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  1. AU=Rajewsky Nikolaus
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  1. Article ; Online: C. elegans

    Froehlich, Jonathan J / Rajewsky, Nikolaus

    microPublication biology

    2023  Volume 2023

    Abstract: Gene regulation has been studied ... ...

    Abstract Gene regulation has been studied in
    Language English
    Publishing date 2023-01-20
    Publishing country United States
    Document type Journal Article
    ISSN 2578-9430
    ISSN (online) 2578-9430
    DOI 10.17912/micropub.biology.000709
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book ; Online ; Thesis: Scalable image analysis for quantitative microscopy

    Preußer, Friedrich [Verfasser] / Rajewsky, Nikolaus [Gutachter] / Preibisch, Stephan [Gutachter] / Reber, Simone [Gutachter]

    2024  

    Author's details Friedrich Ludwig Preußer ; Gutachter: Nikolaus Rajewsky, Stephan Preibisch, Simone Reber
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Humboldt-Universität zu Berlin
    Publishing place Berlin
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  3. Article ; Online: Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease.

    Piwecka, Monika / Rajewsky, Nikolaus / Rybak-Wolf, Agnieszka

    Nature reviews. Neurology

    2023  Volume 19, Issue 6, Page(s) 346–362

    Abstract: In the past decade, single-cell technologies have proliferated and improved from their technically challenging beginnings to become common laboratory methods capable of determining the expression of thousands of genes in thousands of cells simultaneously. ...

    Abstract In the past decade, single-cell technologies have proliferated and improved from their technically challenging beginnings to become common laboratory methods capable of determining the expression of thousands of genes in thousands of cells simultaneously. The field has progressed by taking the CNS as a primary research subject - the cellular complexity and multiplicity of neuronal cell types provide fertile ground for the increasing power of single-cell methods. Current single-cell RNA sequencing methods can quantify gene expression with sufficient accuracy to finely resolve even subtle differences between cell types and states, thus providing a great tool for studying the molecular and cellular repertoire of the CNS and its disorders. However, single-cell RNA sequencing requires the dissociation of tissue samples, which means that the interrelationships between cells are lost. Spatial transcriptomic methods bypass tissue dissociation and retain this spatial information, thereby allowing gene expression to be assessed across thousands of cells within the context of tissue structural organization. Here, we discuss how single-cell and spatially resolved transcriptomics have been contributing to unravelling the pathomechanisms underlying brain disorders. We focus on three areas where we feel these new technologies have provided particularly useful insights: selective neuronal vulnerability, neuroimmune dysfunction and cell-type-specific treatment response. We also discuss the limitations and future directions of single-cell and spatial RNA sequencing technologies.
    MeSH term(s) Humans ; Transcriptome/genetics ; Brain ; Gene Expression Profiling ; Brain Diseases/genetics
    Language English
    Publishing date 2023-05-17
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2491514-2
    ISSN 1759-4766 ; 1759-4758
    ISSN (online) 1759-4766
    ISSN 1759-4758
    DOI 10.1038/s41582-023-00809-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6257: 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)
    Zs.MG 88: Show issues

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  4. Article ; Online: Estimation of

    Froehlich, Jonathan J / Rajewsky, Nikolaus / Ewald, Collin Y

    microPublication biology

    2021  Volume 2021

    Abstract: ... ...

    Abstract Although
    Language English
    Publishing date 2021-01-04
    Publishing country United States
    Document type Journal Article
    ISSN 2578-9430
    ISSN (online) 2578-9430
    DOI 10.17912/micropub.biology.000345
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Rapid nuclear deadenylation of mammalian messenger RNA.

    Alles, Jonathan / Legnini, Ivano / Pacelli, Maddalena / Rajewsky, Nikolaus

    iScience

    2022  Volume 26, Issue 1, Page(s) 105878

    Abstract: Poly(A) tails protect RNAs from degradation and their deadenylation rates determine RNA stability. Although poly(A) tails are generated in the nucleus, deadenylation of tails has mostly been investigated within the cytoplasm. Here, we combined long-read ... ...

    Abstract Poly(A) tails protect RNAs from degradation and their deadenylation rates determine RNA stability. Although poly(A) tails are generated in the nucleus, deadenylation of tails has mostly been investigated within the cytoplasm. Here, we combined long-read sequencing with metabolic labeling, splicing inhibition and cell fractionation experiments to quantify, separately, the genesis and trimming of nuclear and cytoplasmic tails
    Language English
    Publishing date 2022-12-28
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2022.105878
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Generation and Downstream Analysis of Single-Cell and Single-Nuclei Transcriptomes in Brain Organoids.

    Wandres, Miriam / Aigner, Denise / Kastelic, Nicolai / Boltengagen, Anastasiya / Rybak-Wolf, Agnieszka / Rajewsky, Nikolaus

    Journal of visualized experiments : JoVE

    2024  , Issue 205

    Abstract: Over the past decade, single-cell transcriptomics has significantly evolved and become a standard laboratory method for simultaneous analysis of gene expression profiles of individual cells, allowing the capture of cellular diversity. In order to ... ...

    Abstract Over the past decade, single-cell transcriptomics has significantly evolved and become a standard laboratory method for simultaneous analysis of gene expression profiles of individual cells, allowing the capture of cellular diversity. In order to overcome limitations posed by difficult-to-isolate cell types, an alternative approach aiming at recovering single nuclei instead of intact cells can be utilized for sequencing, making transcriptome profiling of individual cells universally applicable. These techniques have become a cornerstone in the study of brain organoids, establishing them as models of the developing human brain. Leveraging the potential of single-cell and single-nucleus transcriptomics in brain organoid research, this protocol presents a step-by-step guide encompassing key procedures such as organoid dissociation, single-cell or nuclei isolation, library preparation and sequencing. By implementing these alternative approaches, researchers can obtain high-quality datasets, enabling the identification of neuronal and non-neuronal cell types, gene expression profiles, and cell lineage trajectories. This facilitates comprehensive investigations into cellular processes and molecular mechanisms shaping brain development.
    MeSH term(s) Humans ; Transcriptome ; Brain ; Organoids ; Gene Expression Profiling ; Cell Nucleus
    Language English
    Publishing date 2024-03-29
    Publishing country United States
    Document type Journal Article ; Video-Audio Media
    ZDB-ID 2259946-0
    ISSN 1940-087X ; 1940-087X
    ISSN (online) 1940-087X
    ISSN 1940-087X
    DOI 10.3791/66225
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Optocoder: computational decoding of spatially indexed bead arrays.

    Senel, Enes / Rajewsky, Nikolaus / Karaiskos, Nikos

    NAR genomics and bioinformatics

    2022  Volume 4, Issue 2, Page(s) lqac042

    Abstract: ... as a stand-alone Python package on GitHub: https://github.com/rajewsky-lab/optocoder. ...

    Abstract Advancing technologies that quantify gene expression in space are transforming contemporary biology research. A class of spatial transcriptomics methods uses barcoded bead arrays that are optically decoded via microscopy and are later matched to sequenced data from the respective libraries. To obtain a detailed representation of the tissue in space, robust and efficient computational pipelines are required to process microscopy images and accurately basecall the bead barcodes. Optocoder is a computational framework that processes microscopy images to decode bead barcodes in space. It efficiently aligns images, detects beads, and corrects for confounding factors of the fluorescence signal, such as crosstalk and phasing. Furthermore, Optocoder employs supervised machine learning to strongly increase the number of matches between optically decoded and sequenced barcodes. We benchmark Optocoder using data from an in-house spatial transcriptomics platform, as well as from Slide-Seq(V2), and we show that it efficiently processes all datasets without modification. Optocoder is publicly available, open-source and provided as a stand-alone Python package on GitHub: https://github.com/rajewsky-lab/optocoder.
    Language English
    Publishing date 2022-06-07
    Publishing country England
    Document type Journal Article
    ISSN 2631-9268
    ISSN (online) 2631-9268
    DOI 10.1093/nargab/lqac042
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Book ; Online ; Thesis: Modelling and Quantification of scRNA-seq Experiments and the Transcriptome Dynamics of the Cell Cycle

    Falcke, Martin [Gutachter] / Rajewsky, Nikolaus [Gutachter] / Klipp, Edda [Gutachter]

    2022  

    Author's details Gutachter: Martin Falcke, Nikolaus Rajewsky, Edda Klipp
    Keywords Naturwissenschaften ; Science
    Subject code sg500
    Language English
    Publisher Humboldt-Universität zu Berlin
    Publishing place Berlin
    Document type Book ; Online ; Thesis
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    Full text online

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  9. Article ; Online: Roles of Long Noncoding RNAs and Circular RNAs in Translation.

    Chekulaeva, Marina / Rajewsky, Nikolaus

    Cold Spring Harbor perspectives in biology

    2019  Volume 11, Issue 6

    Abstract: Most of the eukaryotic genome is pervasively transcribed, yielding hundreds to thousands of long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), some of which are well conserved during evolution. Functions have been described for a few lncRNAs and ...

    Abstract Most of the eukaryotic genome is pervasively transcribed, yielding hundreds to thousands of long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), some of which are well conserved during evolution. Functions have been described for a few lncRNAs and circRNAs but remain elusive for most. Both classes of RNAs play regulatory roles in translation by interacting with messenger RNAs (mRNAs), microRNAs (miRNAs), or mRNA-binding proteins (RBPs), thereby modulating translation in
    MeSH term(s) Humans ; Open Reading Frames ; Protein Biosynthesis/physiology ; RNA, Circular/metabolism ; RNA, Circular/physiology ; RNA, Long Noncoding/metabolism ; RNA, Long Noncoding/physiology ; RNA-Binding Proteins/metabolism
    Chemical Substances RNA, Circular ; RNA, Long Noncoding ; RNA-Binding Proteins
    Language English
    Publishing date 2019-06-03
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 1943-0264
    ISSN (online) 1943-0264
    DOI 10.1101/cshperspect.a032680
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Spacemake: processing and analysis of large-scale spatial transcriptomics data.

    Sztanka-Toth, Tamas Ryszard / Jens, Marvin / Karaiskos, Nikos / Rajewsky, Nikolaus

    GigaScience

    2022  Volume 11

    Abstract: Background: Spatial sequencing methods increasingly gain popularity within RNA biology studies. State-of-the-art techniques quantify messenger RNA expression levels from tissue sections and at the same time register information about the original ... ...

    Abstract Background: Spatial sequencing methods increasingly gain popularity within RNA biology studies. State-of-the-art techniques quantify messenger RNA expression levels from tissue sections and at the same time register information about the original locations of the molecules in the tissue. The resulting data sets are processed and analyzed by accompanying software that, however, is incompatible across inputs from different technologies.
    Findings: Here, we present spacemake, a modular, robust, and scalable spatial transcriptomics pipeline built in Snakemake and Python. Spacemake is designed to handle all major spatial transcriptomics data sets and can be readily configured for other technologies. It can process and analyze several samples in parallel, even if they stem from different experimental methods. Spacemake's unified framework enables reproducible data processing from raw sequencing data to automatically generated downstream analysis reports. Spacemake is built with a modular design and offers additional functionality such as sample merging, saturation analysis, and analysis of long reads as separate modules. Moreover, spacemake employs novoSpaRc to integrate spatial and single-cell transcriptomics data, resulting in increased gene counts for the spatial data set. Spacemake is open source and extendable, and it can be seamlessly integrated with existing computational workflows.
    MeSH term(s) Computational Biology/methods ; RNA, Messenger ; Software ; Transcriptome ; Workflow
    Chemical Substances RNA, Messenger
    Language English
    Publishing date 2022-07-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2708999-X
    ISSN 2047-217X ; 2047-217X
    ISSN (online) 2047-217X
    ISSN 2047-217X
    DOI 10.1093/gigascience/giac064
    Database MEDical Literature Analysis and Retrieval System OnLINE

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