A brief description of the journal club activity is included in the course rules, more details are below.

Groups

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

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
Buchalová, Horváth, Ončák, Podhradský, Pulkin, Zrubák

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
Antony, Hayik, Ishchenko, Komoráš, Saez de Cortazar, Škorňák, Strieška (English speaking)

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
Balan, Bukovinská, Chabadová, Gavura, Guziová, Pilátová, Tibenská

Paper 6 Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF et al. (2007). “Distinguishing protein-coding and noncoding genes in the human genome.”. Proc Natl Acad Sci U S A 104 (49): 19428-33. https://doi.org/10.1073/pnas.0709013104
Hrúzik, Jaremčuková, Kornhauser, Krupa, Ratkovský, Zigman

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
Andraščík, Ayestaran Guillorme, Hladíková, Murua Urizarbarrena, Plachý, Shcherba, Sládek (English speaking)

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
Antlová, Čakurdová, Halmová, Kočalka, Melkovič, Senderák

Group meeting

  • Everyone should read the article before the first meeting.
  • The first meeting should take place no later than November 22. 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.

Journal club report

  • In the report, describe the main methods and results of the article in your own words.
  • The report 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).
  • You do not have to cover the entire content of the article in the report 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 about 1-2 pages per person. However, the report should form one coherent text, so agree well on the outline and division of work and spend some time at the end on combining and editing individual contributions into a coherent report.
  • The report should list the members of the group who have actively participated in its work. Students who are not on this list will receive zero points for the report.

Unused papers

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 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