Thomas J. Mitchell

Multi-scale modeling of human tissues from spatial transcriptomics with TERRA

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

A network medicine framework for multi-modal data integration in therapeutic target discovery

This paper presents a network medicine framework integrating multi-modal data to identify therapeutic targets in clear cell renal cell carcinoma, recovering established targets and predicting five candidates, with ENO2 inhibition showing the strongest anti-tumour effect.

VHL synthetic lethality screens uncover CBF-beta as a negative regulator of STING

The paper identifies CBF-beta as a negative regulator of STING through synthetic lethality screens in VHL-null ccRCC cells, showing its role in type I interferon signaling and tumor growth.

Tumor-infiltrating CD27-IgD- regulatory B cells suppress cytotoxic CD8+T cell responses in renal cell carcinoma

The paper identifies CD27-IgD- regulatory B cells in renal cell carcinoma that suppress CD8+T cell responses, linking them to poor prognosis.

Mapping and reprogramming human tissue microenvironments with MintFlow

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.

Angiogenic and Immune Predictors of Neoadjuvant Axitinib Response in Renal Cell Carcinoma with Venous Tumour Thrombus

The paper assesses neoadjuvant axitinib response in RCC with VTT using multiparametric analysis and identifies angiogenic and immune predictors of treatment response.

Recurrent ERBB2 alterations are associated with esophageal adenocarcinoma brain metastases

The paper identifies ERBB2 alterations as a recurrent oncogene in esophageal adenocarcinoma brain metastases and links them to monoclonal seeding and treatment response.

Accurate de novo detection of somatic mutations in high-throughput single-cell profiling data sets

SComatic detects somatic mutations in single-cell RNA-seq and ATAC-seq data without bulk DNA sequencing, achieving higher precision than existing methods.

X-inactivation states of single cell transcriptomes reveal cellular phylogenies in human females

The paper introduces a method to determine X-inactivation states in single-cell transcriptomes and uses it to infer cellular phylogenies in human females.

The mutational landscape of human somatic and germline cells

This study compares mutational landscapes in somatic and germline cells across 29 anatomical structures, identifying key mutational signatures and their contributions to different cell types.

Clonal dynamics of haematopoiesis across the human lifespan

This study tracks clonal dynamics in human haematopoiesis across age, finding that clonal diversity sharply declines after 70, driven by positive selection on many genes and loss of Y chromosome in males.

Multi-regional characterisation of renal cell carcinoma and microenvironment at single cell resolution

A multi-regional single-cell study of kidney tumours reveals clonotypic heterogeneity, immune cell exhaustion, and potential therapeutic targets through transcriptomic and exomic analysis.

Extensive phylogenies of human development reveal variable embryonic patterns

The paper reconstructs phylogenies of human development using whole-genome sequencing to show variable embryonic patterns and lineage asymmetries across individuals and tissues.