CourseSource: Resources

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Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses

Introductory bioinformatics exercises often walk students through the use of computational tools, but often provide little understanding of what a computational tool does "under the hood." A solid understanding of how a bioinformatics...

Courses: Biochemistry and Molecular Biology Bioinformatics Introductory Biology

BLASTmultiple sequence alignmentsequence similarityphylogramZika virusAlgorithmScoring Matrix

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1566

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300

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Using QIIME to Interpret Environmental Microbial Communities in an Upper Level Metagenomics Course

Metagenomics is rapidly evolving due to advances in sequencing technologies and bioinformatics, but without proper training to interpret these datasets, student understanding remains limited. Aimed at undergraduate juniors and seniors and graduate...

Courses: Biochemistry and Molecular Biology Bioinformatics Ecology Ecology Microbiology Science Process Skills

microbiome

Teaching Tools and Strategies

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356

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DNA Detective: Genotype to Phenotype. A Bioinformatics Workshop for Middle School to College.

Advances in high-throughput techniques have resulted in a rising demand for scientists with basic bioinformatics skills as well as workshops and curricula that teach students bioinformatics concepts. DNA Detective is a workshop we designed to...

Courses: Biochemistry and Molecular Biology Bioinformatics Genetics Plant Biology

geneticsbioinformaticsDNAgenotypephenotypegenegene annotation

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5648

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1168

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Meiosis: A Play in Three Acts, Starring DNA Sequence

Meiosis is well known for being a sticky topic that appears repeatedly in biology curricula. We observe that a typical undergraduate biology major cannot correctly identify haploid and diploid cells or explain how and why chromosomes pair before...

Courses: Cell Biology Genetics Introductory Biology

recombinationmeiosisDNA sequenceCrossingoverchromosome structureHolliday junctionhomology

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1578

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350

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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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1952

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280

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A CURE-based approach to teaching genomics using mitochondrial genomes

There is an abundance (currently over 1016 DNA bases) of publicly available genetic sequence data and a dearth of trained genomicists to process and interpret it, necessitating more trained bioinformaticians with biological expertise. For...

Courses: Bioinformatics Genetics

proteinsMitochondrial GenomesNuclear GenomesrRNAtRNA

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5710

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978

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A clicker-based case study that untangles student thinking about the processes in the central dogma

The central dogma of biology is a foundational concept that provides a scaffold to understand how genetic information flows in biological systems. Despite its importance, undergraduate students often poorly understand central dogma processes (DNA...

Courses: Genetics Introductory Biology

mutationtranscriptionphenotypecentral dogmatranslationDNA replication

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2584

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202

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A Laboratory Module That Explores RNA Interference and Codon Optimization Through Fluorescence Microscopy Using Caenorhabditis elegans

Scientific research experiences are beneficial to students allowing them to gain laboratory and problem-solving skills, as well as foundational research skills in a team-based setting. We designed a laboratory module to provide a guided research...

Courses: Bioinformatics Cell Biology Developmental Biology Genetics Science Process Skills

microscopyC. elegansquantitative analysisinquiry-based learninggene expressionRNA interferenceCodon UsageLaboratory Module

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540

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Using Raw Sequence Data to Analyze Tumor Suppressor Mutations

Learning to identify DNA sequence variants from raw sequencing data (electropherograms) is a basic molecular biology skill with applications to basic research and clinical practice. Yet learning to map DNA sequence variants to functional regions...

Courses: Bioinformatics Genetics

bioinformaticsmutationDNAgenomic visualizationparts of a geneclinical consequencesraw data

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4839

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1206

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Teaching the Central Dogma Using a Case Study of Genetic Variation in Cystic Fibrosis

The central dogma of biology is a foundational concept that is traditionally included in genetics curricula at all academic levels. Despite its ubiquitous presence throughout genetics education, students persistently struggle with both the...

Courses: Genetics

transcriptioncentral dogmatranslationsequence analysisDNA replicationgenetic variants

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2100

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543

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Using computational molecular modeling software to demonstrate how DNA mutations cause phenotypes

Students require a deep understanding of the central dogma before they can understand complex topics such as evolution and biochemical disorders. However, getting undergraduate biology students to apply higher-order thinking skills to the central...

Courses: Bioinformatics Genetics Science Process Skills

Protein Structurecomputational modelingcentral dogmaplant leaf structurePhenotype/Genotype

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617

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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

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Translating Co-Translational Translocation

Understanding the process of proteins targeting to specific locations within a cell is a fundamental part of cell biology. Synthesis of proteins by co-translational translocation, which also determines the resulting protein topology, is a complex...

Courses: Cell Biology

Topologyco-translational translocationendoplasmic reticulumprotease protection assaysecretory proteinssignal sequencetransmembrane proteins

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1246

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My Dog IS My Homework: Exploring Canine Genetics to Understand Genotype-Phenotype Relationships

To facilitate understanding of the fundamental genetic concept of the genotype-phenotype relationship in our introductory biology students, we designed an engaging multi-week series of related lessons about canine genetics in which students...

Courses: Bioinformatics Genetics Introductory Biology Science Process Skills

gel electrophoresissequence analysiscanine geneticsdeoxyribonucleic acid (DNA)dog coat morphologygenotype and phenotypemutationsPolymerase chain reaction (PCR)single nucleotide polymorphism (SNP)

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Tackling "Big Data" with Biology Undergrads: A Simple RNA-seq Data Analysis Tutorial Using Galaxy

Analyzing high-throughput DNA sequence data is a fundamental skill in modern biology. However, real and perceived barriers such as massive file sizes, substantial computational requirements, and lack of instructor background knowledge can...

Courses: Biochemistry and Molecular Biology Bioinformatics

bioinformaticsDNA sequenceRNAseqgene expression

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680

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The Case of the Missing Strawberries: RFLP analysis

While solving the fictional mystery of the missing strawberries, students are engaged in a guided-inquiry lesson featuring small-group and class discussions, hands-on activities, and laboratory exercises related to molecular genotyping by...

Courses: Genetics Science Process Skills

process of scienceDNAforensicsgel electrophoresisMolecular genotypingRestriction endonucleaseRestriction enzymeRestriction fragment length polymorphismRFLP

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A CRISPR/Cas Guide RNA Design In Silico Activity

CRISPR biotechnologies inspired by the Clustered Regularly Interspaced Short Palindromic Repeat RNA-guided nuclease adaptive bacterial immune system have revolutionized biology research and become ubiquitous tools for hypothesis and...

Courses: Biochemistry and Molecular Biology Bioinformatics Cell Biology Genetics

bioinformaticsgene expressiongenetic basis of diseaseCRISPR/Cas9genetic engineeringin silico

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Using CRISPR-Cas9 to teach the fundamentals of molecular biology and experimental design

One of the challenges of inquiry-based research experiences is balancing the instruction on skills and techniques with data generation and analysis. This is especially true in technique heavy disciplines such as molecular biology, where emphasis...

Courses: Biochemistry and Molecular Biology

experimental designcrisprmolecular technique

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Exploration of the Human Genome by Investigation of Personalized SNPs

Students often shy away from tedious bioinformatics approaches to exploring their genomes. However, in our expanding digital world these skills are some of the most relevant and valuable. To increase students' interest in their own genomes, I...

Courses: Bioinformatics Genetics Science Process Skills

UCSC genome browsersingle nucleotide polymorphismGenome wide association studiesGenomic organization

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2357

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286

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You and Your Oral Microflora: Introducing non-biology majors to their “forgotten organ”

With limited time available for laboratory activities, introductory science courses for non-science majors typically use the laboratory period to reinforce material that was previously presented during lecture. This practice was true of a human...

Courses: Genetics Introductory Biology Microbiology Science Process Skills

bacteriamicrobiomeBLASTmicrobesDNA replicationPolymerase chain reaction (PCR)

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Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses

Using QIIME to Interpret Environmental Microbial Communities in an Upper Level Metagenomics Course

DNA Detective: Genotype to Phenotype. A Bioinformatics Workshop for Middle School to College.

Meiosis: A Play in Three Acts, Starring DNA Sequence

Understanding Protein Domains: A Modular Approach

A CURE-based approach to teaching genomics using mitochondrial genomes

A clicker-based case study that untangles student thinking about the processes in the central dogma

A Laboratory Module That Explores RNA Interference and Codon Optimization Through Fluorescence Microscopy Using Caenorhabditis elegans

Using Raw Sequence Data to Analyze Tumor Suppressor Mutations

Teaching the Central Dogma Using a Case Study of Genetic Variation in Cystic Fibrosis

Using computational molecular modeling software to demonstrate how DNA mutations cause phenotypes

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

Translating Co-Translational Translocation

My Dog IS My Homework: Exploring Canine Genetics to Understand Genotype-Phenotype Relationships

Tackling "Big Data" with Biology Undergrads: A Simple RNA-seq Data Analysis Tutorial Using Galaxy

The Case of the Missing Strawberries: RFLP analysis

A CRISPR/Cas Guide RNA Design In Silico Activity

Using CRISPR-Cas9 to teach the fundamentals of molecular biology and experimental design

Exploration of the Human Genome by Investigation of Personalized SNPs

You and Your Oral Microflora: Introducing non-biology majors to their “forgotten organ”

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