The book with a nice explanation of suffix array and BWT is
Bioinformatics Algorithms: An Active Learning Approach by Phillip Compeau & Pavel Pevzner. https://www.bioinformaticsalgorithms.org/
Posts Tagged ‘cbb752’
Suffix Array and BWT Explaination
February 11, 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
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
Fast unfolding of communities in large networks – IOPscience
February 3, 2025Genome-wide association studies | Nature Reviews Methods Primers
January 25, 2025g accounts for the cumulative effect of all other variants on the phenotype besides the effect of the specific variant being tested (SNP s).
Although theoretically we should consider the effect of g when testing for GWAS associations, in practice don’t think this happens in standard GWAS tools, such as PLINK and REGENIE (see below).
PLINK: https://www.cog-genomics.org/plink/2.0/assoc
REGENIE: https://www.nature.com/articles/s41588-021-00870-7#Sec10
https://www.nature.com/articles/s43586-021-00056-9
linkstream2 microblog 