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Single Cell Insights Into Cancer Transcriptomes: A Five-Part Single-Cell RNAseq Case Study Lesson
24 Sep 2021 | Teaching Materials | Contributor(s):
By Leigh Ann Samsa*1, Melissa Eslinger2, Adam Kleinschmit3, Amanda Solem4, Carlos C. Goller*1
1. North Carolina State University 2. United States Military Academy 3. University of Dubuque 4. Hastings College
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...
Renato Augusto Corrêa dos Santos
A CURE for Salmonella: A Laboratory Course in Pathogen Microbiology and Genomics
15 Sep 2021 | Teaching Materials | Contributor(s):
By Sophie K. Jurgensen1, Joseph Harsh2, James B. Herrick*2
1. James Madison University, Louisiana State University 2. James Madison University
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...
An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure
31 Aug 2021 | Teaching Materials | Contributor(s):
By Meg M. Laakso1, Leocadia V. Paliulis2, Paula Croonquist3, Brianna Derr2, Elena Gracheva4, Charles Hauser5, Carina Howell6, Christopher Jones7, Jacob D. Kagey8, Jennifer Kennell9, S. Catherine Silver Key10, Hemlata Mistry11, Srebrenka Robic12, Jamie Sanford13, Marisol Santisteban14, Chiyedza Small15, Rebecca Spokony16, Joyce Stamm17, Melanie Van Stry18, Wilson Leung4, Sarah C.R. Elgin4
1. Eastern University 2. Bucknell University 3. Anoka-Ramsey Community College 4. Washington University in St. Louis 5. St. Edward’s University 6. Lock Haven University 7. Moravian College 8. University of Detroit Mercy 9. Vassar College 10. North Carolina Central University 11. Widener University 12. Agnes Scott College 13. Ohio Northern University 14. The University of North Carolina at Pembroke 15. Medgar Evers College, The City University of New York 16. Baruch College, The City University of New York 17. University of Evansville 18. Lane College
Gene structure, transcription, translation, and alternative splicing are challenging concepts for many undergraduates studying biology. These topics are typically covered in a traditional lecture...
A Fun Introductory Command Line Lesson: Next Generation Sequencing Quality Analysis with Emoji!
30 Aug 2021 | Teaching Materials | Contributor(s):
By Rachael M. St. Jacques †1, William M. Maza †1, Sabrina D. Robertson2, Andrew Lonsdale3, Caylin S. Murray1, Jason J. Williams4, Ray A. Enke*1
1. James Madison University 2. University of North Carolina Chapel Hill 3. University of Melbourne 4. Cold Spring Harbor Laboratory, DNA Learning Center
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...
Mapping a Mutation to its Gene: The "Fly Lab" as a Modern Research Experience
29 Aug 2021 | Teaching Materials | Contributor(s):
By Derek M. Dean*1, David L. Deitcher2, David W. Loehlin1, Lois M. Banta1
1. Williams College 2. Cornell University
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...
A CRISPR/Cas Guide RNA Design In Silico Activity
By Leigh Ann Samsa*1, Linnea Andersen1, Adam Groth1, Carlos Goller1
North Carolina State University
CRISPR biotechnologies inspired by the Clustered Regularly Interspaced Short Palindromic Repeat RNA-guided nuclease adaptive bacterial immune system have revolutionized biology research and become...
DNA Detective: Genotype to Phenotype. A Bioinformatics Workshop for Middle School to College.
By Anne L. Sternberger*1, Sarah E. Wyatt1
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...
CRISPR/Cas9 in yeast: a multi-week laboratory exercise for undergraduate students
28 Aug 2021 | Teaching Materials | Contributor(s):
By Randi J Ulbricht*
Missouri State University
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...
Tackling "Big Data" with Biology Undergrads: A Simple RNA-seq Data Analysis Tutorial Using Galaxy
By Matthew Anthony Escobar*1, William Morgan2, Irina Makarevitch3, Sabrina Robertson4
1. California State University San Marcos 2. The College of Wooster 3. Hamline University 4. North Carolina State University
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...
CURE-all: Large Scale Implementation of Authentic DNA Barcoding Research into First-Year Biology Curriculum
By Oliver Hyman*1, Elizabeth Doyle1, Joseph Harsh1, Joanna Mott2, Andrea Pesce1, Bejan Rasoul1, Kyle Seifert1, Ray Enke1
1. James Madison University 2. California State University
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...
Making toast: Using analogies to explore concepts in bioinformatics
26 Aug 2021 | Teaching Materials | Contributor(s):
By Kate L. Hertweck
University of Texas at Tyler
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...
Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching
22 Aug 2021 | Teaching Materials | Contributor(s):
By Mark Phillip Peterson1, Jacob T Malloy2, Vincent P Buonaccorsi2, James H Marden3
1. Viterbo University 2. Juniata College 3. Pennsylvania State University
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...
Homologous chromosomes? Exploring human sex chromosomes, sex determination and sex reversal using bioinformatics approaches
20 Aug 2021 | Teaching Materials | Contributor(s):
By Kelsey Metzger
University of Minnesota, Rochester
Constructing a robust understanding of homologous chromosomes, sex chromosomes, and the particulate nature of genes is a notoriously difficult task for undergraduate biology students. In this...
RNAseq data analysis using Galaxy
02 Jul 2021 | Teaching Materials | Contributor(s):
By Matthew Escobar1, Sam S Donovan2, Irina Makarevitch3, Bill Morgan4, Sabrina Robertson5
1. California State University San Marcos 2. University of Pittsburgh 3. Hamline University 4. The College of Wooster 5. North Carolina State University
This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.
Inquiry-based hypothesis testing using phylogenetic trees in MEGA
17 Jun 2021 | Teaching Materials | Contributor(s):
By Kristin Hultgren
A key learning objective in biology is applying bioinformatics tools to test a real-life question. These inquiry-based modules have students assemble and align data, and construct simple...