Advanced Topics in Bioinformatics
Tuesdays and Fridays 3-4:30PM
The course is meant to provide students with an overview of and practical experience with bioinformatics techniques. The course consists of 9 modules. The first two and last two modules last 1 week each, and modules 3-7 have the same structure:
At the conclusion of the course, the student will have hands-on experience with common bioinformatics analysis
100% of grade will be determined by projects and course participation
Students will complete projects based on each module. These projects are to be completed in groups of 2-3 that will rotate each week. For each project an analysis plan, a project presentation, and a final report must be completed and submitted by email to the module lecturer, ccing Dr. Ruggles (email@example.com) and Angelina Volkova (firstname.lastname@example.org) by the Tuesday following module completion.
Late/missed work: You must adhere to the due dates for all required submissions.If you miss a deadline, then you will not get credit for that assignment/post. 10 points will be deducted for every day late.
Incompletes: No “Incompletes” will be assigned for this course unless we are at the very end of the course and you have an emergency.
Responding to Messages: I will check e-mails daily during the week, and I will respond to course related questions within 48 hours.
Announcements: I will make announcements throughout the semester by e-mail. Make sure that your email address is updated; otherwise you may miss important emails from me.
Safeguards: Always back up your work on a safe place (electronic file with a backup is recommended) and make a hard copy. Do not wait for the last minute to do your work. Allow time for deadlines.
Plagiarism: Plagiarism, the presentation of someone else's words or ideas as your own, is a serious offense and will not be tolerated in this class. The first time you plagiarize someone else's work, you will receive a zero for that assignment. The second time you plagiarize, you will fail the course with a notation of academic dishonesty on your official record.
Module 1. Historical Overview of Bioinformatics
Hagen JB. The origins of bioinformatics. Nat Rev Genet. 2000 Dec;1(3):231-6.
Searls DB. The roots of bioinformatics. PLoS Comput Biol. 2010 Jun 24;6(6):e1000809. doi: 10.1371/journal.pcbi.1000809.
Hogeweg P. The roots of bioinformatics in theoretical biology. PLoS Comput Biol. 2011 Mar;7(3):e1002021. doi: 10.1371/journal.pcbi.1002021.
Tuesday September 4
Friday September 7
Module 2. Publicly Available Datasets
Langmead and Nellore. Cloud computing for genomic data analysis and collaboration. Nature Reviews Genetics. 2018; 19:208-219
Denk F. Don’t let useful data go to waste. Nature. 2017 Feb 28;
Students present publicly available data sets in their field of interest and a brief overview of studies that have been done using this data (10 minutes per person)
Choose from this list of datasets here and indicate which dataset you will be presenting on
Due September 18th: Identify an additional publicly dataset that was not included on the original list and write up a few sentences explaining what the data is, how it was collected, and what it has been used for at this point.
Tuesday September 11
Presenters: Grivainis, Hong, Narang, Yeaton, Dube
Friday September 14
Presenters: Abebe, McCulloch, Barkley, Devlin, Wang
Module 3: Molecular Classification of Cancer
Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 1999 Oct 15;286(5439):531-7.
Tuesday September 18
Friday September 21
Tuesday September 25
Friday September 28
Group 1: Barkley, Devlin, Wang
Group 2: Abebe, Narang, Hong
Group 3: Grivainis, McCulloch, Yeaton
Module 4: Regulatory Genomics
Core et al., Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nature Genetics. 2014 Dec; 46(12):1311-20
Tuesday October 2
Friday October 5
Tuesday October 9
Friday October 12
Group 1: Wang, Barkley, Abebe
Group 2: Yeaton, Devlin, Grivainis
Group 3: Hong, Narang, McCulloch
Module 5: Cancer Proteogenomics
Mertins et al., Proteogenomics connects somatic mutations to signaling in breast cancer. Nature. 2016 June 2; 534(7605):55-62
Friday October 19
Tuesday October 23
Friday October 26
Group 1: Wang, Yeaton, McCulloch
Group 2: Hong, Devlin, Narang
Group 3: Abebe, Grivainis, Barkley
Module 6: Chromosome Conformation Capture
Rao SS et al., A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014 Dec 18; 159(7):1665-80
Tuesday October 30
Friday November 2
Tuesday November 6
Friday November 9
Group 1: Abebe, Narang, Yeaton
Group 2: Barkley, Devlin, McCulloch
Group 3: Hong, Grivainis, Wang
Module 7: Dynamics of Bacterial Communities
Kelsic ED, Zhao J, Vetsigian K, Kishony R., Counteraction of antibiotic production and degradation stabilizes microbial communities, Nature 521 (2015) 516-519
Tuesday November 13
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----- OFF Tuesday November 20 ----
----- OFF Friday November 22 -----
Tuesday November 27
Friday November 30
Group 1: McCulloch, Grivainis, Wang
Group 2: Devlin, Abebe, Narang
Group 3: Hong, Yeaton, Barkley
Module 8: Software Development Best Practices
Reading List: TBD
Tuesday December 4
Friday December 7
Module 9: Publicly Available Tools
Offord C. Scientists Continue to Use Outdated Methods. (2018) The Scientist
Wadi L, Meyer M, Weiser J, Stein LD, Reimand J. Impact of outdated gene annotations on pathway enrichment analysis (2016) Nature Methods 13(9):705-6
List M, Ebert P, Alberecht F. Ten simple rules for developing usable software in computational biology. (2017) PLOS Computational Biology
Students present publicly available bioinformatics tools in their field of interest and a brief overview of studies that have been done using these tools including an assessment of the positives and negatives of the chosen method (10 minutes per person)
Tuesday December 11
Friday December 14