Proteome-wide model for human disease genetics
Statistics and reproducibility This study is based on analysis of large-scale sequencing and variant annotation datasets (UniRef58, UKBB17,…
Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes
Iyer, L. M., Abhiman, S. & Aravind, L. Natural History of Eukaryotic DNA Methylation Systems, Vol. 101 (Elsevier,…
Genome-wide association analyses identify distinct genetic architectures for early-onset and late-onset depression
Study population To conduct a large GWAS of AAO-based MDD subtypes with consistent phenotypes, we identified nine cohorts…
Epigenetically driven and early immune evasion in colorectal cancer evolution
Sample collection and sequencing Our FF–WGS samples were comprised of processed data from previous sequencing experiments of our…
Cell-type- and locus-specific epigenetic editing of memory expression
All animals and procedures used in this study were approved by the Veterinary Office of the Federal Council…
Pathogenic UNC13A variants cause a neurodevelopmental syndrome by impairing synaptic function
Institute of Medical Genetics, University of Zurich, Zurich, Switzerland Reza Asadollahi, Paranchai Boonsawat, Dennis Kraemer & Anita Rauch Faculty of Engineering and…
Modeling heterogeneity in single-cell perturbation states enhances detection of response eQTLs
Cohorts We used published data (GEO accession no. GSE162632) to study the effect of 12 h of ex vivo…
Redefining cellular reprogramming with advanced genomic technologies
Briggs, R. & King, T. J. Transplantation of living nuclei from blastula cells into enucleated Frogs’ eggs. Proc.…
Characterization of induced cohesin loop extrusion trajectories in living cells
Experiments performed in this study did not require ethics board approval. Cell culture HAP1 cells were cultured in…
Population-scale gene-based analysis of whole-genome sequencing provides insights into metabolic health
Ethics Our research complies with all relevant ethical regulations. All studies included in this research were approved by…
Nucleotide dependency analysis of genomic language models detects functional elements
SpeciesLM training For SpeciesLM metazoa, we obtained metazoan genomes comprising 494 different species from the Ensembl 110 database36.…
Spatial signatures for predicting immunotherapy outcomes using multi-omics in non-small cell lung cancer
Study population We studied three independent cohorts of patients with NSCLC who were treated with PD-1-based immunotherapies in…