David J. Adams

The Human Gut Cell Atlas v1.0: A Unified, Community-Built Reference of Cellular Diversity Across the Gut

The paper presents the Human Gut Cell Atlas v1.0, a unified reference of gut cell diversity, revealing how tissue structure influences cellular composition and enabling disease and organoid analysis.

Function-driven geometry directs human pilosebaceous unit development

The paper builds a spatiotemporal map of human pilosebaceous unit development using single-cell multiomics and machine learning, showing how epithelial-mesenchymal interactions drive organogenesis and how sebaceous gland programs are disrupted in tumors.

A Step-wise, Deterministic and Fatal Mouse Model of Myeloid Neoplasm with Spontaneous Acquisition of Patient-relevant RTK-RAS Mutations

This study creates a mouse model of myeloid neoplasm with spontaneous RTK-RAS mutations, showing a premalignant phase and lineage restriction in tumors.

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.

Clinical validation of large-scale functional assays: insights from 2,120 gene-truthset-assay evaluations

The paper evaluates how different truthset strategies affect evidence points (EPs) in clinical validation of functional assays across 2,120 gene-truthset-assay combinations.

'Truthsets' for clinical validation of large-scale functional assays: Practice recommendations from Cancer Variant Interpretation Group UK (CanVIG-UK)

The paper establishes consensus guidelines for constructing truthsets to validate functional assays in cancer variant interpretation, focusing on missense variants and clinical validation frameworks.

Large distant deletion disrupts CDKN2A enhancer and predisposes to melanoma

The paper identifies a large distant deletion in DMRTA1 upstream of CDKN2A that predisposes to melanoma by disrupting regulatory sequences and reducing p16 expression.

In vivo screening reveals new regulators of Natural Killer cell development and functional response to acute cytomegalovirus infection

The paper identifies novel regulators of NK cell development and antiviral function through in vivo screening in mice, with relevance to human health.

A predicted cancer dependency map for paralog pairs

The paper develops a machine learning classifier to predict cell-line-specific synthetic lethality between paralog pairs and validates its predictions using independent CRISPR screens.

The mouse pangenome reveals the structural complexity of the murine protein coding landscape

The paper presents a mouse pangenome with 17 strains, resolving structural complexity and improving RNA-Seq analysis by identifying non-reference genes and VNTR polymorphisms.

The Onychomys pangenome reveals the unique molecular adaptations that confer toxin resistance

This study identifies molecular adaptations in Onychomys species that confer toxin resistance through genome analysis and positive selection detection.

Comprehensively Testing the Function of Missense Variation in the STK11 Tumour Suppressor

This study functionally tests STK11 missense variants in mammalian cells, identifying pathogenic variants and providing insights for clinical interpretation.

Simulating CD8 T Cell Exhaustion: A Comprehensive Approach

The paper develops an in vitro model of CD8 T cell exhaustion and identifies a gene signature that defines the exhausted state in both in vitro and in vivo settings, with validation in human tumor samples.

Validating data from Multiplex Assays of Variant Effect (MAVEs): A CanVIG-UK National Survey of NHS Clinical Scientists

The paper surveys NHS clinical scientists on their acceptance of MAVE data validation, finding that trusted central bodies are needed for clinical adoption.

Activation of Wnt/β-catenin signalling by mutually exclusive FBXW11 and CTNNB1 hotspot mutations drives salivary gland basal cell adenoma

Exome and transcriptome sequencing of salivary basal cell adenomas reveals a recurrent FBXW11 p.F517S mutation, exclusive with CTNNB1 p.I35T, together accounting for 94% of cases.

The microenvironment of ulcerated acral melanoma is characterised by an inflammatory milieu and an enhanced humoral immune response

This study identifies immunological differences in ulcerated acral melanoma, showing increased humoral immunity and inflammation markers, and proposes potential therapeutic targets.

Genomics-informed Neuropsychiatric Care for Neurodevelopmental Disorders: Results from A Multidisciplinary Clinic

This study evaluates a genomics-informed multidisciplinary clinic for neurodevelopmental disorders, finding that genetic diagnoses lead to significant clinical management changes in most patients.

The structural diversity of telomeres and centromeres across mouse subspecies revealed by complete assemblies

The paper presents T2T mouse genomes for C57BL/6J and CAST/EiJ, revealing structural diversity in telomeres, centromeres, and key loci like PAR and KZFPs.

Impact of Essential Genes on the Success of Genome Editing Experiments Generating 3,313 New Genetically Engineered Mouse Lines

The paper analyzes 3,313 genetically engineered mouse lines to identify gene essentiality as the main factor affecting Cas9-based genome editing success.

Ancestry and somatic profile predict acral melanoma origin and prognosis

This study analyzes acral melanoma genomes and transcriptomes from Mexican patients, finding ancestry-related mutation patterns and survival differences.

IFI207, a young and fast-evolving protein, controls retroviral replication via the STING pathway

The paper identifies IFI207 as a rapidly evolving protein that controls retroviral replication through the STING pathway, highlighting its role in host-pathogen co-evolution.

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

The paper develops methods to model transcription factor binding in modified DNA by expanding the DNA alphabet and adapting existing tools to handle custom alphabets, identifying modification-sensitive motifs and validating them with experimental data.

Saturation genome editing of DDX3X clarifies pathogenicity of germline and somatic variation

The paper uses saturation genome editing to assess DDX3X variants' functional impact, identifies pathogenic variants for neurodevelopmental disorders, and develops a classifier outperforming existing tools.

A Weights-based variant ranking pipeline for familial complex disorders

The paper introduces WARP, a variant ranking pipeline for familial complex disorders, which identifies potential disease-predisposing genes in pedigrees by combining multiple weighted factors.

Towards a Clinically-based Common Coordinate Framework for the Human Gut Cell Atlas - The Gut Models

The paper introduces a 1D coordinate model for the human gut to enable spatial integration and analysis of single-cell data across different anatomical representations.

Population-based analysis of POT1 variants in a cutaneous melanoma case-control cohort

The paper analyzes POT1 variants in a melanoma case-control cohort, finding that pathogenic variants are a minor contributor to melanoma risk but should be screened in high-risk individuals.

Robust genetic analysis of the X-linked anophthalmic (Ie) mouse

This study identifies a critical genomic region on the X chromosome linked to anophthalmia in mice but finds no clear causative mutation, suggesting regulatory changes may underlie the phenotype.

Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

SigProfilerExtractor is a tool for de novo mutational signature extraction that outperforms existing methods and identifies four novel signatures, including one linked to tobacco smoking.

Collateral damage: Identification and characterisation of spontaneous mutations causing deafness from a targeted knockout programme

The paper identifies and characterizes spontaneous mutations causing deafness in mice from a targeted knockout program, showing these mutations are a common side effect of intensive breeding.

Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for Saturation Genome Editing and other Deep Mutational Scanning experiments