Ren Sun

Structures of Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus virions reveal species-specific tegument and envelope features

This study uses cryoET and deep learning to reveal structural differences in the tegument and envelope of EBV and KSHV virions compared to other herpesviruses.

Benchmarking of computational error-correction methods for next-generation sequencing data

This study benchmarks error-correction methods for next-generation sequencing data, finding significant variation in performance across datasets with no single method being optimal overall.

Identifying TCDD-resistance genes via murine and rat comparative genomics and transcriptomics

The paper identifies genes associated with TCDD-response phenotypes by comparing genomic and transcriptomic data from transgenic mice and rats.

BPG: Seamless, Automated and Interactive Visualization of Scientific Data

BPG is an R package that generates publication-quality, customizable plots and offers an interactive web tool for figure customization and integration with computational pipelines.

Accurate Reference-Free Somatic Variant-Calling by Integrating Genomic, Sequencing and Population Data

S22S is a reference-free method for somatic variant calling that uses genomic and population data to accurately identify SNVs without matched normal samples.

Long single-molecule reads can resolve the complexity of the Influenza virus composed of rare, closely related mutant variants

This paper introduces 2SNV, a method to accurately reconstruct rare viral mutant variants from single-molecule sequencing data with high sensitivity and accuracy.

Pathogenesis of Zika Virus Infection via Rectal Route

This study investigates the pathogenesis of Zika virus infection via the rectal route and its potential implications for transmission and disease outcomes.

Adaptive potential of a drug-targeted viral protein as a function of environmental stress

The paper quantifies the adaptive potential of HCV NS5A protein mutations under drug selection and environmental stress, finding increased beneficial mutations and fitness costs.

Adaptation in protein fitness landscapes is facilitated by indirect paths

The paper experimentally characterizes a protein fitness landscape, finding that indirect adaptation paths through extra dimensions can bypass evolutionary traps caused by epistasis.

Rational design and adaptive management of combination therapies for Hepatitis C virus infection

This study develops a model to assess how suboptimal adherence affects HCV resistance and proposes strategies to reduce resistance risk in combination therapies.

High-throughput functional annotation of influenza A virus genome at single-nucleotide resolution

This study presents a platform for high-throughput functional annotation of influenza A virus genome mutations, identifying critical residues and validating mutation effects with high accuracy.