Zhang J - Search Results

1

DeepVelo: Single-cell transcriptomic deep velocity field learning with neural ordinary differential equations.

Chen Z, King WC, Hwang A, Gerstein M, Zhang J. Chen Z, et al. Among authors: zhang j. Sci Adv. 2022 Dec 2;8(48):eabq3745. doi: 10.1126/sciadv.abq3745. Epub 2022 Nov 30. Sci Adv. 2022. PMID: 36449617 Free PMC article.

2

Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data.

Lee CY, Chen Y, Duan Z, Xu M, Girgenti MJ, Xu K, Gerstein M, Zhang J. Lee CY, et al. Among authors: zhang j. PLoS Comput Biol. 2022 Oct 27;18(10):e1010636. doi: 10.1371/journal.pcbi.1010636. eCollection 2022 Oct. PLoS Comput Biol. 2022. PMID: 36301997 Free PMC article.

3

Validation of Enhancer Regions in Primary Human Neural Progenitor Cells using Capture STARR-seq.

Gaynor-Gillett SC, Cheng L, Shi M, Liu J, Wang G, Spector M, Flaherty M, Wall M, Hwang A, Gu M, Chen Z, Chen Y, Consortium P, Moran JR, Zhang J, Lee D, Gerstein M, Geschwind D, White KP. Gaynor-Gillett SC, et al. Among authors: zhang j. bioRxiv [Preprint]. 2024 Mar 18:2024.03.14.585066. doi: 10.1101/2024.03.14.585066. bioRxiv. 2024. PMID: 38562832 Free PMC article. Preprint.

4

Translator: A Transfer Learning Approach to Facilitate Single-Cell ATAC-Seq Data Analysis from Reference Dataset.

Xu S, Skarica M, Hwang A, Dai Y, Lee C, Girgenti MJ, Zhang J. Xu S, et al. Among authors: zhang j. J Comput Biol. 2022 Jul;29(7):619-633. doi: 10.1089/cmb.2021.0596. Epub 2022 May 17. J Comput Biol. 2022. PMID: 35584295 Free PMC article.

5

DIRECT-NET: An efficient method to discover cis-regulatory elements and construct regulatory networks from single-cell multiomics data.

Zhang L, Zhang J, Nie Q. Zhang L, et al. Among authors: zhang j. Sci Adv. 2022 Jun 3;8(22):eabl7393. doi: 10.1126/sciadv.abl7393. Epub 2022 Jun 1. Sci Adv. 2022. PMID: 35648859 Free PMC article.

6

scEpiLock: A Weakly Supervised Learning Framework for cis-Regulatory Element Localization and Variant Impact Quantification for Single-Cell Epigenetic Data.

Gong Y, Srinivasan SS, Zhang R, Kessenbrock K, Zhang J. Gong Y, et al. Among authors: zhang r, zhang j. Biomolecules. 2022 Jun 23;12(7):874. doi: 10.3390/biom12070874. Biomolecules. 2022. PMID: 35883430 Free PMC article.

7

Transcriptomics of the depressed and PTSD brain.

Zhang J, Kaye AP, Wang J, Girgenti MJ. Zhang J, et al. Neurobiol Stress. 2021 Oct 11;15:100408. doi: 10.1016/j.ynstr.2021.100408. eCollection 2021 Nov. Neurobiol Stress. 2021. PMID: 34703849 Free PMC article.

8

iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease.

Duan Z, Dai Y, Hwang A, Lee C, Xie K, Xiao C, Xu M, Girgenti MJ, Zhang J. Duan Z, et al. Among authors: zhang j. PLoS Comput Biol. 2023 Sep 11;19(9):e1011444. doi: 10.1371/journal.pcbi.1011444. eCollection 2023 Sep. PLoS Comput Biol. 2023. PMID: 37695793 Free PMC article.

9

InsuLock: A Weakly Supervised Learning Approach for Accurate Insulator Prediction, and Variant Impact Quantification.

Srinivasan SS, Gong Y, Xu S, Hwang A, Xu M, Girgenti MJ, Zhang J. Srinivasan SS, et al. Among authors: zhang j. Genes (Basel). 2022 Mar 30;13(4):621. doi: 10.3390/genes13040621. Genes (Basel). 2022. PMID: 35456427 Free PMC article.

10

Integrated analysis of multimodal single-cell data with structural similarity.

Cao Y, Fu L, Wu J, Peng Q, Nie Q, Zhang J, Xie X. Cao Y, et al. Among authors: zhang j. Nucleic Acids Res. 2022 Nov 28;50(21):e121. doi: 10.1093/nar/gkac781. Nucleic Acids Res. 2022. PMID: 36130281 Free PMC article.

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