computer-science

January 19, 2025. Class Location: James S. Thomas (JST) Building 225, 400 Magnolia St, Claflin University, South Carolina, USA; Timings: Monday-Friday, 10AM-5PM.

This is the class content for BIOL 620. The GitHub link is Here

Bioinformatics:

https://youtu.be/G6Xh9QJQrjA

https://youtu.be/UlU8GlZP7GU

https://youtu.be/YVMVhcDCMY8

https://youtu.be/OTGJ4355zCQ

https://youtu.be/EYZgSvCS858

https://youtu.be/kGaQ2mG4-9g

https://youtu.be/kIxlNUeG-38

https://youtu.be/bmWCnSMhUDk

https://youtu.be/7UOA1hC2V5k

Phylogenetic Analysis: https://youtu.be/IMIP4la-K84

https://youtu.be/UEsXMfE_7Rg Student Evaluations (2021-2026).

Semester class review: https://youtu.be/Pju8ecWWRAw

Github: https://github.com/spawar2/BTEC-620-Spring-2023

Bioinformatics (topics including Introduction to genomics/proteomics/bioinformatics, pairwise sequence alignment algorithms, scoring matrices, microarray analysis, phylogenetic analysis, bootstrapping, tree building, secondary & tertiary structure prediction, homology modeling, and protein folding)], visualization: heat maps, volcano plots, pie charts, Sequence alignments (Margaret Dayhoff, PAM, blossom scoring matrices, global & local alignment). Gene Expression Omnibus (GEO) datasets mining, Data Visualization (BoxPlots, Scatter Plots), Gene expression Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis. Message-Digest Algorithm 5. File formats (Fasta, etc.). National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) techniques, Sequence alignments (Margaret Dayhoff, PAM, Blossom scoring matrices, global & local alignment): https://youtu.be/Lx1jkr3UKwA

https://campuspress.yale.edu/shrikantpawar/files/2024/05/Student-Evaluations-2021-2024-3df60a3eaf357f31.pdf

https://campuspress.yale.edu/shrikantpawar/files/2025/02/Assignment3-Database-mining-300x98.png

https://campuspress.yale.edu/shrikantpawar/files/2025/03/Microarray-Analysis-300x74.png

https://campuspress.yale.edu/shrikantpawar/files/2025/04/Microarray-analysis-2-1-300x145.png

https://campuspress.yale.edu/shrikantpawar/files/2025/04/Raw-Microarray-Plot.pdfhttps://campuspress.yale.edu/shrikantpawar/files/2025/04/Microarray-analysis-2-2-300x124.png https://campuspress.yale.edu/shrikantpawar/files/2025/04/Normalized-plot.pdf

https://campuspress.yale.edu/shrikantpawar/files/2025/04/Microarray-Analysis-300x143.png

https://campuspress.yale.edu/shrikantpawar/files/2025/04/Fold_changes.csv

https://campuspress.yale.edu/shrikantpawar/files/2025/04/Phylogenetic-Analysis-300x217.png

https://campuspress.yale.edu/shrikantpawar/files/2025/04/Phylogenetic-tree.pdf

https://campuspress.yale.edu/shrikantpawar/files/2025/04/unrooted.pdf

https://campuspress.yale.edu/shrikantpawar/files/2025/04/sample.fasta_-300x69.png

https://github.com/spawar2/BIOL301/blob/main/Sep%208.Rd