Brian D. Marsden
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View article: Interpolation-Based Conditioning of Flow Matching Models for Bioisosteric Ligand Design
Interpolation-Based Conditioning of Flow Matching Models for Bioisosteric Ligand Design Open
A bstract Fast, unconditional 3D generative models can now produce high-quality molecules, but adapting them for specific design tasks often requires costly retraining. To address this, we introduce two training-free, inference-time condit…
View article: Cell type specific analysis of ALS-associated proteins reveals immune-regulated targets
Cell type specific analysis of ALS-associated proteins reveals immune-regulated targets Open
Genetic studies are revolutionizing our understanding of neurodegenerative diseases by identifying hundreds of new genetic risk factors, yet the ability to link these variants to phenotype is constrained by the lack of knowledge on the enc…
View article: Synovial tissue atlas in juvenile idiopathic arthritis reveals pathogenic niches associated with disease severity
Synovial tissue atlas in juvenile idiopathic arthritis reveals pathogenic niches associated with disease severity Open
Precision application of targeted therapies is urgently needed to improve long-term clinical outcomes for children affected by inflammatory arthritis, known as juvenile idiopathic arthritis (JIA). Progress has been hampered by our limited …
View article: CD4+ tissue-resident memory Th17 cells are a major source of IL-17A in Spondyloarthritis synovial tissue
CD4+ tissue-resident memory Th17 cells are a major source of IL-17A in Spondyloarthritis synovial tissue Open
CD4+ TRM17 cells are the predominant source of IL-17A in SpA synovial tissue. TCR stimulation is essential for the secretion of IL-17A by CD4+TRM17-like cells. The epigenetic regulator bromodomain-containing protein 1 (BRD1) contributes to…
View article: MolSnapper: Conditioning Diffusion for Structure-Based Drug Design
MolSnapper: Conditioning Diffusion for Structure-Based Drug Design Open
Generative models have emerged as potentially powerful methods for molecular design, yet challenges persist in generating molecules that effectively bind to the intended target. The ability to control the design process and incorporate pri…
View article: P076 Characterising flare and pain variability in individuals with symptomatic hand osteoarthritis - primary report from the Hand Osteoarthritis: investigating Pain (HOPE) Cohort
P076 Characterising flare and pain variability in individuals with symptomatic hand osteoarthritis - primary report from the Hand Osteoarthritis: investigating Pain (HOPE) Cohort Open
Background/Aims Despite being commonly reported by patients, the occurrence of episodic ‘flare’ and factors affecting it have not previously been studied in hand osteoarthritis. We investigated the associations between short-term fluctuati…
View article: Robustly interrogating machine learning-based scoring functions: what are they learning?
Robustly interrogating machine learning-based scoring functions: what are they learning? Open
Motivation Machine learning-based scoring functions (MLBSFs) have been found to exhibit inconsistent performance on different benchmarks and be prone to learning dataset bias. For the field to develop MLBSFs that learn a generalizable unde…
View article: Fragmenstein: predicting protein–ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding–based methodology
Fragmenstein: predicting protein–ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding–based methodology Open
View article: Toward target 2035: EUbOPEN - a public–private partnership to enable & unlock biology in the open
Toward target 2035: EUbOPEN - a public–private partnership to enable & unlock biology in the open Open
EUbOPEN is a public–private partnership focused on four areas: chemogenomic library collection, chemical probe discovery and technology development, compound profiling in patient-derived assays, and data and reagents collection, storage an…
View article: Development of methodology to support molecular endotype discovery from synovial fluid of individuals with knee osteoarthritis: The STEpUP OA consortium
Development of methodology to support molecular endotype discovery from synovial fluid of individuals with knee osteoarthritis: The STEpUP OA consortium Open
Objectives To develop a protocol for largescale analysis of synovial fluid proteins, for the identification of biological networks associated with subtypes of osteoarthritis. Methods S ynovial Fluid T o detect molecular E ndoty p es by U n…
View article: Early regional lymph node activation drives influenza vaccine responses in an ancestrally diverse cohort
Early regional lymph node activation drives influenza vaccine responses in an ancestrally diverse cohort Open
Early in vivo dynamics of human immune-cell activation across regionally activated lymphoid tissue sites upon immunisation are poorly characterised in ancestrally diverse individuals. Here, we profiled draining and non-draining axillary ly…
View article: A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease
A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease Open
Precision medicine in immune-mediated inflammatory diseases (IMIDs) requires a cellular understanding of treatment response. We describe a therapeutic atlas for Crohn’s disease (CD) and ulcerative colitis (UC) following adalimumab, an anti…
View article: CD4+ tissue-resident memory Th17 cells are a major source of IL-17A in Spondyloarthritis synovial tissue
CD4+ tissue-resident memory Th17 cells are a major source of IL-17A in Spondyloarthritis synovial tissue Open
Objectives Interleukin (IL)-17A is a key driver of Spondyloarthritis (SpA) joint pathology. We aimed to identify its cellular source in synovial tissue from patients with two forms of SpA namely Axial SpA (AxSpA) and Psoriatic arthritis (P…
View article: A data science roadmap for open science organizations engaged in early-stage drug discovery
A data science roadmap for open science organizations engaged in early-stage drug discovery Open
View article: Improving the representativeness of UK’s national COVID-19 Infection Survey through spatio-temporal regression and post-stratification
Improving the representativeness of UK’s national COVID-19 Infection Survey through spatio-temporal regression and post-stratification Open
Population-representative estimates of SARS-CoV-2 infection prevalence and antibody levels in specific geographic areas at different time points are needed to optimise policy responses. However, even population-wide surveys are potentially…
View article: MolSnapper: Conditioning Diffusion for Structure Based Drug Design
MolSnapper: Conditioning Diffusion for Structure Based Drug Design Open
Generative models have emerged as potentially powerful methods for molecular design, yet challenges persist in generating molecules that effectively bind to the intended target. The ability to control the design process and incorporate pri…
View article: Fragmenstein: predicting protein-ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding–based methodology
Fragmenstein: predicting protein-ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding–based methodology Open
Current strategies centred on either merging or linking initial hits from fragment-based drug design (FBDD) crystallographic screens ignore 3D structural information. We show that an algorithmic approach (Fragmenstein) that ‘stitches’ the …
View article: Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population
Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population Open
View article: Toward target 2035: EUbOPEN - a public–private partnership to enable & unlock biology in the open
Toward target 2035: EUbOPEN - a public–private partnership to enable & unlock biology in the open Open
EUbOPEN is a public–private partnership focused on four areas: chemogenomic library collection, chemical probe discovery and technology development, compound profiling in patient-derived assays, and data and reagents collection, storage an…
View article: Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases
Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases Open
Background Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, the diagnostic yields of many studies, particularly those conducted in a healthcare setting, are often disappointingly…
View article: ToolBoxSF: Robustly interrogating machine learning-based scoring functions: what are they learning?
ToolBoxSF: Robustly interrogating machine learning-based scoring functions: what are they learning? Open
This Zenodo repository provides comprehensive resources for the pre-print research paper titled "Robustly interrogating machine learning-based scoring functions: what are they learning?" Our collection includes Singularity containers conta…
View article: ToolBoxSF: Robustly interrogating machine learning-based scoring functions: what are they learning?
ToolBoxSF: Robustly interrogating machine learning-based scoring functions: what are they learning? Open
This Zenodo repository provides comprehensive resources for the pre-print research paper titled "Robustly interrogating machine learning-based scoring functions: what are they learning?" Our collection includes Singularity containers conta…
View article: Persistence of SARS-CoV-2 antibodies over 18 months following infection: UK Biobank COVID-19 Serology Study
Persistence of SARS-CoV-2 antibodies over 18 months following infection: UK Biobank COVID-19 Serology Study Open
Background Little is known about the persistence of antibodies after the first year following SARS-CoV-2 infection. We aimed to determine the proportion of individuals that maintain detectable levels of SARS-CoV-2 antibodies over an 18-mon…
View article: Robustly interrogating machine learning-based scoring functions: what are they learning?
Robustly interrogating machine learning-based scoring functions: what are they learning? Open
Motivation Machine learning-based scoring functions (MLBSFs) have been found to exhibit inconsistent performance on different benchmarks and be prone to learning dataset bias. For the field to develop MLBSFs that learn a generalisable unde…
View article: ToolBoxSF: Robustly interrogating machine learning-based scoring functions: what are they learning?
ToolBoxSF: Robustly interrogating machine learning-based scoring functions: what are they learning? Open
<p>This Zenodo repository provides comprehensive resources for the pre-print research paper titled "Robustly interrogating machine learning-based scoring functions: what are they learning?" Our collection includes Singularity contain…
View article: Integrative GWAS and co-localisation analysis suggests novel genes associated with age-related multimorbidity
Integrative GWAS and co-localisation analysis suggests novel genes associated with age-related multimorbidity Open
View article: Methodological development of molecular endotype discovery from synovial fluid of individuals with knee osteoarthritis: the STEpUP OA Consortium
Methodological development of molecular endotype discovery from synovial fluid of individuals with knee osteoarthritis: the STEpUP OA Consortium Open
Objectives To develop and validate a pipeline for quality controlled (QC) protein data for largescale analysis of synovial fluid (SF), using SomaLogic technology. Design Knee SF and associated clinical data were from partner cohorts. SF sa…
View article: Alterations in the gut microbiome implicate key taxa and metabolic pathways across inflammatory arthritis phenotypes
Alterations in the gut microbiome implicate key taxa and metabolic pathways across inflammatory arthritis phenotypes Open
Musculoskeletal diseases affect up to 20% of adults worldwide. The gut microbiome has been implicated in inflammatory conditions, but large-scale metagenomic evaluations have not yet traced the routes by which immunity in the gut affects i…
View article: Protection against SARS-CoV-2 Omicron BA.4/5 variant following booster vaccination or breakthrough infection in the UK
Protection against SARS-CoV-2 Omicron BA.4/5 variant following booster vaccination or breakthrough infection in the UK Open
View article: Improving the representativeness of UK’s national COVID-19 Infection Survey through spatio-temporal regression and post-stratification
Improving the representativeness of UK’s national COVID-19 Infection Survey through spatio-temporal regression and post-stratification Open
Population-representative estimates of SARS-CoV-2 infection prevalence and antibody levels in specific geographic areas at different time points are needed to optimise policy responses. However, even population-wide surveys are potentially…