Publications

• Praxis-BGM: Clustering of Omics Data Using Semi-Supervised Transfer Learning for Gaussian Mixture Models via Natural-Gradient Variational Inference

  Q. Jia, J. A. Goodrich, D. V. Conti

  Bioinformatics, 42(6), btag395, 2026

  DOIFull textCode

• A False Discovery Rate Control Method Using a Fully Connected Hidden Markov Random Field for Neuroimaging Data

  T. Kim, Q. Jia, M. J. de Leon, H. Shu

  Medical Image Analysis, 113, 104158, 2026

  DOIarXiv

• Integrated Spheroid-to-Population Framework for Evaluating PFHpA-Associated Metabolic Dysfunction and Steatotic Liver Disease

  B. O. Baumert, A. C. Maretti-Mira, D. I. Walker, H. Wang, Q. Jia, et al.

  Research Square (preprint), 2025

  DOI

• The Potential Mediating Role of the Gut Microbiome and Metabolites in the Association Between PFAS and Kidney Function in Young Adults: A Proof-of-Concept Study

  H. E. Hampson, S. Li, D. I. Walker, H. Wang, Q. Jia, et al.

  Science of The Total Environment, 954, 176519, 2024

  DOI

• An Extension of Latent Unknown Clustering Integrating Multi-Omics Data (LUCID) Incorporating Incomplete Omics Data

  Y. Zhao, Q. Jia, J. Goodrich, B. Darst, D. V. Conti

  Bioinformatics Advances, vbae123, 2024

  DOICode

• LUCIDus: An R Package for Implementing Latent Unknown Clustering by Integrating Multi-omics Data (LUCID) With Phenotypic Traits

  Y. Zhao, Q. Jia, J. A. Goodrich, D. V. Conti

  The R Journal, 2024

  DOICode

• DeepFDR: A Deep Learning-based False Discovery Rate Control Method for Neuroimaging Data

  T. Kim, H. Shu, Q. Jia, M. J. de Leon

  Proceedings of Machine Learning Research (AISTATS), 238, 946, 2024

  PaperPDF

• Integrating Multi-Omics with Environmental Data for Precision Health: A Novel Analytic Framework and Case Study on Prenatal Mercury-Induced Childhood Fatty Liver Disease

  J. A. Goodrich, H. Wang, Q. Jia, N. Stratakis, Y. Zhao, L. Maitre, M. Bustamante, et al.

  Environment International, 108930, 2024

  DOI

• mFI-PSO: A Flexible and Effective Method in Adversarial Image Generation for Deep Neural Networks

  H. Shu, R. Shi, Q. Jia, H. Zhu, Z. Chen

  International Joint Conference on Neural Networks (IJCNN), 1–8, 2022

  DOICode

• BiTr-Unet: A CNN-Transformer Combined Network for MRI Brain Tumor Segmentation

  Q. Jia, H. Shu

  International MICCAI Brainlesion Workshop (BrainLes), 3–14, 2021

  DOIarXivCode

Presentations

• Praxis-BGM: A Prior-Augmented and Regularized Natural-Gradient Variational Inference on Gaussian Mixture Models

  Joint Statistical Meetings (JSM) 2025 · Nashville, TN · August 2025

  Code

• BiTr-Unet: A CNN-Transformer Combined Network for MRI Brain Tumor Segmentation for BraTS 2021

  Brain Lesion (BrainLes) Workshop 2021 · Virtual · September 2021

  Code

Software

• LUCIDus

  R package for latent unknown clustering by integrating multi-omics data with phenotypic traits.

  GitHubv3.0

• Praxis-BGM

  Prior-augmented, regularized natural-gradient variational inference on Gaussian mixture models.

  GitHubR interfacePaper

• BiTr-Unet

  CNN + vision transformer network for 3D MRI brain tumor segmentation.

  GitHub