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


Statistical Methodology Work

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. DOI: 10.1093/bioinformatics/btac108.

Ziyi Li, Hao Feng*. A neural network-based method for exhaustive cell label assignment using single cell RNA-seq data. (2022) Scientific Reports. DOI: 10.1038/s41598-021-04473-4.

Hao Feng, Hao Wu. Differential methylation analysis for bisulfite sequencing using DSS. (2019) Quantitative Biology. DOI: 10.1007/s40484-019-0183-8.

Hao Feng, Peng Jin, Hao Wu. Disease prediction by cell-free DNA methylation. (2018) Briefings in Bioinformatics. DOI: 10.1093/bib/bby029.

Weiwei Zhang, Hao Feng, Wu H, Zheng XQ. Accounting for tumor purity improves cancer subtype classification from DNA methylation data. (2017) Bioinformatics. DOI: 10.1093/bioinformatics/btx303.

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. DOI: 10.1093/nar/gku154.

† = co-first authorship; these authors contributed equally

* = corresponding authorship


Collaborative Work

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 DOI: 10.4049/jimmunol.2100771

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 DOI: 10.1002/alz.053211

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 DOI: 10.1038/s41593-021-00913-6

Bin Jiao, Mengli Wang, Hao Feng, Han Bao, Feiran Zhang, Hao Wu, Junling Wang, Beisha Tang, Peng Jin, Lu Shen. A human forebrain organoid model of fragile X syndrome exhibits altered neurogenesis and highlights new treatment strategies. (2021) Human Molecular Genetics DOI: 10.1093/hmg/ddab079

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. Galactic cosmic radiation induces persistent epigenome alterations relevant to human lung cancer. (2021) Nature Communications DOI: 10.1038/s41467-020-20351-5

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. (2018) Addiction Biology DOI: 10.1111/adb.12569

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 DOI: 10.1038/s41598-018-24755-8

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 DOI: 10.1016/j.gendis.2018.02.003

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. DOI: 10.1093/nar/gkw765.

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 DOI: 10.1158/1538-7445.CHROMEPI15-B08

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. DOI: 10.1093/nar/gkv715.

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. DOI: 10.1001/jamapsychiatry.2014.1339.

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. DOI: /10.1016/j.biopsych.2014.01.017.

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. DOI: 10.1002/ajmg.b.32145.


Book Chapter

Hao Feng, Karen Conneely & Hao Wu (2022). Differential Methylation Analysis for Bisulfite Sequencing (BS-Seq) Data. Epigenome-Wide Association Studies. DOI: 10.1007/978-1-0716-1994-0_16 Part of the Methods in Molecular Biology book series. Humana Press, Springer.


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