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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 largely replaced the use of microarrays for...
bioinformatics cancer transcriptomics high-throughput Data wrangling Single cell RNA sequencingq
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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 for students with hands-on experience...
epidemiology research bioinformatics genomics public health Antibiotic Resistant Bacteria Salmonella DNA sequencing pathogenic bacteria
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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 environment, but students often fail to master and...
bioinformatics Genome Browser genomics RNAseq splicing Computer Model Gene Structure
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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 evidence however demonstrates that there are significant...

Courses: BioinformaticsBioinformatics

bioinformatics genomics coding Jupyter notebook command line CyVerse scripting next generation sequencing analysis
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Mapping a Mutation to its Gene: The "Fly Lab" as a Modern Research Experience
Although genetics is an invaluable part of the undergraduate biology curriculum, it can be intimidating to students as well as instructors: Students must reduce their reliance on memorization and dive deep into quantitative analysis, and...
genetics bioinformatics drosophila chi-square analysis complementation mapping mode of inheritance three-point mapping
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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 lessons about canine genetics in which students...
gel electrophoresis sequence analysis canine genetics deoxyribonucleic acid (DNA) dog coat morphology genotype and phenotype mutations Polymerase chain reaction (PCR) single nucleotide polymorphism (SNP)
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Tying it All Together: An Activity to Help Students Connect Course Experiences to Posted Learning Outcomes
Instructors of undergraduate courses in Biology and other Science, Technology, Engineering, and Mathematics (STEM) disciplines face an ongoing challenge to foster higher-order thinking and learning skills while also developing a sound conceptual...
metacognition reflection goals Outcomes
Essay
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Structuring Courses for Equity
As instructors, we continually look for new ways to create equitable learning environments and support learning for all students in our courses. Recently, we have explored ways that we can increase structure to better support students. We have...
Equity metacognition inclusivity course structure
Teaching Tools and Strategies
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DNA Detective: Genotype to Phenotype. A Bioinformatics Workshop for Middle School to College.
Advances in high-throughput techniques have resulted in a rising demand for scientists with basic bioinformatics skills as well as workshops and curricula that teach students bioinformatics concepts. DNA Detective is a workshop we designed to...
genetics bioinformatics DNA genotype phenotype gene gene annotation
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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 bioinformaticians with biological expertise. For...
proteins Mitochondrial Genomes Nuclear Genomes rRNA tRNA
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Training future faculty in 30 minutes a week: A modular framework to provide just-in-time professional development to graduate teaching assistants
Despite increasing recognition of the need to train the teaching assistants (TAs) teaching the majority of STEM lab sections, very few programs report offering sustained teaching professional development opportunities. Here we present a year-long,...
professional development TA Training Teaching Assistants
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CRISPR/Cas9 in yeast: a multi-week laboratory exercise for undergraduate students
Providing undergraduate life-science students with a course-based research experience that utilizes cutting-edge technology, is tractable for students, and is manageable as an instructor is a challenge. Here, I describe a multi-week lesson plan...
bioinformatics PCR phenotyping CRISPR/Cas9 gene editing cloning Genotyping Restriction enzyme
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Tackling "Big Data" with Biology Undergrads: A Simple RNA-seq Data Analysis Tutorial Using Galaxy
Analyzing high-throughput DNA sequence data is a fundamental skill in modern biology. However, real and perceived barriers such as massive file sizes, substantial computational requirements, and lack of instructor background knowledge can...
bioinformatics DNA sequence RNAseq gene expression
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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 student experience, limited resources and...
phylogenetics bioinformatics Biodiversity process of science taxonomy PCR DNA DNA sequence gel electrophoresis
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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 hood." A solid understanding of how a bioinformatics...
BLAST multiple sequence alignment phylogram Zika virus Algorithm Scoring Matrix