Daniel B. Graham

A structure-informed deep learning framework for modeling TCR-peptide-HLA interactions

StriMap models TCR-peptide-HLA interactions using structural and sequence features, achieving state-of-the-art performance and identifying disease-associated peptides in ankylosing spondylitis.

Microbial-associated acylated putrescines as immunomodulatory molecules in inflammatory bowel diseases

The paper identifies N-acyl putrescines, particularly NOP, as immunomodulatory metabolites produced by gut microbiota that suppress inflammation in IBD models.

Peptide-HLA II interaction prediction for post-translationally modified peptides

The paper develops a deep learning model to predict peptide-HLA II interactions for post-translationally modified peptides, showing accurate predictions on unseen modifications.

Protein Language Models Uncover Carbohydrate-Active Enzyme Function in Metagenomic

CAZyLingua uses protein language models to annotate carbohydrate-active enzymes in metagenomic data, outperforming traditional methods and revealing new annotations in disease-related datasets.

Population-scale multiome immune cell atlas reveals complex disease drivers

The paper uses population-scale single-nucleus ATAC-seq and RNA-seq to identify regulatory variants and their disease associations in immune cells.

Prevalent cross-cell type QTL trans-regulatory genetic effects impacting innate lymphoid cells in the small intestine

The paper identifies genetic variants affecting innate lymphoid cells in the gut using single-cell RNA-seq and validates their regulatory roles across cell types.

Sensitive Transcriptomics and Genotyping reveals function of genetic variants in immunity

This study introduces STAG-seq, a method combining transcriptomics and genotyping to functionally analyze genetic variants in immune cells, revealing their impact on gene expression and disease mechanisms.

The Ulcerative Colitis-Associated Gene NXPE1 Catalyzes Glycan Modifications on Colonic Mucin

The paper identifies NXPE1 as an acetyltransferase that modifies mucin glycans in colonic mucus, showing its role in modulating the mucus barrier against commensal microbes in ulcerative colitis.

Sequencing of over 100,000 individuals identifies multiple genes and rare variants associated with Crohns disease susceptibility

The paper identifies ten new genes with coding variants linked to Crohn's disease risk using sequencing data from over 30,000 patients and 80,000 controls.

The schizophrenia-associated variant in SLC39A8 alters N-glycosylation in the mouse brain

This study shows that the schizophrenia-associated SLC39A8 variant A391T alters N-glycosylation in the mouse brain, affecting glycoproteins involved in schizophrenia-related pathways.

The enteric nervous system of the human and mouse colon at a single-cell resolution

The paper profiles the enteric nervous system of human and mouse colon at single-cell resolution, revealing diverse neuron subsets and shared transcriptional programs between species.

Rewiring of the cellular and inter-cellular landscape of the human colon during ulcerative colitis

The paper was withdrawn due to the inclusion of confidential information about a third party.

T helper cells modulate intestinal stem cell renewal and differentiation

This study shows that T helper cells interact with intestinal stem cells via MHCII to regulate their renewal and differentiation, with distinct effects based on Th subtype and cytokine signaling.