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Methods & Resources

  • Genetic ablation of <em>Immt</em> induces a lethal disruption of the MICOS complex
    Open Access
    Genetic ablation of Immt induces a lethal disruption of the MICOS complex

    Stephanie M Rockfield, Meghan E Turnis, Ricardo Rodriguez-Enriquez, Madhavi Bathina, Seng Kah Ng, Nathan Kurtz, Nathalie Becerra Mora, Stephane Pelletier, Camenzind G Robinson, Peter Vogel, Joseph T Opferman

    Stephanie M Rockfield ... Joseph T Opferman

    Published 11 March 2024

    A new conditional mouse model deleting Immt/MIC60 reveals the necessity of this protein in vivo and provides an important resource for future research into the mitochondrial MICOS complex.

  • Ageing-dependent thiol oxidation reveals early oxidation of proteins with core proteostasis functions
    Open Access
    Ageing-dependent thiol oxidation reveals early oxidation of proteins with core proteostasis functions

    Katarzyna Jonak, Ida Suppanz, Julian Bender, Agnieszka Chacinska, Bettina Warscheid, Ulrike Topf

    Katarzyna Jonak ... Ulrike Topf

    Published 21 February 2024

    Proteome-wide analysis of thiol oxidation during chronological ageing of yeast reveals evolutionarily conserved proteins as early-oxidation targets with a potential impact on proteostasis regulation.

  • Extreme trait GWAS (Et-GWAS): Unraveling rare variants in the 3,000 rice genome
    Open Access
    Extreme trait GWAS (Et-GWAS): Unraveling rare variants in the 3,000 rice genome

    Niranjani Gnanapragasam, Vinukonda Vishnu Prasanth, Krishna Tesman Sundaram, Ajay Kumar, Bandana Pahi, Anoop Gurjar, Challa Venkateshwarlu, Sanjay Kalia, Arvind Kumar, Shalabh Dixit, Ajay Kohli, Uma Maheshwer Singh, Vikas Kumar Singh, Pallavi Sinha

    Niranjani Gnanapragasam ... Pallavi Sinha

    Published 26 December 2023

    Using extreme bulk pooling and allele frequency assessment, the graphical user interface (GUI)-enabled association technique successfully revealed relationships between genetic variations and grain yield under drought stress condition.

  • RedRibbon: A new rank–rank hypergeometric overlap for gene and transcript expression signatures
    Open Access
    RedRibbon: A new rank–rank hypergeometric overlap for gene and transcript expression signatures

    Anthony Piron, Florian Szymczak, Theodora Papadopoulou, Maria Inês Alvelos, Matthieu Defrance, Tom Lenaerts, Décio L Eizirik, Miriam Cnop

    Anthony Piron ... Miriam Cnop

    Published 8 December 2023

    RedRibbon is a comparative analysis tool of differential omics analyses to reveal overlapping features between two differential studies, with high performance, accuracy, and simplicity in use.

  • Mitochondrial phosphoproteomes are functionally specialized across tissues
    Open Access
    Mitochondrial phosphoproteomes are functionally specialized across tissues

    Fynn M Hansen, Laura S Kremer, Ozge Karayel, Isabell Bludau, Nils-Göran Larsson, Inge Kühl, Matthias Mann

    Fynn M Hansen ... Matthias Mann

    Published 20 November 2023

    This study explores tissue-specific mitochondrial proteomes and phosphoproteomes in unprecedented depth, offering valuable insights into mitochondrial organization and specialization.

  • CRISPR/Cas9 bioluminescence-based assay for monitoring CFTR trafficking to the plasma membrane
    Open Access
    CRISPR/Cas9 bioluminescence-based assay for monitoring CFTR trafficking to the plasma membrane

    Martin Ondra, Lukas Lenart, Amanda Centorame, Daciana C Dumut, Alexander He, Syeda Sadaf Zehra Zaidi, John W Hanrahan, Juan Bautista De Sanctis, Danuta Radzioch, Marian Hajduch

    Martin Ondra ... Marian Hajduch

    Published 2 November 2023

    A novel CRISPR/Cas9-based bioluminescence system to assess total and live-cell plasma membrane WT-CFTR levels offers a versatile platform for new screening systems in CFTR modulator discovery.

  • Automated staging of zebrafish embryos with deep learning
    Open Access
    Automated staging of zebrafish embryos with deep learning

    Rebecca A Jones, Matthew J Renshaw, David J Barry

    Rebecca A Jones ... David J Barry

    Published 26 October 2023

    Introducing KimmelNet: A deep learning model that accurately stages populations of zebrafish embryos from 2D brightfield images, offering a rapid and objective alternative to manual observations.

  • MICA: a multi-omics method to predict gene regulatory networks in early human embryos
    Open Access
    MICA: a multi-omics method to predict gene regulatory networks in early human embryos

    Gregorio Alanis-Lobato, Thomas E Bartlett, Qiulin Huang, Claire S Simon, Afshan McCarthy, Kay Elder, Phil Snell, Leila Christie, Kathy K Niakan

    Gregorio Alanis-Lobato ... Kathy K Niakan

    Published 25 October 2023

    Our comparative analysis of gene regulatory network predictions defines a pipeline to infer transcription factor–target gene regulatory interactions in early human embryos. Mutual information refined by chromatin accessibility allowed us to construct the first network during early human development.

  • Assessing MAPPs assay as a tool to predict the immunogenicity potential of protein therapeutics
    Open Access
    Assessing MAPPs assay as a tool to predict the immunogenicity potential of protein therapeutics

    Andrea Di Ianni, Tiziana Fraone, Piercesare Balestra, Kyra Cowan, Federico Riccardi Sirtori, Luca Barbero

    Andrea Di Ianni ... Luca Barbero

    Published 13 October 2023

    This work highlights the use of streptavidin magnetic beads as a valuable approach for the immunoaffinity purification of mass spectrometry MHCII-eluted ligands (MAPPs) and their practical application in assessing the drug-induced immunogenicity risk of novel biotherapeutics.

  • Cost-effective DNA methylation profiling by FML-seq
    Open Access
    Cost-effective DNA methylation profiling by FML-seq

    Joseph W Foley, Shirley X Zhu, Robert B West

    Joseph W Foley ... Robert B West

    Published 29 September 2023

    A low-cost, high-throughput method for genome-wide DNA methylation profiling based on methylation-specific restriction digestion and sequencing.

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