Sijie Chen

Building a learnable universal coordinate system for single-cell atlas with a joint-VAE model

The paper introduces UniCoord, a joint-VAE model that learns a universal coordinate system for single-cell transcriptomic data to capture heterogeneity and enable data generation and analysis.

Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes

This paper introduces HapHiC, a reference-independent allele-aware scaffolding tool that improves chromosome assignment and contig ordering, and applies it to construct a haplotype-resolved allotriploid genome.

scDirect: key transcription factor identification for directing cell state transitions based on single-cell multi-omics data

scDirect identifies key transcription factors driving cell state transitions using single-cell multi-omics data, showing robust performance in benchmarking and real-world applications.

A generic reference defined by consensus peaks for scATAC-seq data analysis

The paper constructs a generic chromatin accessibility reference (cPeaks) from bulk ATAC-seq data to improve scATAC-seq analysis and cell type identification.

STEM: A Method for Mapping Single-cell and Spatial Transcriptomics Data with Transfer Learning

STEM maps single-cell and spatial transcriptomics data using transfer learning to create spatially aware embeddings and predict pseudo-spatial adjacencies.

hECA: the cell-centric assembly of a cell atlas

The paper introduces hECA, a cell-centric human Ensemble Cell Atlas, which integrates scRNA-seq data from multiple studies to enable targeted data retrieval, multi-view presentations, and customizable reference creation for cell type annotations.

A new statistic for efficient detection of repetitive sequences

The paper introduces a new statistic for efficiently detecting repetitive sequences in genomic data and demonstrates its effectiveness across multiple scenarios.