Ben Murrell

This paper introduces PhyloTrajectory, a method that uses TCR clonotype frequencies and scRNA-seq to infer T cell differentiation trajectories.

The paper uses spatial and single-cell techniques to show T and B cell clonal expansion in CXCL9-rich niches of sinonasal cancer, linking immune hubs to tumor regions.

The paper uses long-read sequencing to study HIV transmission and population dynamics in acute infection, finding high multilineage transmission rates and rapid viral evolution.

The paper analyzes HIV breakthrough virus populations in antibody-mediated prevention trials, finding high rates of multilineage infections and recombination under VRC01 treatment.

PRIME models physicochemical selection in protein evolution by incorporating biophysical properties, improving model fit and revealing adaptive tuning mechanisms in protein structures.

This paper shows a transformer-based generative model for proteins spontaneously creates symmetry without explicit training or generation constraints.

This study identifies VRC01-mediated viral escape mutations in HIV-infected participants from antibody-mediated prevention trials, showing that VRC01 can select for escape variants with cross-resistance to other CD4bs bnAbs.

This study uses synthetic coevolution to explore mutational trajectories between neutralizing antibodies and SARS-CoV-2 variants, revealing antagonistic and compensatory mutations.

difFUBAR provides a scalable Bayesian method to compare adaptive evolution across different branch sets in phylogenetic trees, showing computational gains and moderate statistical benefits over existing methods.

This paper introduces CHMMAIRRa, a hidden Markov model to detect PCR chimeras in AIRR-seq data, incorporating somatic hypermutation and germline references.

This study shows that antigen affinity and immunization site influence B cell recall responses, with low affinity boosts leading to higher SHM but fewer memory B cells in secondary GCs.

This paper introduces a generative autoregressive language model for protein backbone design, showing it can sample diverse and realistic protein chains.

The paper presents an optimized SMRT-UMI protocol and bioinformatics pipeline to generate highly accurate sequence datasets from diverse pathogens, demonstrated on HIV-1 quasispecies.

This paper introduces a high-throughput platform for identifying host binding factors and antiviral drug targets by overcoming limitations in host plasma membrane complexity.

The paper identifies conserved recombination patterns across six coronavirus subgenera and links them to transcriptional regulatory sequences and sequence features.

This paper introduces a Bayesian method to estimate HIV infection timing from unmutated sequences, avoiding data curation and providing accurate results robust to complications like APOBEC hypermutation.

This paper identifies an alpaca nanobody that neutralizes SARS-CoV-2 by blocking the ACE2 receptor interaction.

MESSI infers coevolution rates of base-pairing interactions in nucleic acid sequences and identifies functionally important substructures.

This paper introduces two methods for denoising long-read amplicon sequencing data, achieving higher accuracy than existing methods.

FLEA is a tool for analyzing long-read sequencing data of HIV-1 env, improving accuracy in reconstructing viral sequences and analyzing evolutionary dynamics.

RIFRAF improves consensus sequence accuracy by resolving frame errors in long-read sequencing data using a two-layer model.