Bao Quoc Tran

Wakhan: reconstruction of chromosome-scale copy number profiles of tumor genomes with long-read sequencing

Wakhan reconstructs chromosome-scale copy number profiles of tumor genomes using long-read sequencing, showing better consistency with data than existing methods.

DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies

DeepSomatic is a deep learning method for detecting somatic variants from short-read and long-read sequencing data, outperforming existing callers, especially for indels.

Long-read sequencing of single cell-derived melanoma subclones reveals divergent and parallel genomic and epigenomic evolutionary trajectories

The paper uses long-read sequencing to analyze genomic and epigenomic changes in melanoma subclones, revealing parallel evolutionary paths and lineage-specific methylation patterns.

The ASNS inhibitor ASX-173 potentiates L-asparaginase anticancer activity

The paper identifies ASX-173 as a potent ASNS inhibitor that enhances the anti-cancer effects of L-asparaginase in leukemia and shows its potential across multiple cancer types.

Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads

Severus detects and characterizes somatic structural variations in tumor genomes using long reads, outperforming existing methods in accuracy and revealing clinically relevant rearrangements.

Ultra-Fast Multi-Organ Proteomics Unveils Tissue-Specific Mechanisms of Drug Efficacy and Toxicity

The paper introduces UFP-MS, a fast proteomics method, and applies it to study drug effects on mouse tissues, revealing tissue-specific metabolic changes.

Structure-guided bifunctional molecules hit a DEUBAD-lacking hRpn13 species upregulated in multiple myeloma

The paper identifies a chemical scaffold targeting hRpn13, revealing a DEUBAD-lacking isoform upregulated in multiple myeloma and demonstrating its potential as a therapeutic target.

Whole Genome and Exome Sequencing Reference Datasets from A Multi-center and Cross-platform Benchmark Study

The paper presents whole-genome and whole-exome sequencing datasets from a multi-center, cross-platform study to benchmark NGS technologies and bioinformatics pipelines in cancer genomics.

Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies

The paper establishes reference samples with high-coverage whole-genome sequencing to create truth sets for somatic mutation and germline variant detection using NGS technologies.

Achieving reproducibility and accuracy in cancer mutation detection with whole-genome and whole-exome sequencing

This study evaluates reproducibility and accuracy of cancer mutation detection using whole-genome and whole-exome sequencing across multiple sequencing centers and bioinformatics pipelines.

Enhanced longitudinal differential expression detection in proteomics with robust reproducibility optimization regression

The paper introduces RolDE, a new differential expression method for longitudinal proteomics data, which outperforms existing methods in handling missing values and reproducibility.

A Multi-center Cross-platform Single-cell RNA Sequencing Reference Dataset

The paper presents a multi-center cross-platform scRNA-seq reference dataset for benchmarking bioinformatics methods across different platforms and centers.

A Comprehensive Multi-Center Cross-platform Benchmarking Study of Single-cell RNA Sequencing Using Reference Samples

This study benchmarks scRNA-seq reproducibility across platforms and pipelines, finding that batch correction methods significantly affect results.

PacBio library preparation using blunt-end adapter ligation produces significant artefactual fusion DNA sequences

The paper identifies artefactual fusion DNA sequences produced by blunt-end adapter ligation in PacBio library preparation and recommends an alternative A/T overhang method to reduce them.