Bioinformatics Journal Club
At the Bioinformatics Journal Club, our aim is to learn about the latest advancements in the field of bioinformatics, and to gain experience in presenting, critical reading, and summarizing key points from research articles. Articles chosen should be from high-impact journals (e.g. Science, Nature, Nature Methods) and published within the past 12 months. The Journal Club is open to everyone interested but please read the article before the club event!
The format of the Bioinformatics Journal Club is as follows: each club session starts with a short introduction by a student (~5 min) to place their chosen article in its wider context within the research discipline, which is followed by an in-depth presentation of the article (~10-15 min). After the presentation, all participants are welcomed to discuss the presented article, its impact and its relation to their own work/studies (~20-30 min). The presentations and discussions are in English.
Organizing team: Antonio Sousa, Sadia Akram, Itana Bojovic.
Bioinformatics Journal Clubs take place in Biocity B stairs, 5th floor seminar room at 13-14 on following Wednesdays:
Schedule, spring 2026
February 11
“Benchmarking informatics workflows for data-independent acquisition single-cell proteomics”
Nature Communications, 2025
https://doi.org/10.1038/s41467-025-65174-4
Presenter: Markus Linden
March 11
“Reproducible single-cell annotation of programs underlying T cell subsets, activation states and functions”
Nature Methods, 2025
https://doi.org/10.1038/s41592-025-02793-1
Presenter: Itana Bojović
April 8
“Deciphering the dark cancer phosphoproteome using machine-learned co-regulation of phosphosites”
Nature Communications, 2025
https://doi.org/10.1038/s41467-025-57993-2
Presenter: Sadia Akram
May 6
“Protein-level batch-effect correction enhances robustness in MS-based proteomics”
Nature Communications, 2025
https://doi.org/10.1038/s41467-025-64718-y
Presenter: Ali Youssef
Schedule, autumn 2025
September 10
“Limitations of cell embedding metrics assessed using drifting islands”
Nature Biotechnology, June 2025
https://doi.org/10.1038/s41587-025-02702-z
Presenter: António Sousa
October 15
“Precision proteogenomics reveals pan-cancer impact of germline variants“
Cell, May 2025
https://doi.org/10.1016/j.cell.2025.03.026
Presenter: Daniel Giesel
November 12
“CellChat for systematic analysis of cell–cell communication from single-cell transcriptomics”
Nature Protocols, September 2024
https://doi.org/10.1038/s41596-024-01045-4
Presenter: Sebastián Zúñiga Norman
December 10
“ProtGraph: a tool for the quick and comprehensive exploration and exploitation of the peptide search space derived from protein sequence databases using graphs”
Briefings in Bioinformatics, January 2025
https://doi.org/10.1093/bib/bbae671
Presenter: Mats Perk
Recommendation for credits
Participating in the journal clubs six times is recommend to equal to 1 credit and credits are accumulated so that 12 times equals 2 credits and so on. Presenting an article in the journal club equals 1 credit. Participation is monitored by a name list that is circulated every time – please contact us to ask for a certificate when you are claiming your credits at the end of your studies.
Contact for more information: mbc (at) utu.fi.