Qin Ma

A kinetic-aware approach to infer metabolic variations and flux using transcriptomics and metabolomics data

This paper introduces mmFEA, a kinetic-aware framework for estimating metabolic flux changes from transcriptomics and metabolomics data, showing improved accuracy over baseline methods.

spaCraft: calibrated power analysis and sample-size planning for multi-sample spatial transcriptomics

spaCraft provides calibrated power analysis and sample-size planning for multi-sample spatial transcriptomics by integrating domain recovery and clustering uncertainty.

An Integrated Multi-omics Single Cell Atlas of the Human RPE and Choroid

The paper constructs a multi-omics single-cell atlas of human RPE and choroid, identifying cell types, aging patterns, and genetic risk factors for AMD.

Human cardiomyocytes with trisomy 21 exhibit heightened susceptibility and immunological response to SARS-CoV-2 infection

This study shows that human cardiomyocytes with trisomy 21 are more susceptible to SARS-CoV-2 infection and show an amplified immune response compared to euploid controls.

DamageFormer: a damage-aware multimodal deep learning framework for DNA lesion identification from nanopore sequencing

DamageFormer detects and localizes DNA lesions from nanopore sequencing with high accuracy and generalization to unseen damage types.

Transcriptional and spatial profiling of fibroblasts from human lungs highlights CTHRC1+ cells as fibrogenic signaling hubs in fibrosis

The paper integrates single-cell RNA sequencing and spatial transcriptomics to identify CTHRC1+ fibroblasts as key fibrogenic cells in IPF, showing how culture affects their transcriptional profile.

Transcriptomics-based modeling of methionine metabolism effectively estimates sample-wise DNA methylation activity and epigenetic aging

This paper develops TDMA, a transcriptomics-based model to estimate DNA methylation activity and epigenetic aging from bulk, single-cell, and spatial transcriptomics data.

GatorST: A Versatile Contrastive Meta-Learning Framework for Spatial Transcriptomic Data Analysis

GatorST improves spatial transcriptomic analysis by integrating graph-based modeling, pseudo-labeling, and contrastive meta-learning to enhance spatial domain identification and downstream tasks.

Gene-centric intra- and inter-clade recombination in a context of Escherichia coli subpopulations

The paper analyzes recombination patterns in Escherichia coli genomes to show extensive intra-clade recombination and reduced inter-clade recombination, establishing genetic barriers between subpopulations.