groups

Journal_club.md

@@ -7,61 +7,53 @@ title: Journal Club
 
 A brief description of the journal club activity is included in the [course rules](./Rules.html#journal-club).
 
+{% if false %}
 ## Submitting preferences
 
 Please submit your preferences regarding these papers using [this form](https://forms.gle/K7BZJD5fA3wRmmXk8) until Wednesday Oct. 23, 2024, 22:00. In the form, include numbers of three papers from this list in the order of preference.
 
 * Students from the same study program will typically not be in the same group.
 * Preferences submitted earlier will be considered with higher priority.
 * Also please indicate if you are willing to work in a group with English-speaking students (this means group discussions and final report in English)
+{% endif %}
 
-## List of papers
 {% if false %}
-## Groups
+## List of papers
 {% endif %}
 
-* All links to papers should work in our University network (e.g.
-    Eduroam or [proxy](https://uniba.sk/index.php?id=6828))
+## Groups
 
-**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>
+* All links to papers should work in our University network (e.g.
+    Eduroam or [proxy](https://uniba.sk/index.php?id=6828))
 
 **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> 
+<br>**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>
+<br>**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>
+<br>**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>
+<br>**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>
+<br>**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> 
-
-**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>
+<br>**Antlová, Čakurdová, Halmová, Kočalka, Melkovič, Senderák**
 
 ## Group meeting 
 
@@ -106,6 +98,22 @@ mechanisms. Science. 2020 Dec 4;370(6521).
     receive zero points for the report.
 
 
-{% if false %}
 ## Unused papers
-{% endif %}
+
+**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>