Glendale Community College Introduction to Bioinformatics

Introduction to the program, mentor introductions and resource account settings Associated online course/resource: Introduction to Bioinformatics Course, Access to the educational portal (edu.t-bio.info) &...

Course structure, expectations and intended outcomes. Topics: Applications of bioinformatics (Introduction to Bioinformatics Course), Examples in Biomedical Research, Pharma R & D and AgricultureAssociated...

Working with sequences DNA, RNA and Protein sequences Associated online course/resource: Working with DNA Sequences in

Pairwise sequence alignment Multiple sequence alignment Clinical Example of DNA variants Associated online course/resource: Introduction to Genomics

Technologies for DNA and RNA sequencing: Microarray, High Throughput Sequencing, qPCR (Introduction to Genomics Course), Advantages and applications of NGS: Illumina, Nanopore and PacBio...

Mapping on genome to separate tumor from microenvironment, Comparison of cancer subtypes (ER and TN), Finding Differentially Expressed Genes Associated online course/resource: Patient Derived...

mRNA library preparation, Mapping on transcriptome TopHat, HiSat, Bowtie 2G, Sailfish, Methods of RNA quantification Associated online course/resource: Transcriptomics 1

Loading CSV, Excel or TXT files. Determine numeric and non-numeric data types. Preparing a matrix and a data frame. Creating variables.  Associated online course/resource:...

Strategies for mapping Exon and Junction detection Quantification strategies and Normalization Associated online course/resource: Transcriptomics 1

Removing NAs, Zero values and filtering Log scale transformation, scaling Computation of summary statistics of data Visualization of Data (Boxplot, Scatterplot, Histogram, Heatmap) Associated...

Statistical Analysis (T-Test), ANOVA, Regression and Factor Regression Analysis, DESEQ2 and EDGER Associated online course/resource: Transcriptomics 2

Differential gene expression: DESEQ and EDGER, Volcano plots, MA Plots, Heatmaps Associated online course/resource: Differential Gene Expression

KEGG pathways annotation for differentially expressed genes; Gene Ontology (GO) Biological Processes, Molecular function and Cellular Components Associated online course/resource: Transcriptomics 2

Planning bioinformatics analysis: literature review, compiling a primary dataset, developing an analysis plan, performing exploratory analysis, data processing and preparation, statistical analysis, biological interpretation...

Overview of unsupervised machine learning methods: Finding patterns and similarity in data Principal Component analysis (PCA) Hierarchical and K-means clustering Associated online course/resource:  Transcriptomics...

Overview of supervised machine learning methods Preparing Training and test datasets Classification: Decision Trees, Random Forest (RF), Support Vector Machine (SVM) Associated online course/resource:...

Omics Data and Precision Medicine PDX model project overview Precision medicine overview Liver cancer Project overview. Associated online course/resource: https://edu.t-bio.info/projects/

Data Pre-processing, Unsupervised analysis Supervised Analysis: Classification and Feature selection, Introduction to Data Integration. Associated online course/resource: Modeling Precision Medicine Publication: Modeling precision treatment...

Dimensionality Reduction: PCA in R and Python PCA with groups, feature selection and confidence. Associated online course/resource: Dimensionality reduction: PCA & visualization

Conventional techniques: Hierarchical and K-means Clustering Big data: PAM and fuzzy clustering Associated online course/resource:Clustering: K-means & Hierarchical clustering & Clustering: K-means (Python)

Data preparation: Training and Test datasets Selecting a model for training and classification Feature selection/Ranking (using RF) Testing Predictions and Performance Assessment (Accuracy, ROC...

Overview of scRNA-Seq capture techniques Sequencing and Data Preparation (UMIs) Analysis and interpretation (PCA, tSNE) Associated online course/resource: Transcriptomics 4

Pan-cancer analysis based on patient samples Stage and Risk factor Classification Multi-omics data integration. Associated online course/resource: Liver Cancer Project: BIOINFORMATICS for Precision Oncology...

Metagenomics sequencing techniques Taxonomic classification Microbiome and Human Health Associated online course/resource:  Introduction to metagenomics

Metagenomics Biological background & methods Metagenomics sequencing analysis: Logics and Concepts, Metagenomics analysis: Practical Associated online course/resource: Metagenomics1

Analysis of 16s rRNA Amplicon data Microbial diversity analysis: Alpha and Beta diversity Visualization of metagenomics data Associated online course/resource: Metagenomics2

Components of bioinformatics analysis: literature review, compiling a primary dataset, developing an analysis plan, performing exploratory analysis, data processing and preparation, statistical analysis, biological...

Taxonomic composition visualization: NMDS Phyloseq analysis of Microbial Diversity: Alpha and beta diversity (Shannon index) Associated online course/resource: Comparing DNA sequences using Phylogenetic Analysis

Overview of DNA structure DNA variations: Point mutations, Deletions, Duplication, Frame Shift Types of Genomics sequencing: Targeted, Whole Genome, Whole Exome Associated online course/resource:...

Multiple sequence alignment Phylogenetic tree reconstruction

Germline and Somatic mutations: Practical Assignment Analysis and Visualization using Genome Browser Associated online course/resource: Ebolavirus: Deadly Mutations