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    Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses
    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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    Biogeography of plant-associated fungi: who lives where and why?
    This dataset of fungal communities associated with the leaves an endemic Hawaiian tree provides students opportunities to explore relationships between environmental variables and microbial...

    Keywords: small group activityinquiry-based learningbiogeographymicrobial ecology

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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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    You and Your Oral Microflora: Introducing non-biology majors to their “forgotten organ”
    With limited time available for laboratory activities, introductory science courses for non-science majors typically use the laboratory period to reinforce material that was previously presented...

    Keywords: bacteriamicrobiomeBLASTmicrobesDNA replicationPolymerase chain reaction (PCR)

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    Hands-On, Hands-Off: The Community College Genomics (ComGen) Course-Based Undergraduate Research Experience
    Science is a process of discovery where failure is inherent and iteration is necessary, yet instructors often teach the scientific process as if it is a controlled, highly supervised, confirmatory...

    Keywords: geneticssequencingDNAbacterium

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    Using genomic data and machine learning to predict antibiotic resistance: a tutorial paper
    Antibiotic resistance is a global public health concern. Bacteria have evolved resistance to most antibiotics, which means that for any given bacterial infection, the bacteria may be resistant to...

    Keywords: Tutorialmachine learningantibiotic-resistanceArtificial Intelligence

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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...

    Keywords: epidemiologyresearchbioinformaticsgenomicspublic healthAntibiotic Resistant BacteriaSalmonellaDNA sequencingpathogenic bacteria

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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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    CURE-all: Large Scale Implementation of Authentic DNA Barcoding Research into First-Year Biology Curriculum
    Growing calls in science education reform have emphasized wide-scale engagement of first-year undergraduate students in authentic research experiences; however, large course enrollments, inadequate...

    Keywords: phylogeneticsbioinformaticsBiodiversityprocess of sciencetaxonomyPCRDNADNA sequencegel electrophoresis

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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...

    Keywords: statisticsbioinformaticsRNAseqgene expressioncomputer programming

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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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    My Dog IS My Homework: Exploring Canine Genetics to Understand Genotype-Phenotype Relationships
    To facilitate understanding of the fundamental genetic concept of the genotype-phenotype relationship in our introductory biology students, we designed an engaging multi-week series of related...

    Keywords: gel electrophoresissequence analysiscanine geneticsdeoxyribonucleic acid (DNA)dog coat morphologygenotype and phenotypemutationsPolymerase chain reaction (PCR)single nucleotide polymorphism (SNP)

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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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    From Dirt to Streptomyces DNA
    The purpose of this semester-long Lesson is to give students an authentic, course-based undergraduate research experience during which they learn basic and advanced microbiological and molecular...

    Keywords: MetabolismAntibiotic productionrRNA genesSecondary metabolitesStreptomyces

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    SOAR - San Francisco Bay Research Coordination Network for Student Opportunities in Avian Research to enhance STEM education and assess human impacts on avian biodiversity (RCN-UBE Introduction)
    The San Francisco Bay Research Coordination Network for Student Opportunities in Avian Research (SOAR) brings together faculty, students, and volunteers to implement an experiential learning and...

    Keywords: RCN-UBE Introduction

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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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    Casting a Wide Net via Case Studies: Educating across the undergraduate to medical school continuum in the biological sciences
    This article seeks to help bridge undergraduate and medical educators by describing shared educational goals and strategies, highlighting resources relevant for both groups, and exemplifying shared...

    Keywords: genetic testingdirect-to-consumer genetic testinginformed consentprenatal screeningsecondary findingswhole genome sequencing

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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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    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...

    Keywords: proteinsMitochondrial GenomesNuclear GenomesrRNAtRNA

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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...

    Keywords: geneticsorganismal biologybioinformaticstaxonomyDNA Barcodingspecies concepts

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