Ting‐Fung Chan

A wild genome of the underutilized legume lablab (Lablab purpureus) reveals the genetic basis of domestication

This paper presents the first chromosome-scale genome of wild lablab and identifies genes and pseudogenes associated with domestication and stress tolerance.

Single-cell analyses reveal scyphozoan conserved and specific genes contribution during tissue regeneration in two jellyfish

This study uses single-cell RNA sequencing to analyze tissue regeneration in two jellyfish species, identifying conserved and lineage-specific genes involved in regeneration processes.

AnAms1.0: A high-quality chromosome-scale assembly of a domestic cat Felis catus of American Shorthair breed

The paper presents a high-quality chromosome-scale genome assembly for the American Shorthair domestic cat breed, improving upon previous fragmented assemblies.

Chromosomal-level reference genome and microRNAs of the ricefield flatsedge Cyperus iria

The paper presents a chromosomal-level genome assembly and microRNA annotation for Cyperus iria, revealing genome duplication and providing resources for weed control research.

Chromosomal-level genome assembly and single-nucleotide polymorphism sites of black-faced spoonbill Platalea minor

This study presents the first chromosomal-level genome assembly and SNP analysis of the black-faced spoonbill, providing genomic resources for conservation and biological research.

Chromosomal-level genome assembly of the long-spined sea urchin Diadema setosum (Leske, 1778)

This paper presents a chromosomal-level genome assembly of the long-spined sea urchin D. setosum using PacBio and Omni-C technologies, providing a resource for ecological and evolutionary studies.

Genome assembly of the edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae)

This study presents the genome assembly of the edible jelly fungus Dacryopinax spathularia using PacBio HiFi and Omni-C data, revealing a high-quality genome with 11,510 protein-coding genes.

Chromosomal-level genome assembly of golden birdwing Troides aeacus (Felder & Felder, 1860)

This paper presents the first chromosomal-level genome assembly of the golden birdwing butterfly, providing a high-quality resource for studying its biology and conservation.

Genome assembly of the milky mangrove Excoecaria agallocha

This study presents a high-quality chromosomal-level genome assembly of the milky mangrove Excoecaria agallocha using PacBio and Omni-C data, revealing 73,740 protein-coding genes.

Accurate identification of structural variations from cancer samples

The paper introduces COMSV, a method for identifying structural variations in cancer samples, showing high sensitivity and specificity and detecting hundreds of novel SVs per sample.

PanGraphViewer: A Versatile Tool to Visualize Pangenome Graphs

PanGraphViewer is a tool for visualizing pangenome graphs, supporting multiple formats and structural variation analysis.

Deep autoencoder for interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis

TAPE deconvolves bulk RNA-seq data into cell-type fractions and gene expression using a deep autoencoder, showing better performance and robustness compared to existing methods.

Self-supervised contrastive learning for integrative single cell RNA-seq data analysis

CLEAR is a self-supervised contrastive learning framework for scRNA-seq that improves clustering, batch correction, and pseudo-time inference by reducing technical noise and heterogeneity.

rG4-seq 2.0: enhanced transcriptome-wide RNA G-quadruplex structure sequencing for low RNA input samples

This study introduces rG4-seq 2.0, an improved method for detecting RNA G-quadruplexes with lower RNA input requirements and better library quality.

A Chromosome-level Assembly of the Japanese Eel Genome, Insights into Gene Duplication and Chromosomal Reorganization

This paper presents a high-quality chromosome-level genome assembly of the Japanese eel and identifies gene duplication events and chromosomal reorganization linked to evolutionary adaptation.

rG4-seeker enables high-confidence identification of novel and non-canonical rG4 motifs from rG4-seq experiments

rG4-seeker improves rG4-seq analysis by reducing false positives and enhancing detection of non-canonical rG4 motifs in human RNA.

OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

OMSV identifies large structural variations from optical maps with high accuracy, outperforming existing methods and detecting many missed by sequencing.

Characterization of Azotobacter vinelandii and Kits for Its Synthetic Biology Applications

The paper characterizes Azotobacter vinelandii for synthetic biology and develops two BioBrick kits for regulated protein expression and magnetosome conjugation.

Systematic selection of reference genes for normalization of circulating RNA transcripts in pregnant women based on RNA-seq data

The paper identifies a panel of stably expressed genes for normalizing circulating RNA transcripts in maternal blood using RNA-seq data from preterm labor samples.