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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...

    Keywords: Rdata analysisRStudio

    2017

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    Making toast: Using analogies to explore concepts in bioinformatics
    Contemporary biology is moving towards heavy reliance on computational methods to manage, find patterns, and derive meaning from large-scale data, such as genomic sequences. Biology teachers are...

    Keywords: bioinformaticsworkflowgenome

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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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    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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    Teaching Protein Structure Modeling
    New strains of microbes have been regularly discovered and brought into a laboratory for study in many different directions. When a new microbial genome is sequenced and assembled, the homologues...

    Keywords: Microbiology Educationbioinformaticsprotein structure modeling

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    Lesson III - Annotation
    Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. Lesson III introduces Annotation, or assigning meaning to all...

    Keywords: Bioinformatics EducationBioinformatics and Genomics

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    Using Bioinformatics to Understand Genetic Diseases: A Practical Guide
    This Practical Guide outlines a number of basic bioinformatics approaches that can be used to understand the molecular basis of genetic diseases.
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    Module 5: The Need for an Open Reading Frame
    In this module, students will learn to identify the open reading frames for a given gene, and define the phases of the splice donor and acceptor sites.

    Keywords: geneticsamino acidsmolecular biologyGenome BrowsergenomicsAssociated Protein Synthesis FactorsCodonMessenger RNARibosomestRNAs

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    Module 3: Transcription, Part II: What Happens to the Initial Transcript Made by RNA pol II?
    This module teaches about the three key steps that are involved in converting the pre-mRNA into a mature mRNA: 1) The addition of a 5’ cap, 2) The addition of a 3’ poly(A) tail, 3) The removal of...

    Keywords: geneticsmolecular biologyGenome BrowsergenomicssplicingmRNAcDNA5' Cap3' Poly(A) TailRNA Maturation

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    Neochromosomes: Creating transcriptional units with yeast Golden Gate assembly
    This resource is a series of protocols using the yeast Golden Gate (yGG) method as developed by Neta Agmon and Leslie Mitchell in Jef Boeke’s lab to assemble a functional yeast gene with...
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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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    BIO 439/539: Big Data Analysis
    Course materials for BIO 439/539: Big Data Analysis

    Keywords: Rdata analysisbig datadata managementstatistical methods

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    Predicting and classifying effects of insertion and deletion mutations on protein coding regions
    Mutations in genes can affect the encoded proteins in multiple ways, and some of these effects are counterintuitive. As for any other knowledge, students must create their own deep understanding of...

    Keywords: mutationcentral dogmatranslationframeshift

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    Chapter 10: Two-way analysis of variance
    Biostatistics Using R: A Laboratory Manual was created with the goals of providing biological content to lab sessions by using authentic research data and introducing R programming language....

    Keywords: biostatisticsR programming language

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    LEAGSEA
    How to perform Leading Edge Analysis in Gene Set Enrichment Analysis by Broad Institute

    Keywords: videosbioinformaticsgenomicsyoutubeLEAGSEAgene set enrichmentLeading Edge Analysis

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    MiniWorkshop Follow-Up October 2, 2020
    A follow up to our mini workshop of August 14, 2020. Further information about the python pipeline for HGT and the new cytoscape lesson.

    Keywords: Bioinformatics Education

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    Lesson VII - Synteny
    The lesson teaches about synteny or the order of genes along a chromosome, which is useful for looking at orthologous genes between two species or strains.

    Keywords: Bioinformatics Education

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    Bioinformatics: CpG Islands
    This is an introductory bioinformatics exercise intended for use in a genetics course.

    Keywords: geneticsepigeneticsbioinformaticsNIBLSEcpggenome database

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    Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses
    Introductory bioinformatics exercises often walk students through the use of computational tools, but often provide little understanding of what a computational tool does "under the...

    Keywords: BLASTmultiple sequence alignmentsequence similarityphylogramZika virusAlgorithmScoring Matrix

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    Exploring Functions for Common Phage Proteins
    This resource is designed to help students better understand the functions of common structural and enzymatic phage proteins, and to relate these functions to phage structure using electron...
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