Yuhan Hao

A multimodal interrogation of Broca's area in the pediatric and adult human brain

The paper provides a high-resolution molecular and cellular analysis of Broca's area and motor cortex across developmental stages, identifying distinct cellular signatures and vulnerabilities to neurodevelopmental disorders.

Molecular dynamics of Brodmann Area 22 in development and autism

The paper identifies transcriptional and epigenomic differences in Brodmann Area 22 in autism, linking them to RFX3-dependent networks and verbal ability.

Microbiota-induced plastic T cells enhance immune control of antigen-sharing tumors

The paper shows that SFB colonization enhances anti-PD-1 therapy efficacy against antigen-sharing tumors by promoting T cell plasticity and immune control.

Reconstructing developmental and disease progression with sample-level embeddings

The paper introduces scSLIDE, a framework that generates sample-level embeddings from single-cell data to analyze variation across samples in disease and development.

Disruption of Cell-Type-Specific Molecular Programs of Medium Spiny Neurons in Autism

The paper identifies cell-type-specific molecular and regulatory changes in D1 striosome medium spiny neurons and astrocytes in ASD using single-nucleus multiomic profiling in human putamen.

Dictionary learning for integrative, multimodal, and scalable single-cell analysis

Dictionary learning enables assumption-free cross-modality single-cell mapping via multi-omic bridge datasets and scales single-modality integration to millions of cells in under an hour via atomic sketching.

CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators

The paper introduces CPA-Perturb-seq, a multiplexed perturbation screen dataset, and uses it to identify polyA site regulators and their functional properties.

Multimodal characterization of antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection.

The paper characterizes antigen-specific CD8+ T cells post-SARS-CoV-2 vaccination and infection using multimodal sequencing, identifying unique biomarkers and clinical predictors.

Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq

The paper introduces CaRPool-seq, a method using Cas13 for combinatorial RNA perturbations in single cells, and applies it to study myeloid differentiation regulators in AML.

Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro

The paper introduces scCUT&Tag-pro and scChromHMM to analyze chromatin states in single cells, showing their ability to characterize dynamic changes and regulatory priming across immune cell types.

Integrated analysis of multimodal single-cell data

Weighted-nearest neighbor (WNN) analysis in Seurat v4 learns per-cell modality weights to define cell states, enabling a 228-antibody human PBMC CITE-seq reference for RNA-only query mapping.

Characterizing the molecular regulation of inhibitory immune checkpoints with multi-modal single-cell screens

The paper uses multi-modal single-cell screens to identify regulators of PD-L1 expression and develops a computational framework to improve analysis of perturbation data.

Comprehensive integration of single cell data

Seurat v3 finds scored mutual-nearest-neighbor anchors in canonical correlation space to integrate scRNA-seq batches and transfer labels, protein levels and transcriptome-wide expression across modalities.

Identification of biomarker and HPV strain for Cervical Cancer from pre-existing RNAseq data

The paper assesses HPViewer's performance on RNA-seq data for HPV strain detection and evaluates p16INK4a as a biomarker for cervical cancer using RNA-seq data from multiple sources.

HPViewer: Sensitive and specific genotyping of human papillomavirus in metagenomic DNA

HPViewer detects HPV types in metagenomic data with high sensitivity and specificity by masking shared sequences and using short reads instead of assembled contigs.

Fast functional annotation of metagenomic shotgun data by DNA alignment to a microbial gene catalog

The paper introduces a fast method for functional annotation of metagenomic shotgun data using DNA-DNA alignment to a microbial gene catalog, enabling efficient detection of differentially abundant gene functions.