Fang Liu

CellMethMarker provides an integrated database of human cell- and tissue-type-specific DNA methylation markers

CellMethMarker provides a database of DNA methylation markers specific to human cell and tissue types, improving deconvolution accuracy in single-cell methylomes.

OTTER: Orchestrated Transcriptomic, Tumor-xenograft (PDX/CDX), and Epigenomic Reporting Workflow

OTTER improves bisulfite deconvolution in tumor xenograft sequencing by restoring recall to 52%-54% while preserving transcriptomic accuracy.

Xenograft supervision and joint methylation-fragment-end encoding define a reusable molecular scoring layer for cell-free tumor DNA

ctDNA-BERT scores individual bisulfite reads for cell-free DNA methylation analysis, achieving high accuracy in cancer staging without cohort-specific retraining.

Comparative scototaxis among four honey bee species

This study compares scototaxis behavior in four honey bee species, finding stronger orientation in open-nesting species and suggesting ancestral trait reduction in cavity-nesting lineages.

EpicTope: predicting and validating non-disruptive epitope tagging sites

EpicTope predicts and validates epitope tagging sites by analyzing structural and functional features, showing effectiveness in zebrafish proteins.

Multi-tissue Transcriptomic and Pan-genomic Analyses Reveal Reciprocal Selective Retention Drives the Phenotypic Trade-off in Gossypium hirsutum and Gossypium barbadense

This study identifies reciprocal selective retention of transcription factors in Upland and Sea Island cotton, explaining the yield-quality trade-off through genomic and transcriptomic analyses.

mRNA interactions promote cotranslational association of heteromeric membrane proteins

The paper shows that mRNA interactions promote cotranslational association of heteromeric hERG1a/1b ion channels, with structural diversity and mRNA interactions influencing translation modes.

SPAC: a scalable, integrated enterprise platform for end-to-end single cell spatial analysis of multiplexed tissue imaging

SPAC provides a scalable platform for end-to-end single-cell spatial analysis of multiplexed tissue imaging data, enabling efficient processing and visualization of large datasets.

Genetic Diagnosis of Facioscapulohumeral Muscular Dystrophy Type 1 Using Rare Variant Linkage Analysis and Long Read Genome Sequencing

This study uses rare variant linkage analysis and long-read sequencing to identify a pathogenic FSHD1 allele in a family, mapping the disease locus to chromosome 4q35.2.

A comprehensive overview and benchmarking analysis of fast algorithms for genome-wide association studies

This study benchmarks 33 GWAS algorithms to evaluate their performance in identifying QTLs across plant species and simulated data.

Spatiotemporal functional organization of excitatory synaptic inputs onto macaque V1 neurons

This study maps excitatory synaptic inputs on V1 neurons in awake macaques, revealing functional clustering and spatial distribution patterns of visual features.

Cullin1 represses systematic inflammasome activation by binding and catalyzing NLRP3 ubiquitination

This study identifies CUL1 as a repressor of NLRP3 inflammasome activation by ubiquitinating NLRP3, showing its role in controlling immune responses under physiological and inflammatory conditions.

Collinearity Analysis of Allotetraploid Gossypium Tomentosum and Gossypium Darwinii

This study compares genetic linkage maps of G. tomentosum and G. darwinii with G. hirsutum to identify chromosomal inversions and translocations, revealing G. tomentosum's closer genetic relationship to G. hirsutum.