There are four small groups (A, B, C, D), each with 5 students. For the first class period, students are responsible for reading the paper labeled with their small group letter below. For the second class period, one student in the small group will present the paper (see the presentation schedule on ELMS).

Updates: I will try to provide questions to guide the small group discussion and short presentations. This is also a friendly reminder to use pictures in your presentation. These could be figures you make or figures from papers, lecture slides, etc. (cite your source). This greatly helps with everyone's understanding of the material - so thank you!

Oct 25,27: Multiple Sequence Alignment

  1. Lee et al., 2002, Multiple sequence alignment using partial order graphs, Bioinformatics. [link]
  2. Kececioglu and Starrett, 2004, Aligning alignments exactly, RECOMB. [link]
  3. Smirnov and Warnow, 2020, MAGUS: Multiple sequence Alignment using Graph clUStering, Bioinformatics. [link]
  4. Garriga et al., 2019, Large multiple sequence alignments with a root-to-leaf regressive method, Nature Biotechnology. [link]

Nov 1,3: Plant Evolution and Gene Duplication and Loss

  1. Li et al., 2015, Early genome duplications in conifers and other seed plants, Scientific Advances. [link] [Note: focus on their method: MAPS]
  2. Aluru and Singh, 2021, Improved inference of tandem domain duplications, Bioinformatics/ISMB. [link]
  3. Rabier et al., 2013, Detecting and Locating Whole Genome Duplications on a Phylogeny: A Probabilistic Approach, Molecular Biology and Evolution. [link]
  4. Qiao et al., 2019, Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants, Genome Biology. [link] [Note: focus on their pipeline: DupGen finder)

Nov 8,10: Bacteria Evolution and Horizontal Gene Transfer

  1. Sela et al., 2021, Assessment of assumptions underlying models of prokaryotic pangenome evolution, . [link]
  2. Bansal et al., 2012, Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss, Bioinformatics. [link]
  3. Oliveira et al., 2017, The chromosomal organization of horizontal gene transfer in bacteria, Nature Communications. [link]
  4. Jeong et al., 2019, Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation, Scientific Reports. [link]

Nov 15,17: Virus Evolution and Recombination [Q's]

  1. Forster et al., 2020, Phylogenetic network analysis of SARS-CoV-2 genomes, PNAS. [link] Note: We have intentionally picked a contentious paper; read/present the paper as well as the letters in response.
  2. Wertheim et al., 2021, Accuracy in Near-Perfect Virus Phylogenies, Systematic Biology. [link]
  3. Boni et al., 2020, Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic, Nature Microbiology. [link]
  4. Li et al., 2020, Phylogenetic supertree reveals detailed evolution of SARS-CoV-2, Scientific Reports. [link]

Nov 29, Dec 1: Presenter's Choice [Q's]

  1. Malikic et al., 2019, Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data, Nature Communications. [link]
  2. Simonsen et al., 2008, Rapid Neighbour-Joining, WABI. [link]
  3. Wittler, 2020, Alignment- and reference-free phylogenomics with colored de Bruijn graphs, Algorithms for Molecular Biology. [link]
  4. Casanellas et al., 2021, SAQ: semi-algebraic quartet reconstruction, IEEE/ACM TCBB. [link]