cross-species

Code for "Whole brain alignment of spatial transcriptomics between humans and mice with BrainAlign"

Cell-type Assignment and Module Extraction based on a heterogeneous graph neural network.

This is the lesson repository for the Workshop on Computational Techniques and Resources for Effective Translational Research in Alzheimer's Disease.

Reproducible R workflow for background-aware, multi-context functional enrichment of non-model and reference-based transcriptomic datasets, integrating GOseq, g:Profiler, RRvGO, consensus scoring, and GO-term networks.

This project is a part of BRAIN Initiative Cell Census Network (2017-2022)

Adaptive elastic-net sparse PCA for robust cross-species, cross-platform analysis of complex gene expression data in Alzheimer’s disease

Cross-species integration of single cell RNA-seq data from the primary motor cortex between human, mouse and drosophila using expiMap and SATURN

Independence-guarded meta-analysis of rodent-to-human directional chemical-gene effects in the Comparative Toxicogenomics Database (CTD).

Study-aware reconstruction and cross-species benchmarking of mammalian mRNA half-life PC1 labels

Static, client-side Fusarium gene analysis tool: ortholog mapping, PPI networks, phylogenetic trees, and GO/KEGG enrichment across 20 species — no backend required.

Reproducible cross-species benchmark of Geneformer, scGPT and UCE single-cell embeddings against PCA and scVI in developmental D. discoideum and C. elegans atlases.

Philip Ahmadzada, Perry Moerland: Comparative single-cell analysis of macrophages and macrophage subtypes in atherosclerotic mice and humans

Re-analysis of the Crinier et al. 2018 (Immunity) human & mouse NK-cell scRNA-seq datasets

A gene regulation model reveals an ancestral adaptation response to particulate exposure triggered by nanomaterials

Scan genomes for internally repeated sequences, elements which are repetitive in another species, or high-identity HGT candidate regions between species.

Workflow to identify functional cis-regulatory regions for each annotated cell type

Reproducible Python workflow for ortholog-resolved cross-species proteomic analysis of human and mouse dorsal root ganglia (DRG), including differential abundance testing, enrichment analysis, GSEA, and systems-level comparison.

Incorporating Triplet Error for Predicting PPIs using Deep Learning

Static, client-side bioinformatics tool for cross-species gene analysis centered on S. pombe. Integrates ortholog mapping, PPI networks, GO/KEGG enrichment, and phylogenetic trees across 7 model organisms — entirely in-browser, no server required. Built on STRING v12.0, KEGG, and eggNOG v7.