Bioinformatic Methods II from Coursera

Large-scale biology projects such as the sequencing of the human genome and gene expression surveys using RNA-seq, microarrays and other technologies have created a wealth of data for biologists. However, the challenge facing scientists is analyzing and even accessing these data to extract useful information pertaining to the system being studied. This course focuses on employing existing bioinformatic resources – mainly web-based programs and databases – to access the wealth of data to answer questions relevant to the average biologist, and is highly hands-on.

Topics covered include multiple sequence alignments, phylogenetics, gene expression data analysis, and protein interaction networks, in two separate parts.

The first part, Bioinformatic Methods I, dealt with databases, Blast, multiple sequence alignments, phylogenetics, selection analysis and metagenomics.

This, the second part, Bioinformatic Methods II, will cover motif searching, protein-protein interactions, structural bioinformatics, gene expression data analysis, and cis-element predictions.

This pair of courses is useful to any student considering graduate school in the biological sciences, as well as students considering molecular medicine.

These courses are based on one taught at the University of Toronto to upper-level undergraduates who have some understanding of basic molecular biology. If you're not familiar with this, something like https://learn.saylor.org/course/bio101 might be helpful. No programming is required for this course although some command line work (though within a web browser) occurs in the 5th module.

Bioinformatic Methods II is regularly updated, and was last updated for January 2023.

What's inside

Syllabus

Protein Motifs

In this module we'll be exploring conserved regions within protein families. Such regions can help us understand the biology of a sequence, in that they are likely important for biological function, and also be used to help ascribe function to sequences where we can't identify any homologs in the databases. There are various ways of describing the conserved regions from simple regular expressions to profiles to profile hidden Markov models (HMMs).

Protein-Protein Interactions

In this module we'll be exploring protein-protein interactions (PPIs). Protein-protein interactions are important as proteins don't act in isolation, and often an examination of the interaction partners (determined in an unbiased, perhaps high throughput way) of a given protein can tell us a lot about its biology. We'll talk about some different methods used to determine PPIs and go over their strengths and weaknesses. In the lab we'll use 3 different tools and two different databases to examine interaction partners of BRCA2, a protein that we examined in last module's lab. Finally, we'll touch on a "foundational" concept, Gene Ontology (GO) term enrichment analysis, to help us understand in an overview way the proteins interacting with our example.

Protein Structure

The determination of a protein's tertiary structure in three dimensions can tell us a lot about the biology of that protein. In this module's mini-lecture, we'll talk about some different methods used to determine a protein's tertiary structure and cover the main database for protein structure data, the PDB. In the lab we'll explore the PDB and an online tool for searching for structural (as opposed to sequence) similarity, VAST. We'll then use a nice piece of stand-alone software, PyMOL, to explore several protein structures in more detail.

Review: Protein Motifs, Protein-Protein Interactions, and Protein Structure

Gene Expression Analysis I

When and where genes are expressed (active) in tissues or cells is one of the main determinants of what makes that tissue or cell the way it is, both in terms of morphology and in terms of response to external stimuli. Several different methods exist for generating gene expression levels for all of the genes in the genome in tissues or even at cell-type-specific resolution. In this class we'll be processing and then examining some gene expression data generated using RNA-seq. We'll explore one of the main databases for RNA-seq expression data, the Sequence Read Archive (SRA), and then use an open-source suite of programs in R called BioConductor to process the raw reads from 4 RNA-seq data sets, to summarize their expression levels, to select significantly differentially expressed genes, and finally to visualize these as a heat map.

Gene Expression Analysis II

When and where genes are expressed (active) in tissues or cells is one of the main determinants of what makes that tissue or cell the way it is, both in terms of morphology and in terms of response to external stimuli. Several different methods exist for generating gene expression levels for all of the genes in the genome in tissues or even at cell-type-specific resolution. In this class we'll be hierarchically clustering our significantly differentially expressed genes from last time using BioConductor and the built-in function of an online tool, called Expression Browser. Then we'll be using another online tool that uses a similarity metric, the Pearson correlation coefficient, to identify genes responding in a similar manner to our gene of interest, in this case AP3. We'll use a second tool, ATTED-II to corroborate our gene list. We'll also be exploring some online databases of gene expression and an online tool for doing a Gene Ontology enrichment analysis.

Cis Regulatory Systems

When and where genes are expressed in tissues or cells is one of the main determinants of what makes that tissue or cell the way it is, both in terms of morphology and in terms of response to external stimuli. Gene expression is controlled in part by the presence of short sequences in the promoters (and other parts) of genes, called cis-elements, which permit transcription factors and other regulatory proteins to bind to direct the patterns of expression in certain tissues or cells or in response to environmental stimuli: We'll explore a couple of sets of promoters of genes that are coexpressed with AP3 from Arabidopsis, and with INSULIN from human, for the presence of known cis-elements, and we'll also try to predict some new ones using a couple of different methods.

Review: Gene Expression Analysis and Cis Regulatory Systems + Final Assignment

Good to know

Know what's good

, what to watch for

, and possible dealbreakers

Follows a structured, linear path from the foundational to the advanced

Covers advanced topics in bioinformatics, including motif searching, protein-protein interactions, structural bioinformatics, gene expression data analysis, and cis-regulatory systems

Provides hands-on labs and interactive materials to reinforce concepts and skills

Taught by instructors with expertise in bioinformatics

Requires a basic understanding of molecular biology, which may exclude beginners

Reviews summary

Bioinformatics ii: engaging and beneficial

According to students, Bioinformatic Methods II offers a detailed and straightforward introduction to the field. The course is engaging, with a beneficial lab section and encouraging instructors like Professor Provart. While the exercises can be confusing at times, learners can seek support from the active discussion forums.

Learners find this course interesting and engaging.

"I just loved the course"

The lab section is seen as the most beneficial part of the course.

"the most beneficial and in the same time interesting part was the lab section"

Learners can easily get help from discussion forums with active participation from Professor Provart.

"there are plenty of discussion forums where help can be easily obtained - Prof Provart himself follows the forums very closely and is not hesitant to step in with further explanations"

Professor Provart's explanations are clear and easy to follow.

"simple straightforward way"

"simple way of explaining"

Some learners find following the exercises difficult.

"The way in which the exercises are designed can sometimes be confusing to follow"

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 Bioinformatic Methods II with these activities:

Review molecular biology

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This course builds upon the basics of molecular biology, so it is imperative that you are familiar with these concepts before starting the course.

Browse courses on Molecular Biology

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Review your notes from a previous molecular biology course or textbook.
Take some practice quizzes or tests to assess your understanding of the material.
Meet with a tutor or teaching assistant to go over any areas where you are struggling.

Read 'Molecular Biology of the Cell'

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This book is a comprehensive overview of molecular biology and will help you to solidify your understanding of the basic concepts that will be covered in this course.

View Molecular Biology of the Cell on Amazon

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Read one chapter per week.
Take notes on the most important concepts.
Discuss the material with a classmate or study group.

Follow tutorials on bioinformatics tools

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This course will introduce you to a variety of bioinformatics tools, and it is important to get some hands-on experience with these tools before starting the course.

Browse courses on Bioinformatics

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Identify a few bioinformatics tools that you are interested in learning more about.
Find tutorials for these tools online.
Follow the tutorials and complete the exercises.

Five other activities

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Practice multiple sequence alignment

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Multiple sequence alignment is a fundamental skill in bioinformatics, and it is important to get plenty of practice before starting this course.

Browse courses on Multiple Sequence Alignment

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Find a dataset of multiple sequences.
Use a multiple sequence alignment tool to align the sequences.
Analyze the alignment and identify conserved regions.

Join a study group

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Joining a study group can be a great way to review the material, get help with difficult concepts, and stay motivated throughout the course.

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Find a study group that meets regularly.
Attend study group meetings and participate in discussions.
Work with your study group members to review the material and prepare for exams.

Create a mind map of the course material

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Creating a mind map can help you to visualize the relationships between different concepts in the course and improve your understanding of the material.

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Start by writing down the main topic of the course in the center of a piece of paper.
Draw branches off of the main topic for each of the major subtopics.
Continue to add branches and sub-branches until you have a complete map of the course material.

Review statistics

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This course will use some basic statistical concepts, so it is important to review these concepts before starting the course.

Browse courses on Statistics

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Review your notes from a previous statistics course or textbook.
Take some practice quizzes or tests to assess your understanding of the material.
Meet with a tutor or teaching assistant to go over any areas where you are struggling.

Participate in a bioinformatics competition

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Participating in a bioinformatics competition can be a great way to test your skills and knowledge, and to learn from other bioinformaticians.

Browse courses on Bioinformatics

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Find a bioinformatics competition that you are interested in participating in.
Register for the competition and download the data.
Analyze the data and develop a solution to the problem.
Submit your solution to the competition.

Career center

Learners who complete Bioinformatic Methods II will develop knowledge and skills that may be useful to these careers:

Geneticist

Geneticists study the genes of living things, their functions, and how they are passed down from generation to generation. They learn about the genetic causes of diseases and develop new treatments. A course in bioinformatic methods can be extremely helpful for this career as it will help you develop the skills needed to analyze and interpret genetic data.

See salaries and explore the career path for Geneticist

Computational Biologist

Computational biologists use computer science and mathematics to solve problems in biology. They develop new methods for analyzing and interpreting biological data, and they work with biologists to solve complex problems. A course in bioinformatic methods can be very helpful for this career, as it will help you develop the skills needed to work with biological data.

See salaries and explore the career path for Computational Biologist

Bioinformatician

Bioinformaticians use computer science and mathematics to analyze and interpret biological data. They develop new methods for storing and analyzing this data, and they work with biologists to solve complex problems. A course in bioinformatic methods can be very helpful for this career, as it will help you develop the skills needed to work with biological data.

See salaries and explore the career path for Bioinformatician

Data Scientist

Data scientists use computer science and mathematics to analyze and interpret data. They develop new methods for storing and analyzing this data, and they work with businesses to solve complex problems. A course in bioinformatic methods can be very helpful for this career, as it will help you develop the skills needed to work with data.

See salaries and explore the career path for Data Scientist

Biostatistician

Biostatisticians use statistics to analyze and interpret biological data. They develop new methods for storing and analyzing this data, and they work with biologists to solve complex problems. A course in bioinformatic methods can be very helpful for this career, as it will help you develop the skills needed to work with biological data.

See salaries and explore the career path for Biostatistician

Epidemiologist

Epidemiologists study the causes of diseases and develop new ways to prevent and treat them. They use statistics and other methods to analyze data on the spread of diseases, and they work with public health officials to develop policies to prevent and control diseases. A course in bioinformatic methods can be very helpful for this career, as it will help you develop the skills needed to analyze and interpret data on the spread of diseases.

See salaries and explore the career path for Epidemiologist

Toxicologist

Toxicologists study the effects of toxic substances on living things. They develop new ways to protect people from toxic substances, and they work with government agencies to set standards for the safe use of toxic substances. A course in bioinformatic methods can be helpful for this career, as it will help you develop the skills needed to analyze and interpret data on the effects of toxic substances on living things.

See salaries and explore the career path for Toxicologist

Pharmacologist

Pharmacologists study the effects of drugs on living things. They develop new drugs and treatments, and they work with doctors to determine the best way to use drugs to treat diseases. A course in bioinformatic methods can be helpful for this career, as it will help you develop the skills needed to analyze and interpret data on the effects of drugs on living things.

See salaries and explore the career path for Pharmacologist

Medical Researcher

Medical researchers study the causes and treatments of diseases. They develop new drugs and treatments, and they work with doctors to determine the best way to use drugs to treat diseases. A course in bioinformatic methods can be helpful for this career, as it will help you develop the skills needed to analyze and interpret data on the causes and treatments of diseases.

See salaries and explore the career path for Medical Researcher

Science Writer

Science writers write about scientific topics for the general public. They work with scientists to understand complex scientific concepts and translate them into clear and concise writing. A course in bioinformatic methods can be helpful for this career, as it will help you develop the skills needed to understand and write about complex scientific concepts.

See salaries and explore the career path for Science Writer

Science Teacher

Science teachers teach science to students at all levels. They develop lesson plans and teach students about the principles of science. A course in bioinformatic methods can be helpful for this career, as it will help you develop the skills needed to teach students about complex scientific concepts.

See salaries and explore the career path for Science Teacher

Science Communicator

Science communicators communicate scientific information to the public. They work with scientists to understand complex scientific concepts and translate them into clear and concise language. A course in bioinformatic methods can be helpful for this career, as it will help you develop the skills needed to understand and communicate complex scientific concepts.

See salaries and explore the career path for Science Communicator

Science Journalist

Science journalists write about scientific topics for the general public. They work with scientists to understand complex scientific concepts and translate them into clear and concise writing. A course in bioinformatic methods can be helpful for this career, as it will help you develop the skills needed to understand and write about complex scientific concepts.

See salaries and explore the career path for Science Journalist

Policy Analyst

Policy analysts develop and evaluate policies for government agencies. They use data and research to analyze the impact of policies, and they work with policymakers to develop new policies. A course in bioinformatic methods can be helpful for this career, as it will help you develop the skills needed to analyze and interpret data.

See salaries and explore the career path for Policy Analyst

Science Administrator

Science administrators manage science programs and activities. They work with scientists to develop and implement research programs, and they work with government agencies to secure funding for research. A course in bioinformatic methods can be helpful for this career, as it will help you develop the skills needed to manage science programs and activities.

See salaries and explore the career path for Science Administrator