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

  1. 14
    January
    Orientation Webinar
    10:00 - 11:00
    Online

    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) &...

  2. 19
    January
    Course Overview
    10:00 - 11:00
    Online

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

  3. 21
    January
    Bioinformatics in R and Python
    10:00 - 11:00
    Online

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

  4. 26
    January
    Introduction to Sequence Analysis
    10:00 - 11:00
    Online

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

  5. 28
    January
    Next Generation Sequencing Data: Overview
    10:00 - 11:00
    Online

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

  6. 02
    February
    Case Study: Patient Derived Xenograft Models for tumor microenvironment studies
    10:00 - 11:00
    Online

    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...

  7. 04
    February
    Processing Transcriptomic Data (Transcriptomics 1 A)
    10:00 - 11:00
    Online

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

  8. 09
    February
    Loading a dataset (Open and view a table of expression in R and Python)
    10:00 - 11:00
    Online

    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:...

  9. 11
    February
    Mapping and Quantification (Transcriptomics 1)
    10:00 - 11:00
    Online

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

  10. 16
    February
    Data Normalization and Visualization (Excel, R & Python)
    10:00 - 11:00
    Online

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

  11. 18
    February
    Regression Analysis (Transcriptomics 2B)
    10:00 - 11:00
    Online

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

  12. 23
    February
    Differential Gene Expression in R and Python
    10:00 - 11:00
    Online

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

  13. 25
    February
    Biological Interpretation
    10:00 - 11:00
    Online

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

  14. 02
    March
    Introduction to Projects using Bioinformatics
    10:00 - 11:00
    Online

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

  15. 04
    March
    Big Data Analysis: Data Mining (Transcriptomics 3A)
    10:00 - 11:00
    Online

    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...

  16. 09
    March
    Machine Learning: Classification (Transcriptomics 3B)
    10:00 - 11:00
    Online

    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:...

  17. 11
    March
    Overview of practical biological applications
    10:00 - 11:00
    Online

    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/

  18. 23
    March
    Case Study: Modeling Precision Medicine
    10:00 - 11:00
    Online

    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...

  19. 25
    March
    Principal Component Analysis in R and Python
    10:00 - 11:00
    Online

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

  20. 30
    March
    Clustering in R and Python
    10:00 - 11:00
    Online

    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)

  21. 01
    April
    Classification in R & Python
    10:00 - 11:00
    Online

    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...

  22. 06
    April
    Single Cell RNA-seq (Trans 4)
    10:00 - 11:00
    Online

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

  23. 08
    April
    Cancer Genome Atlas
    10:00 - 11:00
    Online

    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...

  24. 13
    April
    Introduction to Metagenomics
    10:00 - 11:00
    Online

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

  25. 15
    April
    Metagenomics Databases
    10:00 - 11:00
    Online

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

  26. 20
    April
    16s rRNA Sequencing
    10:00 - 11:00
    Online

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

  27. 22
    April
    Project Proposal Review
    10:00 - 11:00
    Online

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

  28. 27
    April
    Metagenomics in R
    10:00 - 11:00
    Online

    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

  29. 29
    April
    Introduction to Genomics
    10:00 - 11:00
    Online

    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:...

  30. 04
    May
    Sequence analysis
    10:00 - 11:00
    Online

    Multiple sequence alignment Phylogenetic tree reconstruction

  31. 05
    May
    Mutation Analysis
    10:00 - 11:00
    Online

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

  32. 06
    May
    Course and Progress Review
    10:00 - 11:00
    Online

    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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Glendale Bioinformatics
$335.00
74 Days

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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.
Introduction to Metagenomics
Patient Derived Xenograft Models
Transcriptomics 3
Transcriptomics 2
Transcriptomics 1
Introduction to Genomics
Introduction to Bioinformatics

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