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  1. Book: Limb malformations

    Mundlos, Stefan / Horn, Denise

    an atlas of genetic disorders of limb development

    2014  

    Author's details Stefan Mundlos ; Denise Horn
    Keywords Extremities (Anatomy)--Abnormalities--Atlases
    Subject code 617.58
    Language English
    Size XVI, 267 S. : zahlr. Ill., graph. Darst., 26 cm
    Publisher Springer
    Publishing place Heidelberg u.a.
    Publishing country Germany
    Document type Book
    HBZ-ID HT018635247
    ISBN 978-3-540-95927-4 ; 3-540-95927-0 ; 9783540959281 ; 3540959289
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    2015 A 2118 available for loan (reading room) Lesesaal EG

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  2. Article ; Online: Disruption of regulatory domains and novel transcripts as disease-causing mechanisms.

    Allou, Lila / Mundlos, Stefan

    BioEssays : news and reviews in molecular, cellular and developmental biology

    2023  Volume 45, Issue 10, Page(s) e2300010

    Abstract: Deletions, duplications, insertions, inversions, and translocations, collectively called structural variations (SVs), affect more base pairs of the genome than any other sequence variant. The recent technological advancements in genome sequencing have ... ...

    Abstract Deletions, duplications, insertions, inversions, and translocations, collectively called structural variations (SVs), affect more base pairs of the genome than any other sequence variant. The recent technological advancements in genome sequencing have enabled the discovery of tens of thousands of SVs per human genome. These SVs primarily affect non-coding DNA sequences, but the difficulties in interpreting their impact limit our understanding of human disease etiology. The functional annotation of non-coding DNA sequences and methodologies to characterize their three-dimensional (3D) organization in the nucleus have greatly expanded our understanding of the basic mechanisms underlying gene regulation, thereby improving the interpretation of SVs for their pathogenic impact. Here, we discuss the various mechanisms by which SVs can result in altered gene regulation and how these mechanisms can result in rare genetic disorders. Beyond changing gene expression, SVs can produce novel gene-intergenic fusion transcripts at the SV breakpoints.
    MeSH term(s) Humans ; Chromosome Mapping ; Genome, Human/genetics ; Base Sequence ; Gene Expression Regulation/genetics
    Language English
    Publishing date 2023-06-29
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 50140-2
    ISSN 1521-1878 ; 0265-9247
    ISSN (online) 1521-1878
    ISSN 0265-9247
    DOI 10.1002/bies.202300010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2024: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: 3D or Not 3D: Shaping the Genome during Development.

    Glaser, Juliane / Mundlos, Stefan

    Cold Spring Harbor perspectives in biology

    2022  Volume 14, Issue 5

    Abstract: One of the most fundamental questions in developmental biology is how one fertilized cell can give rise to a fully mature organism and how gene regulation governs this process. Precise spatiotemporal gene expression is required for development and is ... ...

    Abstract One of the most fundamental questions in developmental biology is how one fertilized cell can give rise to a fully mature organism and how gene regulation governs this process. Precise spatiotemporal gene expression is required for development and is believed to be achieved through a complex interplay of sequence-specific information, epigenetic modifications,
    MeSH term(s) Chromatin ; DNA Transposable Elements ; Embryo, Mammalian ; Epigenesis, Genetic ; Gene Expression Regulation
    Chemical Substances Chromatin ; DNA Transposable Elements
    Language English
    Publishing date 2022-05-27
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ISSN 1943-0264
    ISSN (online) 1943-0264
    DOI 10.1101/cshperspect.a040188
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Protocol for chromatin accessibility profiling of human endothelial cells cultured under fluid shear stress using ATAC-seq.

    Raaz, Lion / Mendez, Paul-Lennard / Mundlos, Stefan / Knaus, Petra / Jatzlau, Jerome

    STAR protocols

    2024  Volume 5, Issue 1, Page(s) 102859

    Abstract: Chromatin accessibility influences gene regulation and can be quantified using assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). Recapitulating in vivo fluid shear stress (FSS) mechano-regimes in vitro allows the ... ...

    Abstract Chromatin accessibility influences gene regulation and can be quantified using assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). Recapitulating in vivo fluid shear stress (FSS) mechano-regimes in vitro allows the study of atheroprone and atheroprotective mechanisms. In this protocol, we show how to culture and harvest endothelial cells from microfluidic channels for the preparation of ATAC-seq, highlighting optional growth factor stimulation and different FSS rates. This extends the application of ATAC-seq to the analysis of in vitro mechanically stimulated cells. For complete details on the use and execution of this protocol, please refer to Jatzlau et al.
    MeSH term(s) Humans ; Chromatin/genetics ; Chromatin Immunoprecipitation Sequencing ; Endothelial Cells ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods
    Chemical Substances Chromatin
    Language English
    Publishing date 2024-02-07
    Publishing country United States
    Document type Journal Article
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2024.102859
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Book ; Online: Fünfter Gentechnologiebericht : Sachstand und Perspektiven für Forschung und Anwendung

    Fehse, Boris / Hucho, Ferdinand / Bartfeld, Sina / Clemens, Stephan / Erb, Tobias / Fangerau, Heiner / Hampel, Jürgen / Korte, Martin / Marx-Stölting, Lilian / Mundlos, Stefan / Osterheider, Angela / Pichl, Anja / Reich, Jens / Schickl, Hannah / Schicktanz, Silke / Taupitz, Jochen / Walte, Jörn / Winkler, Eva / Zenke, Martin

    2021  

    Keywords MBP, KCQ, JFMG ; Biologie Ethik Forschung Gene Gesundheit Medizin Gentechnologie Grüne Gentechnik Synthetische Biologie Epigenetik Einzelzellanalyse Gene Drives Organoide Stammzellforschung Hirnorganoide Embryoide Datenschutz Monitoring Genbegriff Genom Gendeterminismus
    Size 1 electronic resource (592 pages)
    Publishing place Baden-Baden
    Document type Book ; Online
    Note German ; Open Access
    HBZ-ID HT021229742
    ISBN 978-3-7489-2724-2 ; 3-7489-2724-X
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  6. Book: Fünfter Gentechnologiebericht

    Fehse, Boris / Hucho, Ferdinand / Bartfeld, Sina / Clemens, Stephan / Erb, Tobias / Fangerau, Heiner / Hampel, Jürgen / Korte, Martin / Marx-Stölting, Lilian / Mundlos, Stefan / Osterheider, Angela / Pichl, Anja / Reich, Jens / Schickl, Hannah / Schicktanz, Silke / Taupitz, Jochen / Walter, Jörn / Winkler, Eva / Zenke, Martin

    Sachstand und Perspektiven für Forschung und Anwendung

    2021  

    Abstract: Im „Fünften Gentechnologiebericht“ bieten namhafte Expertinnen und Experten einen Überblick über aktuelle Entwicklungen des dynamischen Forschungsfeldes der Gen- und Biotechnologien und ihrer Anwendungen. -- In den Blick genommen werden u. a. genetische ... ...

    Abstract Im „Fünften Gentechnologiebericht“ bieten namhafte Expertinnen und Experten einen Überblick über aktuelle Entwicklungen des dynamischen Forschungsfeldes der Gen- und Biotechnologien und ihrer Anwendungen. -- In den Blick genommen werden u. a. genetische Diagnostik, somatische Gentherapie, Impfstoffentwicklung, Stammzell- und Organoidforschung, Grüne Gentechnik, Synthetische Biologie, Gene Drives, Genome-Editing, Epigenetik und Einzelzellanalyse. Neben Sachstandsberichten werden auch die gese...
    Keywords Gentechnologie ; Grüne Gentechnik ; Synthetische Biologie ; Epigenetik ; Einzelzellanalyse ; Gene Drives ; Organoide ; Stammzellforschung ; Hirnorganoide ; Embryoide ; Datenschutz ; Monitoring ; Genbegriff ; Genom ; Gendeterminismus ; Gene ; Biologie ; Ethik ; Medizin ; Forschung ; Gesundheit
    Language German
    Size 592 p.
    Edition 1
    Publisher Nomos
    Document type Book
    Note Hochschulschriften Medizin
    Format 153 x 227
    ISBN 9783848783373 ; 3848783371
    Database PDA

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  7. Article ; Online: Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs.

    Berghöfer, Jan / Khaveh, Nadia / Mundlos, Stefan / Metzger, Julia

    BMC genomics

    2022  Volume 23, Issue 1, Page(s) 564

    Abstract: Background: Past selection events left footprints in the genome of domestic animals, which can be traced back by stretches of homozygous genotypes, designated as runs of homozygosity (ROHs). The analysis of common ROH regions within groups or ... ...

    Abstract Background: Past selection events left footprints in the genome of domestic animals, which can be traced back by stretches of homozygous genotypes, designated as runs of homozygosity (ROHs). The analysis of common ROH regions within groups or populations displaying potential signatures of selection requires high-quality SNP data as well as carefully adjusted ROH-defining parameters. In this study, we used a simultaneous testing of rule- and model-based approaches to perform strategic ROH calling in genomic data from different pig populations to detect genomic regions under selection for specific phenotypes.
    Results: Our ROH analysis using a rule-based approach offered by PLINK, as well as a model-based approach run by RZooRoH demonstrated a high efficiency of both methods. It underlined the importance of providing a high-quality SNP set as input as well as adjusting parameters based on dataset and population for ROH calling. Particularly, ROHs ≤ 20 kb were called in a high frequency by both tools, but to some extent covered different gene sets in subsequent analysis of ROH regions common for investigated pig groups. Phenotype associated ROH analysis resulted in regions under potential selection characterizing heritage pig breeds, known to harbour a long-established breeding history. In particular, the selection focus on fitness-related traits was underlined by various ROHs harbouring disease resistance or tolerance-associated genes. Moreover, we identified potential selection signatures associated with ear morphology, which confirmed known candidate genes as well as uncovered a missense mutation in the ABCA6 gene potentially supporting ear cartilage formation.
    Conclusions: The results of this study highlight the strengths and unique features of rule- and model-based approaches as well as demonstrate their potential for ROH analysis in animal populations. We provide a workflow for ROH detection, evaluating the major steps from filtering for high-quality SNP sets to intersecting ROH regions. Formula-based estimations defining ROHs for rule-based method show its limits, particularly for efficient detection of smaller ROHs. Moreover, we emphasize the role of ROH detection for the identification of potential footprints of selection in pigs, displaying their breed-specific characteristics or favourable phenotypes.
    MeSH term(s) Animals ; Genome ; Genomics ; Genotype ; Homozygote ; Inbreeding ; Polymorphism, Single Nucleotide ; Swine/genetics
    Language English
    Publishing date 2022-08-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041499-7
    ISSN 1471-2164 ; 1471-2164
    ISSN (online) 1471-2164
    ISSN 1471-2164
    DOI 10.1186/s12864-022-08801-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: TADA-a machine learning tool for functional annotation-based prioritisation of pathogenic CNVs.

    Hertzberg, Jakob / Mundlos, Stefan / Vingron, Martin / Gallone, Giuseppe

    Genome biology

    2022  Volume 23, Issue 1, Page(s) 67

    Abstract: Few methods have been developed to investigate copy number variants (CNVs) based on their predicted pathogenicity. We introduce TADA, a method to prioritise pathogenic CNVs through assisted manual filtering and automated classification, based on an ... ...

    Abstract Few methods have been developed to investigate copy number variants (CNVs) based on their predicted pathogenicity. We introduce TADA, a method to prioritise pathogenic CNVs through assisted manual filtering and automated classification, based on an extensive catalogue of functional annotation supported by rigourous enrichment analysis. We demonstrate that our classifiers are able to accurately predict pathogenic CNVs, outperforming current alternative methods, and produce a well-calibrated pathogenicity score. Our results suggest that functional annotation-based prioritisation of pathogenic CNVs is a promising approach to support clinical diagnostics and to further the understanding of mechanisms controlling the disease impact of larger genomic alterations.
    MeSH term(s) DNA Copy Number Variations ; Genomics ; Machine Learning
    Language English
    Publishing date 2022-03-01
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-022-02631-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: TADA—a machine learning tool for functional annotation-based prioritisation of pathogenic CNVs

    Hertzberg, Jakob / Mundlos, Stefan / Vingron, Martin / Gallone, Giuseppe

    Genome biology. 2022 Dec., v. 23, no. 1

    2022  

    Abstract: Few methods have been developed to investigate copy number variants (CNVs) based on their predicted pathogenicity. We introduce TADA, a method to prioritise pathogenic CNVs through assisted manual filtering and automated classification, based on an ... ...

    Abstract Few methods have been developed to investigate copy number variants (CNVs) based on their predicted pathogenicity. We introduce TADA, a method to prioritise pathogenic CNVs through assisted manual filtering and automated classification, based on an extensive catalogue of functional annotation supported by rigourous enrichment analysis. We demonstrate that our classifiers are able to accurately predict pathogenic CNVs, outperforming current alternative methods, and produce a well-calibrated pathogenicity score. Our results suggest that functional annotation-based prioritisation of pathogenic CNVs is a promising approach to support clinical diagnostics and to further the understanding of mechanisms controlling the disease impact of larger genomic alterations.
    Keywords automation ; diagnostic techniques ; genome ; genomics ; pathogenicity ; prioritization
    Language English
    Dates of publication 2022-12
    Size p. 67.
    Publishing place BioMed Central
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-022-02631-z
    Database NAL-Catalogue (AGRICOLA)

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  10. Article ; Online: The role of 3D chromatin domains in gene regulation: a multi-facetted view on genome organization.

    Ibrahim, Daniel M / Mundlos, Stefan

    Current opinion in genetics & development

    2020  Volume 61, Page(s) 1–8

    Abstract: The causal relationship between 3D chromatin domains and gene regulation has been of considerable debate in recent years. Initial Hi-C studies profiling the 3D chromatin structure of the genome described evolutionarily conserved Topologically Associating ...

    Abstract The causal relationship between 3D chromatin domains and gene regulation has been of considerable debate in recent years. Initial Hi-C studies profiling the 3D chromatin structure of the genome described evolutionarily conserved Topologically Associating Domains (TADs) that correlated with gene expression. Subsequent evidence from mouse models and human disease directly linked TADs to gene regulation. However, a number of focused genetic and genome-wide studies questioned the relevance of 3D chromatin domains for orchestrating gene expression, ultimately yielding a more multi-layered view of 3D chromatin structure and gene regulation. We review the evidence for and against the importance of 3D chromatin structure for gene regulation and argue for a more comprehensive classification of regulatory chromatin domains that integrates 3D chromatin structure with genomic, functional, and evolutionary conservation.
    MeSH term(s) Animals ; Chromatin/genetics ; Chromatin/ultrastructure ; Chromatin Assembly and Disassembly/genetics ; Evolution, Molecular ; Gene Expression Regulation/genetics ; Genome/genetics ; Humans ; Mice
    Chemical Substances Chromatin
    Language English
    Publishing date 2020-03-19
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1077312-5
    ISSN 1879-0380 ; 0959-437X
    ISSN (online) 1879-0380
    ISSN 0959-437X
    DOI 10.1016/j.gde.2020.02.015
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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    Jg. 1995 - 2021: Lesesall (2.OG)
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