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
Group: Harmanová, Kubranová, Novotný, Šimkovič, Beliaeva

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
Group: Donets, Karakaya, Revajová, Gurová, Patka

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
Group: Ivantaeva, Kun, Makarová, Orlova

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
Group: Bublavý, Klymova, Kvasnakova, Seleng, Králiková

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
Group: Madzin, Podskalka, Abliasova, Antony, Blašková

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
Group: Knapec, Galková, Jaroš, Nagy, Sidorov

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
Group: Kendereš, Kurimaiová, Villányiová, Zetocha, Zhaken

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
Group: Drugda, Dolaberidze, Miendiukov, Murajda, Richnakova

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
Group: Antonova, Klimo, Kuzmenko, Liiv, Orságová

Submitting preferences

Please submit your preferences regarding these papers using this form until Wednesday Oct. 21, 2026, 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.

Group meeting

  • Everyone should read the article before the first meeting.
  • The first meeting should take place no later than November 20. The meeting can be online (e.g. in MS Teams) or in person. Try to choose a time suitable for all members of the group.
  • At least 24 hours before the first group meeting, post its date, time and location to the discussion forum in Moodle.
  • After the first meeting, one representative of the group will post a short summary to Moodle stating who attended the meeting, who apologized and who did not respond to the group and what was the outcome of the meeting - whether the group had problems with some parts of the article, whether it plans to meet again, etc. You do not need to report subsequent meetings.
  • If you need help from instructors, please contact us by email.
  • Failure to hold the first meeting according to these rules may affect the grade of the final report.

Presentation

  • The group has to prepare slides to present the article in accessible terms to students of this course (both computer scientists and biologists).
  • The presentation should be understandable for students of this course (both computer scientists and biologists), so explain the necessary terms that are not explained in the article and were not explained in class (do not repeat material from lectures).
  • The presentation must be in English.
  • You do not have to cover the entire content of the article in the presentation and, conversely, you can use other resources. Cite all sources you have used.
  • You should include the following (not necessarily in this order):
    • a brief overall description of the contents of the paper,
    • a detailed explanation of at least one computational method,
    • a detailed explanation of at least one biological result or evaluation of the method on data,
    • an explanation how the paper relates to the course material,
    • examples of other papers citing your paper and using or improving its results.
  • The recommended length is 1 slide per minute plus title slide and the “Active participation” slide, which list the members of the group who have actively participated (students who are not on this list will receive zero points).
  • Oral presentations will take place either during the last lecture, or during the exam session (TBA).
  • Presenter and presentation duration: TBA

Grading

  • Slides have to be submitted prior the presentation date (TBA). The oral presentation is mandatory.
  • Grades come from a) quality of the slides themselves, b) quality of the oral presentation.
  • Points are assigned equally to the members of the group who have actively participated in the group activities (if present at the presentation, otherwise zero points unless she has good reasons for an absence).