C. R. Weber

Untangling the Role of Pathobionts from Bacteroides Species in Inflammatory Bowel Diseases

This study shows that Bacteroides fragilis from UC patients promotes colitis in genetically susceptible mice, suggesting a role for pathobionts in IBD.

Deep learning-guided selection of antibody therapies with enhanced resistance to current and prospective SARS-CoV-2 Omicron variants

This study uses deep learning to identify antibodies resistant to SARS-CoV-2 Omicron variants by predicting their binding and escape from mutations.

Molecular dynamics analyses of CLDN15 pore size and charge selectivity

The paper uses molecular dynamics simulations and cell culture experiments to study how the D55 residue in CLDN15 affects ion size and charge selectivity in tight junctions.

A novel triptolide analog downregulates NF-κB and induces mitochondrial apoptosis pathways in human pancreatic cancer

This paper describes a novel triptolide analog, CK21, which downregulates the NF-κB pathway and induces mitochondrial apoptosis in human pancreatic cancer cells.

Intestinal Epithelial Heat Shock Protein 25/27 integrates host and microbial drivers of mucosal restitution following inflammatory injury

This study identifies Hsp25/27 as a key mediator of mucosal healing by integrating host and microbial signals in intestinal epithelial cells following inflammatory injury.

Pancreatic tumors activate arginine biosynthesis to adapt to myeloid-driven amino acid stress

The paper develops a cell culture medium mimicking the PDAC tumor microenvironment and identifies arginine biosynthesis as a metabolic adaptation to myeloid-driven arginine starvation.

Molecular mechanism of claudin-15 strand flexibility

This study uses molecular dynamics simulations to investigate the flexibility of claudin-15 strands and identifies interfacial interaction networks as the source of their lateral flexibility.

The Physiological Landscape and Specificity of Antibody Repertoires

This study analyzes antibody repertoires across multiple lymphoid organs in immunized mice, finding that strong humoral responses lead to consolidated, overlapping B-cell clones and a uniform but redundant physiological landscape.

In silico proof of principle of machine learning-based antibody design at unconstrained scale

This paper demonstrates that deep generative models can design high-affinity, developable antibodies at scale using synthetic data and transfer learning.

Individualized VDJ recombination predisposes the available Ig sequence space

The paper shows that VDJ recombination rules vary between individuals, leading to individual-specific Ig sequence spaces.

A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients

This study uses single-cell sequencing to analyze immune repertoires and transcriptomes in convalescent COVID-19 patients, revealing age-related differences in T and B cell responses.

Single-cell sequencing of plasma cells from COVID-19 patients reveals highly expanded clonal lineages produce specific and neutralizing antibodies to SARS-CoV-2

Single-cell sequencing and screening identify expanded plasma cell clones in COVID-19 patients producing SARS-CoV-2-specific neutralizing antibodies.

CRISPR-targeted display of functional T cell receptors enables engineering of enhanced specificity and prediction of cross-reactivity

The paper introduces a CRISPR-based platform to engineer TCRs with enhanced specificity and predict cross-reactivity by profiling mutational landscapes and screening TCR libraries.

A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding

The paper identifies a compact vocabulary of paratope-epitope interaction motifs that enables machine learning prediction of antibody-antigen binding.

Pancreatic adenocarcinoma human organoids share structural and genetic features with primary tumors

This study shows that pancreatic cancer organoids closely match primary tumors in molecular features, genetic diversity, and drug responses, suggesting their use in personalized therapy prediction.

High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis

This paper develops a high-throughput method for antibody engineering in mammalian cells using CRISPR/Cas9-mediated homology-directed mutagenesis, demonstrating improved efficiency and applicability for variant discovery and optimization.