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  1. Module 5: The Need for an Open Reading Frame

    Module 5: The Need for an Open Reading Frame

    2020-07-25 20:07:05 | Teaching Materials | Contributor(s): Carina Howell, Leocadia Paliulis, Anne Rosenwald | doi:10.25334/N11Z-PK53

    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.

  2. Module 4: Removal of Introns from pre-mRNA by Splicing

    Module 4: Removal of Introns from pre-mRNA by Splicing

    2020-07-25 20:06:06 | Teaching Materials | Contributor(s): Meg Laakso, Anne Rosenwald | doi:10.25334/030X-Q219

    In this module, students will learn to identify splice donor and acceptor sites that are best supported by RNA-Seq data, and use the canonical splice donor and splice acceptor sequences to identify intron-exon boundaries.

  3. Module 3: Transcription, Part II: What Happens to the Initial Transcript Made by RNA pol II?

    Module 3: Transcription, Part II: What Happens to the Initial Transcript Made by RNA pol II?

    2020-07-25 20:05:01 | Teaching Materials | Contributor(s): Cathy Silver Key, Chiyedza Small, Laura Reed | doi:10.25334/PYZN-JQ45

    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 introns through splicing.

  4. Module 2: Transcription Part I: From DNA Sequence to Transcription Unit

    Module 2: Transcription Part I: From DNA Sequence to Transcription Unit

    2020-07-25 20:04:08 | Teaching Materials | Contributor(s): Maria Santisteban, Alexa Sawa | doi:10.25334/53EH-4602

    This module illustrates how a primary transcript (pre-mRNA) is synthesized using a DNA molecule as the template. Students will learn about the importance of the 5' and 3' regions of the gene for initiation and termination of transcription.

  5. Module 1: Introduction to the Genome Browser: What is a Gene?

    Module 1: Introduction to the Genome Browser: What is a Gene?

    2020-07-25 20:03:07 | Teaching Materials | Contributor(s): Joyce Stamm, Jennifer Kennell, Wilson Leung, Leocadia Paliulis, Srebrenka Robic, Anne Rosenwald | doi:10.25334/N0PH-7508

    This lesson introduces the University of California Santa Cruz genome browser to students, walking them through some of the key features so that it can be used for analysis of gene structure.

  6. GEA Introductory lesson on RNA-Seq

    GEA Introductory lesson on RNA-Seq

    2020-07-25 20:01:56 | Teaching Materials | Contributor(s): Jason Williams, Judy Brusslan, Ray Enke, Matthew Escobar, Vince Buonaccorsi | doi:10.25334/GM6A-VC81

    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. normal diet) and disease (cancer vs. normal tissue).

  7. GEA Introductory lesson on BLAST

    GEA Introductory lesson on BLAST

    2020-07-25 20:00:58 | Teaching Materials | Contributor(s): Justin DiAngelo, Alexis Nagengast, Wilson Leung, Douglas L Chalker | doi:10.25334/WQ1J-PW32

    The "Introduction to BLAST using Human Leptin" exercise aims to introduce students to the use of the Basic Local Alignment Search Tool (BLAST) to identify related sequences and compare similarity between them.

  8. Encouraging student collaboration and networking and improving student access to undergraduate research opportunities.

    Encouraging student collaboration and networking and improving student access to undergraduate research opportunities.

    2020-07-25 01:40:49 | Teaching Materials | Contributor(s): Gary Laverty, Metehan Cebeci, Jessica Rainey, R Rodney Cooper | doi:10.25334/DKZ3-R852

    We describe, as a case study, work done by two undergraduate students on a specific enzyme in the ciliate Tetrahymena thermophila.

  9. Exploring multiple approaches to engage underrepresented students in research with natural history collections.

    Exploring multiple approaches to engage underrepresented students in research with natural history collections.

    2020-07-24 19:04:22 | Teaching Materials | Contributor(s): Molly Phillips, Adania Flemming, Jeanette Pirlo, David Blackburn | doi:10.25334/1FPC-KQ95

    The iDigBio team has leveraged natural history collections in a 3-pronged approach designed to engage undergraduates from underrepresented groups in collections-based research.

  10. Genome Solver: Building faculty skills in bioinformatics

    Genome Solver: Building faculty skills in bioinformatics

    2020-07-24 02:15:09 | Teaching Materials | Contributor(s): Vinayak Mathur, Gaurav Arora, Vinodh Ganesan, Hita Gupta, Mariana Kazarian, Anne Rosenwald | doi:10.25334/G1B6-JJ53

    Genome Solver (GS) began in 2011 as an NSF-funded project for faculty training in basic web-based bioinformatics skills.

  11. NEON Data in the Classroom: Quantifying Spatial Patterns

    NEON Data in the Classroom: Quantifying Spatial Patterns

    2020-07-23 21:58:03 | Teaching Materials | Contributor(s): Kusum Naithani | doi:10.25334/AJBF-AZ49

    Students build on fundamental concepts of spatial patterns and combine this knowledge with the open-data from the National Ecological Observatory Network to quantify spatial autocorrelation and complexity.

  12. Genomics Education Alliance: A Collection of Posters for the 2020 BIOME Institute.

    Genomics Education Alliance: A Collection of Posters for the 2020 BIOME Institute.

    2020-07-23 14:47:36 | Teaching Materials | Contributor(s): Vince Buonaccorsi, Marcella Denise Cervantes, Douglas L Chalker, Anne Rosenwald, Emily Wiley, Jason Williams | doi:10.25334/90HY-1188

    This is a collection of posters from members of the Genomics Education Alliance (GEA) that will be presented at the 2020 BIOME Institute.

  13. Integration of Bioinformatics into Life Science Curricula: Community Development, Dissemination, and Assessment of a NIBLSE Learning Resource

    Integration of Bioinformatics into Life Science Curricula: Community Development, Dissemination, and Assessment of a NIBLSE Learning Resource

    2020-07-23 14:24:32 | Teaching Materials | Contributor(s): Adam Kleinschmit, Rachel Cook, Barbara Murdoch, Elizabeth F Ryder, William Tapprich | doi:10.25334/F138-SS53

    Big data and computational tools have transformed the way we address biological questions. To prepare undergraduates for tomorrow’s challenges, life science curricula should integrate the understanding and use of these tools at all levels.

  14. Using genome browsers constructed by G-OnRamp to provide students with a Course-based Undergraduate Research Experience in genome annotation

    Using genome browsers constructed by G-OnRamp to provide students with a Course-based Undergraduate Research Experience in genome annotation

    2020-07-23 14:23:11 | Teaching Materials | Contributor(s): Wilson Leung, Luke Sargent, Yating Liu, Nathan Mortimer, David Lopatto, Jeremy Goecks, Sarah Elgin | doi:10.25334/A57B-W632

    G-OnRamp (http://g-onramp.org) provides an easy-to-use web platform for educators to create genome browsers to engage undergraduate students in research projects, both collaborative annotation of eukaryotic genes/genomes and “big data” biomedical analyses

  15. The Genomics Education Partnership:  Introducing Undergraduates to Research by Engaging Them in Genome Annotation

    The Genomics Education Partnership: Introducing Undergraduates to Research by Engaging Them in Genome Annotation

    2020-07-23 14:22:53 | Teaching Materials | Contributor(s): Sarah Elgin, Wilson Leung, Anne Rosenwald, David Lopatto, Charles Hauser, Catherine Reinke, Laura Reed | doi:10.25334/SFXW-PZ41

    Since 2006, the Genomics Education Partnership (GEP; http://gep.wustl.edu) has helped faculty bring genomics research experiences into the undergraduate curriculum.

  16. The Network for Integrating Bioinformatics into Life Sciences Education  (NIBLSE): Barriers to Integration

    The Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE): Barriers to Integration

    2020-07-23 14:22:36 | Teaching Materials | Contributor(s): Anne Rosenwald, Elizabeth Dinsdale, William Morgan, Mark A. Pauley, William Tapprich, Eric Triplett, Jason Williams | doi:10.25334/NHB4-X766

    The Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) seeks to promote the use of bioinformatics and data science as a way to teach biology.

  17. Incubators: Building community networks and developing open educational resources to integrate bioinformatics into life sciences education

    Incubators: Building community networks and developing open educational resources to integrate bioinformatics into life sciences education

    2020-07-23 14:22:20 | Teaching Materials | Contributor(s): William Morgan, Sam S Donovan, Hayley Orndorf, Sabrina Robertson, Elizabeth F Ryder, Michael Sierk, Anne Rosenwald, Elizabeth Dinsdale, Eric Triplett, Mark Pauley, William Tapprich | doi:10.25334/A6NR-TT57

    To efficiently and effectively integrate bioinformatics instruction into undergraduate life science curricula, educators would benefit from open access, high-quality learning resources (LRs) for use in existing biology classes.

  18. The Genomics Education Partnership: Exploring best practices in  implementation of a genomics CURE

    The Genomics Education Partnership: Exploring best practices in implementation of a genomics CURE

    2020-07-23 14:21:53 | Teaching Materials | Contributor(s): Matthew Wawersik, Anna Allen, Cindy Arrigo, Andrew Arsham, Daron Barnard, Rebecca Burgess, Justin DiAngelo, Jennifer Jemc, Christopher Jones, Lisa Kadlec, Adam Kleinschmit, Judith Leatherman, David Lopatto, Mollie Manier, Hemlata Mistry, Nathan Mortimer, Alexis Nagengast, Susan Parish, Anne Rosenwald, Joyce Stamm, Sarah Elgin, Laura Reed | doi:10.25334/6HS9-XM77

    Since 2006, the Genomics Education Partnership (GEP) has incorporated authentic genomics research experiences into the undergraduate curriculum.

  19. Ciliate Genomics Consortium: a professional learning community sharing modular curricula to support undergraduate research in the classroom

    Ciliate Genomics Consortium: a professional learning community sharing modular curricula to support undergraduate research in the classroom

    2020-07-23 14:20:46 | Teaching Materials | Contributor(s): Douglas L Chalker, Emily Wiley | doi:10.25334/CNPE-4M14

    The Ciliate Genomics Consortium (CGC) employs an integrative teaching and research model that combines both inquiry-driven class laboratory activities and collaborative consortium pedagogies to advance faculty research.

  20. Genomics Education Alliance: Towards Genomics CURE templates

    Genomics Education Alliance: Towards Genomics CURE templates

    2020-07-23 14:20:00 | Teaching Materials | Contributor(s): Vince Buonaccorsi, Arthur Hunt, Emily Wiley, Sandesh Subramanya, Wilson Leung, Sally Elgin | doi:10.25334/VV4Q-K260

    Here we present major findings of a national survey of faculty teaching genomics CUREs conducted by the GEA, and our work on presenting relevant resources on the QUBES web portal.