Mariike Kuijjer

Check out this new map of nationalities in the group on an AuthaGraph projection of the world, with color priority as follows: current (dark green) and co-supervised (light green) members, former core (dark blue) and students and co-supervised members (light blue)

Oslo Bioinformatics Workshop Week 2025 - Bioinformatics in Life Science – BiLS December 8th-12th 2025 will see the fourth edition of the Oslo Bioinformatics Workshop Week at the University of Oslo, Norway. This event is organised by the Trainee Committee of BiLS (Bioinformatics ...

Great program at OBiWoW, the Oslo Bioinformatics Workshop Week 2025. Various workshops today/tomorrow are given by Oslo group members, including modeling and analysis of single-sample regulatory networks, Python development in VS code, and software testing. Welcome!
www.mn.uio.no/bils/english...

Not a bad place to work 🍂🍁🌥🇩🇪

This work was led by 𝐍𝐨𝐥𝐚𝐧, with contributions from 𝐓𝐚𝐭𝐢𝐚𝐧𝐚. Thanks also to many group members for testing and providing feedback on the method. Funding from Kreftforeningen, NFR, Familien Blix Fond, and iCAN 🙏

📖 In the manuscript, we walk the user through a tutorial on how to run the SiSaNA pipeline, interpret the results, and obtain high-quality figures summarized in a single HTML file as output. 🌐

Would you like to model and analyze sample-specific regulatory networks? Check out our latest BioRxiv pre-print in which we present 𝐒𝐢𝐒𝐚𝐍𝐀, a command line workflow that makes modeling and analysis of single-sample networks really easy, transparent, and reproducible 🪄: www.biorxiv.org/content/10.1...

This work was led by 𝐍𝐨𝐥𝐚𝐧, with contributions from 𝐓𝐚𝐭𝐢𝐚𝐧𝐚. Thanks also to many group members for testing and providing feedback on the method. Funding from Kreftforeningen, NFR, Familien Blix Fond, and iCAN 🙏

📖 In the manuscript, we walk the user through a tutorial on how to run the SiSaNA pipeline, interpret the results, and obtain high-quality figures summarized in a single HTML file as output. 🌐

Cancer genomics

I am very much looking forward to next week's EMBL conference on cancer genomics! Proud that some of the group's recent work will be presented in a selected talk by Tatiana and a poster and flash talk by Ine 🤩
www.embl.org/about/info/c...

Side-by-side Q&A: Connecting Labs and Learning Across Borders PhD student Iga Niemiec and postdoctoral fellow Ladislav Hovan on their UiO:Life Science Internationalisation experiences.

Read their side-by-side Q&A on how international mobility builds both skills and community:

🔗 projects.au.dk/nordic-embl-...

@mkuijjer.bsky.social @afarkkila.bsky.social @embl.org @mimsumea.bsky.social @dandrite.bsky.social

This work presents a major milestone by the group, led by Tatiana Belova, with contributions from current and former group members. Funding sources incl the Norwegian Research Council, Norwegian Cancer Society, iCAN, and NCMBM 🙏 Code is available in Snakemake 🐍 pipeline: github.com/kuijjerlab/P...

Finally, we mapped TFs modulating PD-L1, with their regulatory profiles linked to survival. Recurrent TFs included both known modulators (incl with/without known binding sites) and TFs with yet unknown role in PD-L1 regulation, highlighting candidate targets for modulating immune checkpoint activity

Strikingly, PD1 signaling heterogeneity associated with survival in about half of these (12/23) cancer types, but only associated with immune infiltrate in a subset (5/12, 👇), suggesting that, in many cancers, dysregulation may arise from tumor-intrinsic regulatory programs

This motivated us to map the regulatory heterogeneity per cancer type with our tool PORCUPINE, analyzing the complete networks. This identified several recurrently heterogeneously regulated pathways (categories and pathways from top category 👇), with PD1 signaling dysregulated in 23/33 cancer types!

We reconstructed sample-specific networks with our NetZoo tools PANDA and LIONESS: nearly 10k networks for 33 cancer types. Visualizing and clustering these networks on Gene Targeting Scores indicated that, for most cancer types, networks stratify patients distinctly from expression data (e.g. 👇)

Until now, patient-specific regulatory networks have mostly been studied in individual cancer types. In our latest BioRxiv pre-print, we took this to the next level, performing a large-scale, pan-cancer network analysis of patient-specific regulatory landscapes: www.biorxiv.org/content/10.1...

New group members Kuijjer Lab website

October welcomes 2 new group members in the Kuijjer group! Welcome Samantha Martin and Turan Koç! More info: www.kuijjerlab.org/blog/new-gro...

€10 Million in Grants – Focus on Children’s Physical Activity, Psychiatry, and Cancer Research - Jane and Aatos Erkko Foundation The Jane and Aatos Erkko Foundation has awarded €9.9 million in grants to 13 projects in the fields of medicine, science, arts, and culture. The announcement coincides with International Foundations D...

Grateful for funding from the Jane & Aatos Erkko Foundation for our project NETMET! We will develop AI and network science methods to map gene regulation at the patient and cell level, to understand cancer aggressiveness and improve patient stratification:
jaes.fi/en/topics/me...

Poster discussion ongoing, with our iCANDOC PhD student Panos presenting benchmarking of single sample network subtyping 📜

Nice location for the iCAN 2025 symposium!

Great spot for a pause and outdoor dinner in between work and dance, in beautiful Copenhagen 🧜‍♀️🇩🇰

Touring the Nordics and Europe for science in early fall brings sundogs, rainbows, and beautiful clouds 🇸🇪🇫🇮🇩🇪🇳🇴🇩🇰 Also good to have packed rain gear 🚲🌦

New group member Kuijjer Lab website

We are growing the wet-lab 🧪 Welcome Atefeh to the Oslo group! More info 👉 www.kuijjerlab.org/blog/atefeh-...

New group members Kuijjer Lab website

September starts strong! Welcome Ceren Pajanoja to our Helsinki group as postdoc, and congrats to Romana Pop for continuing as a joint NCMBM/OUS postdoc with our Oslo group & Anita Sveen. Excited to see the science they’ll drive in the years ahead! Info 👇
www.kuijjerlab.org/blog/new-gro...

Back from a wonderful joint group retreat in Fornebu 🌊🇳🇴 We had lots of pork neck, 🌶️ gossip, and fruitful discussions. Hope to do this again soon to keep connections strong 💪 So lucky to be part of this brilliant team of scientists 💫 Read more here: www.kuijjerlab.org/blog/group-r...

At the Meilahti campus bus stop, on my way to the group retreat in Fornebu 😍

I’m surprised to see that some funders still ask for impact factors in grant applications, even though institutions like @helsinki.fi have signed DORA. It puts applicants in an awkward spot

iCANDOC doctoral education pilot - iCAN The iCANDOC Precision Cancer Medicine (PCM) pilot is the largest Ministry of Education and Culture’s doctoral education pilots, awarded a total of

Happy to have started as director of the iCANDOC doctoral education pilot in precision cancer medicine! Looking forward to supporting the development of doctoral training in 🇫🇮🧑‍🎓 More info: ican.fi/icandoc/

Sundog above Helsinki 🌈🌥🇫🇮

SPONGE: simple prior omics network GEnerator AbstractSummary. Gene regulatory networks modelled from experimental data can be improved through the use of prior biological knowledge, e.g. transcription

GRN inference algorithms often build on prior knowledge of e.g. TF binding. Build up-to-date priors with our new tool SPONGE, now out in Bioinformatics: academic.oup.com/bioinformati...