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    Introductory Video and worksheets on Module 1 and 2 on "Sequence Similarity: An inquiry based and under the hood..."
    The video walks the students to complete Module 1 and 2 on Sequence Similarly and Alignment adapted from Tapprich (2019) and Hudson Alpha that teaches these modules within the context of the...

    Keywords: bioinformaticssequencingFASTANCBINIBLSEalgorithmsBLASTmultiple sequence alignmentsequence similarityBLOSUM scoring matrixCourseSource

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    Sequence Similarity: Introducing Biological Databases to Community College Biology Students
    This laboratory module, published on CourseSource, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.

    Keywords: phylogeneticsbioinformaticssequencingFASTANCBINIBLSEalgorithmsincubatorsBLASTmultiple sequence alignmentsequence similarityBLOSUM scoring matrixneighbor-joining distance matrixCourseSourcephylogramZika virus

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    Bioinformatics: Investigating Sequence Similarity - A Plant Biology Approach
    This laboratory module is a modification of the original published on CourseSource with a focus on plant biology. In the final activity, students conduct a BLAST to compare histone protein...

    Keywords: phylogeneticsbioinformaticssequencingFASTANCBIplant biologyNIBLSEalgorithmsincubatorsPlant and Fungal EvolutionBLASTmultiple sequence alignmentsequence similarityBLOSUM scoring matrixneighbor-joining distance matrixCourseSourcephylogram

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    Sequence Similarity Resource Adaptation: Exploring Ebola Virus
    This adaptation of the sequence similarity resource provides biology students with a basic set of bioinformatics concepts and tools. These concepts and tools are used to explore relationships...

    Keywords: phylogeneticsbioinformaticsEbolasequencingFASTANCBINIBLSEalgorithmsincubatorsBLASTmultiple sequence alignmentsequence similarityBLOSUM scoring matrixneighbor-joining distance matrixCourseSourcephylogram

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    Phage Comparative Genomics Lab Manual
    A lab manual containing detailed instructions for several bioinformatics tools (dot plots, Phamerator maps, phylogenetic trees, and gene content similarity), all of which enable students to perform...

    Keywords: phageCUREcourse-based research experiences (CUREs)Comparative genomicsSEA-PHAGES

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    Using computational molecular modeling software to demonstrate how DNA mutations cause phenotypes
    This lesson is a five-week series of laboratory activities designed to help students transition from applying lower order thinking skills to the central dogma to applying higher-order thinking skills.

    Keywords: bioinformaticsNIBLSEProtein StructureDNAmolecular modelinggenotypephenotypeCourseSourcecomputational modelingcentral dogmaplant leaf structure

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    MathBench: Biodiversity Assessment of Stream Biota
    The MathBench module, "The Case of the Missing Mountaintop" introduces students to the concept of biodiversity and measures used to quantify biodiversity and stream health. Students investigate the...

    Keywords: ecology labCommunity Ecologyenvironmental scienceconservation ecologyStream ecology

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    Microbiome Analysis with Oxford Nanopore 16S amplicon sequencing data
    The resource is a brief description of an analysis pipeline for microbiome analysis of Oxford Nanopore 16S amplicon sequence data. We tested the Kraken 2 and Krona pipeline from nanogalaxy with...

    Keywords: microbiome analysis toolNanopore

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    Lesson V - Phylogenetics
    Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. Lesson V is an introduction to Phylogenetics.

    Keywords: Bioinformatics EducationBioinformatics and Genomics

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    Lesson IV - Comparative Genomics
    Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. Lesson IV, Comparative Genomics, discusses some of the tools...

    Keywords: Bioinformatics EducationBioinformatics and Genomics

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    REMNet Tutorial, R Part 3: Creating Alpha Diversity Plots in R 5.2.19
    Video on creating alpha diversity plots in R from the Research Experiences in Microbiomes Network

    Keywords: VideoMicrobiology EducationR programming languagemicrobiomesCoastal wetlandsmanagementnortheastsea-level risesalt marshresearch in the classroomREMNeturban microbiomes

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    Genome Sequence Data in R using Biostrings (Swirl Lesson)
    By the end of this lesson, students should be able to load FASTA files into R as DNAStringSets and use width() and alphabetFrequency(), combined with other functions like sum() and mean(), to...

    Keywords: R programming languagecourse-based undergraduate research experienceBioinformatics and GenomicsCURECUREscourse-based research experiences (CUREs)STEM CUREsComparative genomicsBioconductor

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    Quantifying Bacterial Growth in the Guts and Hemolymph of Fruit Flies: Mathematical Modeling and Data Interpolation/Extrapolation
    In this activity, students will analyze raw data obtained from an experiment that explores the effect of overexpressing the Ssk protein in order to strengthen the intestinal barrier and prevent...

    Keywords: graphingexponential growthlinear modelsqbccinterpolationConcepts in Statistics and Precalculus Understanding exponential rates and linear slopesExtrapolation

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    When tests disagree, how do I know if I have COVID-19?
    Students will learn about infectious disease and the immune response to infection by investigating different types of tests (PCR, antigen, and antibody tests) to detect the SARS-CoV-2 viral genetic...

    Keywords: geneticsVision and Changeintroductory biologyinfectious diseasemolecular biologycore competenciesRT-PCRviruscore conceptsnon-majors biologySARS-CoV-2antibodyAntigenImmunoReachmolecular DiagnosticsCOVID-19 transmission

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    The Human Microbiome Biodiversity in Health and Disease
    The students will analyze the human gut and vaginal microbiomes in healthy and diseased states using diversity of bacteria as determined by 16SrRNA sequence.
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    Louse Genetics, Genomics, and Gene Function...Oh My!
    In this module, students will be investigating a louse gene with an unknown function to determine if it might be important in the evolution of the louse ecomorphs.

    Keywords: parasitesgenomicsgene sequence analysisFunctional Genomics

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    Exploring the evolution of caffeine biosynthesis enzymes
    Caffeine is a very common stimulant consume worldwide as tea, coffee, mate, cocoa, and chocolate. Ever wondered why plants make caffeine? Do all caffeine producing plants have the same enzymes for...

    Keywords: Bioinformatics EducationBioinformatics and Genomics

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    Building creatures with the central dogma of biology
    Activity that demonstrates how nucleotide changes can affect phenotypes

    Keywords: amino acidsnucleotidesRNADNAgenotypephenotypecentral dogma

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    Phylogenetic analysis using collections material: interpreting trait evolution by comparison of morphological and molecular genetic hypotheses
    Exercise spans two weeks, includes homework, and involves some groups of animals as well as plants. Emphasizes re-interpretation of morphological trait evolution following molecular genetic...

    Keywords: Evolutionmorphologyphylogenylaboratoryplantsbiological collectionsmolecular analysis

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    BSL-4: Authorized Personnel Only
    National Center for Case Study Teaching in Science resource on the 2014 Ebola epidemic. This resource is also included in the NIBLSE Learning Resource Collection

    Keywords: infectious diseaseexperimental designbioinformaticsEbolaNIBLSECase It!PCRBLASTmultiple sequence alignmentPublished in National Center for Case Study Teaching in Sciencepolymerase chain reactionfebrile illnessvirusELISAenzyme linked immunosorbent assayfilovirusAfrica

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