Yaping Liu

This study identifies a novel cfDNA fragmentomic metric, rMDS, that distinguishes immunotherapy responders from non-responders in HNSCC with high accuracy.

The paper identifies an NTRK2 isoform switch in BPD lungs that impairs endothelial regeneration and shows that restoring full-length NTRK2 mRNA can reverse alveolar damage.

This study identifies circulating cell-free DNA methylation profiles as potential non-invasive biomarkers for multiple sclerosis, showing their ability to classify subtypes, estimate severity, and predict progression.

The paper introduces GenomeOcean, a large-scale generative model trained on metagenomic data, to explore the genomic manifold hypothesis and demonstrates its alignment with another model.

FinaleToolkit accelerates cfDNA fragmentation analysis by generating comprehensive features efficiently, improving processing speed by up to 50-fold for large datasets.

This study uses iPSC-derived neurons to show that FMRP deficiency in fragile X syndrome leads to m6A-mediated transcriptome dysregulation, causing synaptic dysfunction and suggesting therapeutic targets.

The paper identifies DoG RNAs as noncoding transcripts that are differentially expressed in cancer and linked to poor prognosis and carcinogenesis.

FinaleMe predicts DNA methylation and tissues-of-origin from plasma whole-genome sequencing by using a non-homogeneous Hidden Markov Model.

The paper identifies that reduced nephron numbers in Six2-TGCtg mice result from Six3 misexpression due to aberrant enhancer-promoter interactions in the transgene.

NOMe-HiC jointly profiles genetic variants, DNA methylation, chromatin accessibility, and 3D genome structure from the same DNA molecule, showing high concordance with mono-omic assays and revealing coordinated chromatin accessibility in spatially proximal regions.

FinaleDB provides a database and browser for cfDNA fragmentation patterns, enabling integration with other omics data to study gene regulation and disease.

The paper develops a method to identify cell-free DNA fragmentation hotspots in plasma whole-genome sequencing and shows their utility in detecting early-stage cancers with high specificity and sensitivity.

The paper introduces Methyl-HiC, a method that simultaneously profiles DNA methylation and chromatin architecture, revealing coordinated methylation and dynamic chromatin contacts in mouse embryonic stem cells.