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Genome Biology|July 11, 2023
CMOT: Cross-Modality Optimal Transport for multimodal inferenceSayali Anil Alatkar, Daifeng WangBiorxiv : the Preprint Server for Biology|February 3, 2025
ARTEMIS integrates autoencoders and Schrödinger Bridges to predict continuous dynamics of gene expression, cell population and perturbation from time-series single-cell dataSayali Anil Alatkar, Daifeng WangBioinformatics (Oxford, England)|October 8, 2020
Varmole: a biologically drop-connect deep neural network model for prioritizing disease risk variants and genesNam D Nguyen, Ting Jin, Daifeng WangBMC Cancer|December 8, 2017
Comparative gene co-expression network analysis of epithelial to mesenchymal transition reveals lung cancer progression stagesDaifeng Wang, John D Haley, Patricia ThompsonNature Computational Science|April 28, 2022
A deep manifold-regularized learning model for improving phenotype prediction from multi-modal dataNam D Nguyen, Jiawei Huang, Daifeng WangNature Machine Intelligence|August 23, 2024
Joint variational autoencoders for multimodal imputation and embeddingNoah Cohen Kalafut, Xiang Huang, Daifeng WangBiorxiv : the Preprint Server for Biology|July 1, 2024
Single-cell multi-omics analysis reveals cooperative transcription factors for gene regulation in oligodendrocytesJerome J Choi, John Svaren, Daifeng WangCommunications Biology|February 5, 2025
CoTF-reg reveals cooperative transcription factors in oligodendrocyte gene regulation using single-cell multi-omicsJerome J Choi, John Svaren, Daifeng WangIEEE/ACM Transactions on Computational Biology and Bioinformatics|April 10, 2017
Multiple-Swarm Ensembles: Improving the Predictive Power and Robustness of Predictive Models and Its Use in Computational BiologyPedro Alves, Shuang Liu, Daifeng Wang, et al.Biorxiv : the Preprint Server for Biology|November 24, 2025
Dynamic landscapes of gene regulatory networks in early mammalian neurogenesis: Insights into brain evolution and disorder riskKalpana Hanthanan Arachchilage, Ryan D Risgaard, Jie Sheng, et al.Pageof 89