Bioinformatics: Introduction and Methods 生物信息学: 导论与方法 from Coursera

What's inside

Syllabus

Introduction and History of Bioinformatics

Welcome to “Bioinformatics: Introduction and Methods! Upon completion of this module you will be able to: become familiar with the essential concepts of bioinformatics; explore the history of this young area; experience how rapidly bioinformatics is growing. Our supplementary materials will give you a better understanding of the course lectures through they are not required in quizzes or exams

Sequence Alignment

Upon completion of this module, you will be able to: describe dynamic programming based sequence alignment algorithms; differentiate between the Needleman-Wunsch algorithm for global alignment and the Smith-Waterman algorithm for local alignment; examine the principles behind gap penalty and time complexity calculation which is crucial for you to apply current bioinformatic tools in your research; experience the discovery of Smith-Waterman algorithm with Dr. Michael Waterman himself.

Sequence Database Search

Upon completion of this module, you will be able to: become familiar with sequence databse search and most common databases; explore the algoritm behind BLAST and the evaluation of BLAST results; ajdust BLAST parameters base on your own research project.

Markov Model

Upon completion of this module, you will be able to: recognize state transitions, Markov chain and Markov models; create a hidden Markov model by yourself; make predictuions in a real biological problem with hidden Markov model.

Next Generation Sequencing (NGS): Mapping of Reads From Resequencing and Calling of Genetic Variants

Upon completion of this module, you will be able to: describe the features of NGS; associate NGS results you get with the methods for reads mapping and models for variant calling; examine pipelines in NGS data analysis; experience how real NGS data were analyzed using bioinformatic tools. This module is required before entering Module 8.

Functional Prediction of Genetic Variants

Upon completion of this module you will able to: describe what is variant prediction and how to carry out variant predictions; associate variant databases with your own research projects after you get a list of variants; recognize different principles behind prediction tools and know how to use tools such as SIFT, Polyphen and SAPRED according to your won scientific problem.

Mid-term Exam

The description goes here

Next Generation Sequencing: Transcriptome Analysis, and RNA-Seq

Upon completion of this module, you will be able to: describe how transcriptome data were generated; master the algorithm used in transcriptome analysis; explore how the RNA-seq data were analyzed. This module is required before entering Module 9.

Prediction and Analysis of Noncoding RNA

Upon completion of this module, you will be able to: Analyze non-coding RNAs from transcriptome data; identify long noncoding RNA (lncRNA) from NGS data and predict their functions.

Ontology and Identification of Molecular Pathways

Upon completion of this module, you will be able to: define ontology and gene ontology, explore KEGG pathway databses; examine annotations in Gene Ontology; identify pathways with KOBAS and apply the pipeline to drug addition study.

Bioinformatics Database and Software Resources

Upon completion of this module, you will be able to describe the most important bioinformatic resources including databases and software tools; explore both centralized resources such as NCBI, EBI, UCSC genome browser and lots of individual resources; associate all your bioinformatic problems with certain resources to refer to.

Origination of New Genes

Upon completion of this case study module, you will be able to: experience how to apply bioinformatic data, methods and analyses to study an important problem in evolutionary biology; examine how to detect and study the origination, evolution and function of species-specific new genes; create phylogenetic trees with your own data (not required) with Dr. Manyuan Long, a world-renowned pioneer and expert on new genes from University of Chicago.

Evolution function analysis of DNA methyltransferase

Upon completion of this case study module, you will be able to: experience how to use bioinformatic methods to study the function and evolution of DNA methylases; share with Dr. Gang Pei, president of Tongji University and member of the Chinese Academy of Science, the experiences in scientific research and thought about MOOC.

Final Exam

Good to know

Know what's good

, what to watch for

, and possible dealbreakers

Builds a strong foundation for beginners in the field

Taught by recognized experts in the field: Ge Gao and Liping Wei

Affiliated with Peking University, a highly reputable institution

Covers the essential concepts of bioinformatics

Provides practical experience through interactive materials

Emphasizes applications in biology

Reviews summary

Bioinformatics intro: accessible yet rigorous

This course serves as a good introduction to the fundamentals of bioinformatics. Beginners may particularly appreciate this course for that reason. However, more experienced learners should be aware that the later modules may not be as rigorous as they might expect.

Course is accessible for beginners

"the first part is very good for beginners"

Less content in later modules

"not so good in later parts"

Activities

Be better prepared before your course. Deepen your understanding during and after it. Supplement your coursework and achieve mastery of the topics covered in Bioinformatics: Introduction and Methods 生物信息学: 导论与方法 with these activities:

Review of Basic Bioinformatics Concepts

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Get familiar with fundamental concepts in bioinformatics to enhance understanding of course content.

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Read assigned course materials (e.g., textbooks, articles) or watch introductory videos on bioinformatics.
Identify and define key terms (e.g., DNA, RNA, proteins, genetic code).
Explore online resources (e.g., NCBI, EMBL-EBI) to familiarize yourself with bioinformatics databases and tools.
Attend the first few lectures or tutorials to gain basic knowledge of bioinformatics concepts.

Multiple Sequence Alignment Practice

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Develop proficiency in sequence alignment algorithms to better comprehend subsequent sections on sequence analysis.

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Solve practice problems on multiple sequence alignment using dynamic programming.
Use online tools (e.g., ClustalW, T-Coffee) to perform sequence alignments and analyze results.
Attend workshops or tutorials to enhance understanding of sequence alignment techniques.

Bioinformatics Conference Attendance

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Expand understanding of the field, connect with professionals, and learn about recent advancements in bioinformatics.

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Attend a bioinformatics conference related to the course topics.
Attend presentations and listen to experts in the field.
Interact with researchers and professionals to exchange ideas and learn about new projects and collaborations.

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Bioinformatics Software Tool Comparison

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Enhance understanding of bioinformatics software tools and their applications by conducting a comparative analysis.

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Identify a specific bioinformatics task (e.g., sequence analysis, genome assembly).
Research and select several popular software tools for the task.
Download and install the software tools.
Test and evaluate each tool using benchmark datasets or real-world data.
Compare and contrast the features, performance, and strengths and weaknesses of each tool.
Write a report or create a presentation summarizing the findings and recommendations.

Next-Generation Sequencing Data Analysis Exercise

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Develop practical skills in analyzing next-generation sequencing data to strengthen understanding of genome analysis methods.

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Obtain a dataset from a public repository (e.g., NCBI Sequence Read Archive).
Install and use bioinformatics software (e.g., BWA, SAMtools) to map reads and identify variants.
Analyze the variants and identify potential mutations or genetic polymorphisms.

Advanced Sequence Analysis Techniques

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Enhance analytical skills in bioinformatics by exploring advanced techniques and algorithms for sequence analysis.

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Review online tutorials or attend workshops on topics such as hidden Markov models (HMMs) or machine learning for sequence analysis.
Implement algorithms for HMMs or other advanced techniques using programming languages (e.g., Python, R).
Apply these techniques to real-world biological datasets and analyze the results.

Bioinformatics Community Involvement

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Gain practical experience and contribute to the bioinformatics community by volunteering in relevant projects.

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Identify open-source bioinformatics projects or organizations that align with your interests.
Contact the project leaders or organizers to inquire about volunteer opportunities.
Contribute to the project by participating in discussions, testing software, or writing documentation.

Bioinformatics Case Study Presentation

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Deepen understanding of bioinformatics applications by conducting a case study and presenting findings.

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Choose a bioinformatics case study (e.g., disease diagnosis, drug discovery) that aligns with course topics.
Conduct research to gather relevant data and information.
Create a presentation that summarizes the case study, methods used, and key findings.
Present the case study to the class or a designated group for feedback and discussion.

Career center

Learners who complete Bioinformatics: Introduction and Methods 生物信息学: 导论与方法 will develop knowledge and skills that may be useful to these careers:

Bioinformatician

Bioinformaticians use their knowledge of computer science and biology to develop and apply computational techniques to biological data. This course will teach you the essential concepts of bioinformatics, including sequence alignment, sequence database search, and Markov models. These concepts are fundamental to bioinformatics, and this course will help you build a strong foundation for a career in this field. Furthermore, the course will cover topics such as Next Generation Sequencing (NGS) and the analysis of RNA-Seq data, which are increasingly important in bioinformatics.

See salaries and explore the career path for Bioinformatician

Computational Biologist

Computational biologists use their knowledge of computer science and biology to develop and apply computational techniques to biological problems. This course will teach you the essential concepts of bioinformatics, including sequence alignment, sequence database search, and Markov models. These concepts are fundamental to computational biology, and this course will help you build a strong foundation for a career in this field. Furthermore, the course will cover topics such as Next Generation Sequencing (NGS) and the analysis of RNA-Seq data, which are increasingly important in computational biology.

See salaries and explore the career path for Computational Biologist

Molecular Biologist

Molecular biologists use their knowledge of molecular biology to study the structure, function, and regulation of biological molecules. This course will teach you the essential concepts of bioinformatics, including sequence alignment, sequence database search, and Markov models. These concepts are fundamental to molecular biology, and this course will help you build a strong foundation for a career in this field. Furthermore, the course will cover topics such as Next Generation Sequencing (NGS) and the analysis of RNA-Seq data, which are increasingly important in molecular biology.

See salaries and explore the career path for Molecular Biologist

Geneticist

Geneticists use their knowledge of genetics to study the inheritance and variation of genes. This course will teach you the essential concepts of bioinformatics, including sequence alignment, sequence database search, and Markov models. These concepts are fundamental to genetics, and this course will help you build a strong foundation for a career in this field. Furthermore, the course will cover topics such as Next Generation Sequencing (NGS) and the analysis of RNA-Seq data, which are increasingly important in genetics.

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Biomedical Engineer

Biomedical engineers use their knowledge of engineering and biology to design and develop medical devices and technologies. This course will teach you the essential concepts of bioinformatics, including sequence alignment, sequence database search, and Markov models. These concepts are fundamental to biomedical engineering, and this course will help you build a strong foundation for a career in this field. Furthermore, the course will cover topics such as Next Generation Sequencing (NGS) and the analysis of RNA-Seq data, which are increasingly important in biomedical engineering.

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Biostatistician

Biostatisticians use their knowledge of statistics and biology to design experiments, collect data, and analyze biological information. This course will teach you the essential concepts of bioinformatics, including sequence alignment, sequence database search, and Markov models. These concepts are fundamental to biostatistics, and this course will help you build a strong foundation for a career in this field. Furthermore, the course will cover topics such as Next Generation Sequencing (NGS) and the analysis of RNA-Seq data, which are increasingly important in biostatistics.

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Data Scientist

Data scientists use their knowledge of statistics, computer science, and domain expertise to extract insights from data. This course will teach you the essential concepts of bioinformatics, including sequence alignment, sequence database search, and Markov models. These concepts are fundamental to data science, and this course will help you build a strong foundation for a career in this field. Furthermore, the course will cover topics such as Next Generation Sequencing (NGS) and the analysis of RNA-Seq data, which are increasingly important in data science.

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Pharmacist

Pharmacists use their knowledge of pharmacology to dispense and administer medications. This course will teach you the essential concepts of bioinformatics, including sequence alignment, sequence database search, and Markov models. These concepts are fundamental to pharmacology, and this course will help you build a strong foundation for a career in this field. Furthermore, the course will cover topics such as Next Generation Sequencing (NGS) and the analysis of RNA-Seq data, which are increasingly important in pharmacology.

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Physician

Physicians use their knowledge of medicine to diagnose and treat diseases. This course may be useful for physicians who want to learn more about bioinformatics and how it can be used to improve patient care. The course will cover topics such as Next Generation Sequencing (NGS) and the analysis of RNA-Seq data, which are increasingly important in medicine.

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Nurse

Nurses use their knowledge of nursing to provide care to patients. This course may be useful for nurses who want to learn more about bioinformatics and how it can be used to improve patient care. The course will cover topics such as Next Generation Sequencing (NGS) and the analysis of RNA-Seq data, which are increasingly important in nursing.

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Healthcare Administrator

Healthcare administrators use their knowledge of healthcare administration to manage healthcare organizations. This course may be useful for healthcare administrators who want to learn more about bioinformatics and how it can be used to improve healthcare delivery. The course will cover topics such as Next Generation Sequencing (NGS) and the analysis of RNA-Seq data, which are increasingly important in healthcare administration.

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Science Writer

Science writers use their knowledge of science to communicate scientific information to the public. This course may be useful for science writers who want to learn more about bioinformatics and how it is used to advance scientific research. The course will cover topics such as Next Generation Sequencing (NGS) and the analysis of RNA-Seq data, which are increasingly important in science writing.

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Teacher

Teachers use their knowledge of education to teach students. This course may be useful for teachers who want to learn more about bioinformatics and how it can be used to teach biology. The course will cover topics such as Next Generation Sequencing (NGS) and the analysis of RNA-Seq data, which are increasingly important in biology education.

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Librarian

Librarians use their knowledge of library science to manage libraries and provide information services to the public. This course may be useful for librarians who want to learn more about bioinformatics and how it is used to organize and disseminate scientific information. The course will cover topics such as Next Generation Sequencing (NGS) and the analysis of RNA-Seq data, which are increasingly important in library science.

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Patent Attorney

Patent attorneys use their knowledge of law and science to obtain and defend patents for inventions. This course may be useful for patent attorneys who want to learn more about bioinformatics and how it is used to develop and protect intellectual property in the life sciences. The course will cover topics such as Next Generation Sequencing (NGS) and the analysis of RNA-Seq data, which are increasingly important in patent law.

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