Binomial models uncover biological variation during feature selection of droplet-based single-cell RNA sequencing.

Autor: Sparta B; Department of Integrative Biology and Physiology, University of California, Los Angeles, California, United States of America.; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America., Hamilton T; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America.; Bioinformatics Interdepartmental Program, University of California, Los Angeles, California, United States of America., Natesan G; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America., Aragones SD; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America., Deeds EJ; Department of Integrative Biology and Physiology, University of California, Los Angeles, California, United States of America.; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America.

Publikováno v: PLoS computational biology [PLoS Comput Biol] 2024 Sep 06; Vol. 20 (9), pp. e1012386. Date of Electronic Publication: 2024 Sep 06 (Print Publication: 2024).

Clustering and visualization of single-cell RNA-seq data using path metrics.

Autor: Manousidaki, Andriana¹ (AUTHOR), Little, Anna² (AUTHOR) little@math.utah.edu, Xie, Yuying^1,3 (AUTHOR) little@math.utah.edu

Publikováno v: PLoS Computational Biology. 5/29/2024, Vol. 20 Issue 5, p1-19. 19p.

High order expression dependencies finely resolve cryptic states and subtypes in single cell data.

Autor: Jansma A; MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK.; Higgs Centre for Theoretical Physics, School of Physics & Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK., Yao Y; MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK.; School of Informatics, University of Edinburgh, Edinburgh, EH8 9AB, UK., Wolfe J; MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK., Del Debbio L; Higgs Centre for Theoretical Physics, School of Physics & Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK., Beentjes SV; MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK.; School of Mathematics, University of Edinburgh, Edinburgh, EH9 3FD, UK., Ponting CP; MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK. chris.ponting@ed.ac.uk., Khamseh A; MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK. ava.khamseh@ed.ac.uk.; Higgs Centre for Theoretical Physics, School of Physics & Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK. ava.khamseh@ed.ac.uk.; School of Informatics, University of Edinburgh, Edinburgh, EH8 9AB, UK. ava.khamseh@ed.ac.uk.

Publikováno v: Molecular systems biology [Mol Syst Biol] 2025 Jan 02. Date of Electronic Publication: 2025 Jan 02.

Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods.

Autor: Bulygin, Ivan, Shatov, Vladislav, Rykachevskiy, Anton, Raiko, Arsenii, Bernstein, Alexander, Burnaev, Evgeny, Gelfand, Mikhail S.

Publikováno v: PeerJ; Sep2023, p1-30, 30p