This is the first version in English language of the Bioinformatics course. The main subject is “metagenomics”. We will learn how to handle the output of DNA sequencing machines, how to assemble the chromosome, how to find genes and how to determine the probable function of the proteins they encode. If time allows, we will also study phylogenetic trees and microarray analysis.
Classes are held each week on Mondays at 13:00 for about 90 minutes, followed by 90 minutes of practice. Please bring your own computer since the ones in the lab cannot run our software.
Please register yourself in the course forum at https://groups.google.com/d/forum/iu-bioinfo. You can also participate writing an email to iu-bioinfo@googlegroups.com.
This page will be updated during the semester. Please check it regularly.
Homework
All homeworks should be sent to andres.aravena+bioinfo@istanbul.edu.tr before the deadline to get a grade. Please be careful, otherwise you will get a grade zero.
Semester Project
The challenge is to sequence your own samples. For this, during the semester, you have to work as a team and follow these steps:
- Learn what technologies exist for DNA sequencing (Deadline: September 25th)
- Learn which companies provide sequencing services, in the country and abroad
- Learn the prices of the service
- Decide the target to sequence and the scientific question to answer
- Decide the sampling and DNA extraction protocols
- Decide how to get money to cover the expenses
- Perform the sampling and DNA extraction
- Send the DNA and receive the sequences
- Analyze and conclude
- Deposit the sequences in an international database
Classes
Here you find the slides that have been used in classes. Notice that usually they are not published immediately, so you better take good notes. We recommend taking notes with pen and paper using the Cornell Method.
Class 1: Why do we care about Bioinformatics?. (Sep 18, 2017). [Slides].
A personal perspective on Metagenomics and BioinformaticsClass 8: Primer Design. (Nov 20, 2017). [Slides].
Class 10: Working with multiple sequences. (Dec 4, 2017). [Slides].
Class 11: Alignment free methods. (Dec 11, 2017). [Slides].
Finding Motifs and Taxonomy Identification without alignment.Class 12: NCBI website. (Dec 18, 2017). [Slides].
Entrez.
Bibliography
- Dina Fine Maron. “Dirty Money.” Scientific American, 2017. https://www.scientificamerican.com/article/dirty-money/.
- Jeff Leach. “Going Feral: My One-Year Journey to Acquire the Healthiest Gut Microbiome in the World,” January 2014. http://humanfoodproject.com/going-feral-one-year-journey-acquire-healthiest-gut-microbiome-world-heard/.
- Phillippy, Adam M. “New Advances in Sequence Assembly.” Genome Research 27, no. 5 (May 1, 2017): xi–xiii. doi:10.1101/gr.223057.117.
- Tyson, Gene W, Jarrod Chapman, Philip Hugenholtz, Eric E Allen, Rachna J Ram, Paul M Richardson, Victor V Solovyev, Edward M Rubin, Daniel S Rokhsar, and Jillian F Banfield. “Community Structure and Metabolism through Reconstruction of Microbial Genomes from the Environment.” Nature 428, no. 6978 (2004): 37–43. doi:10.1038/nature02340.
- Qin, Junjie, Ruiqiang Li, Jeroen Raes, Manimozhiyan Arumugam, Kristoffer Solvsten Burgdorf, Chaysavanh Manichanh, Trine Nielsen, et al. “A Human Gut Microbial Gene Catalogue Established by Metagenomic Sequencing.” Nature 464, no. 7285 (March 4, 2010): 59–65. doi:10.1038/nature08821.
- Ünal, Burcu. “Phylogenetic Analysis of Bacterial Communities in Kefir by Metagenomics.” Izmir Institute of Technology, Turkey, 2008.
- Ünal, Burcu Ünsal, and Alper Arslanoğlu. “Phylogenetic Identification of Bacteria within Kefir by Both Culture-Dependent and Culture-Independent Methods.” African Journal of Microbiology Research 7, no. 36 (2013): 4533–38. doi:10.5897/AJMR2013.6064.
- Handelsman, Jo. “Metagenomics: Application of Genomics to Uncultured Microorganisms.” Microbiology and Molecular Biology Reviews 68, no. 4 (2004): 669–85. doi:10.1128/MMBR.68.4.669-685.2004.
- Baker, Brett J., and Jillian F. Banfield. “Microbial Communities in Acid Mine Drainage.” FEMS Microbiology Ecology 44, no. 2 (2003): 139–52. doi:10.1016/S0168-6496(03)00028-X.
- Wooley, John C., and Yuzhen Ye. “Metagenomics: Facts and Artifacts, and Computational Challenges.” Journal of Computer Science and Technology 25, no. 1 (2009): 71–81. doi:10.1007/s11390-010-9306-4.
- Sharpton, Thomas J. “An Introduction to the Analysis of Shotgun Metagenomic Data.” Frontiers in Plant Science 5 (June 16, 2014): 209. doi:10.3389/fpls.2014.00209.
- Hunter, Chris I, Alex Mitchell, Philip Jones, Craig McAnulla, Sebastien Pesseat, Maxim Scheremetjew, and Sarah Hunter. “Metagenomic Analysis: The Challenge of the Data Bonanza.” Briefings in Bioinformatics 13, no. 6 (November 1, 2012): 743–46. doi:10.1093/bib/bbs020.
- Teeling, Hanno, and Frank Oliver Glöckner. “Current Opportunities and Challenges in Microbial Metagenome Analysis–a Bioinformatic Perspective.” Briefings in Bioinformatics 13, no. 6 (December 1, 2012): 728–42. doi:10.1093/bib/bbs039.
- Mande, Sharmila S, Monzoorul Haque Mohammed, and Tarini Shankar Ghosh. “Classification of Metagenomic Sequences: Methods and Challenges.” Briefings in Bioinformatics 13, no. 6 (November 1, 2012): 669–81. doi:10.1093/bib/bbs054.