PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization

Integrated analysis of multimodal single-cell data

Yuhan Hao, Stephanie Hao, Erica Andersen‐Nissen et al. · Cell · 2021 · 14.9K citations · Full text

Gephi: An Open Source Software for Exploring and Manipulating Networks

Mathieu Bastian, Sébastien Heymann, Mathieu Jacomy · Proceedings of the International AAAI Conference on Web and Social Media · 2009 · 11K citations · Full text

Engineering, Interaction Network, Network Analysis +19

SCANPY: large-scale single-cell gene expression data analysis

F. Alexander Wolf, Philipp Angerer, Fabian J. Theis · Genome biology · 2018 · 8.6K citations · Full text

Variational Inference: A Review for Statisticians

Journal of the American Statistical Association · 2017 · 3.5K citations · Full text

Metagenes and molecular pattern discovery using matrix factorization

Jean-Philippe Brunet, Pablo Tamayo, Todd R. Golub et al. · Proceedings of the National Academy of Sciences · 2004 · 2.2K citations · Full text

Engineering, Machine Learning, Molecular Biology +21