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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...

    Keywords: computationpythonJupyter notebookFunctionscentral dogmaDictionaries

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    2018-Eduardo-Sontag-Lecture_Notes_on_Mathematical_Systems_Biology
    I am often asked if it is OK to use these notes in courses at other universities. The answer is “of course!” though I strongly suggest that a link to my website be provided, so that students can...

    Keywords: biologytextbooksystemsdyanmical system

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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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    A Muscular Dystrophy Case Study Illustrating the Phenotypic Effects of Mutation
    Mutations in genes can lead to a variety of phenotypes, including various human diseases. Students often understand that a particular mutation in a single gene causes a disease phenotype, but it is...

    Keywords: mutationProtein Structureethicscentral dogmahuman disease

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    Splicing it Together: Using Primary Data to Explore RNA Splicing and Gene Expression in Large-Lecture Introductory Biology
    At the heart of scientific ways of knowing is the systematic collection and analysis of data, which is then used to propose an explanation of how the world works. In this two-day module, students...

    Keywords: gene regulationtranscriptiongene expressioncentral dogmarepressoralternative splicingmRNA processingActivatorTranscription factors

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    Forensic Phylogenetics: Implementing Tree-thinking in a Court of Law
    Here we describe an in-class activity developed for Evolutionary Biology and Biodiversity (BioEE1780) at Cornell University, an introductory course required of all biology majors. This activity...

    Keywords: phylogeneticsTree thinkingparaphyly

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    Investigating Gene Expression and Cell Specialization in Axolotl Embryos
    The process of cell specialization is critical to the formation and function of tissues in animals and plants. Although gene expression, including the regulation of transcription, is taught in most...

    Keywords: developmenttranscriptiongene expressionmodel organismembryo

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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...

    Keywords: bioinformaticsgene expressiongenetic basis of diseaseCRISPR/Cas9genetic engineeringin silico

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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...

    Keywords: Speciationgenome evolutiongenetic variation

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    A virtual laboratory on cell division using a publicly-available image database
    Cell division is a key concept in cell biology. While there are many popular activities to teach students the stages of mitosis, most make use of simple schematics, cartoons, or textbook diagrams....

    Keywords: image analysismicroscopymitosisCellular Processes

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    Mock Drug Activity Enhances Student Learning About the Challenges of HIV/AIDS Therapy
    While traditional didactic coursework is important for learning about the scientific aspects of HIV/AIDS, it is difficult to convey social aspects of the epidemic. Due to effective drug therapies,...

    Keywords: drug resistanceRetrovirusViral replication

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    Fragile States: A Case Study Exploring Genetics, Molecular Biology, and Biochemistry Through the Lens of Fragile X Syndrome
    This case aims to strengthen students’ understanding of molecular biology concepts through study of Fragile X Syndrome (FXS). Students begin by learning the cause and phenotypes of FXS and...

    Keywords: gene regulationtranscriptiontranslationFragile X syndrometriplet repeat expansionsex linkagemetabolic pathway

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    Make It Stick: Teaching Gene Targeting with Ribbons and Fasteners
    Manipulating gene expression is a commonly used tool to study the effect of a single gene or the hierarchy of gene networks in many different biological disciplines. When working with mice, the...

    Keywords: mathematical modelhomologous recombinationCre/loxgene targeting

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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...

    Keywords: bioinformaticsGenome BrowsergenomicsRNAseqsplicingComputer ModelGene Structure

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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...

    Keywords: EvolutionmutationcompetitionNatural Selectionregulationstructure and functionreproductive fitnessgenotype to phenotypehomologs

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    Using Immunocytochemistry and Fluorescence Microscopy Imaging to Explore the Mechanism of Action of Anti-Cancer Drugs on the Cell Cycle
    Understanding and visualizing the cell cycle and mitosis is an essential concept of cell biology. This multi-week lab module has students investigate the mechanism of action of anti-cancer drugs...

    Keywords: fluorescence microscopymitosisCell StructureCell ImagingImmunocytochemistryQuantitative microscopySTEM skills

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    Cutthroat trout in Colorado: A case study connecting evolution and conservation
    Evaluation of evidence is a key process skill for the core competencies of applying the process of science and using quantitative reasoning. This case study enables upper-division biology students...

    Keywords: population geneticsphylogeneticsSpeciationdivergencegene flow

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    Investigating Cell Signaling with Gene Expression Datasets
    Modern molecular biology is a data- and computationally-intensive field with few instructional resources for introducing undergraduate students to the requisite skills and techniques for analyzing...

    Keywords: genomicstranscriptionsignaling

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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...

    Keywords: microbiome

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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...

    Keywords: bioinformaticsgenomicscodingJupyter notebookcommand lineCyVersescriptingnext generation sequencing analysis

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