Jay W. Shin

HARP integrates PBMC data from multiple studies to create a reference atlas with consensus annotations and identifies age, sex, and disease-related cellular modules.

The paper profiles NHD microglia and shows they adopt an antigen-presenting state without TREM2 dependence, triggering glial-to-neuronal changes.

The paper presents the first single-cell immune atlas of a Mainland Southeast Asian population, showing genetic ancestry shapes innate immune profiles and highlights sex-by-ancestry interactions in immune activation.

The paper performs a federated cis-eQTL meta-analysis across single-cell datasets to identify cell-type-specific genetic effects and link them to disease mechanisms.

The paper maps RNA-chromatin interactions in human prefrontal cortex, revealing co-regulatory changes linked to brain evolution and disease pathways.

The paper identifies ASCL1 as a key regulator of mTEC function and central tolerance by analyzing single-cell RNA sequencing data from thymoma patients and mouse models.

The paper develops a machine learning method to identify cis-regulatory element profiles and their sequence features during neuronal differentiation using single-cell ATAC-seq and RNA-seq data.

The paper identifies trans-contacting intronic RNAs (TIRs) in neuronal cells that form nuclear scaffolds called introsomes, influencing 3D genome organization and gene expression.

Bambu-Clump improves transcript discovery and quantification from single-cell and spatial long-read RNA-seq data by leveraging cell and cluster information.

This paper introduces CFC-seq and SALA to sequence non-poly(A) RNAs, identifies 39,425 novel transcriptional units, and reveals a genomic code governing enhancer RNA fate based on promoter architecture.

This study identifies FBXO22 deficiency as a cause of a pleiotropic syndrome with growth restriction and neurodevelopmental delay, linked to an epigenetic signature involving histone demethylase KDM4B.

The paper presents AIDA, a diverse single-cell RNA-seq atlas of immune cells, revealing sub-continental diversity impacts on immune cell properties and identifying functional genetic variants.

The paper identifies altered layer 1 astrocytes in schizophrenia using spatial and single-nucleus transcriptomics of the anterior cingulate cortex.

The paper constructs a single-cell atlas of transcribed cis-regulatory elements in the human genome, revealing gene regulation patterns and trait-gene relationships across cell populations.

The paper introduces scLinaX, a method to quantify X chromosome inactivation escape using scRNA-seq, revealing heterogeneity across cell types and tissues.

Monopogen calls single nucleotide variants from single-cell sequencing data, achieving high accuracy in germline variant detection and enabling ancestry inference and variant association analysis.

The paper performs knockdown of 200 lncRNAs in human iPS cells, identifies 36 with growth inhibition, and finds molecular phenotypes in 29.3% of cases, with higher agreement in molecular than cell growth phenotypes across cell types.

This study integrates human iPSC-derived microglia into midbrain organoids, enhancing neuronal maturation and functionality through effects on synaptic remodeling and excitability.

The paper establishes genetically modified mouse embryonic stem cell lines for autism spectrum disorder research and uses single-cell RNA sequencing to identify cell-type and CNV-specific molecular features.

This paper introduces sc-end5-seq and SCAFE to profile transcribed cis-regulatory elements in single cells, showing tCREs improve prediction of CRE interactions and disease heritability.

The paper identifies cis-interacting lncRNAs and their targets using RNA-chromatin and Hi-C data across 18 human cell types.

This study compares single-cell transcriptomes of human brainstem and midbrain organoids, identifying unique cell types and similarities with fetal midbrain data.

The paper uses single-cell RNA-sequencing to identify multiple neuronal cell types in human midbrain organoids, including dopaminergic, GABAergic, and glutamatergic neurons.

The paper presents FC-R2, an expanded transcriptome atlas of over 109,000 genes, including lncRNAs, and demonstrates its utility in analyzing gene expression across normal and diseased human samples.

This study develops human brainstem organoids containing neural crest cells and various neuron types, validated by single-cell RNA sequencing, proteomics, and electrophysiology.

This study introduces Convert-seq, a method combining scRNA-seq and ectopic gene expression to identify gene regulatory networks during cell reprogramming.

C1 CAGE detects transcription start sites and enhancer activity in lung cancer cells, revealing subpopulations with distinct responses to TGF-β and enhancer RNA dynamics.

The paper proposes the Human Cell Atlas project to catalog all human cell types through molecular profiling and connects this data with classical cellular descriptions.

The paper generates a single-cell RNA-seq dataset of HeLa cells labeled with Fucci reporters and provides an open workflow for data processing and quality control.