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1. A Critical Guide to BLAST

   04 Dec 2020 | Teaching Materials | Contributor(s):

   By Teresa Attwood¹, GOBLET Foundation

   The University of Manchester, Manchester, UK

   This Critical Guide in the Introduction to Bioinformatics series provides an overview of the BLAST similarity search tool, briefly examining the underlying algorithm and its rise to popularity.

   https://qubeshub.org/publications/2172/?v=1

2. A Critical Guide to the PDB

   05 Dec 2020 | Teaching Materials | Contributor(s):

   By Teresa Attwood¹, GOBLET Foundation

   The University of Manchester, Manchester, UK

   This Critical Guide in the Introduction to Bioinformatics series provides a brief outline of the Protein Data Bank – the PDB – the world’s primary repository of biological macromolecular structures.

   https://qubeshub.org/publications/2174/?v=1

3. Behavioral Genetics: Investigating the genes of a complex phenotype in fruit flies

   03 Jan 2019 | Teaching Materials | Contributor(s):

   By Craig E. Stanley, Jr., Charles Hadley S. King, IV, Michelle Thornton, Rob J. Kulathinal

   Introductory genetics laboratory published as GSA Learning Resource

   https://qubeshub.org/publications/988/?v=1

4. Bioinformatics / Neuroinformatics

   03 Jan 2019 | Teaching Materials | Contributor(s):

   By William Grisham

   University of California, Los Angeles

   This module is a computer-based introduction to bioinformatics resources. This easy-to-adopt module weaves together several important bioinformatic tools so students can grasp how each is used in...

   https://qubeshub.org/publications/990/?v=1

5. Bioinformatics: An Interactive Introduction to NCBI

   03 Jan 2019 | Teaching Materials | Contributor(s):

   By Seth Bordenstein

   Marine Biological Laboratory

   Modules showing how the NCBI database classifies and organizes information on DNA sequences, evolutionary relationships, and scientific publications. And a module working to identify a nucleotide...

   https://qubeshub.org/publications/989/?v=1

6. Bioinformatics: Investigating Sequence Similarity - A Plant Biology Approach

   29 May 2019 | Teaching Materials | Contributor(s):

   By Ami Erickson

   This laboratory module is a modification of the original published on CourseSource with a focus on plant biology. In the final activity, students conduct a BLAST to compare histone protein...

   https://qubeshub.org/publications/1247/?v=1

7. Bioinformatics: the Power of Computers in Biology – a Practical Guide

   03 Dec 2020 | Teaching Materials | Contributor(s):

   By Daniel Barker¹, Heleen Plaisier², Stevie Anne Bain¹, Teresa Attwood

   1. The University of Edinburgh, Edinburgh, UK 2. Royal Botanic Garden, Edinburgh, UK

   This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces simple bioinformatics approaches for database searching and sequence analysis.

   https://qubeshub.org/publications/2159/?v=1

8. DNA Subway Learning Resources

   18 Oct 2017 | Teaching Materials | Contributor(s):

   By Jason Williams

   DNA Learning Center

   DNA Subway is a NIBLSE Recommended resource. This is a collection of learning resources associated with DNA Subway.

   https://qubeshub.org/publications/164/?v=2

9. Exploring HIV Evolution

   05 Aug 2016 | Teaching Materials | Contributor(s):

   By Sam S Donovan¹, Tony Weisstein²

   1. University of Pittsburgh 2. Truman State University

   In this activity you will study aspects of sequence evolution by working with a set of HIV sequence data from 15 different subjects (Markham, et al., 1998). You will first learn about the dataset,...

   https://qubeshub.org/publications/24/?v=1

10. Exploring HIV Evolution

    05 Jun 2017 | Teaching Materials | Contributor(s):

    By Sam S Donovan¹, Tony Weisstein²

    1. University of Pittsburgh 2. Truman State University

    In this activity you will study aspects of sequence evolution by working with a set of HIV sequence data from 15 different subjects (Markham, et al., 1998). You will first learn about the dataset,...

    https://qubeshub.org/publications/24/?v=2

11. Homologous chromosomes? Exploring human sex chromosomes, sex determination and sex reversal using bioinformatics approaches

    04 Jan 2019 | Teaching Materials | Contributor(s):

    By Kelsey Metzger

    University of Minnesota, Rochester

    In this four- part guided activity, students will learn about the structure and function of human autosomal and sex chromosomes, view and interpret gene maps, and gain familiarity with basic...

    https://qubeshub.org/publications/1000/?v=1

12. Infectious Chocolate Joy with a Side of Poissonian Statistics: An activity connecting life science students with subtle physics concepts

    04 Jan 2019 | Teaching Materials | Contributor(s):

    By Eric T. Holland¹, Greg Manley¹, Tamara Chiba¹, Rona Ramos¹, Simon Mochrie¹, Jennifer Frederick¹

    Yale University

    Lesson on what it means for biological processes to be Poissonian, published in CourseSource

    https://qubeshub.org/publications/1001/?v=1

13. RNAseq data analysis using Galaxy

    03 Jul 2017 | Teaching Materials | Contributor(s):

    By Matthew Escobar

    California State University - San Marcos

    This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.

    https://qubeshub.org/publications/118/?v=1

14. RNAseq data analysis using Galaxy

    01 Aug 2017 | Teaching Materials | Contributor(s):

    By Matthew Escobar

    California State University - San Marcos

    This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.

    https://qubeshub.org/publications/118/?v=2

15. RNAseq data analysis using Galaxy

    13 Nov 2017 | 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.

    https://qubeshub.org/publications/118/?v=3

16. Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching

    04 Jan 2019 | 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

    This lesson plan was created to teach RNAseq analysis as a part of GCAT-SEEK network. It is provided here, both in finished form and with the modifiable source code, to allow flexible adaptation to...

    https://qubeshub.org/publications/1005/?v=1

17. Using Bioinformatics to Understand Genetic Diseases: A Practical Guide

    03 Dec 2020 | Teaching Materials | Contributor(s):

    By Marie-Claude Blatter¹, Patricia Palagi¹, Teresa Attwood²

    1. SIB Swiss Institute of Bioinformatics, Geneva, Lausanne (CH). 2. School of Computer Science, The University of Manchester, Oxford Road, Manchester M13 9PL (UK)

    This Practical Guide outlines a number of basic bioinformatics approaches that can be used to understand the molecular basis of genetic diseases.

    https://qubeshub.org/publications/2154/?v=1

18. Using DNA Subway to Analyze Sequence Relationships

    18 Oct 2017 | Teaching Materials | Contributor(s):

    By Jason Williams

    DNA Learning Center

    This is a bioinformatics exercise using DNA Subway

    https://qubeshub.org/publications/165/?v=1

19. Using DNA Subway to Analyze Sequence Relationships

    28 May 2018 | Teaching Materials | Contributor(s):

    By Jason Williams¹, Ray A. Enke², Oliver Hyman², Emily Lescak³, Sam S Donovan⁴, William Tapprich⁵, Elizabeth F Ryder⁶

    1. DNA Learning Center 2. The Department of Biology, James Madison University; The Center for Genome & Metagenome Studies, James Madison University 3. University of Alaska 4. University of Pittsburgh 5. University of Nebraska-Omaha 6. Worcester Polytechnic Institute

    This is a bioinformatics exercise using the DNA Subway Blue Line, a user-friendly pipeline of bioinformatics tools, to analyze a collection of mosquito DNA bar-code sequences.

    https://qubeshub.org/publications/165/?v=2

20. Using Synthetic Biology to Teach Data Science

    26 Jun 2019 | Teaching Materials | Contributor(s):

    By Margaret S Saha¹, Beteel Abu-Ageel¹, Sanjana Challa¹, Xiangyi Fang¹, Chai Hibbert¹, Anna Isler¹, Elias Nafziger¹, Adam Oliver¹, Hanqiu Peng¹, Julia Urban¹, Vivian Zhu¹

    College of William and Mary

    Abstract for poster on using synthetic biology to introduce students to meaningful data mining, analysis, and application to engineering novel biological constructs.

    https://qubeshub.org/publications/1326/?v=1