Huanming Yang

LucaCell: a sequence-centric foundation model for cross-species single-cell analysis

LucaCell is a sequence-centric foundation model that improves cross-species single-cell analysis by using mRNA sequence embeddings instead of fixed gene identifiers.

The genetic repertoire of the deep sea: from sequence to structure and function

This study analyzes the genetic diversity of the deep sea, linking protein structures to genetic variants and identifying biotechnologically relevant features.

Intra-host Variation and Evolutionary Dynamics of SARS-CoV-2 Population in COVID-19 Patients

This study characterizes intra-host SARS-CoV-2 genomic variants and their evolutionary dynamics in COVID-19 patients using deep sequencing data.

LFMD: detecting low-frequency mutations in high-depth genome sequencing data without molecular tags

LFMD improves low-frequency mutation detection in high-depth sequencing by combining duplex sequencing and bottleneck sequencing to enhance sensitivity and specificity.

Spatially resolved gene regulatory and disease vulnerability map of the adult Macaque cortex

The paper integrates single-cell ATAC and transcriptomic data with spatial transcriptomics to map regulatory features and disease vulnerabilities in macaque cortex.

PALM-Seq: simultaneous sequencing of cell-free long RNA and small RNA

PALM-Seq simultaneously sequences cell-free long and small RNA, identifying pregnancy-related RNAs and sample-specific signatures in plasma, amniotic fluid, leukocytes, and placentas.

Single-cell RNA-seq reveals distinct dynamic behavior of sex chromosomes during early human embryogenesis

The paper analyzes single-cell RNA-seq data from human embryos to compare gene expression between males and females, identifying differences in sex chromosome activation and dosage compensation during early development.

The mitochondrial DNA content can not predict the embryo viability

This study investigates whether mitochondrial DNA content can predict embryo viability and finds no significant association with chromosome status or other factors.

Comprehensive analysis of immune evasion in breast cancer by single-cell RNA-seq

This study uses single-cell RNA-seq to analyze the tumor microenvironment of breast cancer, revealing cell type diversity and immune evasion mechanisms.

Recovered and dead outcome patients caused by influenza A (H7N9) virus infection show different pro-inflammatory cytokine dynamics during disease progress and its application in real-time prognosis

This study analyzes cytokine dynamics in H7N9-infected patients with different outcomes, identifying predictors and a real-time prognosis model.

A Complete Public Domain Family Genomics Dataset

This paper presents a publicly available family genomics dataset under CC0 license, including SNP genotypes, exomes, metagenomic data, and derived phenotypes, enabling heritability studies and tool testing.