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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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    The Case of the Missing Strawberries: RFLP analysis
    While solving the fictional mystery of the missing strawberries, students are engaged in a guided-inquiry lesson featuring small-group and class discussions, hands-on activities, and laboratory...

    Keywords: process of scienceDNAforensicsgel electrophoresisMolecular genotypingRestriction endonucleaseRestriction enzymeRestriction fragment length polymorphismRFLP

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    An Interactive Protocol for In-Classroom DNA Extraction
    Using commonly available materials, this tool allows students to extract DNA, exploring DNA chemistry and the principles of experimental design and execution. We take a “Choose Your Own...

    Keywords: geneticsDNAbiochemical structure and function

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    Using CRISPR-Cas9 to teach the fundamentals of molecular biology and experimental design
    One of the challenges of inquiry-based research experiences is balancing the instruction on skills and techniques with data generation and analysis. This is especially true in technique heavy...

    Keywords: experimental designcrisprmolecular technique

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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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    A Hands-on Introduction to Hidden Markov Models
    In this Lesson, we describe a classroom activity that demonstrates how a Hidden Markov Model (HMM) is applied to predict a eukaryotic gene, focusing on predicting one exon-intron boundary. This HMM...

    Keywords: transcriptionexonintronsplicing

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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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    Exploration of the Human Genome by Investigation of Personalized SNPs
    Students often shy away from tedious bioinformatics approaches to exploring their genomes. However, in our expanding digital world these skills are some of the most relevant and valuable. To...

    Keywords: UCSC genome browsersingle nucleotide polymorphismGenome wide association studiesGenomic organization

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    Split Decomp
    This Excel worksheet performs split decomposition on a set of four DNA sequences and their associated amino acid sequences. The user can type in the sequences or paste them in from a text file.

    Keywords: phylogenyDNA sequenceamino acid sequencesplit decomposition

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    Calculating Lifetime Cancer Risk Resulting from DNA Replication
    An expanded case study adapted from an HHMI Data Point on Cell Division and Cancer Risk using Figure 1 from Tomasetti, C. and Vogelstein, B. (2015).

    Keywords: cancerScientific ProcessStatistics and MathScientific Methodologybiology of cellscell growth and divisionHigh School

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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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    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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    GEA Introductory lesson on RNA-Seq
    This RNA-Seq lesson uses the CyVerse VICE Platform and Jupyter notebooks to examine the expression of the leptin gene in samples from a mouse experimental design evaluating diet (high-fat vs....

    Keywords: data sciencebioinformaticsGenome BrowserRNAseqhigh throughput sequencingmRNAAlignmentNCBI Sequence Read Archive

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    A Fun Introductory Command Line Exercise: Next Generation Sequencing Quality Analysis with Emoji!
    This resource is a fun computer-based intro to command line programming. The activity takes FASTQ NGS data files and runs a fun program called FASTQE.

    Keywords: data sciencebioinformaticsnext generation sequencingquality controlFASTQgenomicsprogrammingNIBLSElinuxmicrobiomeIllumina sequencingcommand lineFASTQEFASTPNGS analysisterminalMacemojiPhred scoreTrimmingshort read

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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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    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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    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...
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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...
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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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    Learn genomics and bioinformatics through scientific thinking, creation and analysis (virtual and hands-on)
    Nucleic acid are biological molecules composed of nitrogen-containing bases, phosphate groups, and sugar molecules. The complimentary chemical bonding results in formation of double stranded DNA....

    Keywords: data analysisbioinformaticsnucleotidesproteinsRNAgenomicsScientific communicationscientific writingDNAmodelling scientific thinkinggenescientific thinkingcreation

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