Jeremy Wang

Memory-safe high-performance sequence mapping with rammap

The paper introduces rammap, a Rust reimplementation of minimap2 with improved performance and memory safety, demonstrating compatibility and efficiency improvements.

Long-read analysis of tetrameric microsatellites with vmwhere supports GGAA repeat length-dependent chromatin state association in Ewing sarcoma

The paper introduces vmwhere, a tool for analyzing tetrameric microsatellites from long-read sequencing data, and shows its application in linking GGAA repeat structure to chromatin state in Ewing sarcoma.

Shared PRAME Epitopes are T-Cell Targets in NUT Carcinoma

This study identifies PRAME as a therapeutic target in NUT carcinoma, showing its high expression and susceptibility to T-cell mediated cytotoxicity via PRAME epitopes presented by HLA Class I molecules.

Extrachromosomal DNA Gives Cancer a New Evolutionary Pathway

The paper shows that ecDNA allows tumors to adapt rapidly by maintaining a spectrum of gene expression levels across cells, rather than relying on clonal expansion.

Sex differentiation, divergence, and introgression in the leishmaniasis vector Lutzomyia longipalpis

The paper investigates genetic diversity and sex differentiation in Lutzomyia longipalpis, identifying sex chromosomes and population structure across South America.

Real-time genomic characterization of pediatric acute leukemia using adaptive sampling

This study demonstrates real-time genomic classification of pediatric acute leukemia using long-read sequencing with adaptive sampling, identifying key alterations faster than traditional methods.

The cell biology and genome of Stentor pyriformis, a giant cell that embeds symbiotic algae in a microtubule meshwork

This paper describes the cell biology and genome of Stentor pyriformis, a mixotrophic ciliate, revealing unique features of its endosymbiotic relationship with Chlorella variabilis.

Polishing de novo nanopore assemblies of bacteria and eukaryotes with FMLRC2

The paper introduces FMLRC2, a tool for polishing de novo nanopore assemblies, and demonstrates its effectiveness for bacterial and eukaryotic genomes.

Plastid Genome Assembly Using Long-read Data (ptGAUL)

The paper introduces ptGAUL, a pipeline for assembling plastomes from long-read data, showing it produces accurate assemblies and revealing long repeats and rearrangements in Juncus plastomes.

Long-read sequencing to interrogate strain-level variation among adherent-invasive Escherichia coli isolated from human intestinal tissue

The paper develops a long-read sequencing method to identify and distinguish AIEC strains in intestinal tissue, showing their ability to colonize IBD-susceptible mice and induce inflammation.

Genomic Epidemiology of Escherichia coli Isolates from a Tertiary Referral Center in Lilongwe, Malawi

This study uses whole genome sequencing to analyze the prevalence and spread of antimicrobial resistance genes in E. coli isolates from Malawi, showing increased prevalence of ST131 and blaCTX-M-15.

Non-linear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains

The paper shows non-linear sequence similarity between Xist and Rsx repeat domains, suggesting shared functional roles through similar protein-binding motif enrichments.