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Cells|February 25, 2023
SINFONIA: Scalable Identification of Spatially Variable Genes for Deciphering Spatial DomainsRui Jiang, Zhen Li, Yuhang Jia, et al.Genome Research|March 26, 2026
High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBONDKehan Lang, Chenyang Jia, Siyu Li, et al.Interdisciplinary Sciences, Computational Life Sciences|September 30, 2024
scCrab: A Reference-Guided Cancer Cell Identification Method based on Bayesian Neural NetworksHeyang Hua, Wenxin Long, Yan Pan, et al.Nature Communications|July 27, 2025
Triple-effect correction for Cell Painting data with contrastive and domain-adversarial learningChengwei Yan, Yu Zhang, Jiuxin Feng, et al.Briefings in Bioinformatics|December 13, 2022
RefTM: reference-guided topic modeling of single-cell chromatin accessibility dataZheng Zhang, Shengquan Chen, Zhixiang LinBMC Bioinformatics|September 17, 2020
EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomesXiaoyang Chen, Shengquan Chen, Rui JiangBriefings in Bioinformatics|March 17, 2025
Graph neural networks for single-cell omics data: a review of approaches and applicationsSijie Li, Heyang Hua, Shengquan ChenBioinformatics Advances|April 22, 2024
OpenAnnotateApi: Python and R packages to efficiently annotate and analyze chromatin accessibility of genomic regionsZijing Gao, Rui Jiang, Shengquan ChenBioinformatics (Oxford, England)|January 7, 2023
ASTER: accurately estimating the number of cell types in single-cell chromatin accessibility dataShengquan Chen, Rongxiang Wang, Wenxin Long, et al.Genomics, Proteomics & Bioinformatics|February 13, 2021
DeepCAPE: A Deep Convolutional Neural Network for the Accurate Prediction of EnhancersShengquan Chen, Mingxin Gan, Hairong Lv, et al.Pageof 71