M. Thomson

Unexplored regions of the protein sequence-structure map revealed at scale by a library of foldtuned language models

This paper introduces foldtuning, a method to generate novel protein sequences with target structures, bypassing evolutionary barriers and enabling synthetic biology applications.

Identifying perturbations that boost T-cell infiltration into tumours via counterfactual learning of their spatial proteomic profiles

The paper develops a deep-learning model to identify minimal tumour perturbations that enhance T-cell infiltration using spatial proteomic data from cancer samples.

Configurational entropy is an intrinsic driver of tissue structural heterogeneity

The paper uses human mammary organoids to show that configurational entropy drives tissue structural heterogeneity by linking structural parameters to molecular and microenvironmental factors.

A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice

A prebiotic diet reduces motor deficits and microglial activation in α-synuclein overexpressing mice by altering gut microbiota and microglial states.

A universal stress protein acts as a metabolic rheostat controlling carbon flux in mycobacteria

This study identifies a universal stress protein in mycobacteria that regulates carbon flux by acting as a metabolic rheostat, demonstrated through 13C-stable isotope tracing and protein interactions.

Motor processivity and speed determine structure and dynamics of microtubule-motor assemblies

The paper investigates how motor protein properties affect microtubule assembly dynamics and structure, showing that motor speed and processivity determine aster size and contraction rates.

Commensal bacteria promote type I interferon signaling to maintain immune tolerance

This study shows that commensal bacteria promote type I interferon signaling to support immune tolerance by enhancing T regulatory cell function.

Deep parallel characterization of AAV tropism and AAV-mediated transcriptional changes via single-cell RNA sequencing

The paper develops a scRNA-seq pipeline to characterize AAV tropism and transcriptional responses at single-cell resolution, revealing cell-type-specific targeting and gene expression changes.

cis dominantly explains regulatory divergence between two indica rice genotypes; drought further enhances regulatory differences

This study identifies cis and trans regulatory divergence between two indica rice genotypes under stress and non-stress conditions, showing cis dominance under normal conditions and increased trans effects under drought.

Modulation of the cAMP levels with a conserved actinobacteria phosphodiesterase enzyme reduces antimicrobial tolerance in mycobacteria

This study identifies a phosphodiesterase enzyme that reduces cAMP levels in mycobacteria, increasing antimicrobial susceptibility and revealing a new target for antimicrobial development.

Enabling out-of-clinic human immunity studies via single-cell profiling of capillary blood

The paper develops a platform for single-cell immune profiling using capillary blood to study gene expression variability across individuals and time.

The antibiotic bedaquiline activates host macrophage innate immune resistance to bacterial infection

The paper shows that bedaquiline reprograms macrophages to enhance bactericidal activity against bacteria through metabolic and lysosomal pathways.

Controlling Organization and Forces in Active Matter Through Optically-Defined Boundaries

This paper demonstrates the use of optically-defined boundaries to control active matter systems of microtubules and motor proteins, enabling the creation of contractile networks and fluid flows.

Diffusion as a ruler: modeling kinesin diffusion as a length sensor for intraflagellar transport

The paper models kinesin diffusion as a mechanism for measuring flagellar length during intraflagellar transport, showing it can achieve stable length regulation without additional signaling.

Transient Thresholding: A Mechanism Enabling Non-Cooperative Transcriptional Circuitry To Form A Switch

The paper identifies a transient activation threshold in the HIV Tat circuit that enables temporary latency despite lacking cooperativity and deterministic bistability.

Maintaining their genetic distance; limited gene flow between widely hybridising species of Geum with contrasting mating systems

The paper measures gene flow between two hybridizing Geum species with different mating systems and finds limited genetic exchange despite frequent hybridization.