Gene regulatory networks
Links:
- Software: https://git.embl.de/grp-zaugg/GRaNIE
- Software: https://git.embl.de/grp-zaugg/GRaNPA
- Resources and description
- Publication: GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks applied to study macrophages (Molecular Systems Biology 2023)
DeePiCt: supervised models for segmentation of cryo-electron tomograms
Links:
- Software: https://github.com/ZauggGroup/DeePiCt
- Publication: Convolutional networks for supervised mining of molecular patterns within cellular context (Nature Methods 2023)
Transcription factor cooperative binding
Links:
- Resources and description
- Publication: Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions (Nature Communications 2020)
Predictive features of gene expression variation
Links:
- Resources and description
- Publication: Predictive features of gene expression variation reveal mechanistic link with differential expression (Mol. Sys. Biol. 2020)
Quantification of differential transcription factor activity
Links:
- Software: https://git.embl.de/grp-zaugg/diffTF
- Resources and description
- Publication: Quantification of differential transcription factor activity and multiomic-based classification into activators and repressors: diffTF (Cell Reports 2019)
CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals
Links:
- Resources and description
- Publication: CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals (Cell Systems 2017)