iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease
Duan, Ziheng, Dai, Yi, Hwang, Ahyeon, Lee, Cheyu, Xie, Kaichi, Xiao, Chutong, Xu, Min, Girgenti, Matthew J, Zhang, Jing
Published in PLoS computational biology (11.09.2023)
Published in PLoS computational biology (11.09.2023)
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Characterizing dysregulations via cell-cell communications in Alzheimer's brains using single-cell transcriptomes
Lee, Che Yu, Riffle, Dylan, Xiong, Yifeng, Momtaz, Nadia, Lei, Yutong, Pariser, Joseph M, Sikdar, Diptanshu, Hwang, Ahyeon, Duan, Ziheng, Zhang, Jing
Published in BMC neuroscience (13.05.2024)
Published in BMC neuroscience (13.05.2024)
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Single Cell Genomic Analysis Reveals Cell Type-Specific Molecular Signatures in the Human PTSD Prefrontal Cortex
Girgenti, Matthew, Zhang, Jing, Skarica, Mario, Hwang, Ahyeon, Xu, Ke, Young, Keith, Zhao, Hongyu, Sestan, Nenad, Krystal, John
Published in Biological psychiatry (1969) (01.05.2023)
Published in Biological psychiatry (1969) (01.05.2023)
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iHerd: an i ntegrative h i e rarchical graph r epresentation learning framework to quantify network changes and prioritize risk genes in d isease
Duan, Ziheng, Dai, Yi, Hwang, Ahyeon, Lee, Cheyu, Xie, Kaichi, Xiao, Chutong, Xu, Min, Girgenti, Matthew J, Zhang, Jing
Published in PLoS computational biology (01.09.2023)
Published in PLoS computational biology (01.09.2023)
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scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding
Duan, Ziheng, Xu, Siwei, Sai Srinivasan, Shushrruth, Hwang, Ahyeon, Lee, Che Yu, Yue, Feng, Gerstein, Mark, Luan, Yu, Girgenti, Matthew, Zhang, Jing
Published in Briefings in bioinformatics (22.01.2024)
Published in Briefings in bioinformatics (22.01.2024)
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Translator: A Trans fer L earning Approach to Facilitate Single-Cell AT AC-Seq Data Analysis fr o m R eference Dataset
Xu, Siwei, Skarica, Mario, Hwang, Ahyeon, Dai, Yi, Lee, Cheyu, Girgenti, Matthew J, Zhang, Jing
Published in Journal of computational biology (01.07.2022)
Published in Journal of computational biology (01.07.2022)
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Validation of Enhancer Regions in Primary Human Neural Progenitor Cells using Capture STARR-seq
Gaynor-Gillett, Sophia C, Cheng, Lijun, Shi, Manman, Liu, Jason, Wang, Gaoyuan, Spector, Megan, Flaherty, Mary, Wall, Martha, Hwang, Ahyeon, Gu, Mengting, Chen, Zhanlin, Chen, Yuhang, Consortium, PsychENCODE, Moran, Jennifer R, Zhang, Jing, Lee, Donghoon, Gerstein, Mark, Geschwind, Daniel, White, Kevin P
Published in bioRxiv : the preprint server for biology (18.03.2024)
Published in bioRxiv : the preprint server for biology (18.03.2024)
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