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Methods & Resources

  • 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.

  • Harnessing reaction-based probes to preferentially target pancreatic β-cells and β-like cells
    Open Access
    Harnessing reaction-based probes to preferentially target pancreatic β-cells and β-like cells

    Sevim Kahraman, Debasish Manna, Ercument Dirice, Basudeb Maji, Jonnell Small, Bridget K Wagner, Amit Choudhary, Rohit N Kulkarni

    Sevim Kahraman ... Rohit N Kulkarni

    Published 29 January 2021

    The study uses a reaction probe to target insulin-expressing pancreatic β-cells and β-like cells derived from pluripotent stem cells by harnessing high intracellular Zn(II) concentration.

  • A FIJI macro for quantifying pattern in extracellular matrix
    Open Access
    A FIJI macro for quantifying pattern in extracellular matrix

    Esther Wershof, Danielle Park, David J Barry, Robert P Jenkins, Antonio Rullan, Anna Wilkins, Karin Schlegelmilch, Ioannis Roxanis, Kurt I Anderson, Paul A Bates, Erik Sahai

    Esther Wershof ... Erik Sahai

    Published 27 January 2021

    This work provides a quantitative tool for the analysis of fibrillar patterns in biology. We demonstrates its utility on in vitro generated extracellular matrices, mouse tissues, and patient samples. The tool is already publicly available to the research community.

  • FIREWORKS: a bottom-up approach to integrative coessentiality network analysis
    Open Access
    FIREWORKS: a bottom-up approach to integrative coessentiality network analysis

    David R Amici, Jasen M Jackson, Mihai I Truica, Roger S Smith, Sarki A Abdulkadir, Marc L Mendillo

    David R Amici ... Marc L Mendillo

    Published 16 December 2020

    A tool to create bias-adjusted coessentiality networks reveals functional relationships between genes, context-specific rewiring of genetic networks, determinants of essentiality, and therapeutic targets for challenging proteins.

  • ESI mutagenesis: a one-step method for introducing mutations into bacterial artificial chromosomes
    Open Access
    ESI mutagenesis: a one-step method for introducing mutations into bacterial artificial chromosomes

    Arnaud Rondelet, Andrei Pozniakovsky, Devika Namboodiri, Richard Cardoso da Silva, Divya Singh, Marit Leuschner, Ina Poser, Andrea Ssykor, Julian Berlitz, Nadine Schmidt, Lea Röhder, Gerben Vader, Anthony A Hyman, Alexander W Bird

    Arnaud Rondelet ... Alexander W Bird

    Published 8 December 2020

    A simple and efficient recombineering-based method for introducing point mutations into bacterial artificial chromosomes using an artificial intron cassette.

  • Predicting gene regulatory networks from cell atlases
    Open Access
    Predicting gene regulatory networks from cell atlases

    Andreas Fønss Møller, Kedar Nath Natarajan

    Andreas Fønss Møller ... Kedar Nath Natarajan

    Published 21 September 2020

    Integrated single-cell gene regulatory network from three mouse cell atlases captures global and cell type–specific regulatory modules and crosstalk, important for cellular identity.

  • Profiles of histidine-rich glycoprotein associate with age and risk of all-cause mortality
    Open Access
    Profiles of histidine-rich glycoprotein associate with age and risk of all-cause mortality

    Mun-Gwan Hong, Tea Dodig-Crnković, Xu Chen, Kimi Drobin, Woojoo Lee, Yunzhang Wang, Fredrik Edfors, David Kotol, Cecilia Engel Thomas, Ronald Sjöberg, Jacob Odeberg, Anders Hamsten, Angela Silveira, Per Hall, Peter Nilsson, Yudi Pawitan, Mathias Uhlén, Nancy L Pedersen, Sara Hägg, Patrik KE Magnusson, Jochen M Schwenk

    Mun-Gwan Hong ... Jochen M Schwenk

    Published 31 July 2020

    Affinity-based proteomics assays identify particular profiles of the circulating histidine-rich glycoprotein to increase with age and elevated levels to indicate a higher risk of all-cause mortality.

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