Ka Ming Nip

Genomic structures and regulation patterns at HPV integration sites in cervical cancer

The paper uses long-read sequencing to analyze HPV integration sites in cervical cancer genomes, identifying structural and epigenetic impacts of integration.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

ntEmbd: Deep learning embedding for nucleotide sequences

ntEmbd is a deep learning tool for nucleotide sequence embedding, demonstrating utility in RNA classification and adapter sequence identification.

GoldRush: A de novo long read genome assembler with linear time complexity

GoldRush is a de novo long read genome assembler with linear time complexity, achieving efficient assembly of large genomes with high contiguity and low memory usage.

Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2

RNA-Bloom2 is a reference-free transcriptome assembler for long-read data, showing competitive performance with reference-based methods and lower resource usage.

Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim

Meta-NanoSim simulates and characterizes nanopore metagenomic data to improve microbial abundance estimation and guide algorithm development.

RNA-Bloom provides lightweight reference-free transcriptome assembly for single cells

RNA-Bloom is a de novo RNA-seq assembler for scRNA-seq data that reconstructs cell-specific isoforms and detects gene fusions, outperforming bulk RNA-seq methods.

Trans-NanoSim characterizes and simulates nanopore RNA-seq data

Trans-NanoSim simulates nanopore RNA-seq reads using features learned from real data, enabling cost-effective development of analytical tools.

Terminitor: Cleavage Site Prediction Using Deep Learning Models

Terminitor predicts polyadenylation cleavage sites from RNA-seq data, outperforming existing tools in sensitivity and precision on experimental data.

Pan-cancer analysis reveals complex tumor-specific alternative polyadenylation

The paper analyzes APA patterns in 114 cancer-related genes across 33 cancer types to show complex 3 UTR cleavage changes in tumors.