A brief description of the journal club activity is included in the course rules, more details will be added later.

Submitting preferences

Please submit your preferences regarding these papers using this form until Wednesday Oct. 22, 2025, 22:00. In the form, include numbers of three papers from this list in the order of preference. We will try to take your preferences into account, but we also need to balance group sizes and composition.

  • Groups will typically include students with different backgrounds.
  • Preferences submitted earlier will be considered with a higher priority.

List of papers

  • All links to papers should work in our University network (e.g. Eduroam or proxy)

Paper 1 Curry, K.D., Wang, Q., Nute, M.G., Tyshaieva, A., Reeves, E., Soriano, S., Wu, Q., Graeber, E., Finzer, P., Mendling, W. and Savidge, T., 2022. Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data. Nature methods, 19(7), pp.845-853. https://doi.org/10.1038/s41592-022-01520-4

Paper 2 Edgar, R.C., Taylor, J., Lin, V., Altman, T., Barbera, P., Meleshko, D., Lohr, D., Novakovsky, G., Buchfink, B., Al-Shayeb, B. and Banfield, J.F., 2022. Petabase-scale sequence alignment catalyses viral discovery. Nature, 602(7895), pp.142-147. https://doi.org/10.1038/s41586-021-04332-2

Paper 3. Bradley, P., Den Bakker, H.C., Rocha, E.P., McVean, G. and Iqbal, Z., 2019. Ultrafast search of all deposited bacterial and viral genomic data. Nature biotechnology, 37(2), pp.152-159. https://doi.org/10.1038/s41587-018-0010-1

Paper 4 Hauser, M., Steinegger, M. and Söding, J., 2016. MMseqs software suite for fast and deep clustering and searching of large protein sequence sets. Bioinformatics, 32(9), pp.1323-1330. https://doi.org/10.1093/bioinformatics/btw006

Paper 5 Wapinski, I., Pfeffer, A., Friedman, N. and Regev, A., 2007. Automatic genome-wide reconstruction of phylogenetic gene trees. Bioinformatics, 23(13), pp.i549-i558. https://doi.org/10.1093/bioinformatics/btm193

Paper 6 Kress, A., Poch, O., Lecompte, O. and Thompson, J.D., 2023. Real or fake? Measuring the impact of protein annotation errors on estimates of domain gain and loss events. Frontiers in Bioinformatics, 3, p.1178926. https://doi.org/10.3389/fbinf.2023.1178926

Paper 7 Gearing, L.J., Cumming, H.E., Chapman, R., Finkel, A.M., Woodhouse, I.B., Luu, K., Gould, J.A., Forster, S.C. and Hertzog, P.J., 2019. CiiiDER: A tool for predicting and analysing transcription factor binding sites. PloS one, 14(9), p.e0215495. https://doi.org/10.1371/journal.pone.0215495

Paper 8 Huang, K.L., Scott, A.D., Zhou, D.C., Wang, L.B., Weerasinghe, A., Elmas, A., Liu, R., Wu, Y., Wendl, M.C., Wyczalkowski, M.A. and Baral, J., 2021. Spatially interacting phosphorylation sites and mutations in cancer. Nature communications, 12(1), p.2313. https://doi.org/10.1038/s41467-021-22481-w

Paper 9 Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 Dec 4;370(6521). https://doi.org/10.1126/science.abe9403