Statistical Methodology

Feng H, Jin P, Wu H. Disease prediction by cell-free DNA methylation. Briefings in Bioinformatics. doi: 10.1093/bib/bby029. 2018.

Zhang WW, Feng H, Wu H, Zheng XQ. Accounting for tumor purity improves cancer subtype classification from DNA methylation data. Bioinformatics. 33 (17), 2651-2657. doi: 10.1093/bioinformatics/btx303. 2017.

Wu H, Xu T, Feng H, Chen L, Li B, Yao B, Qin ZS, Jin P, Conneely KN. Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates. Nucleic Acids Research 43 (21): e141. doi: 10.1093/nar/gkv715. 2015.

Feng H, Conneely KN, Wu H. A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data. Nucleic Acids Research 42 (8): e69. doi: 10.1093/nar/gku154. 2014.

† = co-first authorship; these authors contributed equally

Protocol

Feng H, Wu H. Differential methylation analysis for bisulfite sequencing using DSS. Quantitative Biology. To appear. 2019

Collaborative

Kennedy EM, Powell DR, Li Z, Bell JSK, Barwick BG, Feng H, McCrary MR, Dwivedi B, Kowalski J, Dynan WS, Conneely KN, Vertino PM (2018) Galactic cosmic radiation induces persistent epigenome alterations relevant to human lung cancer. Scientific Reports doi: 10.1038/s41598-018-24755-8

Qin Y, Feng H, Chen M, Wu H and Zheng X (2018) InfiniumPurify: An R package for estimating and accounting for tumor purity in cancer methylation research. Genes & Diseases Volume 5, Issue 1, pages 43-45. doi: 10.1016/j.gendis.2018.02.003

Almli L, Lori A, Meyers J, Shin J, Fani N, Maihofer A, Nievergelt C, Smith A, Mercer K, Kerley K Leveille J, Feng H, … , Conneely KN and Ressler K (2017) Problematic alcohol use associates with sodium channel and clathrin linker 1 (SCLT1) in trauma-exposed populations. Addiction biology doi: 10.1111/adb.12569

Zhang F, Hammack C, Ogden SC, Cheng Y, Lee EM, Wen Z, Qian X, Nguyen H, Li Y, Yao B, Xu M, Xu T, Chen L, Wang Z, Feng H, Huang W, Yoon K, Shan C, Huang L, Qin ZS, Christian KM, Shi PY, Xu M, Xia M, Zheng W, Wu H, Song H, Tang H, Ming G, Jin P (2016) Molecular signatures associated with ZIKV exposure in human cortical neural progenitors. Nucleic Acids Research doi: 10.1093/nar/gkw765

Kennedy E, Powell DR, Li Z, Bell JSK, Feng H, Dynan W, Dwivedi B, Kowalski J, Conneely KN and Vertino PM (2016) Space radiation exposure induces stable epigenome alterations relevant to human lung cancer. [abstract nr B08] Cancer Research doi: 10.1158/1538-7445.CHROMEPI15-B08

Almli LM, Duncan R, Feng H, Ghosh D, Binder EB, Bradley B, Ressler KJ, Conneely KN, Epstein MP (2014) Correcting systematic inflation in genetic association tests that consider interaction effects: application to a genome-wide association study of posttraumatic stress disorder. JAMA Psychiatry 71(12):1392-9. doi: 10.1001/jamapsychiatry.2014.1339

Almli LM, Srivastava A, Fani N, Kerley K, Mercer KB, Feng H, Bradley B, Ressler KJ (2014) Correspondence. Biological psychiatry 76(4): e3-e4. doi: 10.1016/j.biopsych.2014.01.017

Almli LM, Mercer KB, Kerley K, Feng H, Bradley B, Conneely KN, Ressler KJ (2013) ADCYAP1R1 genotype associates with post-traumatic stress symptoms in highly traumatized African-American females. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics doi: 10.1002/ajmg.b.32145