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    Building a Model of Tumorigenesis: A small group activity for a cancer biology/cell biology course
    The multistep nature of tumorigenesis is a foundational concept in the context of Cancer Biology. Many students do not appreciate the complex nature of cancer development nor do they understand how...

    Keywords: pathwayscancerMolecular AlterationsRetrospective dataTumorigenesis

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    Integrating Manipulatives and Animations to Visualize Holliday Junctions
    The complex molecular architecture of Holliday junctions is often challenging for undergraduate biochemistry students to conceptualize. In particular, they have difficulty translating from...

    Keywords: dna structureDNA damageDNA recombinationGene crossoverHolliday junction

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    Evaluating the potential for immune escape: how likely is an antibody to protect against a specific SARS-CoV-2 variant?
    Commercial antibodies to the SARS-CoV-2 spike protein have been successfully used to treat people with COVID-19. Unfortunately, as the SARS-CoV-2 virus evolves, new variants have appeared that can...

    Keywords: course based undergraduate research experiencesBLASTmolecular modelingSARS-CoV-2antibodyNextstrainiCn3DSequence alignmentStructure alignment

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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...

    Keywords: bioinformaticscancertranscriptomicshigh-throughputData wranglingSingle cell RNA sequencingq

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    Using Undergraduate Molecular Biology Labs to Discover Targets of miRNAs in Humans
    In this lesson, we describe an easily adaptable lab module that can be used in existing undergraduate molecular biology lab courses to conduct authentic scientific research, published in CourseSource

    Keywords: molecular biologybioinformaticsNIBLSEgene regulationmicroRNAsgene expressionCourseSourcemiRNA

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    2017-Brian_Winkel-Let_Us_Do_It_Using_Modeling_in_the_Classroom
    In this article the author, Brian Winkel, Director of SIMIODE, attempts to make the case for modeling in the differential equations classroom by giving both rationale and examples.

    Keywords: differential equationsmodelingclassroom

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    Happy Blue Baby
    This case, about a specific mutant of hemoglobin, focuses on visualizing and understanding the molecular basis of why an infant turned blue soon after birth and how the cyanosis resolved on its own...

    Keywords: mutationHemoglobinmolecular visualization and analysisgenetic basisPDBMolecular Case StudyMol*

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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...

    Keywords: bioinformaticsmutationDNAgenomic visualizationparts of a geneclinical consequencesraw data

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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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    CRISPR Gene Editing: Designing the gRNA and Donor Template
    In this adaptation, students learn how CRISPR/Cas9 is used in bacterial immunity and gene editing. Students create both a gRNA target and a donor template to edit a gene. Mutations can be from the...

    Keywords: geneticseducationcell biologymolecular biologymutationStem cellsstructure-functionmolecular visualization and analysis3D protein structure /function analysisCRISPR/Cas9crisprDNA mutationPiwiPDBMolecular Case StudyPiwi Matters

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    Piwi Matters
    This case focuses on understanding structure and function relationships in Piwi, a protein that is critical for germline stem cell function and development of eggs in the fruit fly ovary.

    Keywords: Stem cellsmolecular visualization and analysis3D protein structure /function analysisPiwiPDBMolecular Case Study

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    Happy Blue Baby
    This case, about a specific mutant of hemoglobin, focuses on visualizing and understanding the molecular basis of why an infant turned blue soon after birth and how the cyanosis resolved on its own...

    Keywords: mutationHemoglobinmolecular visualization and analysisPDBMolecular Case Study

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    Morphological, Anatomical and Molecular Analysis of Plant Phylogeny and Diversity
    In this lab, students perform phylogenetic analyses on morphological, anatomical and molecular data, and compare.

    Keywords: morphologyphylogenylaboratoryplantsmolecular analysisstele architecture

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    Discovering Prokaryotic Gene Regulation by Building and Investigating a Computational Model of the lac Operon
    The ability to construct and reason through a biological system is an important skill to develop in science education. This level of understanding forces students to recognize the interrelatedness...

    Keywords: prokaryotesgene regulationLac Operoninducible operon

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    Introduction to the Math Modeling Hub
    The Math Modeling Hub (MMHub) is an online community of practice and OER resource repository for math modeling educators at all grade levels. We have been a partner with QUBES since our initial...
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    List of models in which observed patterns are Important
    Supplemental material for ABM

    Keywords: textbookNetLogoagent-based modelingIndividual & Agent Based Modelingin-class activityproblem set

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    Breeding synchrony in colonial birds: from local stress to global harmony
    This is a supplemental resource for ABM

    Keywords: NetLogoagent-based modelingIndividual & Agent Based Modeling

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    NetLogo refresher course
    This is a supplemental resource from ABM

    Keywords: moduletextbookNetLogoagent-based modelingIndividual & Agent Based Modelingin-class activityproblem set

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    Marriage age model ODD
    Supplemental resource from ABM

    Keywords: case studytextbookNetLogoagent-based modelingIndividual & Agent Based ModelingODD protocol

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    My Experiences in a Faculty Mentoring Network for Mathematical Modeling
    Talk given as a part of the Symposium - Communities of Practice for Math Modeling Education at the SIAM 2018 Conference

    Keywords: SIAMfaculty mentoring networksfaculty communitiesResources @ MMHubResources @ SIAMEd 2018

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