Marcus Ho

Peripheral Complement C4 Protein in Schizophrenia: Association with Gene Copy Number and Immune Cell Subtypes

This study identifies C4 protein expression in neutrophils and monocytes in schizophrenia, linking it to C4A gene copy number only in patients.

Effect of cortisol on cortical organoids: Building a "stress in a dish" model system

This study develops a 'Stress-in-a-dish' model using cortical organoids to investigate the molecular effects of cortisol on gene expression and potential PTSD-related mechanisms.

Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex

The paper identifies 46,802 enhancers and 164 psychiatric disorder variants with regulatory effects in the developing cortex and organoids using massively parallel reporter assays and deep learning.

Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex

The paper generates a molecular neuroanatomical map of the human prefrontal cortex using spatial transcriptomics and single nucleus RNA-sequencing, revealing novel spatial domains and cell-cell interactions linked to psychiatric disorders.

The ENCODE Uniform Analysis Pipelines

ENCODE's containerised Workflow Description Language pipelines for ChIP-seq, ATAC-seq, DNase-seq, RNA-seq variants, Hi-C and bisulfite sequencing run on cloud or local clusters, with documented compute costs and provenance.

Network effects of the neuropsychiatric 15q13.3 microdeletion on the transcriptome and epigenome in human induced neurons

This study examines the transcriptome and epigenome effects of the 15q13.3 microdeletion in human induced neurons, identifying gene expression and pathway changes linked to neuropsychiatric disorders.

Complete and haplotype-specific sequence assembly of segmental duplication-mediated genome rearrangements using CRISPR-targeted ultra-long read sequencing (CTLR-Seq)

The paper introduces CTLR-Seq, a method to resolve complex genomic regions with high accuracy, and applies it to study CNVs associated with schizophrenia and autism.

Haplotype-phased common marmoset embryonic stem cells for genome editing using CRISPR/Cas9

This study provides haplotype-resolved genome characterization of a marmoset ESC line and demonstrates CRISPR/Cas9 targeting and neuronal differentiation capabilities.

Genome-wide molecular effects of the neuropsychiatric 16p11 CNVs in an iPSC-to-iN neuronal model

The paper investigates the molecular effects of 16p11.2 CNVs on gene expression and DNA methylation using an iPSC-to-iN model and identifies potential contributing genes.

SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata

The paper introduces SnoVault, a metadata storage system, and encodeD, a tool for genomic data storage, both designed for the ENCODE project's data management needs.