课程信息
4.5
119 个评分
15 个审阅

第 3 门课程(共 6 门)

100% 在线

立即开始,按照自己的计划学习。

可灵活调整截止日期

根据您的日程表重置截止日期。

完成时间大约为27 小时

建议:6-8 hours/week...

英语(English)

字幕:英语(English)

第 3 门课程(共 6 门)

100% 在线

立即开始,按照自己的计划学习。

可灵活调整截止日期

根据您的日程表重置截止日期。

完成时间大约为27 小时

建议:6-8 hours/week...

英语(English)

字幕:英语(English)

教学大纲 - 您将从这门课程中学到什么

1
完成时间为 2 小时

Course Overview and Introductions

The 'Introduction to Complex Systems' module discusses complex systems and leads to the idea that a cell can be considered a complex system or a complex agent living in a complex environment just like us. The 'Introduction to Biology for Engineers' module provides an introduction to some central topics in cell and molecular biology for those who do not have the background in the field. This is not a comprehensive coverage of cell and molecular biology. The goal is to provide an entry point to motivate those who are interested in this field, coming from other disciplines, to begin studying biology....
3 个视频 (总计 52 分钟), 4 个阅读材料, 3 个测验
3 个视频
Introduction to Cell Biology16分钟
Introduction to Molecular Biology19分钟
4 个阅读材料
Course Logistics10分钟
Grading Policy10分钟
Resources and Links to Additional Materials10分钟
MATLAB License10分钟
3 个练习
Introduction to Complex Systems20分钟
Introduction to Cell Biology18分钟
Introduction to Molecular Biology20分钟
2
完成时间为 2 小时

Topological and Network Evolution Models

In the 'Topological and Network Evolution Models' module, we provide several lectures about a historical perspective of network analysis in systems biology. The focus is on in-silico network evolution models. These are simple computational models that, based of few rules, can create networks that have a similar topology to the molecular networks observed in biological systems. ...
4 个视频 (总计 45 分钟), 4 个测验
4 个视频
Duplication-Divergence and Network Motifs8分钟
Large Size Motifs and Complex Models of Network Evolution10分钟
Network Properties of Biological Networks11分钟
4 个练习
Rich-Get-Richer14分钟
Duplication-Divergence and Network Motifs16分钟
Large Size Motifs16分钟
Topological Properties of Biological Networks18分钟
3
完成时间为 2 小时

Types of Biological Networks

The 'Types of Biological Networks' module is about the various types of networks that are typically constructed and analyzed in systems biology and systems pharmacology. This lecture ends with the idea of functional association networks (FANs). Following this lecture are lectures that discuss how to construct FANs and how to use these networks for analyzing gene lists. ...
4 个视频 (总计 58 分钟), 4 个测验
4 个视频
Genes2Networks and Network Visualization16分钟
Sets2Networks - Creating Functional Association Networks14分钟
Genes2FANs - Analyzing Gene Lists with Functional Association Networks14分钟
4 个练习
Types of Biological Networks16分钟
Genes2Networks and Network Visualization14分钟
Functional Association Networks with Sets2Networks16分钟
Functional Association Networks with Genes2FANs16分钟
4
完成时间为 1 小时

Data Processing and Identifying Differentially Expressed Genes

This set of lectures in the 'Data Processing and Identifying Differentially Expressed Genes' module first discusses data normalization methods, and then several lectures are devoted to explaining the problem of identifying differentially expressed genes with the focus on understanding the inner workings of a new method developed by the Ma'ayan Laboratory called the Characteristic Direction. ...
5 个视频 (总计 41 分钟), 2 个测验
5 个视频
Characteristic Direction Method - Part 18分钟
Characteristic Direction Method - Part 27分钟
Characteristic Direction Method - Part 310分钟
Characteristic Direction Method - Part 45分钟
2 个练习
Data Normalization14分钟
Characteristic Direction12分钟
5
完成时间为 4 小时

Gene Set Enrichment and Network Analyses

In the 'Gene Set Enrichment and Network Analyses' module the emphasis is on tools developed by the Ma'ayan Laboratory to analyze gene sets. Several tools will be discussed including: Enrichr, GEO2Enrichr, Expression2Kinases and DrugPairSeeker. In addition, one lecture will be devoted to a method we call enrichment vector clustering we developed, and two lectures will describe the popular gene set enrichment analysis (GSEA) method and an improved method we developed called principal angle enrichment analysis (PAEA)....
9 个视频 (总计 139 分钟), 1 个阅读材料, 8 个测验
9 个视频
GEO2Enrichr: A Google Chrome Extension for Gene Set Extraction and Enrichment7分钟
Gene Set Enrichment Analysis (GSEA) - Preliminaries13分钟
Gene Set Enrichment Analysis (GSEA) - Part 28分钟
Principal Angle Enrichment Analysis (PAEA)18分钟
Network2Canvas (N2C) and Enrichment Analysis with N2C17分钟
Expression2Kinases: Inferring Pathways from Differentially Expressed Genes24分钟
DrugPairSeeker and the New CMAP17分钟
Classifying Patients/Tumors from TCGA11分钟
1 个阅读材料
GATE Desktop Software Tool10分钟
8 个练习
The Fisher Exact Test and Enrichr18分钟
Gene Set Enrichment Analysis (GSEA) - Part 112分钟
Gene Set Enrichment Analysis (GSEA) - Part 210分钟
Principal Angle Enrichment Analysis (PAEA)10分钟
GATE and Network2Canvas14分钟
Expression2Kinases20分钟
DrugPairSeeker and the New CMAP16分钟
Classifying Patients from TCGA16分钟
6
完成时间为 4 小时

Deep Sequencing Data Processing and Analysis

A set of lectures in the 'Deep Sequencing Data Processing and Analysis' module will cover the basic steps and popular pipelines to analyze RNA-seq and ChIP-seq data going from the raw data to gene lists to figures. These lectures also cover UNIX/Linux commands and some programming elements of R, a popular freely available statistical software. Note that since these lectures were developed and recorded during the Fall of 2013, it is possible that there are better tools that should be used now since the field is rapidly advancing. ...
7 个视频 (总计 125 分钟), 7 个测验
7 个视频
RNA-seq Analysis - Using TopHat and Cufflinks21分钟
RNA-seq Analysis - R Basics23分钟
RNA-seq Analysis - CummeRbund23分钟
STAR: An Ultra-fast RNA-seq Aligner13分钟
ChIP-seq Analysis - Part 113分钟
ChIP-seq Analysis - Part 212分钟
7 个练习
RNA-seq and UNIX/Linux Commands16分钟
RNA-seq Pipeline20分钟
CummeRbund and R Programming20分钟
CummeRbund - Demo18分钟
RNA-seq STAR10分钟
ChIP-seq Analysis - Part 118分钟
ChIP-seq Analysis - Part 216分钟
7
完成时间为 3 小时

Principal Component Analysis, Self-Organizing Maps, Network-Based Clustering and Hierarchical Clustering

This module is devoted to various method of clustering: principal component analysis, self-organizing maps, network-based clustering and hierarchical clustering. The theory behind these methods of analysis are covered in detail, and this is followed by some practical demonstration of the methods for applications using R and MATLAB....
6 个视频 (总计 90 分钟), 1 个阅读材料, 6 个测验
6 个视频
Principal Component Analysis (PCA) - Part 28分钟
Principal Component Analyis (PCA) Plotting in MATLAB15分钟
Clustergram in MATLAB14分钟
Self-Organizing Maps14分钟
Network-Based Clustering24分钟
1 个阅读材料
MATLAB License10分钟
6 个练习
Principal Component Analysis (PCA) - Part 112分钟
Principal Component Analysis (PCA) - Part 214分钟
Principal Component Analysis (PCA) with MATLAB18分钟
Hierarchical Clustering (HC) with MATLAB16分钟
Self-Organizing Maps12分钟
Network-Based Clustering10分钟
8
完成时间为 1 小时

Resources for Data Integration

The lectures in the 'Resources for Data Integration' module are about the various types of networks that are typically constructed and analyzed in systems biology and systems pharmacology. These lectures start with the idea of functional association networks (FANs). Following this lecture are several lectures that discuss how to construct FANs from various resources and how to use these networks for analyzing gene lists as well as to construct a puzzle that can be used to connect genomic data with phenotypic data. ...
5 个视频 (总计 49 分钟), 2 个测验
5 个视频
Resources for Data Integration - Part 110分钟
Resources for Data Integration - Part 212分钟
Resources for Data Integration - Part 39分钟
Resources for Data Integration - Part 410分钟
2 个练习
Big Data in Biology and Data Integration16分钟
Resources for Data Integration24分钟
9
完成时间为 1 小时

Crowdsourcing: Microtasks and Megatasks

The final set of lectures presents the idea of crowdsourcing. MOOCs provide the opportunity to work together on projects that are difficult to complete alone (microtasks) or compete for implementing the best algorithms to solve hard problems (megatasks). You will have the opportunity to participate in various crowdsourcing projects: microtasks and megatasks. These projects are designed specifically for this course....
2 个视频 (总计 19 分钟), 1 个测验
2 个视频
Crowdsourcing Tasks for this Course3分钟
1 个练习
Crowdsourcing: Microtasks and Megatasks16分钟
10
完成时间为 2 小时

Final Exam

The final exam consists of multiple choice questions from topics covered in all of modules of the course. Some of the questions may require you to perform some of the analysis methods you learned throughout the course on new datasets. ...
1 个测验
1 个练习
Final Exam50分钟
4.5
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创建者 FPJun 3rd 2016

Excellent course to get deep into the data analysis of system biology experimentation.

创建者 CCApr 6th 2016

Its really a very interesting course ,and very informative

讲师

Avatar

Avi Ma’ayan, PhD

Director, Mount Sinai Center for Bioinformatics
Professor, Department of Pharmacological Sciences

关于 西奈山伊坎医学院

The Icahn School of Medicine at Mount Sinai, in New York City is a leader in medical and scientific training and education, biomedical research and patient care....

关于 系统生物学与生物技术 专项课程

Design systems-level experiments using appropriate cutting edge techniques, collect big data, and analyze and interpret small and big data sets quantitatively. The Systems Biology Specialization covers the concepts and methodologies used in systems-level analysis of biomedical systems. Successful participants will learn how to use experimental, computational and mathematical methods in systems biology and how to design practical systems-level frameworks to address questions in a variety of biomedical fields. In the final Capstone Project, students will apply the methods they learned in five courses of specialization to work on a research project....
系统生物学与生物技术

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