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Genome Biology|May 21, 2021
MichiGAN: sampling from disentangled representations of single-cell data using generative adversarial networksHengshi Yu, Joshua D WelchMolecular Systems Biology|July 10, 2025
PerturbNet predicts single-cell responses to unseen chemical and genetic perturbationsHengshi Yu, Weizhou Qian, Yuxuan Song, et al.Communications in Statistics: Simulation and Computation|December 26, 2022
A note on the estimation and inference with quadratic inference functions for correlated outcomesHengshi Yu, Guangyu Tong, Fan LiContemporary Clinical Trials Communications|July 31, 2020
An evaluation of quadratic inference functions for estimating intervention effects in cluster randomized trialsHengshi Yu, Fan Li, Elizabeth L TurnerBioinformatics (Oxford, England)|May 13, 2022
PyLiger: scalable single-cell multi-omic data integration in PythonLu Lu, Joshua D WelchBioinformatics (Oxford, England)|January 17, 2025
Integrating single-cell multimodal epigenomic data using 1D convolutional neural networksChao Gao, Joshua D WelchBiorxiv : the Preprint Server for Biology|March 11, 2024
Integrating single-cell multimodal epigenomic data using 1D-convolutional neural networksChao Gao, Joshua D WelchThe Stata Journal|August 20, 2021
cvcrand and cptest: Commands for efficient design and analysis of cluster randomized trials using constrained randomization and permutation testsJohn A Gallis, Fan Li, Hengshi Yu, et al.Nature Communications|February 10, 2022
UINMF performs mosaic integration of single-cell multi-omic datasets using nonnegative matrix factorizationApril R Kriebel, Joshua D WelchGenome Biology|November 27, 2025
Molecular effects of transposable element sequences in mammalian cellsMing-Ching C Wen, Joshua D WelchPageof 7