2024
Benchmarking Machine Learning Missing Data Imputation Methods in Large-Scale Mental Health Survey Databases
Preethi Prakash, Kelly Street, Shrikanth Narayanan, Bridget A Fernandez, Yufeng Shen, Chang Shu
medRxiv, https://doi.org/10.1080/17501911.2024.2343276
A review of single-cell transcriptomics and epigenomics studies in maternal and child health
Chang Shu, Kelly Street, Carrie V Breton, Theresa M Bastain and Melissa L Wilson
Epigenomics, https://doi.org/10.1080/17501911.2024.2343276
Predicting autism severity classification by machine learning models
Qi Zhang (advised by Chang Shu, Kelly Street and Nicholas Mancuso)
Department of Population and Public Health Sciences Master of Science Thesis
Climate factors associated with cancer incidence: An ecological study covering 33 cancers from population-based registries in 37 countries
Haowen Wang, Hongmei Zeng, Hui Miao, Chang Shu, Yuming Guo, John S Ji
PLOS Climate, 3(3), e0000362. https://doi.org/10.1371/journal.pclm.0000362
2022
Integrating de novo and inherited variants in over 42,607 autism cases identifies mutations in new moderate risk genes
Xueya Zhou*, Pamela Feliciano*, Chang Shu*, Tianyun Wang*, Irina Astrovskaya*, ... , Brian J O’Roak, Daniel H Geschwind, Jacob J Michaelson, Natalia Volfovsky, Evan E Eichler, Yufeng Shen, Wendy K Chung (*contribute equally)
Nature Genetics, 1-15. https://doi.org/10.1038/s41588-022-01148-2
Imputing cognitive impairment in SPARK, a large autism cohort
Chang Shu, LeeAnne Green Snyder, Yufeng Shen, Wendy K Chung & The SPARK Consortium
Autism research, 15(1), 156-170. https://doi.org/10.1002/aur.2622
Epigenome-wide association analyses of active injection drug use
Chang Shu, Andrew E Jaffe, Sarven Sabunciyan, Hongkai Ji, Jacquie Astemborski, Jing Sun, Kelly M Bakulski, David W Sosnowski, Shruti H Mehta, Gregory D Kirk, Brion S Maher
Drug and alcohol dependence, 235, 109431. https://doi.org/10.1016/j.drugalcdep.2022.109431
Differential expression of NPAS4 in the dorsolateral prefrontal cortex following opioid overdose
David W Sosnowski, Andrew E Jaffe, Ran Tao, Amy Deep-Soboslay, Chang Shu, Sarven Sabunciyan, Joel E Kleinman, Thomas M Hyde, Brion S Maher
Drug and Alcohol Dependence Reports, 3, 100040. https://doi.org/10.1016/j.dadr.2022.100040
Sex Difference and Interaction of SIRT1 and FOXO3 Candidate Longevity Genes on Life Expectancy: A 10-year Prospective Longitudinal Cohort Study
John S Ji, Linxin Liu, Chang Shu, Lijing L Yan, Yi Zeng
The Journals of Gerontology: Series A, 77(8), 1557-1563. https://doi.org/10.1093/gerona/glab378
2021
DNA methylation biomarker selected by an ensemble machine learning approach predicts mortality risk in an HIV-positive veteran population
Chang Shu, Amy C Justice, Xinyu Zhang, Vincent C Marconi, Dana B Hancock, Eric O Johnson, Ke Xu
Epigenetics, 1-13. https://doi.org/10.1080/15592294.2020.1824097
Epigenome-wide study of brain DNA methylation following acute opioid intoxication
Chang Shu, David W Sosnowski, Ran Tao, Amy Deep-Soboslay, Joel E Kleinman, Thomas M Hyde, Andrew E Jaffe, Sarven Sabunciyan, Brion S Maher
Drug and alcohol dependence, 221, 108658. https://doi.org/10.1016/j.drugalcdep.2021.108658
Interaction of greenness and polygenic risk score of Alzheimer's disease on risk of cognitive impairment
Xurui Jin, Chang Shu, Yi Zeng, Liming Liang, John S Ji
The Science of the total environment, 796, 148767. https://doi.org/10.1016/j.scitotenv.2021.148767
Gene–Environment Interaction of FOXO and Residential Greenness on Mortality Among Older Adults
Linxin Liu, Anna Zhu, Chang Shu, Yi Zeng, John S Ji
Rejuvenation Research, 24(1), 49-61. http://doi.org/10.1089/rej.2019.2301
2020
DNA methylation mediates the effect of cocaine use on HIV severity
Chang Shu, Amy C Justice, Xinyu Zhang, Zuoheng Wang, Dana B Hancock, Eric O Johnson, Ke Xu
Clinical Epigenetics 12, 140. https://doi.org/10.1186/s13148-020-00934-1
Comparison of methylation capture sequencing and Infinium MethylationEPIC array in peripheral blood mononuclear cells
Chang Shu, Xinyu Zhang, Bradley E Aouizerat, Ke Xu
Epigenetics and Chromatin, 13(1), 1-15. https://doi.org/10.1186/s13072-020-00372-6
Epigenome-wide association scan identifies methylation sites associated with HIV infection
Chang Shu, Andrew E Jaffe, Sarven Sabunciyan, Hongkai Ji, Jacquie Astemborski, Jing Sun, Kelly M Bakulski, Shruti H Mehta, Gregory D Kirk, Brion S Maher
Epigeneomics, 12(21), 1917-1927. https://doi.org/10.2217/epi-2020-0123
Single-cell transcriptome mapping identifies common and cell-type specific genes affected by acute delta9-tetrahydrocannabinol in humans
Ying Hu, Mohini Ranganathan, Chang Shu, Xiaoyu Liang, Suhas Ganesh, Awo Osafo-Addo, Chunhua Yan, Xinyu Zhang, Bradley E Aouizerat, John H Krystal, Deepak C D’Souza, Ke Xu
Scientific Reports, 10(1), 1-14. https://doi.org/10.1038/s41598-020-59827-1
Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data
Jovan Tanevski, Thin Nguyen, Buu Truong, Nikos Karaiskos, Mehmet Eren Ahsen, Xinyu Zhang, Chang Shu, Ke Xu, Xiaoyu Liang, ..., Pablo Meyer, DREAM SCTC Consortium
Life science alliance, 3(11). http://doi.org/10.26508/lsa.202000867
APOE ε4 modifies effect of residential greenness on cognitive function among older adults: a longitudinal analysis in China
Anna Zhu, Lijing Yan, Chang Shu, Yi Zeng, John S Ji
Scientific Reports 10, 82. https://doi.org/10.1038/s41598-019-57082-7
2014-2019
Examining the association between substance use disorder treatment and smoking cessation (2015)
Chang Shu, Benjamin Lê Cook
Addiction, 110(6), 1015-1024. https://doi.org/10.1111/add.12879
Presence of an epigenetic signature of prenatal cigarette smoke exposure in childhood (2016)
Christine Ladd-Acosta, Chang Shu, Brian K Lee, Nicole Gidaya, Alison Singer, Laura A Schieve, Diana E Schendel, Nicole Jones, Julie L Daniels, Gayle C Windham, Craig J Newschaffer, Lisa A Croen, Andrew P Feinberg, M Daniele Fallin
Environmental research, 144, 139-148. https://doi.org/10.1016/j.envres.2015.11.014
Trends in smoking among adults with mental illness and association between mental health treatment and smoking cessation (2014)
Benjamin Lê Cook, Geoff Ferris Wayne, E Nilay Kafali, Zimin Liu, Chang Shu, Michael Flores
JAMA, 311(2), 172-182. https://doi.org/10.1001/jama.2013.284985
NIDA Genomics Consortium White Paper: Coordinating Efforts Between Human and Animal Addiction Studies (2019)
Hannah M Cates, Chelsie E Benca‐Bachman, Giordano de Guglielmo, Sarah A Schoenrock, Chang Shu, Marsida Kallupi
Genes, Brain and Behavior, e12577. https://doi.org/10.1111/gbb.12577