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    Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching
    Next-generation sequencing is radically changing the study of biology, but there are currently few resources aimed at teaching the required laboratory and data-analysis skills to undergraduate students. This gap is especially true at primarily...

    Courses: BioinformaticsBioinformatics Introductory BiologyIntroductory Biology

    statisticsbioinformaticsRNAseqgene expressioncomputer programming
    Lesson
    2711

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    429

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    An Introduction to Eukaryotic Genome Analysis in Non-model Species for Undergraduates: A tutorial from the Genome Consortium for Active Teaching
    Advances in Next Generation Sequencing (NGS) technology have led to development of many research methods for analyzing genomic data. Students studying biology at the undergraduate level must hone their skills at genomic analysis to participate in...

    Courses: BioinformaticsBioinformatics GeneticsGenetics Science Process SkillsScience Process Skills

    Speciationgenome evolutiongenetic variation
    Essay
    923

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    202

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    Thinking deeply about quantitative analysis: Building a Biologist's Toolkit
    Vision and Change in Undergraduate Biology Education encouraged faculty to focus on core concepts and competencies in undergraduate curriculum. We created a sophomore-level course, Biologists' Toolkit, to focus on the competencies of...

    Courses: Introductory BiologyIntroductory Biology

    Vision and ChangeRRStudioquantitative literacystatistical analysisScientific communication
    Lesson
    2992

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    549

    downloads

    2

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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: BioinformaticsBioinformatics

    bioinformaticsgenomicscodingJupyter notebookcommand lineCyVersescriptingnext generation sequencing analysis
    Teaching Tools and Strategies
    976

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    311

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    A Customizable Inquiry-Based Statistics Teaching Application for Introductory Biology Students
    Building strong quantitative skills prepares undergraduate biology students for successful careers in science and medicine. While math and statistics anxiety can negatively impact student learning within biology classrooms, instructors may reduce...

    Courses: Introductory BiologyIntroductory Biology

    introductory biologyQuantitative reasoningInclusive teachingauthentic inquiryInferential statisticsInstructional scaffolding
    Lesson
    1281

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    169

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    0

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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
    3074

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    453

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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...

    Courses: BioinformaticsBioinformatics EcologyEcology EvolutionEvolution Science Process SkillsScience Process Skills

    modelingEvolutionecologyagent-based modelingGenetic Driftenvironmental scienceNatural Selectioncompetitive coevolutionsimulation modelingevolutionary reasoning
    Lesson
    1514

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    210

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    Modeling Strep Throat Detection, Infection, and Spread Using an SIR Model and the Vensim Simulation Software
    The overarching goal of this lesson is to provide students with an opportunity to gain experience making and using biological models. Biological modeling can be used to investigate complex, real-world problems so that predictions can be made about...

    Courses: Cell BiologyCell Biology ImmunologyImmunology Introductory BiologyIntroductory Biology MicrobiologyMicrobiology

    infectious diseasebiological modelingSIR model
    Lesson
    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 BiologyBiochemistry and Molecular Biology BioinformaticsBioinformatics EcologyEcology MicrobiologyMicrobiology Science Process SkillsScience Process Skills

    microbiome
    Lesson
    2274

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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-PhysiologyAnatomy-Physiology BioinformaticsBioinformatics EcologyEcology GeneticsGenetics

    Rdata analysisRStudio
    Lesson
    2045

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    890

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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: BioinformaticsBioinformatics GeneticsGenetics Science Process SkillsScience Process Skills

    UCSC genome browsersingle nucleotide polymorphismGenome wide association studiesGenomic organization
    Lesson
    1757

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    286

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    Using Gamification to Teach Undergraduate Students about Scientific Writing
    Despite its importance, scientific writing is often deprioritized in undergraduate biology classes. Reasons include assumed prior knowledge, lack of class time, tedious grading, and the complexity and challenges associated with quality writing. To...

    Courses: Science Process SkillsScience Process Skills

    gamificationscientific writingE-LearningInstant FeedbackInteractive LearningReading Scientific PapersVIdeo/computer game
    Lesson
    3686

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    200

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    Three Research-Based Quantitative Reasoning Modules for Introductory Organismal Biology Laboratories
    We have designed three laboratory modules for an introductory organismal biology course with an emphasis on quantitative reasoning and data analysis skills. Module 1 tests for dimorphism in crayfish chelae using a paired statistical design. Module...

    Courses: Introductory BiologyIntroductory Biology Science Process SkillsScience Process Skills

    allometryplantsAnatomytranspirationdimorphisminvertebrate biologyarthropodsplatyhelminths
    Lesson
    6614

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    1646

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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...

    Courses: Biochemistry and Molecular BiologyBiochemistry and Molecular Biology BioinformaticsBioinformatics Cell BiologyCell Biology GeneticsGenetics Introductory BiologyIntroductory Biology

    bioinformaticscancertranscriptomicshigh-throughputData wranglingSingle cell RNA sequencingq
    Lesson
    6121

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    1235

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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...

    Courses: Biochemistry and Molecular BiologyBiochemistry and Molecular Biology BioinformaticsBioinformatics EcologyEcology MicrobiologyMicrobiology

    epidemiologyresearchbioinformaticsgenomicspublic healthAntibiotic Resistant BacteriaSalmonellaDNA sequencingpathogenic bacteria
    Lesson
    3505

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    1299

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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 BiologyBiochemistry and Molecular Biology BioinformaticsBioinformatics Cell BiologyCell Biology GeneticsGenetics

    bioinformaticsgene expressiongenetic basis of diseaseCRISPR/Cas9genetic engineeringin silico
    Lesson
    3677

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    678

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    0

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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: BioinformaticsBioinformatics GeneticsGenetics Science Process SkillsScience Process Skills

    transcriptionexonintronsplicing
    Lesson
    1529

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    305

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    Promoting Climate Change Literacy for Non-majors: Implementation of an atmospheric carbon dioxide modeling activity as an inquiry-based classroom activity
    Students who are directly involved in scientific activities develop a deeper understanding and appreciation of both scientific knowledge and the scientific process. This understanding is critically important in scientific areas like climate change...

    Courses: Introductory BiologyIntroductory Biology Science Process SkillsScience Process Skills

    modelingExcelquantitativeclimate changeEnvironmental Biologyatmospheric carbon dioxide
    Lesson
    2821

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    554

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    Developing Data Literacy Skills and Connecting the Student Experience in the Classroom to the Community Through Biodiversity Projects
    Undergraduate education and long-term science literacy are enhanced by integrating data projects with public datasets and creating analysis summaries. Underutilized public datasets are often generated by community-based or citizen science projects...

    Courses: EcologyEcology Plant BiologyPlant Biology

    species richnessBiodiversitydisturbanceHabitat rangePopulation abundance
    Lesson
    1955

    views

    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: BioinformaticsBioinformatics GeneticsGenetics

    proteinsMitochondrial GenomesNuclear GenomesrRNAtRNA