Archive for February, 2025
Transformer | Nick Lane | W. W. Norton & Company
February 4, 2025Principal component analysis | Nature Reviews Methods Primers
February 4, 2025https://www.nature.com/articles/s43586-022-00184-w
Greenacre, M., Groenen, P. J. F., Hastie, T., D’Enza, A. I., Markos, A., & Tuzhilina, E. (2022). Principal component analysis. Nature Reviews Methods Primers, 2(1).
https://doi.org/10.1038/s43586-022-00184-w
Network Analysis as a Grand Unifier in Biomedical Data Science | Annual Reviews
February 4, 2025https://www.annualreviews.org/content/journals/10.1146/annurev-biodatasci-080917-013444
McGillivray, P., Clarke, D., Meyerson, W., Zhang, J., Lee, D., Gu, M., Kumar, S., Zhou, H., & Gerstein, M. (2018). Network analysis as a grand unifier in biomedical data science. Annual Review of Biomedical Data Science, 1(1), 153–180.
https://doi.org/10.1146/annurev-biodatasci-080917-013444
Lox vs. Smoked Salmon: What’s the Difference? | Vital Choice
February 4, 2025Pool, Gym, & Fitness Class Schedules at the West Side YMCA
February 4, 2025https://ymcanyc.org/locations/west-side-ymca/schedules
5 W 63rd St., New York, NY 10023
Scale-free networks – PubMed
February 3, 2025https://pubmed.ncbi.nlm.nih.gov/12701331/
Barabási, A., & Bonabeau, E. (2003). Scale-Free networks. Scientific American, 288(5), 60–69.
https://doi.org/10.1038/scientificamerican0503-60
Comprehensive integration of single-cell data – PMC
February 3, 2025https://pmc.ncbi.nlm.nih.gov/articles/PMC6687398/
(Description of cell type annotation. See fig. 1, which is explained in the beginning of Results section)
Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P., & Satija, R. (2019). Comprehensive integration of Single-Cell data. Cell, 177(7), 1888-1902.e21. https://doi.org/10.1016/j.cell.2019.05.031
Diffusion pseudotime robustly reconstructs lineage branching | Nature Methods
February 3, 2025https://www.nature.com/articles/nmeth.3971
Haghverdi, L., Büttner, M., Wolf, F. A., Buettner, F., & Theis, F. J. (2016). Diffusion pseudotime robustly reconstructs lineage branching. Nature Methods, 13(10), 845–848. https://doi.org/10.1038/nmeth.3971
(first page summarizes the Pseudotime algorithm)
Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data | Nature Protocols
February 3, 2025https://www.nature.com/articles/s41596-020-00409-w
(Single Cell overview; goes over every step)
Andrews, T. S., Kiselev, V. Y., McCarthy, D., & Hemberg, M. (2020). Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data. Nature Protocols, 16(1), 1–9.
https://doi.org/10.1038/s41596-020-00409-w
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