CourseSource: Resources

Teaching Tools and Strategies

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Making toast: Using analogies to explore concepts in bioinformatics

Contemporary biology is moving towards heavy reliance on computational methods to manage, find patterns, and derive meaning from large-scale data, such as genomic sequences. Biology teachers are increasingly compelled to prepare students with...

Courses: Bioinformatics

bioinformaticsworkflowgenome

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A Fun Introductory Command Line Lesson: Next Generation Sequencing Quality Analysis with Emoji!

Radical innovations in DNA sequencing technology over the past decade have created an increased need for computational bioinformatics analyses in the 21st century STEM workforce. Recent evidence however demonstrates that there are significant...

Courses: Bioinformatics

bioinformaticsgenomicscodingJupyter notebookcommand lineCyVersescriptingnext generation sequencing analysis

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An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure

Gene structure, transcription, translation, and alternative splicing are challenging concepts for many undergraduates studying biology. These topics are typically covered in a traditional lecture environment, but students often fail to master and...

Courses: Biochemistry and Molecular Biology Bioinformatics Genetics

bioinformaticsGenome BrowsergenomicsRNAseqsplicingComputer ModelGene Structure

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Homologous chromosomes? Exploring human sex chromosomes, sex determination and sex reversal using bioinformatics approaches

Constructing a robust understanding of homologous chromosomes, sex chromosomes, and the particulate nature of genes is a notoriously difficult task for undergraduate biology students. In this lesson, students expand their knowledge of human...

Courses: Bioinformatics Genetics Introductory Biology Science Process Skills

bioinformaticsautosomehomologous chromosomeshomologous recombinationsex chromosomesex determinationsex reversal mutations

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A Hands-on Introduction to Hidden Markov Models

In this Lesson, we describe a classroom activity that demonstrates how a Hidden Markov Model (HMM) is applied to predict a eukaryotic gene, focusing on predicting one exon-intron boundary. This HMM lesson is part of the BIOL/CS 370...

Courses: Bioinformatics Genetics Science Process Skills

transcriptionexonintronsplicing

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Understanding Protein Domains: A Modular Approach

An understanding of protein structure, function, and interaction is central to biochemistry. One angle into this topic is to engage students in considering protein domains as modules that develop form and execute function semi-independently. Here,...

Courses: Biochemistry and Molecular Biology Cell Biology Science Process Skills

Protein Structure

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Using Open-Source Bioinformatics and Visualization Tools to Explore the Structure and Function of SARS-CoV-2 Spike Protein

The relationship between protein structure and function is a foundational concept in undergraduate biochemistry. We find this theme is best presented with assignments that encourage exploration and analysis. Here, we share a series of four...

Courses: Biochemistry and Molecular Biology Bioinformatics Science Process Skills

bioinformaticsmolecular modelingCOVID19protein structure and functionUCSF ChimeraSARS-CoV-2 spike proteinACE2 receptor

Teaching Tools and Strategies

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A 360˚ View of COVID-19

In March 2020, institutions underwent a massive transition to distance learning as a result of the COVID-19 pandemic. With so little time to devise new materials to maximize learning in the new virtual environment, instructors devised a variety of...

Courses: Biochemistry and Molecular Biology Bioinformatics Cell Biology Evolution Genetics Immunology Introductory Biology Microbiology Science Process Skills

geneticsImmunologyBiochemistrybioinformaticsmolecular evolutionpublic healthvirusCOVID19

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How to Find a Gene: Retrieving Information From Gene Databases

A strong understanding of distinct gene components and the ability to retrieve relevant information from gene databases are necessary to answer a diverse set of biological questions. However, often there is a considerable gap between...

Courses: Biochemistry and Molecular Biology Bioinformatics Cell Biology Genetics Introductory Biology

NCBItranscriptiontranslationGene StructureGene databasesEnsembl

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351

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Learning R for Biologists: A Mini Course Grab-Bag for Instructors

As biology becomes more data driven, teaching students data literacy skills has become central to biology curriculum. Despite a wealth of online resources that teach researchers how to use R, there are few that offer practical laboratory-based...

Courses: Anatomy-Physiology Bioinformatics Ecology Ecology Genetics

Rdata analysisRStudio

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Manuscript 101: A Data-Driven Writing Exercise for Beginning Scientists

Learning to write a scientific manuscript is one of the most important and rewarding scientific training experiences, yet most young scientists only embark on this experience relatively late in graduate school after gathering sufficient data in...

Courses: Bioinformatics Cell Biology Developmental Biology Genetics Microbiology Science Process Skills

geneticsanimaldevelopmentcompetitionbacterial

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Does Organelle Shape Matter?: Exploring Patterns in Cell Shape and Structure with High-Throughput (HT) Imaging

Organelle structure has been studied and visualized for decades; however, publicly available databases that use improved high-throughput microscopy of gene-edited cell lines have recently revolutionized the amount and quality of information now...

Courses: Biochemistry and Molecular Biology Bioinformatics Cell Biology Genetics Science Process Skills

modelingcase studymicroscopystructureOrganellesHigh-throughput (HT)Endoplasmic Reticulum (ER)Fluorescent microscopyHuman Cell Biology

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Tying it All Together: An Activity to Help Students Connect Course Experiences to Posted Learning Outcomes

Instructors of undergraduate courses in Biology and other Science, Technology, Engineering, and Mathematics (STEM) disciplines face an ongoing challenge to foster higher-order thinking and learning skills while also developing a sound conceptual...

Courses: Anatomy-Physiology Bioinformatics Cell Biology Developmental Biology Ecology Ecology Genetics Introductory Biology Microbiology Neurobiology Plant Biology Science Process Skills

metacognitionreflectiongoalsOutcomes

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Infectious Chocolate Joy with a Side of Poissonian Statistics: An activity connecting life science students with subtle physics concepts

Introductory physics courses are required for many programs in the life sciences, yet traditional curricula fail to help students meaningfully connect physical concepts with biological systems. In this lesson, we describe an activity taught...

Courses: Bioinformatics Microbiology Science Process Skills

quantitative biologyHIVmultiplicity of infectionPoisson DistributionPhysics for biologists

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Predicting and classifying effects of insertion and deletion mutations on protein coding regions

Mutations in genes can affect the encoded proteins in multiple ways, and some of these effects are counterintuitive. As for any other knowledge, students must create their own deep understanding of the Central Dogma. Students may not develop this...

Courses: Bioinformatics Genetics Science Process Skills

mutationcentral dogmatranslationframeshift

Teaching Tools and Strategies

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Fostering Student to Student Collaboration Across Institutions in a Protein Centric CURE

Collaboration is an essential component of research because it allows scientists to share expertise and tackle difficult scientific questions. While many undergraduate science courses include inquiry-based or authentic research projects,...

Courses: Biochemistry and Molecular Biology Genetics Introductory Biology Professional Development and Career Planning Science Process Skills

communicationBiochemistrycollaborationCUREhypothesisStudent to StudentInter institutionalProtein CentricAssignments

Teaching Tools and Strategies

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A Journal Club Project to Promote Interpreting and Presenting Information From the Primary Scientific Literature

Many undergraduate students receive little guidance on how to critically read, interpret data within, or present information from the primary scientific literature before they begin senior independent research experiences or enter professional or...

Courses: Developmental Biology Neurobiology

primary literaturejournal clubScience CommunicationfeedbackPeer reviewgroup workOral presentationProcess skillsPeer evaluationDevelopmental neurobiology

Teaching Tools and Strategies

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A How to Guide and Template for Designing a Puzzle Based Escape Room Game

Educational games are one active and effective way of engaging students with material while also providing additional motivation to tackle challenging concepts. A particularly popular game concept is the escape room, where students need to work in...

Courses: Biochemistry and Molecular Biology Bioinformatics Ecology Ecology Evolution Genetics Science Process Skills

Problem SolvingCollaborative WorkCorrect Misconceptions

Teaching Tools and Strategies

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The Pipeline CURE: An Iterative Approach to Introduce All Students to Research Throughout a Biology Curriculum

Participation in research provides personal and professional benefits for undergraduates. However, some students face institutional barriers that prevent their entry into research, particularly those from underrepresented groups who may stand to...

Courses: Developmental Biology Genetics Introductory Biology Science Process Skills

epigeneticsundergraduate researchmendelian inheritanceSelf-EfficacyCUREsnature of scienceResiliencecurriculum strategiesreprogramming

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Investigating the Function of a Transport Protein: Where is ABCB6 Located in Human Cells?

One of the challenges of teaching Cell Biology is helping students understand important research methods used to study cells. The goal of understanding cell biology methods is especially challenging in courses without a laboratory...

Courses: Cell Biology

ABC transporter familyDifferential centrifugationImmunoblottingImmunofluorescence assayProtein localizationPurifying organellesSDS-PAGE

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Making toast: Using analogies to explore concepts in bioinformatics

A Fun Introductory Command Line Lesson: Next Generation Sequencing Quality Analysis with Emoji!

An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure

Homologous chromosomes? Exploring human sex chromosomes, sex determination and sex reversal using bioinformatics approaches

A Hands-on Introduction to Hidden Markov Models

Understanding Protein Domains: A Modular Approach

Using Open-Source Bioinformatics and Visualization Tools to Explore the Structure and Function of SARS-CoV-2 Spike Protein

A 360˚ View of COVID-19

How to Find a Gene: Retrieving Information From Gene Databases

Learning R for Biologists: A Mini Course Grab-Bag for Instructors

Manuscript 101: A Data-Driven Writing Exercise for Beginning Scientists

Does Organelle Shape Matter?: Exploring Patterns in Cell Shape and Structure with High-Throughput (HT) Imaging

Tying it All Together: An Activity to Help Students Connect Course Experiences to Posted Learning Outcomes

Infectious Chocolate Joy with a Side of Poissonian Statistics: An activity connecting life science students with subtle physics concepts

Predicting and classifying effects of insertion and deletion mutations on protein coding regions

Fostering Student to Student Collaboration Across Institutions in a Protein Centric CURE

A Journal Club Project to Promote Interpreting and Presenting Information From the Primary Scientific Literature

A How to Guide and Template for Designing a Puzzle Based Escape Room Game

The Pipeline CURE: An Iterative Approach to Introduce All Students to Research Throughout a Biology Curriculum

Investigating the Function of a Transport Protein: Where is ABCB6 Located in Human Cells?

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