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Network Analysis in Systems Biology
  • Level Professional
  • Duration 30 hours
  • Course by Icahn School of Medicine at Mount Sinai
  • Offered by

About

An introduction to data integration and statistical methods used in contemporary Systems Biology, Bioinformatics and Systems Pharmacology research. The course covers methods to process raw data from genome-wide mRNA expression studies (microarrays and RNA-seq) including data normalization, differential expression, clustering, enrichment analysis and network construction. The course contains practical tutorials for using tools and setting up pipelines, but it also covers the mathematics behind the methods applied within the tools. The course is mostly appropriate for beginning graduate students and advanced undergraduates majoring in fields such as biology, math, physics, chemistry, computer science, biomedical and electrical engineering. The course should be useful for researchers who encounter large datasets in their own research. The course presents software tools developed by the Ma’ayan Laboratory (http://labs.icahn.mssm.edu/maayanlab/) from the Icahn School of Medicine at Mount Sinai, but also other freely available data analysis and visualization tools. The ultimate aim of the course is to enable participants to utilize the methods presented in this course for analyzing their own data for their own projects. For those participants that do not work in the field, the course introduces the current research challenges faced in the field of computational systems biology.

Modules

Course Overview

    • 4 Readings
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4 Readings

  • Course Logistics
  • Grading Policy
  • Resources and Links to Additional Materials
  • MATLAB License

Introduction to Complex Systems

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Introduction to Complex Systems

1 Videos

  • Design Principles of Complex Systems

Introduction to Biology for Engineers

    • 2 Videos
    • 2 Assignment
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2 Assignment

  • Introduction to Cell Biology
  • Introduction to Molecular Biology

2 Videos

  • Introduction to Cell Biology
  • Introduction to Molecular Biology

Rich-Get-Richer

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Rich-Get-Richer

1 Videos

  • Small-World and Scale-Free Networks

Duplication-Divergence and Network Motifs

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Duplication-Divergence and Network Motifs

1 Videos

  • Duplication-Divergence and Network Motifs

Large Size Motifs

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Large Size Motifs

1 Videos

  • Large Size Motifs and Complex Models of Network Evolution

Topological Properties of Biological Networks

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Topological Properties of Biological Networks

1 Videos

  • Network Properties of Biological Networks

Types of Biological Networks

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Types of Biological Networks

1 Videos

  • Types of Biological Networks

Genes2Networks and Network Visualization

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Genes2Networks and Network Visualization

1 Videos

  • Genes2Networks and Network Visualization

Functional Association Networks with Sets2Networks

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Functional Association Networks with Sets2Networks

1 Videos

  • Sets2Networks - Creating Functional Association Networks

Functional Association Networks with Genes2FANs

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Functional Association Networks with Genes2FANs

1 Videos

  • Genes2FANs - Analyzing Gene Lists with Functional Association Networks

Concepts on Data Normalization

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Data Normalization

1 Videos

  • Data Normalization

Characteristic Direction Method to Identify Differentially Expressed Genes

    • 4 Videos
    • 1 Assignment
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1 Assignment

  • Characteristic Direction

4 Videos

  • Characteristic Direction Method - Part 1
  • Characteristic Direction Method - Part 2
  • Characteristic Direction Method - Part 3
  • Characteristic Direction Method - Part 4

Fisher Exact Test and Enrichr

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • The Fisher Exact Test and Enrichr

1 Videos

  • Enrichment Analysis and Enrichr

GEO2Enrichr

    • 1 Videos
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1 Videos

  • GEO2Enrichr: A Google Chrome Extension for Gene Set Extraction and Enrichment

Gene Set Enrichment Analysis (GSEA)

    • 2 Videos
    • 2 Assignment
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2 Assignment

  • Gene Set Enrichment Analysis (GSEA) - Part 1
  • Gene Set Enrichment Analysis (GSEA) - Part 2

2 Videos

  • Gene Set Enrichment Analysis (GSEA) - Preliminaries
  • Gene Set Enrichment Analysis (GSEA) - Part 2

Principal Angle Enrichment Analysis (PAEA)

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Principal Angle Enrichment Analysis (PAEA)

1 Videos

  • Principal Angle Enrichment Analysis (PAEA)

Network2Canvas: Network Visualization on a Canvas

    • 1 Videos
    • 1 Readings
    • 1 Assignment
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1 Assignment

  • GATE and Network2Canvas

1 Videos

  • Network2Canvas (N2C) and Enrichment Analysis with N2C

1 Readings

  • GATE Desktop Software Tool

Expression2Kinases

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Expression2Kinases

1 Videos

  • Expression2Kinases: Inferring Pathways from Differentially Expressed Genes

DrugPairSeeker and the New CMAP

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • DrugPairSeeker and the New CMAP

1 Videos

  • DrugPairSeeker and the New CMAP

Classifying Patients from TCGA

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Classifying Patients from TCGA

1 Videos

  • Classifying Patients/Tumors from TCGA

RNA-seq and UNIX/Linux Commands

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • RNA-seq and UNIX/Linux Commands

1 Videos

  • RNA-seq Analysis - Preliminaries

RNA-seq Pipeline

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • RNA-seq Pipeline

1 Videos

  • RNA-seq Analysis - Using TopHat and Cufflinks

CummeRbund and R Programming

    • 2 Videos
    • 2 Assignment
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2 Assignment

  • CummeRbund and R Programming
  • CummeRbund - Demo

2 Videos

  • RNA-seq Analysis - R Basics
  • RNA-seq Analysis - CummeRbund

RNA-seq Analysis with STAR

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • RNA-seq STAR

1 Videos

  • STAR: An Ultra-fast RNA-seq Aligner

ChIP-seq Analysis

    • 2 Videos
    • 2 Assignment
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2 Assignment

  • ChIP-seq Analysis - Part 1
  • ChIP-seq Analysis - Part 2

2 Videos

  • ChIP-seq Analysis - Part 1
  • ChIP-seq Analysis - Part 2

Principal Component Analysis (PCA)

    • 3 Videos
    • 1 Readings
    • 3 Assignment
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3 Assignment

  • Principal Component Analysis (PCA) - Part 1
  • Principal Component Analysis (PCA) - Part 2
  • Principal Component Analysis (PCA) with MATLAB

3 Videos

  • Principal Component Analysis (PCA) - Part 1
  • Principal Component Analysis (PCA) - Part 2
  • Principal Component Analyis (PCA) Plotting in MATLAB

1 Readings

  • MATLAB License

Hierarchical Clustering (HC) with MATLAB

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Hierarchical Clustering (HC) with MATLAB

1 Videos

  • Clustergram in MATLAB

Self-Organizing Maps

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Self-Organizing Maps

1 Videos

  • Self-Organizing Maps

Network-Based Clustering

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Network-Based Clustering

1 Videos

  • Network-Based Clustering

Big Data in Biology and Data Integration

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Big Data in Biology and Data Integration

1 Videos

  • Big Data in Biology and Data Integration

Resources for Data Integration

    • 4 Videos
    • 1 Assignment
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1 Assignment

  • Resources for Data Integration

4 Videos

  • Resources for Data Integration - Part 1
  • Resources for Data Integration - Part 2
  • Resources for Data Integration - Part 3
  • Resources for Data Integration - Part 4

Crowdsourcing: Microtasks and Megatasks

    • 2 Videos
    • 1 Assignment
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1 Assignment

  • Crowdsourcing: Microtasks and Megatasks

2 Videos

  • Crowdsourcing in Bioinformatics
  • Crowdsourcing Tasks for this Course

Final Exam

    • 1 Assignment
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1 Assignment

  • Final Exam

Auto Summary

Unlock the power of data analysis in systems biology with this immersive course. Dive into bioinformatics and systems pharmacology research, mastering techniques like data normalization, clustering, and network construction. Ideal for advanced undergraduates, graduate students, and researchers across biology, statistics, and engineering disciplines. Taught by experts from the Icahn School of Medicine, this course offers practical tutorials and deep mathematical insights. Available on Coursera with flexible subscription options, start your journey in computational systems biology today.

Avi Ma’ayan, PhD
Instructor

Avi Ma’ayan, PhD