Seminar

Seminar Metagenomics

Despite the title of this seminar being "metagenomics", the main focus will be on viruses and bioinformatics questions related to viruses, in particular human associated viruses such as HIV.

Each participant will be given one-three papers to read and to present to the class. In addition, a write-up of the presentation is expected. All participants are required to attend all talks and to actively participate in discussions.

Important Dates:

• After determining the literature and sources that you will use, please contact your tutor to discuss them with him or her (at the latest three weeks before your presentation).
• One week before the presentation hand in a pre-final version of the required 10-15 page report (a summary of the topics in style of a scientific presentation).
• The report should describe and discuss the topic logically, didactically and structured.
• On the day of the presentation hand in the final version of the report so that it can be distributed to the other participants
• One week before the presentation, hand in a penultimate version of your slides.
• The presentation should take 20 minutes + 5 minutes of discussion

Dates and presentations

Topics:

Here we list the possible topics or more papers related to the topic. Students are encouraged to do their literature search to find additional sources.

How old are measles? Estimation of divergence dates

Wertheim, Joel O., and Sergei L. Kosakovsky Pond. “Purifying Selection Can Obscure the Ancient Age of Viral Lineages.” Molecular Biology and Evolution 28, no. 12 (December 1, 2011): 3355–3365. doi:10.1093/molbev/msr170.

Furuse, Yuki, Akira Suzuki, and Hitoshi Oshitani. “Origin of Measles Virus: Divergence from Rinderpest Virus Between the 11th and 12th Centuries.” Virology Journal 7 (March 4, 2010): 52. doi:10.1186/1743-422X-7-52.

Flu: where does it come from and how does it change?

Gong, L. I., M. A. Suchard, and J. D. Bloom. “Stability-mediated Epistasis Constrains the Evolution of an Influenza Protein.” eLife 2, no. 0 (May 14, 2013): e00631–e00631. doi:10.7554/eLife.00631.

Russell, Colin A., Terry C. Jones, Ian G. Barr, Nancy J. Cox, Rebecca J. Garten, Vicky Gregory, Ian D. Gust, et al. “The Global Circulation of Seasonal Influenza A (H3N2) Viruses.” Science 320, no. 5874 (April 18, 2008): 340–346. doi:10.1126/science.1154137.

Reconstructing ancestral states

Pupko, Tal, Itsik Pe, Ron Shamir, and Dan Graur. “A Fast Algorithm for Joint Reconstruction of Ancestral Amino Acid Sequences.” Molecular Biology and Evolution 17, no. 6 (June 1, 2000): 890–896.

Determining protein structure with phylogenetics

Hopf, Thomas A., Lucy J. Colwell, Robert Sheridan, Burkhard Rost, Chris Sander, and Debora S. Marks. “Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing.” Cell 149, no. 7 (June 22, 2012): 1607–1621. doi:10.1016/j.cell.2012.04.012.

Morcos, Faruck, Andrea Pagnani, Bryan Lunt, Arianna Bertolino, Debora S. Marks, Chris Sander, Riccardo Zecchina, José N. Onuchic, Terence Hwa, and Martin Weigt. “Direct-coupling Analysis of Residue Coevolution Captures Native Contacts Across Many Protein Families.” Proceedings of the National Academy of Sciences 108, no. 49 (December 6, 2011): E1293–E1301. doi:10.1073/pnas.1111471108.

Viral metagenomics

Hurwitz BL, Sullivan MB (2013) The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology. PLoS ONE 8(2): e57355. doi:10.1371/journal.pone.0057355

Reyes, Alejandro, Matthew Haynes, Nicole Hanson, Florent E. Angly, Andrew C. Heath, Forest Rohwer, and Jeffrey I. Gordon. “Viruses in the Fecal Microbiota of Monozygotic Twins and Their Mothers.” Nature 466, no. 7304 (July 15, 2010): 334–338. doi:10.1038/nature09199.

Reassortment

McHardy AC, Adams B (2009) The Role of Genomics in Tracking the Evolution of Influenza A Virus. PLoS Pathog 5(10): e1000566. doi:10.1371/journal.ppat.1000566

Co-evolution of HIV and immune system

Liao, Hua-Xin, Rebecca Lynch, Tongqing Zhou, Feng Gao, S. Munir Alam, Scott D. Boyd, Andrew Z. Fire, et al. “Co-evolution of a Broadly Neutralizing HIV-1 Antibody and Founder Virus.” Nature advance online publication (April 3, 2013). doi:10.1038/nature12053.

Zhu, Jiang, Gilad Ofek, Yongping Yang, Baoshan Zhang, Mark K. Louder, Gabriel Lu, Krisha McKee, et al. “Mining the Antibodyome for HIV-1–neutralizing Antibodies with Next-generation Sequencing and Phylogenetic Pairing of Heavy/light Chains.” Proceedings of the National Academy of Sciences 110, no. 16 (April 16, 2013): 6470–6475. doi:10.1073/pnas.1219320110.

Inference of human evolutionary history

Li, Heng, and Richard Durbin. “Inference of Human Population History from Individual Whole-genome Sequences.” Nature 475, no. 7357 (July 28, 2011): 493–496. doi:10.1038/nature10231.

Who infected whom? Inferring transmission chains of viruses

Thomas Leitner and Jan Albert. “Reconstruction of HIV-1 Transmission Chains for Forensic Purposes”. AIDS reviews. Vol 2, 2000

Evolutionary history of SIV

Worobey, Michael, Paul Telfer, Sandrine Souquière, Meredith Hunter, Clint A. Coleman, Michael J. Metzger, Patricia Reed, et al. “Island

Biogeography Reveals the Deep History of SIV.” Science 329, no. 5998 (September 17, 2010): 1487–1487. doi:10.1126/science.1193550.

The ancient history of viruses: Analysis of integrated retroviruses

Katzourakis, Aris, Robert J. Gifford, Michael Tristem, M. Thomas P. Gilbert, and Oliver G. Pybus. “Macroevolution of Complex Retroviruses.” Science 325, no. 5947 (September 18, 2009): 1512–1512. doi:10.1126/science.1174149.