
Glendale Bioinformatics
This course is designed for students who don’t have a background in bioinformatics and experienced biologists who are eager to learn about data analysis. We will cover such topics as genomics, transcriptomics, and metagenomics. The sessions will introduce statistical analysis methods, visualization, and an introduction to popular machine learning techniques for omics data analysis. Students will also learn about public data repositories and understand the various file formats used in bioinformatics for storing and efficient processing of omics data. Big data analysis tools as well as scripting will be introduced using online resources developed by Pine Biotech and our partners.
Upcoming Events
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14January
Orientation Webinar
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) &...
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19January
Course Overview
Course structure, expectations and intended outcomes. Topics: Applications of bioinformatics (Introduction to Bioinformatics Course), Examples in Biomedical Research, Pharma R & D and AgricultureAssociated...
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21January
Bioinformatics in R and Python
Working with sequences DNA, RNA and Protein sequences Associated online course/resource: Working with DNA Sequences in
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26January
Introduction to Sequence Analysis
Pairwise sequence alignment Multiple sequence alignment Clinical Example of DNA variants Associated online course/resource: Introduction to Genomics
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28January
Next Generation Sequencing Data: Overview
Technologies for DNA and RNA sequencing: Microarray, High Throughput Sequencing, qPCR (Introduction to Genomics Course), Advantages and applications of NGS: Illumina, Nanopore and PacBio...
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02February
Case Study: Patient Derived Xenograft Models for tumor microenvironment studies
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...
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04February
Processing Transcriptomic Data (Transcriptomics 1 A)
mRNA library preparation, Mapping on transcriptome TopHat, HiSat, Bowtie 2G, Sailfish, Methods of RNA quantification Associated online course/resource: Transcriptomics 1
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09February
Loading a dataset (Open and view a table of expression in R and Python)
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:...
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11February
Mapping and Quantification (Transcriptomics 1)
Strategies for mapping Exon and Junction detection Quantification strategies and Normalization Associated online course/resource: Transcriptomics 1
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16February
Data Normalization and Visualization (Excel, R & Python)
Removing NAs, Zero values and filtering Log scale transformation, scaling Computation of summary statistics of data Visualization of Data (Boxplot, Scatterplot, Histogram, Heatmap) Associated...
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18February
Regression Analysis (Transcriptomics 2B)
Statistical Analysis (T-Test), ANOVA, Regression and Factor Regression Analysis, DESEQ2 and EDGER Associated online course/resource: Transcriptomics 2
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23February
Differential Gene Expression in R and Python
Differential gene expression: DESEQ and EDGER, Volcano plots, MA Plots, Heatmaps Associated online course/resource: Differential Gene Expression
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25February
Biological Interpretation
KEGG pathways annotation for differentially expressed genes; Gene Ontology (GO) Biological Processes, Molecular function and Cellular Components Associated online course/resource: Transcriptomics 2
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02March
Introduction to Projects using Bioinformatics
Planning bioinformatics analysis: literature review, compiling a primary dataset, developing an analysis plan, performing exploratory analysis, data processing and preparation, statistical analysis, biological interpretation...
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04March
Big Data Analysis: Data Mining (Transcriptomics 3A)
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...
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09March
Machine Learning: Classification (Transcriptomics 3B)
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:...
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11March
Overview of practical biological applications
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/
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23March
Case Study: Modeling Precision Medicine
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...
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25March
Principal Component Analysis in R and Python
Dimensionality Reduction: PCA in R and Python PCA with groups, feature selection and confidence. Associated online course/resource: Dimensionality reduction: PCA & visualization
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30March
Clustering in R and Python
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)
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01April
Classification in R & 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...
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06April
Single Cell RNA-seq (Trans 4)
Overview of scRNA-Seq capture techniques Sequencing and Data Preparation (UMIs) Analysis and interpretation (PCA, tSNE) Associated online course/resource: Transcriptomics 4
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08April
Cancer Genome Atlas
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...
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13April
Introduction to Metagenomics
Metagenomics sequencing techniques Taxonomic classification Microbiome and Human Health Associated online course/resource: Introduction to metagenomics
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15April
Metagenomics Databases
Metagenomics Biological background & methods Metagenomics sequencing analysis: Logics and Concepts, Metagenomics analysis: Practical Associated online course/resource: Metagenomics1
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20April
16s rRNA Sequencing
Analysis of 16s rRNA Amplicon data Microbial diversity analysis: Alpha and Beta diversity Visualization of metagenomics data Associated online course/resource: Metagenomics2
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22April
Project Proposal Review
Components of bioinformatics analysis: literature review, compiling a primary dataset, developing an analysis plan, performing exploratory analysis, data processing and preparation, statistical analysis, biological...
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27April
Metagenomics in R
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
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29April
Introduction to Genomics
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:...
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04May
Sequence analysis
Multiple sequence alignment Phylogenetic tree reconstruction
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05May
Mutation Analysis
Germline and Somatic mutations: Practical Assignment Analysis and Visualization using Genome Browser Associated online course/resource: Ebolavirus: Deadly Mutations
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06May
Course and Progress Review
Activity and Progress review on educational portal (edu.t-bio.info) & analytical server (server.t-bio.info) & https://code.omicslogic.com
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