For the most up-to-date publications, please see my Google Scholar


Statistical Methodology Publications

Guanqun Meng, Yue Pan, Wen Tang, Lijun Zhang, Ying Cui, Fredrick R. Schumacher, Ming Wang, Rui Wang, Sijia He, Jeffrey Krischer, Qian Li*, Hao Feng*. imply: improving cell-type deconvolution accuracy using personalized reference profiles. (2024). Genome Medicine.

Zhenxing Guo, Daoyu Duan, Wen Tang, Julia Zhu, William S. Bush, Liangliang Zhang, Xiaofeng Zhu, Fulai Jin, Hao Feng*. magpie: a power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing. (2024). PLOS Computational Biology.

Hao Feng*, Guanqun Meng, Tong Lin, Hemang Parikh, Yue Pan, Ziyi Li, Jeffery Krischer, Qian Li*. ISLET: individual-specific reference panel recovery improves cell-type-specific inference. (2023). Genome Biology.

Daoyu Duan, Wen Tang, Runshu Wang, Zhenxing Guo*, Hao Feng*. Evaluation of epitranscriptome-wide N6-methyladenosine differential analysis methods. (2023). Briefings in Bioinformatics.

Guanqun Meng, Wen Tang, Emina Huang, Ziyi Li, Hao Feng*. A comprehensive assessment of cell type-specific differential expression methods in bulk data. (2023). Briefings in Bioinformatics.

Daoyu Duan, Sijia He, Emina Huang, Ziyi Li*, Hao Feng*. NeuCA web server: a neural network-based cell annotation tool with web-app and GUI. (2022). Bioinformatics.

Ziyi Li*, Hao Feng*. A neural network-based method for exhaustive cell label assignment using single cell RNA-seq data. (2022). Scientific Reports.

Hao Feng, Hao Wu. Differential methylation analysis for bisulfite sequencing using DSS. (2019). Quantitative Biology.

Hao Feng, Peng Jin, Hao Wu. Disease prediction by cell-free DNA methylation. (2018). Briefings in Bioinformatics.

Weiwei Zhang, Hao Feng, Hao Wu, Xiaoqi Zheng. Accounting for tumor purity improves cancer subtype classification from DNA methylation data. (2017). Bioinformatics.

Hao Feng, Karen N. Conneely, Hao Wu. A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data. (2014). Nucleic Acids Research.

† = co-first authorship; these authors contributed equally

* = corresponding authorship


Book Chapter

Hao Feng, Karen Conneely & Hao Wu. Differential Methylation Analysis for Bisulfite Sequencing (BS-Seq) Data. (2022). Epigenome-Wide Association Studies Part of the Methods in Molecular Biology book series. Humana Press, Springer.


Team Science Publications

Daxuan Deng, Lijun Zhang, Hao Feng, Vern M. Chinchilli, Chixiang Chen, Ming Wang. Improving Estimation Efficiency for Survival Data Analysis by Integrating a Coarsened Time-to-Event Outcome from an External Study. (2023) Submitted.

Ximena Ruden, Aditi Singh, Teya Marben, Wen Tang, Awoniyi Awpnuga, Douglas Ruden, Elizabeth Puscheck, Hao Feng, Daniel Rappolee. A single cell transcriptomic fingerprint of stressed premature, imbalanced differentiation of embryonic stem cells. (2023) Submitted.

Moeez Rathore, Michel’le Wright, Wei Huang, Daniel Martin, Derek Taylor, Masaru Miyagi, Wen Tang, Hao Feng, Yamu Li, Zhenghe Wang, Lee M Ellis, Jordan Winter, Stephen E Moss, John Greenwood, Rui Wang. LRG1 is a novel HER3 ligand to promote growth in colorectal cancer. (2023) Submitted.

Daxuan Deng, Vern M. Chinchilli, Hao Feng, Chixiang Chen, Ming Wang. Robust Integration of Secondary Data Information into Main Outcome Analysis in the Presence of Missing Data. (2023) Submitted.

Wenzhang Wang, Fanpeng Zhao, Yubing Lu, Sandra L. Siedlak, Hisashi Fujioka, Hao Feng, George Perry, Xiongwei Zhu. Damaged Mitochondria Coincide with Presynaptic Vesicle Loss and Abnormalities in Alzheimer’s Disease Brain. (2023). Acta Neuropathologica Communications.

Moeez Rathore, Wei Zhang, Michel’le Wright, Mehrdad Zarei, Ali Vaziri-Gohar, Omid Hajihassani, Ata Abbas, Hao Feng, Jonathan Brody, Sandy D. Markowit, Jordan Winter, Rui Wang. Liver Endothelium Microenvironment Promotes HER3-mediated Cell Growth in Pancreatic Ductal Adenocarcinoma. (2022). Journal of Cancer Science and Clinical Therapeutics.

Grace E Weber, Maria Khrestian, Elizabeth D Tuason, Yvonne Shao, Jagan Pillai, Stephen Rao, Hao Feng, Yadi Zhou, Feixiong Cheng, Tara M DeSilva, Shaun Stauffer, James B Leverenz, Lynn M Bekris. Peripheral sTREM2-Related Inflammatory Activity Alterations in Early-Stage Alzheimer’s Disease. (2022). The Journal of Immunology.

Grace E Weber, Maria Khrestian, Elizabeth D Tuason, Yvonne Shao, Jagan A Pillai, Stephen M Rao, Hao Feng, Tara M DeSilva, Shaun Stauffer, James B Leverenz, Lynn M Bekris. Peripheral sTREM2-Related Inflammatory Activity Alterations in Early-Stage Alzheimer’s Disease. (2021). Alzheimer’s & Dementia.

Yunhee Kang, Ying Zhou, Yujing Li, Yanfei Han, Jie Xu, Weibo Niu, Ziyi Li, Shiying Liu, Hao Feng, Wen Huang, Ranhui Duan, Tianmin Xu, Nisha Raj, Feiran Zhang, Juan Dou, Chongchong Xu, Hao Wu, Gary J Bassell, Stephen T Warren, Emily G Allen, Peng Jin, Zhexing Wen. A human forebrain organoid model of fragile X syndrome exhibits altered neurogenesis and highlights new treatment strategies. (2021). Nature Neuroscience.

Bin Jiao, Mengli Wang, Hao Feng, Han Bao, Feiran Zhang, Hao Wu, Junling Wang, Beisha Tang, Peng Jin, Lu Shen. Downregulation of TOP2 modulates neurodegeneration caused by GGGGCC expanded repeats. (2021). Human Molecular Genetics.

Samaneh K Sarvestani, Steven Signs, Bo Hu, Yunku Yeu, Hao Feng, Ying Ni, David R Hill, Robert C Fisher, Sylvain Ferrandon, Reece K DeHaan, Jennifer Stiene, Michael Cruise, Tae Hyun Hwang, Xiling Shen, Jason R Spence, Emina H Huang. Induced organoids derived from patients with ulcerative colitis recapitulate colitic reactivity. (2021). Nature Communications.

E. M. Kennedy, D. R. Powell, Z. Li, J. S. K. Bell, B. G. Barwick, Hao Feng, M. R. McCrary, B. Dwivedi, J. Kowalski, W. S. Dynan, K. N. Conneely, P. M. Vertino. Galactic Cosmic Radiation Induces Persistent Epigenome Alterations Relevant to Human Lung Cancer. (2018). Scientific Reports.

Yufang Qin, Hao Feng, Ming Chen, Hao Wu, Xiaoqi Zheng. InfiniumPurify: An R package for estimating and accounting for tumor purity in cancer methylation research. (2018). Genes & Diseases.

Lynn M Almli, Adriana Lori, Jacquelyn L Meyers, Jaemin Shin, Negar Fani, Adam X Maihofer, Caroline M Nievergelt, Alicia K Smith, Kristina B Mercer, Kimberly Kerley, Jennifer M Leveille, Hao Feng, Duna Abu‐Amara, Janine D Flory, Rachel Yehuda, Charles R Marmar, Dewleen G Baker, Bekh Bradley, Karestan C Koenen, Karen N Conneely, Kerry J Ressler. Problematic alcohol use associates with sodium channel and clathrin linker 1 (SCLT1) in trauma‐exposed populations. (2017). Addiction Biology.

Feiran Zhang, Christy Hammack, Sarah C Ogden, Yichen Cheng, Emily M Lee, Zhexing Wen, Xuyu Qian, Ha Nam Nguyen, Yujing Li, Bing Yao, Miao Xu, Tianlei Xu, Li Chen, Zhiqin Wang, Hao Feng, Wei-Kai Huang, Ki-jun Yoon, Chao Shan, Luoxiu Huang, Zhaohui Qin, Kimberly M Christian, Pei-Yong Shi, Mingjiang Xu, Menghang Xia, Wei Zheng, Hao Wu, Hongjun Song, Hengli Tang, Guo-Li Ming, Peng Jin. Molecular signatures associated with ZIKV exposure in human cortical neural progenitors. (2016). Nucleic Acids Research.

E Kennedy, DR Powell, Z Li, JSK Bell, Hao Feng, W Dynan, B Dwivedi, J Kowalski, KN Conneely, PM Vertino. Space radiation exposure induces stable epigenome alterations relevant to human lung cancer. (2016). Cancer Research.

Hao Wu, Tianlei Xu, Hao Feng, Li Chen, Ben Li, Bing Yao, Zhaohui Steve Qin, Peng Jin, Karen N. Conneely. Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates. (2015). Nucleic Acids Research.

Lynn M Almli, Richard Duncan, Hao Feng, Debashis Ghosh, Elisabeth B Binder, Bekh Bradley, Kerry J Ressler, Karen N Conneely, Michael P Epstein. Correcting systematic inflation in genetic association tests that consider interaction effects: Application to a genome-wide association study of posttraumatic stress disorder. (2014). JAMA Psychiatry.

Lynn M Almli, Amita Srivastava, Negar Fani, Kimberly Kerley, Kristina B Mercer, Hao Feng, Bekh Bradley, Kerry J Ressler. Follow-up and Extension of a Prior Genome-wide Association Study of Posttraumatic Stress Disorder: Gene × Environment Associations and Structural Magnetic Resonance Imaging in a Highly Traumatized African-American Civilian Population. (2014). Biological Psychiatry.

Lynn M Almli, Kristina B Mercer, Kimberly Kerley, Hao Feng, Bekh Bradley, Karen N Conneely, Kerry J Ressler. ADCYAP1R1 genotype associates with post‐traumatic stress symptoms in highly traumatized African‐American females. (2013). American Journal of Medical Genetics Part B: Neuropsychiatric Genetics.


Thesis

Hao Feng. Statistical Methods for High-throughput Epigenomics Data. Ph.D. Dissertation. Emory University. 2019

Hao Feng. A Hierarchical Bayesian Approach to Detect Differentially Methylated Loci from Bisulfite Sequencing Data. Master’s Thesis. Emory University. 2013