The paper introduces Hi-Plex CUT&Tag, a method to detect co-localization of over 600 CRF pairs, enabling comprehensive analysis of chromatin regulatory interactions in a single experiment.

bioRxiv · Oct 6, 2025 · PreprintGenetics

Genetics of cardiovascular outcomes in individuals with chronic kidney disease: the Chronic Renal Insufficiency Cohort (CRIC) study

Jia Wen, Bridget M. Lin, Quan Sun, Min-Zhi Jiang, Gregorio V. Linchangco, Gang Li, R Chen, Alan S. Go, Tyne W. Miller‐Fleming, Megan M. Shuey, Debbie L. Cohen, Panduranga S. Rao, Mahboob Rahman, Nancy Jean Cox, James Phillip Lash, , Million Veteran Program and the CRIC Study Investigators

The paper performs GWAS on cardiovascular outcomes in CKD patients, identifying stroke-associated SNVs but not replicating CHD findings, and finding genetic correlations with published GWAS.

medRxiv · Feb 19, 2025 · PreprintGenetic & Genomic Medicine

A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies

Xihao Li, Han Chen, Margaret Sunitha Selvaraj, Eric Van Buren, Hufeng Zhou, Yuxuan Wang, Ryan Sun, Zachary Ryan McCaw, Zhi Yu, Min-Zhi Jiang, DANIEL A. DICORPO, Sheila M. Gaynor, Rounak Dey, Donna K. Arnett, Emelia J. Benjamin, , Amber L. Beitelshees

The paper introduces MultiSTAAR, a statistical framework for multi-trait rare variant analysis in WGS studies, identifying new lipid trait associations in diverse populations.

Nature Computational Science · Feb 7, 2025Peer-reviewedGenetics

Whole Genome Sequencing Based Analysis of Inflammation Biomarkers in the Trans-Omics for Precision Medicine (TOPMed) Consortium

Min-Zhi Jiang, Sheila M. Gaynor, Xihao Li, Eric Van Buren, A.M. Stilp, Erin Buth, Fei Fei Wang, Regina Manansala, Stephanie M. Gogarten, Zilin Li, Linda M. Polfus, Shabnam Salimi, Joshua C. Bis, Nathan Pankratz, Lisa R. Yanek, , TOPMed Inflammation Working Group

The paper analyzes inflammation biomarkers using whole-genome sequencing from the TOPMed consortium, identifying both single-variant and rare variant associations with inflammatory traits.

bioRxiv · Sep 10, 2023 · PreprintGenetics

Cell composition inference and identification of layer-specific spatial transcriptional profiles with POLARIS

Jiawen Carmen Chen, Tianyou Luo, Min-Zhi Jiang, Jiandong Liu, Gaorav P. Gupta, Yun Li

POLARIS infers cell composition from histology images and identifies layer-specific differentially expressed genes in spatial transcriptomics data.

bioRxiv · Dec 8, 2022 · PreprintGenetics

Uncovering Cross-Cohort Molecular Features with Multi-Omics Integration Analysis

Min-Zhi Jiang, François Aguet, Kristin Ardlie, Jiawen Carmen Chen, Elaine S. Cornell, Dan Cruz, Peter Durda, Stacey Gabriel, Robert Edgardo Gerszten, Xiuqing Guo, Craig W Johnson, Silva Kasela, Leslie A. Lange, Tuuli Lappalainen, Yongmei Liu, , TOPMed Analysis Working Group

This paper improves multi-omics integration by enhancing orthogonality in canonical vectors and demonstrates transferability across cohorts for proteomics and methylomics data.

bioRxiv · Nov 10, 2022 · PreprintGenomics

A comprehensive comparison on cell type composition inference for spatial transcriptomics data

Jiawen Chen, Weifang Liu, Tianyou Luo, Zhentao Yu, Min-Zhi Jiang, Jia Wen, Gaorav P. Gupta, Paola Giusti‐Rodríguez, Hongtu Zhu B, Yuchen Yang, Yun Li

This paper compares eight ST deconvolution methods using four real datasets to evaluate their performance in inferring cell type composition from spatial transcriptomics data.

Briefings in Bioinformatics · Jun 26, 2022Peer-reviewedGenetics

Whole genome sequencing identifies common and rare structural variants contributing to hematologic traits in the NHLBI TOPMed program

Marsha M. Wheeler, Adrienne M. Stilp, Shuquan Rao, Bjarni V. Halldórsson, Doruk Beyter, Jia Wen, Anna V. Mikhaylova, Caitlin McHugh, John Lane, Min-Zhi Jiang, Laura M. Raffield, Goo Jun, Fritz Joachim Sedlazeck, Ginger Metcalf, Yao Yao, , Alex P. Reiner

medRxiv · Dec 16, 2021 · PreprintGenetic & Genomic Medicine