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2021
Gene Expression Analysis through Parallel Non-Negative Matrix Factorization
Computation
2021
Simultaneous Learning the Dimension and Parameter of a Statistical Model with Big Data
Statistics in Biosciences
2021
The triumphs and limitations of computational methods for scRNA-seq
Nature Methods
2021
SC-JNMF: single-cell clustering integrating multiple quantification methods based on joint non-negative matrix factorization
PeerJ
2021
Single-Cell Transcriptomic Heterogeneity in Invasive Ductal and Lobular Breast Cancer Cells
Cancer Research
2021
From bench to bedside: Single-cell analysis for cancer immunotherapy
Cancer Cell
2021
scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling
Bioinformatics
2021
Similarity and Dissimilarity Regularized Nonnegative Matrix Factorization for Single-Cell RNA-seq Analysis
Interdisciplinary Sciences: Computational Life Sciences
2020
CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures
BMC Bioinformatics
2020
Joint learning dimension reduction and clustering of single-cell RNA-sequencing data
Bioinformatics
2020
Interpretable factor models of single-cell RNA-seq via variational autoencoders
Bioinformatics
2020
Exploring generative deep learning for omics data using log-linear models
Bioinformatics
2020
Single‐cell transcriptomics uncover distinct innate and adaptive cell subsets during tissue homeostasis and regeneration
Journal of Leukocyte Biology
2020
Evaluation of Cell Type Annotation R Packages on Single-cell RNA-seq Data
Genomics, Proteomics & Bioinformatics
2020
Non-invasive characterization of human bone marrow stimulation and reconstitution by cell-free messenger RNA sequencing
Nature Communications
2020
BEM: Mining Coregulation Patterns in Transcriptomics via Boolean Matrix Factorization
Bioinformatics
2020
An Adaptive Sparse Subspace Clustering for Cell Type Identification
Frontiers in Genetics
2019
Single-Cell Omics
2019
Single-Cell RNA Sequencing Data Interpretation by Evolutionary Multiobjective Clustering
IEEE/ACM Transactions on Computational Biology and Bioinformatics
2019
DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data
Genome Biology
2019
Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species
Cell Systems
2019
Unified single-cell analysis of testis gene regulation and pathology in five mouse strains
eLife
2019
De novo prediction of cell-type complexity in single-cell RNA-seq and tumor microenvironments
Life Science Alliance
2019
Single-cell RNA-seq interpretations using evolutionary multiobjective ensemble pruning
Bioinformatics
2018
The Human Cell Atlas: Technical approaches and challenges
Briefings in Functional Genomics
2018
Enter the Matrix: Factorization Uncovers Knowledge from Omics
Trends in Genetics
2018
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
2018
Detection of correlated hidden factors from single cell transcriptomes using Iteratively Adjusted-SVA (IA-SVA)
Scientific Reports
2018
Metabotypes Related to Meat and Vegetable Intake Reflect Microbial, Lipid and Amino Acid Metabolism in Healthy People
Molecular Nutrition & Food Research
2018
2018 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)
2018
Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance
Genome Medicine
2018
Single-cell RNA sequencing for the study of development, physiology and disease
Nature Reviews Nephrology
2017
Single cell transcriptome analysis of muscle satellite cells reveals widespread transcriptional heterogeneity
Gene
2017
Using single‐cell multiple omics approaches to resolve tumor heterogeneity
Clinical and Translational Medicine
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