Mengyang Xu

This study reconstructs 3D spatial transcriptomic models of planarians to map cell type distribution and positional gene regulation, identifying candidate genes involved in regeneration.

This study constructs a 4D spatiotemporal transcriptomic map of planarian regeneration using Stereo-seq, identifying dynamic gradients and an injury-induced regenerative zone.

The paper develops ACCESS, a multimodal graph neural network to annotate functional dark matter proteins from extreme environments beyond homology-based methods.

This study determines the structural basis of DNA N6-adenine methylation by modeling the AMT1 complex and validating its function through mutagenesis.

Stereopy provides a framework for analyzing multi-sample spatial transcriptomics data to model comparative and spatiotemporal cellular heterogeneity through three key algorithms.

SpaGRN predicts spatially informed gene regulatory networks from spatial transcriptomics data, revealing spatiotemporal regulatory patterns in Drosophila development.

ST-GEARS improves spatial information recovery in 3D spatial transcriptomics by aligning sections and correcting distortions, enhancing accuracy for downstream analysis.

This paper introduces new randstrobe construction methods, identifies biases in previous approaches, and improves accuracy in short-read mapping.

MetaTrass improves metagenome assembly by binning first and assembling later, producing more high-quality draft genomes from human gut microbiome samples.

The paper introduces a de novo scaffolding tool for synthetic long reads that improves assembly quality significantly, especially for assemblies from next-generation sequencing reads.

This study compares three long-read sequencing technologies for de novo assembly of the Macadamia jansenii genome, evaluating contiguity, accuracy, completeness, cost, and DNA requirements.

Symbiont-Screener separates host sequences from contaminants in long reads or co-barcoded reads using unsupervised clustering without reference alignment, achieving high accuracy in simulated and real data.

The paper introduces HAST, a tool for haplotype-resolved assembly using trio binning, achieving high accuracy and completeness in haplotype reconstruction from synthetic long reads.

TGS-GapCloser closes gaps in genome assemblies using error-prone long reads, improving contig N50 and gene completeness while being faster than existing tools.

This paper presents the first de novo genome assembly of the porcupinefish, Diodon holocanthus, using long-read sequencing technologies and provides annotations of repetitive sequences and protein-coding genes.