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    Central Dogma, Dictionaries, and Functions: Using Programming Concepts to Simulate Biological Processes
    Technologies like next-generation sequencing, proteomics, and high-throughput phenotyping have transformed the way we do biology. There is a continued need for scientists with computational skills to analyze biological data while understanding the...

    Courses: BioinformaticsBioinformatics

    computationpythonJupyter notebookFunctionscentral dogmaDictionaries
    Lesson
    8550

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    440

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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...
    geneticsanimaldevelopmentcompetitionbacterial
    Lesson
    1469

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    182

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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...
    Rdata analysisRStudio
    Lesson
    996

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    274

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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...
    NCBItranscriptiontranslationGene StructureGene databasesEnsembl
    Lesson
    3849

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    230

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    Analysis of Microbiomes Using Free Web-Based Tools in Online and In-Person Undergraduate Science Courses
    Our understanding of microbiomes, or the collection of microorganisms and their genes in a given environment, has been revolutionized by technological and computational advances. However, many undergraduate students do not get hands-on experiences...
    microbiomeDNA SubwayCyVerseCourse based undergraduate researchQIIME2ranacapa
    Lesson
    1449

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    180

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    Bioinformatics is a BLAST: Engaging First-Year Biology Students on Campus Biodiversity Using DNA Barcoding
    In order to introduce students to the concept of molecular diversity, we developed a short, engaging online lesson using basic bioinformatics techniques. Students were introduced to basic bioinformatics while learning about local on-campus species...
    geneticsorganismal biologybioinformaticstaxonomyDNA Barcodingspecies concepts
    Lesson
    2609

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    201

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    Application of a Bacterial Experimental Evolution System to Visualize and Teach Evolution in Action: A Course-Based Undergraduate Research Experience
    Concepts of evolution are typically taught through examples of extremely long timescales, which do not always resonate broadly. Here, we describe a course-based undergraduate research experience tailored for junior and senior undergraduate biology...
    EvolutionmutationcompetitionNatural Selectionregulationstructure and functionreproductive fitnessgenotype to phenotypehomologs
    Review
    1225

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    156

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    Workshop Report: Summer 2020 Virtual CRISPR in the Classroom
    As innovations and developments in genome editing technologies using CRISPR-Cas systems progress, the need to disseminate relevant knowledge and build skills among the next generation of young scientists in undergraduate classrooms is vital. Our...
    geneticscrisprGenome Analysisgene editingbacterial immunity
    Review
    1537

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    93

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    Making Change Sustainable: Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) Meeting Review
    The purpose of the meeting described in this review was to decide how best to ensure the sustainability of the Network for Integrating Bioinformatics into Life Science Education (NIBLSE; pronounced “nibbles”). Biology research today...

    Courses: BioinformaticsBioinformatics

    meetingsustainabilityfmnNIBLSEincubator
    Lesson
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    136

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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...
    microscopyC. elegansquantitative analysisinquiry-based learninggene expressionRNA interferenceCodon UsageLaboratory Module
    Lesson
    1761

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    146

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    Sequences and Properties of Gluten Proteins From Different Grains: A Virtual-Friendly Protein Laboratory
    The COVID-19 pandemic has forced much university instruction into virtual modes. As a result, many laboratory courses have either dropped content altogether or replaced hands-on activities with simulations and “dry” labs. Our goal was...
    protein structure and functionProtein sequenceintermolecular forcesBiomacromolecules
    Lesson
    3195

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    328

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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...
    bioinformaticsmolecular modelingCOVID19protein structure and functionUCSF ChimeraSARS-CoV-2 spike proteinACE2 receptor
    Teaching Tools and Strategies
    2066

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    249

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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...
    Problem SolvingCollaborative WorkCorrect Misconceptions
    Lesson
    4120

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    402

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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...
    modelingcase studymicroscopystructureOrganellesHigh-throughput (HT)Endoplasmic Reticulum (ER)Fluorescent microscopyHuman Cell Biology
    Lesson
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    546

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    Using Bioinformatics and Molecular Visualization to Develop Student Hypotheses in a Malate Dehydrogenase Oriented CURE
    Developing student creativity and ability to develop a testable hypothesis represents a significant challenge in most laboratory courses. This lesson demonstrates how students use facets of molecular evolution and bioinformatics approaches...
    bioinformaticsNoncovalent InteractionsEnzyme CatalysisProtein Structure/function
    Teaching Tools and Strategies
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    1624

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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...
    geneticsImmunologyBiochemistrybioinformaticsmolecular evolutionpublic healthvirusCOVID19
    Lesson
    2580

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    388

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    Moths and Frogs and E. coli, Oh My!: Agent-based Modeling of Evolutionary Systems
    In evolution classrooms, introducing and reinforcing the idea of genetic drift and random selection can be challenging, as can be reinforcing appropriate mental models of evolution. Agent-based models offer students the opportunity to conduct a...
    modelingEvolutionecologyagent-based modelingGenetic Driftenvironmental scienceNatural Selectioncompetitive coevolutionsimulation modelingevolutionary reasoning
    Lesson
    5688

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    1501

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    Single Cell Insights Into Cancer Transcriptomes: A Five-Part Single-Cell RNAseq Case Study Lesson
    There is a growing need for integration of “Big Data” into undergraduate biology curricula. Transcriptomics is one venue to examine biology from an informatics perspective. RNA sequencing has largely replaced the use of microarrays for whole...
    bioinformaticscancertranscriptomicshigh-throughputData wranglingSingle cell RNA sequencingq
    Lesson
    5289

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    1088

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    A CURE for Salmonella: A Laboratory Course in Pathogen Microbiology and Genomics
    Rapid advances in genomics and bioinformatics, the vast amount of data generated by next-generation sequencing, and the penetration of the ‘-omics’ into many areas of biology have created a need for students with hands-on experience with...
    epidemiologyresearchbioinformaticsgenomicspublic healthAntibiotic Resistant BacteriaSalmonellaDNA sequencingpathogenic bacteria
    Lesson
    6779

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    1325

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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...
    bioinformaticsGenome BrowsergenomicsRNAseqsplicingComputer ModelGene Structure