Author

Zitong He

Johns Hopkins UniversityORCID 0000-0002-9308-2003Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Organism:human· 2 Assay:whole-genome sequencing· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:differential expression· 1 Assay:DNA methylation· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Liliana FloreaiD· 3 shared Giulia Irene Maria PasquesiiD· 1 shared Guangyu YangiD· 1 shared Noelani Phillips· 1 shared Ou CheniD· 1 shared Sarven SabunciyaniD· 1 shared Wui Wang LuiiD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

7 top collaborators · 13 mutual co-author links

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3 shared papersBioinformatics

Liliana FloreaORCID

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Author profile →

3 papers

Recent·Most cited

Benchmarking foundation models for splice site and exon annotation

Zitong He, Liliana Florea

This study benchmarks foundation models for splice site and exon annotation, finding performance varies greatly depending on exon type and training data representation.

bioRxiv · Feb 23, 2026 · PreprintBioinformatics

MntJULiP and Jutils: Differential splicing analysis of RNA-seq data with covariates

Wui Wang Lui, Guangyu Yang, Zitong He, Liliana Florea

The paper introduces MntJULiP and Jutils for differential splicing analysis of RNA-seq data, incorporating covariates to identify age and sex-related splicing patterns in GTEx brain samples.

NAR Genomics and Bioinformatics · Sep 30, 2025Peer-reviewedBioinformatics

Predicting Alu exonization in the human genome with a deep learning model

Zitong He, Ou Chen, Noelani Phillips, Giulia Irene Maria Pasquesi, Sarven Sabunciyan, Liliana Florea

The paper develops a deep learning model, eXAlu, to predict Alu exonization events in the human genome and estimates their prevalence to be 55-110K, significantly higher than in GENCODE.

bioRxiv · Jan 3, 2024 · PreprintBioinformatics