This paper introduces a Bayesian framework for detecting circadian rhythmicity biomarkers across the genome, showing improved false discovery rate control and performance in RNA-sequencing data.

Briefings in Bioinformatics · Aug 31, 2025Peer-reviewedBioinformatics

New role of cardiomyocyte Bmal1 in the regulation of sex-specific heart transcriptomes

Xiping Zhang, Spencer B. Procopio, Haocheng Ding, Maya G. Semel, Elizabeth A. Schroder, Mark R. Viggars, Tanya S. Seward, Ping Du, Kevin G. Wu, Sidney R. Johnson, Abhilash Prabhat, David J. Schneider, Isabel G. Stumpf, Ezekiel R. Rozmus, Zhiguang Huo, , Karyn Ann Esser

This study shows that cardiomyocyte Bmal1 is essential for sex-specific gene expression in the adult mouse heart, as its loss reduces sex differences in circadian transcriptomes.

Function · Dec 9, 2024Peer-reviewedPhysiology

CosinorTest: An R Shiny App for Cosinor-model-based circadian and differential analysis in transcriptomic applications

Haocheng Ding, Yutao Zhang, Lingsong Meng, Chengguo Xing, Karyn Ann Esser, Zhiguang Huo

CosinorTest is an R Shiny app for circadian and differential analysis of transcriptomic data using Cosinor models, offering tools for rhythmicity detection, differential pattern assessment, and visualization.

bioRxiv · Nov 6, 2024 · PreprintBioinformatics

AB-free kava enhances resilience against the adverse health effects of tobacco smoke in mice

Tengfei Bian, Allison M. Lynch, Kayleigh Ballas, Jessica Mamallapalli, Breanne Freeman, Alexander Scala, Yifan Wang, Hussein Traboulsi, Ranjith kumar Chellian, Amy Fagan, Zhixin Tang, Haocheng Ding, Umasankar De, Kristianna M. Fredenburg, Zhiguang Huo, , Chengguo Xing

This study evaluates AB-free kava's effects on tobacco smoke-exposed mice, showing it mitigates health deficits with safety, suggesting potential for reducing tobacco-related harm.

ACS Pharmacology & Translational Science · Oct 2, 2024Peer-reviewedPharmacology & Toxicology

Profiling plasma extracellular vesicle-derived microRNAs for noninvasive diagnosis of alpha-1 antitrypsin deficiency associated liver disease

Regina A. Oshins, Zhiguang Huo, Brittney Poole, Virginia Clark, Huiping Zhou, Jesse West, Matthew Wheeler, Mahya Aghaee, Mei He, Mark Brantly, Nazli Khodayari

This study identifies miRNA biomarkers in plasma extracellular vesicles for noninvasive detection of AATD liver disease, achieving an AUC of 0.751 with a four-miRNA model.

bioRxiv · Aug 31, 2023 · PreprintMolecular Biology

Defining the age-dependent and tissue-specific circadian transcriptome in male mice

Christopher A. Wolff, Miguel A. Gutierrez‐Monreal, Lingsong Meng, Xiping Zhang, Lauren G. Douma, Hannah M. Costello, Collin M. Douglas, Elnaz Ebrahimi, Ann T. Pham, Aline Cristina da Silva Oliveira, Chunhua Fu, Amy Nguyen, Bryan R. Alava, Stuart J. Hesketh, Andrew R. Morris, , Karyn Ann Esser

This study identifies age-dependent and tissue-specific changes in the circadian transcriptome of male mice, showing reduced rhythmic gene expression and increased variability in aged tissues.

Cell Reports · Jan 1, 2023Peer-reviewedGenomics

Statistical Methods for Detecting Circadian Rhythmicity and Differential Circadian Patterns with Repeated Measurement in Transcriptomic Applications

Haocheng Ding, Lingsong Meng, Chengguo Xing, Karyn Ann Esser, Zhiguang Huo

The paper develops linear mixed model methods to detect circadian rhythmicity and differential circadian patterns using repeated measurements, showing improved statistical power and validity.

bioRxiv · Jun 5, 2022 · PreprintBioinformatics

Experimental Design and Power Calculation in Omics Circadian Rhythmicity Detection

Wei Zong, Marianne L. Seney, Kyle D. Ketchesin, Michael T. Gorczyca, Andrew C. Liu, Karyn Ann Esser, George C. Tseng, Colleen A. McClung, Zhiguang Huo

This paper introduces CircaPower, a statistical method for power calculation in circadian rhythmicity detection, validated through simulations and real data.

bioRxiv · Jan 19, 2022 · PreprintGenomics

NF-κB modifies the mammalian circadian clock through interaction with the core clock protein BMAL1

Yang Shen, Mehari Endale, Wei Wang, Andrew R. Morris, Lauren J. Francey, Rachel L. Harold, David W. Hammers, Zhiguang Huo, Carrie L. Partch, John B. Hogenesch, Zhao‐Hui Wu, Andrew C. Liu

This study shows NF-κB interacts with BMAL1 to regulate circadian clock function through transcriptional repression at E-box elements.

PLoS Genetics · Nov 22, 2021Peer-reviewedMolecular Biology

Likelihood-based Tests for Detecting CircadianRhythmicity and Differential Circadian Patterns in Transcriptomic Applications

Haocheng Ding, Lingsong Meng, Andrew C. Liu, Michelle L. Gumz, Andrew J. Bryant, Colleen A. McClung, George C. Tseng, Karyn Ann Esser, Zhiguang Huo

This paper introduces likelihood-based methods to detect circadian rhythmicity and differential circadian patterns in transcriptomic data, showing improved error control and power in simulations and real data.

Briefings in Bioinformatics · May 24, 2021Peer-reviewedBioinformatics

Metabolites associated with early cognitive changes implicated in Alzheimer’s disease

Burcu F. Darst, Zhiguang Huo, Erin McMullen Jonaitis, Rebecca L. Koscik, Lindsay R. Clark, Qiongshi Lu, William S. Kremen, Carol E. Franz, Brinda K. Rana, Michael J. Lyons, Kirk J. Hogan, Jinying Zhao, Sterling C. Johnson, Corinne D. Engelman

The paper identifies seven metabolites associated with executive function decline in early Alzheimer’s disease using longitudinal plasma samples from the WRAP cohort.

Journal of Alzheimer s Disease · Jan 8, 2021Peer-reviewedNeuroscience