Tak‐Wah Lam

ClairS is a deep-learning method for long-read somatic variant calling that outperforms existing tools on synthetic and short-read datasets.

AutoPM3 automates PM3 evidence extraction from scientific literature using LLMs, improving variant interpretation for rare diseases.

ClusterV-Web provides a user-friendly web interface for analyzing Nanopore long-read data to profile HIV quasispecies and generate drug resistance reports.

This study improves variant calling by integrating Oxford Nanopore and Illumina data using Clair3-MP, showing benefits in difficult genomic regions.

This study uses ultra-low coverage whole genome sequencing on embryo samples to perform GWAS and identifies genetic loci associated with gestational age.

This paper introduces Clair3, a deep learning-based variant caller that combines pile-up and full-alignment methods, achieving faster performance and better accuracy, especially at lower coverage.

This study compares Oxford Nanopore adaptive sequencing and PCR amplicon sequencing for detecting Mycobacterium Tuberculosis in metagenomic samples and calls variants, with an open-source analysis framework.

Duet improves structural variant calling and phasing using low-coverage Oxford Nanopore sequencing data, outperforming existing tools at 8X coverage and maintaining strong performance at higher coverage.

This study identifies novel human DNA sequences using long reads and shows that assembly-free methods capture more novel sequences than assemblers.

Clair3-Trio improves variant calling in family trios using Nanopore long-reads with a Trio-to-Trio neural network and a novel loss function.

SENSV detects structural variations with high sensitivity and precise breakpoints using low-depth Oxford Nanopore WGS data from a single MinION flowcell, outperforming existing tools in pathogenic SV detection.

HKG is a variant database of 205 Hong Kong Cantonese exomes that fills a gap in southern Chinese genetics, showing unique variants and improving variant imputation.

RENET2 extracts gene-disease associations from full-text articles with higher accuracy than existing tools, identifying 3.72M associations from 1.89M PMC articles.

The paper tracks cytosine depletion in SARS-CoV-2 over time using genomic data from GISAID and finds a monthly loss of cytosine correlated with mortality.

Clair is a germline small variant caller using single-molecule sequencing data that achieves high precision, recall, and speed, approaching the accuracy limit for pileup-based deep learning methods.

Skyhawk is an AI tool that quickly reviews genomic variants, reducing manual review time by identifying false positives and flagging uncertain variants for further analysis.

Clairvoyante is a deep learning model for variant calling in single molecule sequencing that achieves high accuracy across multiple sequencing technologies.