Applied Bioinformatics, BIOL441 Fall 2024 (4 credit) (5 students) *Graduate Class (Masters & Ph.D. Level): https://www.claflin.edu/ Claflin University, Orangeburg, South Carolina, United States of America. https://www.claflin.edu/academics-research/schools-departments/school-of-natural-sciences-and-mathematics/department-of-mathematics-computer-science/computer-science
January 9 2023.
This is the class content for BIOL441. The GitHub link is Here
Bioinformatics:
Phylogenetic Analysis: https://youtu.be/IMIP4la-K84
Semester class review: https://youtu.be/Pju8ecWWRAw
Github: https://github.com/spawar2/BTEC-620-Spring-2023
Bioinformatics (topics including Introduction to genomics/proteomics/bioinformatics, 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, Blast, Sequence alignments (Margaret Dayhoff, PAM, blossom scoring matrices, global & local alignment).Gene Expression Omnibus (GEO) datasets mining, 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. 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
Print statement: https://campuspress.yale.edu/shrikantpawar/files/2024/08/Screenshot-2024-08-19-at-9.51.47%E2%80%AFAM-300x61.png
Set working directory: https://campuspress.yale.edu/shrikantpawar/files/2024/08/Correlatin-300x187.png
https://campuspress.yale.edu/shrikantpawar/files/2024/09/Affy-Read-300x134.png
Raw microarray plot: https://campuspress.yale.edu/shrikantpawar/files/2024/09/Raw-data.pdf
Box plot code: https://campuspress.yale.edu/shrikantpawar/files/2024/09/Screenshot-2024-09-06-at-9.49.11%E2%80%AFAM-300x191.png
Robust Multiarray Normalized (RMA) plot: https://campuspress.yale.edu/shrikantpawar/files/2024/09/Nomalized-Plot.pdf
https://campuspress.yale.edu/shrikantpawar/files/2024/09/Program-300x207.png​https://campuspress.yale.edu/shrikantpawar/files/2024/09/Screenshot-2024-09-11-at-9.45.39%E2%80%AFAM-300x178.png
​Fold Change Analysis: https://campuspress.yale.edu/shrikantpawar/files/2024/09/Fold-Change-Analysis-Microarray-300x214.png
Phylogenetic-Analysis: https://campuspress.yale.edu/shrikantpawar/files/2024/09/Phylogenetic-Analysis-300x142.png
https://campuspress.yale.edu/shrikantpawar/files/2024/09/Phylogenetic-Analysis-1-300x206.png
https://campuspress.yale.edu/shrikantpawar/files/2024/09/Phylogenetic-tree.pdf
https://campuspress.yale.edu/shrikantpawar/files/2024/11/Unknown-Gene-Sequence-300x243.png
All Videos
All Videos
WorldS4 2023
Madhuhas-Stanford-Testimonial
K-Fold Semi-Supervised-Video
