Daniyal J. Jafree

TERRA is a foundation model for spatial transcriptomics that predicts tissue behavior under perturbation and identifies multi-scale biological insights across tissues.

This study constructs a cross-model spatial and single-cell atlas of PKD, identifying Spp1 (osteopontin) as a conserved driver of disease progression through its signaling to Ly6clo monocytes.

Human Developmental Cell Atlas integrates ~4.6 million cells/nuclei from 4-22 post-conception weeks into 454 refined cell types and maps 114 spatial niches across 6PCW whole-embryo sections.

Tripso, a self-supervised transformer model, identifies gene program-specific embeddings and discovers novel gene programs, revealing biological insights in hematopoietic development and disease.

PerturbGen predicts how genetic perturbations affect cellular trajectories across time in human datasets, showing effects on immune responses, hematopoiesis, and skin development.

The paper develops multi-regional gastric assembloids from patient-derived organoids to model parietal cell maturation and antral foveolar hyperplasia in genetic disorders.

The paper develops an in silico framework to model human kidney haemodynamics using HiP-CT data, showing vascular geometry and resistance scaling influence kidney function.

The paper develops a nanobody-based method to label kidney lymphatic vessels in mice, revealing spatially restricted LYVE1 expression unique to the kidney.

This study identifies two progenitor sources for kidney lymphatics in mice: Tie2 endothelial lineage and Osr1 intermediate mesoderm, showing a dual origin for kidney lymphatic formation.

MintFlow is a generative AI algorithm that predicts how tissue perturbations reprogram cell states in disease, revealing novel cell populations and therapeutic targets in three human conditions.

The paper identifies a unique pericystic endothelium in ADPKD that contributes to microvascular remodelling and impaired perfusion, suggesting vascular targets for early intervention.

This study examines the phenotypic effects of SNX14 loss-of-function mutations in mice and zebrafish, revealing species-specific consequences despite conserved biochemical roles.