, has the potential to provide new insights into the regulation of gene expression for many genes at once while simultaneously retaining information regarding the position of each nucleus prior to dissociation based on patterned gene expression. In order to establish the use of single-nucleus RNA sequencing in Drosophila embryos prior to cellularization, here we look at gene expression in control and insulator protein, dCTCF, maternal null embryos during zygotic genome activation at nuclear cycle 14. We find that early embryonic nuclei can be grouped into distinct clusters according to gene expression. From both virtual and published in situ hybridizations, we also find that these clusters correspond to spatial regions of the embryo. Lastly, we provide a resource of candidate differentially expressed genes that might show local changes in gene expression between control and maternal dCTCF null nuclei with no detectable differential expression in bulk. These results highlight the potential for single-nucleus RNA-sequencing to reveal new insights into the regulation of gene expression in the early Drosophila melanogaster embryo.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 612 ; 570
    Sprache Englisch
    Erscheinungsdatum 2022-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  8. Artikel ; Online: Atlas…t, patterns from every cell.

    Stadler, Michael R / Eisen, Michael B

    Science (New York, N.Y.)

    2017  Band 358, Heft 6360, Seite(n) 172–173

    Mesh-Begriff(e) Animals ; DNA ; Drosophila melanogaster/embryology ; Gene Expression Regulation, Developmental ; RNA
    Chemische Substanzen RNA (63231-63-0) ; DNA (9007-49-2)
    Sprache Englisch
    Erscheinungsdatum 2017--13
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Comment
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.aap8493
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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    Verfügbar in ZB MED Köln/Königswinter

    Zs.A 27: Hefte anzeigen Standort:
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  9. Artikel: Genome-wide measurement of spatial expression in patterning mutants of

    Combs, Peter A / Eisen, Michael B

    F1000Research

    2017  Band 6, Seite(n) 41

    Abstract: Patterning in ... ...

    Abstract Patterning in the
    Sprache Englisch
    Erscheinungsdatum 2017
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2699932-8
    ISSN 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.9720.1
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  10. Artikel ; Online: Whole Genome Sequences of 23 Species from the

    Bronski, Michael J / Martinez, Ciera C / Weld, Holli A / Eisen, Michael B

    G3 (Bethesda, Md.)

    2020  Band 10, Heft 5, Seite(n) 1443–1455

    Abstract: Large groups of species with well-defined phylogenies are excellent systems for testing evolutionary hypotheses. In this paper, we describe the creation of a comparative genomic resource consisting of 23 genomes from the species- ... ...

    Abstract Large groups of species with well-defined phylogenies are excellent systems for testing evolutionary hypotheses. In this paper, we describe the creation of a comparative genomic resource consisting of 23 genomes from the species-rich
    Mesh-Begriff(e) Animals ; Drosophila/genetics ; Drosophila melanogaster/genetics ; Genome ; Genomics ; Phylogeny
    Sprache Englisch
    Erscheinungsdatum 2020-05-04
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1534/g3.119.400959
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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