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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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