A. Stern

Using big sequencing data to identify chronic SARS-Coronavirus-2 infections

The paper identifies chronic SARS-CoV-2 infections by analyzing phylogenetic clades with identical metadata and finds that chronic-like clades predict adaptive mutations in circulating variants.

Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation

This paper infers mutation rates and selection parameters from RNA virus haplotypes using neural posterior estimation, revealing epistasis in MS2 bacteriophage evolution.

Elevated genetic risk for multiple sclerosis originated in Steppe Pastoralist populations

This study identifies the origin of genetic risk variants for multiple sclerosis in Steppe pastoralist populations and traces their spread into Europe through migration.

#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

This paper uses AI-enabled multiscale computational microscopy to study SARS-CoV-2 Delta variant in respiratory aerosols, revealing atomic-level insights into airborne transmission.

Development of GPC2-directed chimeric antigen receptors using mRNA for pediatric brain tumors

This study develops mRNA chimeric antigen receptor T cells targeting GPC2 on pediatric brain tumors, showing significant tumor regression and prolonged survival without toxicity.

In vivo engineered B cells retain memory and secrete high titers of anti-HIV antibodies in mice

AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics

This paper develops an AI-driven workflow to simulate SARS-CoV-2 spike protein dynamics, revealing glycan shield structure, spike glycans' role in infectivity, and spike-ACE2 interactions.

Globally defining the effects of mutations in a picornavirus capsid

The paper defines the effects of mutations in a picornavirus capsid by analyzing >90% of single amino acid mutations, identifying sequence determinants, and developing a bioinformatic approach to predict host protein targets.

Unsupervised cellular phenotypic hierarchy enables spatial intratumor heterogeneity characterization, recurrence-associated microdomains discovery, and harnesses network biology from hyperplexed in-situ fluorescence images of colorectal carcinoma

LEAPH identifies spatial microdomains and recurrence-associated signaling networks in colorectal carcinoma using hyperplexed fluorescence images.

Inferring Population Genetics Parameters of Evolving Viruses Using Time-series Data

This paper introduces FITS, a computational framework for inferring virus population genetics parameters from time-series data, demonstrating high accuracy in classifying mutations as advantageous, neutral, or deleterious.

Evolutionary rate shifts suggest species-specific adaptation events in HIV-1 and SIV

The paper identifies evolutionary rate decelerations in HIV-1 and SIV proteins linked to cross-species adaptation, finding more decelerations in non-pandemic HIV-1 group O than in pandemic group M.

Within-patient HIV mutation frequencies reveal fitness costs of CpG dinucleotides, drastic amino acid changes and G->A mutations

The paper estimates the fitness costs of 870 HIV mutations in vivo by analyzing mutation frequencies in the pol gene across 160 patients, finding higher costs for non-synonymous, drastic amino acid changes, and CpG-creating mutations.