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CSC 334: Topics in Computational Biology

Homework 5: In-class paper presentation

The goal of this assignment is to help you get started on a potential final project topic, by reading a paper that interests you. This assignment is designed to help you practice distilling information and making it understandable to an audience. I will give you feedback on both your understanding of the material and your presentation style. The goal is to prepare and improve for the final presentation.

1. Choose a paper from the list below, or another paper related to the course material. Email me your choice and schedule a meeting with me (in the next week or so). We'll discuss what might be good to focus on when preparing your presentation of that particular topic, and also how it might relate to a final project.
2. Prepare and give your 10-15 minute presentation in class (we'll set up a schedule over the next 2-3 weeks). Things to think about: do you want to use slides and/or the board? How will you explain a difficult part of the paper in a way that makes sense to the class? Make sure to clearly explain the motivation, methods, results, and discussion sections of the paper.
3. The last part is to participate in the presentations of your classmates and read the papers they present *before* class! Ask questions if you don't understand something they explain. Ask them how this paper relates to the class material. Questions can help the presenter feel more comfortable and adjust their pace.

PAPER LIST:

• Local string alignment:

  Basic local alignment search tool (BLAST)

• Genome assembly for single cells:

  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

• BWT combined with Smith-Waterman alignment:

  Fast and accurate long-read alignment with Burrows-Wheeler transform

• UPGMA applied to data sampled over time:

  Reconstructing Genealogies of Serial Samples Under the Assumption of a Molecular Clock Using Serial-Sample UPGMA

• Neighbor-Joining applied to proteins:

  QuickTree: building huge Neighbour-Joining trees of protein sequences

• Phylogenetics and geography:

  Bayesian Phylogeography Finds Its Roots

• Bayesian phylogenetic methods:

  Bayesian Phylogenetic Inference Using DNA Sequences: A Markov Chain Monte Carlo Method

• PCA (future topic) applied to population structure:

  Genes mirror geography within Europe

• Population history methods (future topic):

  Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

• Estimating population size changes (future topic):

  Inference of human population history from individual whole-genome sequences

  Deep resequencing reveals excess rare recent variants consistent with explosive population growth

• Identifying genes under natural selection (future topic):

  Genetic signatures of strong recent positive selection at the lactase gene

  Learning Natural Selection from the Site Frequency Spectrum

• Ancient genomics (future topic):

  The complete genome sequence of a Neanderthal from the Altai Mountains

• GWAS (future topic) for human diseases:

  A new multipoint method for genome-wide association studies by imputation of genotypes