Author

Ching‐Huang Ho

Benaroya Research InstituteORCID 0000-0001-8359-8068Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Organism:human· 4 Research Focus:differential expression· 3 Research Focus:gene regulatory network inference· 3 Approach:statistical model· 3 Assay:bulk RNA-seq· 2 Assay:ChIP-seq· 2 Approach:deep learning· 2 Research Focus:variant effect prediction· 2

Frequent Co-Authors

John P. RayiD· 3 shared Ryan TewheyiD· 3 shared Harshpreet ChandokiD· 2 shared Maxwell A. Dippel· 2 shared Susan KalesiD· 2 shared Adriana Estela Sedeño-CortésiD· 1 shared Andrew B. StergachisiD· 1 shared Andrew J. HendersoniD· 1 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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3 shared papersMicrobiology

John P. RayORCID

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4 papers

Recent·Most cited

MicrobiologybioRxivPreprintApr 6, 2026

Atlas of HIV cis-regulatory elements reveals extensive transcriptional variation across clades, isolates, and within individuals

Berkay ENGİN, Mohamed Yousry ElSadec, Joseph Alexander Finkelberg…·Juan I. Fuxman Bass

The paper creates a regulatory atlas of HIV-1 and HIV-2 by analyzing transcriptional variation across clades, isolates, and individuals using MPRAs and predictive models.

DOI 10.64898/2026.04.03.716403

humanbulk RNA-seq

𝕏 PostBluesky

GeneticsNature GeneticsPeer-reviewedSep 18, 2025

Linking candidate causal autoimmune variants to T cell networks using genetic and epigenetic screens in primary human T cells.

Ching‐Huang Ho, Maxwell A. Dippel, Meghan S. McQuade…·John P. Ray

The paper identifies 545 expression-modulating variants in CD4+ T cells linked to autoimmune diseases and shows they regulate genes in a lymphocyte activation network.

11 citationstop 2%

humanbulk RNA-seq

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GenomicsbioRxivPreprintJul 9, 2025

Expanding the DNA Motif Lexicon of the Transcriptional Regulatory Code

Jing‐Yu Fan, Virendra K. Chaudhri, Deepa Bisht…·Harinder Singh

The paper expands the DNA motif lexicon of transcriptional regulatory code by identifying composite elements and using a deep learning model to predict their activity and impact of variants.

1 citation

humanDNA methylation

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GenomicsbioRxivPreprintJun 14, 2024

Somatic epimutations cap genetic determinism in the human diploid chromatin epigenome

Mitchell Robert Vollger, Elliott G. Swanson, Shane J. Neph…·Andrew B. Stergachis

The paper introduces FIRE to comprehensively map haplotype-selective chromatin accessibility in diploid human genomes, revealing somatic epimutations that contribute to non-genetic chromatin alterations.

30 citations

humanChIP-seq

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