Methods & Resources
- Reverse-engineering the anti-MUC1 antibody 139H2 by mass spectrometry–based de novo sequencing
A widely used anti-MUC1 antibody (139H2) is sequenced by mass spectrometry, revealing the molecular basis of its glycosylation-independent binding to this tumor-associated antigen.
- Genetic ablation of Immt induces a lethal disruption of the MICOS complex
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
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
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
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
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
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
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
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
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.