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Methods & Resources

  • Subgenomic RNA profiling suggests novel mechanism in coronavirus gene regulation and host adaption
    Open Access
    Subgenomic RNA profiling suggests novel mechanism in coronavirus gene regulation and host adaption

    Lin Lyu, Ru Feng, Mingnan Zhang, Xiaoqing Xie, Yinjing Liao, Yanjiao Zhou, Xiaokui Guo, Bing Su, Yair Dorsett, Lei Chen

    Lin Lyu ... Lei Chen

    Published 25 April 2022

    CORONATATOR, developed to analyze the subgenomic RNA of coronavirus, was applied on large number of sequencing data sets from coronaviruses, and shed light on viral gene regulation.

  • LuminoCell: a versatile and affordable platform for real-time monitoring of luciferase-based reporters
    Open Access
    LuminoCell: a versatile and affordable platform for real-time monitoring of luciferase-based reporters

    Kamila Weissová, Bohumil Fafílek, Tomasz Radaszkiewicz, Canan Celiker, Petra Macháčková, Tamara Čechová, Jana Šebestíková, Aleš Hampl, Vítězslav Bryja, Pavel Krejčí, Tomáš Bárta

    Kamila Weissová ... Tomáš Bárta

    Published 19 April 2022

    Description of affordable ($40) open-source platform for real-time in-cell monitoring of luciferase activity.

  • Evaluation of the correctable decoding sequencing as a new powerful strategy for DNA sequencing
    Open Access
    Evaluation of the correctable decoding sequencing as a new powerful strategy for DNA sequencing

    Chu Cheng, Pengfeng Xiao

    Chu Cheng ... Pengfeng Xiao

    Published 14 April 2022

    This article proposed the correctable decoding sequencing technology with conservative theoretical error rate of 0.0009%, and evaluated its robustness by simulation. This technology can provide a powerful new protocol for NGS platforms, enabling accurate identification of rare mutations in medicine.

  • Tracking connectivity maps in human stem cell–derived neuronal networks by holographic optogenetics
    Open Access
    Tracking connectivity maps in human stem cell–derived neuronal networks by holographic optogenetics

    Felix Schmieder, Rouhollah Habibey, Johannes Striebel, Lars Büttner, Jürgen Czarske, Volker Busskamp

    Felix Schmieder ... Volker Busskamp

    Published 13 April 2022

    Holographic optogenetic stimulation of human iPSC–derived neuronal networks was exploited to map precise functional connectivity motifs and their long-term dynamics during network development.

  • Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH
    Open Access
    Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH

    Elena Rensen, Stefano Pietropaoli, Florian Mueller, Christian Weber, Sylvie Souquere, Sina Sommer, Pierre Isnard, Marion Rabant, Jean-Baptiste Gibier, Fabiola Terzi, Etienne Simon-Loriere, Marie-Anne Rameix-Welti, Gérard Pierron, Giovanna Barba-Spaeth, Christophe Zimmer

    Elena Rensen ... Christophe Zimmer

    Published 7 January 2022

    We design an RNA-FISH method to target the plus and minus strands of SARS-CoV-2 RNA, and apply it to image the virus in cell lines, lung tissue, and nasal swabs, by fluorescence and electron microscopy.

  • SnRNA sequencing defines signaling by RBC-derived extracellular vesicles in the murine heart
    Open Access
    SnRNA sequencing defines signaling by RBC-derived extracellular vesicles in the murine heart

    Nedyalka Valkov, Avash Das, Nathan R Tucker, Guoping Li, Ane M Salvador, Mark D Chaffin, Getulio Pereira De Oliveira Junior, Ivan Kur, Priyanka Gokulnath, Olivia Ziegler, Ashish Yeri, Shulin Lu, Aushee Khamesra, Chunyang Xiao, Rodosthenis Rodosthenous, Srimeenakshi Srinivasan, Vasilis Toxavidis, John Tigges, Louise C Laurent, Stefan Momma, Robert Kitchen, Patrick Ellinor, Ionita Ghiran, Saumya Das

    Nedyalka Valkov ... Saumya Das

    Published 18 October 2021

    In a unique model of fluorescent based mapping of EV recipient cells, RBC-EVs were found to signal to cardiac cells and regulate gene expression in a model of ischemic heart failure.

  • An extended DNA-free intranuclear compartment organizes centrosome microtubules in malaria parasites
    Open Access
    An extended DNA-free intranuclear compartment organizes centrosome microtubules in malaria parasites

    Caroline S Simon, Charlotta Funaya, Johanna Bauer, Yannik Voβ, Marta Machado, Alexander Penning, Darius Klaschka, Marek Cyrklaff, Juyeop Kim, Markus Ganter, Julien Guizetti

    Caroline S Simon ... Julien Guizetti

    Published 17 September 2021

    Malaria arises during the proliferation of Plasmodium spp. in human blood, whereas the underlying atypical cell division mechanisms remain poorly understood. This study uses advanced imaging to dissect dynamics and organization of the centrosome, a key division regulator.

  • Statistical guidelines for quality control of next-generation sequencing techniques
    Open Access
    Statistical guidelines for quality control of next-generation sequencing techniques

    Maximilian Sprang, Matteo Krüger, Miguel A Andrade-Navarro, Jean-Fred Fontaine

    Maximilian Sprang ... Jean-Fred Fontaine

    Published 30 August 2021

    Condition-specific statistical guidelines and accurate classification trees for quality control of functional genomics NGS files (RNA-seq, ChIP-seq and DNase-seq) have been generated using thousands of reference files from the ENCODE project and made available to the community.

  • Dissection-independent production of <em>Plasmodium</em> sporozoites from whole mosquitoes
    Open Access
    Dissection-independent production of Plasmodium sporozoites from whole mosquitoes

    Joshua Blight, Katarzyna A Sala, Erwan Atcheson, Holger Kramer, Aadil El-Turabi, Eliana Real, Farah A Dahalan, Paulo Bettencourt, Emma Dickinson-Craig, Eduardo Alves, Ahmed M Salman, Chris J Janse, Frances M Ashcroft, Adrian VS Hill, Arturo Reyes-Sandoval, Andrew M Blagborough, Jake Baum

    Joshua Blight ... Jake Baum

    Published 16 June 2021

    Overcoming limitations of traditional dissection-dependent methods for malarial sporozoite isolation from mosquitoes, a new dissection-free method is presented that yields pure, infective sporozoites.

  • CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data
    Open Access
    CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data

    Almut Lütge, Joanna Zyprych-Walczak, Urszula Brykczynska Kunzmann, Helena L Crowell, Daniela Calini, Dheeraj Malhotra, Charlotte Soneson, Mark D Robinson

    Almut Lütge ... Mark D Robinson

    Published 23 March 2021

    A systematic comparison of batch effect metrics for single cell data is performed. The new cell-specific mixing score from the R/Bioconductor CellMixS package performs well across various tasks.

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