Publications
Journal Publications #
Deep learning for psychiatric genomics: from tools to applications 📄
Junhao Liu, Siwei Xu, Dongbo Sun, Chaoyang Wang, Jing Zhang
Current Opinion in Genetics & Development
2026
Central amygdala single-nucleus atlas reveals chromatin and gene transcription dynamics in human alcohol use disorder 📄
Che Yu Lee et al.
Nature Communications
2026
Transcriptomic and Chromatin Dynamics of the Human PTSD Brain at Single Cell Resolution 📄
Matthew Girgenti et al.
European Neuropsychopharmacology
2025
Combined single-cell profiling of chromatin–transcriptome and splicing across brain cell types, regions and disease state 📄
Wen Hu et al.
Nature Biotechnology
2025
Single cell transcriptomic and chromatin dynamics of the human PTSD brain 📄
Ahyeon Hwang et al.
Nature
2025
Single-cell genomics and regulatory networks for 388 human brains 📄
Prashant S Emani et al.
Science
2024
scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding 📄
Ziheng Duan et al.
Briefings in Bioinformatics
2024
Translator: A Transfer Learning Approach to Facilitate Single-Cell ATAC-Seq Data Analysis from Reference Dataset 📄
Siwei Xu et al.
Journal of Computational Biology
2022
InsuLock: A Weakly Supervised Learning Approach for Accurate Insulator Prediction, and Variant Impact Quantification 📄
Shushrruth Sai Srinivasan et al.
Genes
2022
Integrating longitudinal clinical and microbiome data to predict growth faltering in preterm infants 📄
Jose Lugo-Martinez et al.
Journal of Biomedical Informatics
2022
Conference Publications #
Multimodal Cell Context Instruction Tuning for Conditional DNA Regulatory Sequence Generation with Large Language Models 📄
Junhao Liu et al.
IEEE International Conference on Image Processing (ICIP)
2025
CytoFlow: A Novel Computational Method to Construct Signal Transduction Networks at Single-Cell Resolution based on Flow Networks 📄
Yi Dai, Ziheng Duan, Siwei Xu, Jing Zhang
IEEE International Conference on Medical Artificial Intelligence (MedAI)
2024
Understanding Transcriptional Regulatory Redundancy by Learnable Global Subset Perturbations 📄
Junhao Liu et al.
Asian Conference on Machine Learning (ACML)
2024
iHAST: Integrating Hybrid Attention for Super-Resolution in Spatial Transcriptomics 📄
Xi Li, Jing Zhang, Ziheng Duan, Yi Dai, Siwei Xu
British Machine Vision Conference (BMVC)
2024
Learnable Subset Perturbations for Understanding Transcriptional Regulatory Redundancy 📄
Junhao Liu, Siwei Xu, Dylan Riffle, Ziheng Duan, Jing Zhang
NeurIPS 2024 Workshop on Data-driven and Differentiable Simulations, Surrogates, and Solvers
2024
scACT: Accurate Cross-modality Translation via Cycle-consistent Training from Unpaired Single-cell Data 📄
Siwei Xu, Junhao Liu, Jing Zhang
ACM International Conference on Information and Knowledge Management (CIKM)
2024
iMIRACLE: An Iterative Multi-View Graph Neural Network to Model Intercellular Gene Regulation From Spatial Transcriptomic Data 📄
Ziheng Duan, Siwei Xu, Cheyu Lee, Dylan Riffle, Jing Zhang
ACM International Conference on Information and Knowledge Management (CIKM)
2024
Consortium Publications #
The single-cell opioid responses in the context of HIV (SCORCH) consortium 📄
SCORCH Consortium
Molecular Psychiatry
2024
Transcriptomic sex differences in postmortem brain samples from patients with psychiatric disorders 📄
PsychENCODE Consortium
Science Translational Medicine
2024
Single-cell multi-cohort dissection of the schizophrenia transcriptome 📄
PsychENCODE Consortium
Science
2024
A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex 📄
PsychENCODE Consortium
Science
2024
Massively parallel characterization of regulatory elements in the developing human cortex 📄
PsychENCODE Consortium
Science
2024
Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain 📄
PsychENCODE Consortium
Science
2024
Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements 📄
PsychENCODE Consortium
Science Advances
2024
Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data 📄
PsychENCODE Consortium
Science Advances
2024
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