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Mariike Kuijjer @mkuijjer.bsky.social · 1d

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...

Mariike Kuijjer @mkuijjer.bsky.social · 1d

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

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Mariike Kuijjer @mkuijjer.bsky.social · 1d

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

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Mariike Kuijjer @mkuijjer.bsky.social · 1d

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!

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Mariike Kuijjer @mkuijjer.bsky.social · 1d

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. 👇)

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Mariike Kuijjer @mkuijjer.bsky.social · 1d

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...

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Mariike Kuijjer @mkuijjer.bsky.social · 2d

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

New group members

Kuijjer Lab website

www.kuijjerlab.org

Mariike Kuijjer @mkuijjer.bsky.social · 7d

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...

€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...

jaes.fi

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Mariike Kuijjer @mkuijjer.bsky.social · 13d

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

Mariike Kuijjer @mkuijjer.bsky.social · 13d

Nice location for the iCAN 2025 symposium!

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Mariike Kuijjer @mkuijjer.bsky.social · 21d

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

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Mariike Kuijjer @mkuijjer.bsky.social · 22d

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

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Mariike Kuijjer @mkuijjer.bsky.social · 22d

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

New group member

Kuijjer Lab website

www.kuijjerlab.org

Mariike Kuijjer @mkuijjer.bsky.social · Sep 3

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...

New group members

Kuijjer Lab website

www.kuijjerlab.org

Mariike Kuijjer @mkuijjer.bsky.social · Aug 24

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...

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Mariike Kuijjer @mkuijjer.bsky.social · Aug 20

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

Mariike Kuijjer @mkuijjer.bsky.social · Aug 14

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

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Mariike Kuijjer @mkuijjer.bsky.social · Aug 7

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/

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

ican.fi

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Mariike Kuijjer @mkuijjer.bsky.social · Aug 4

Sundog above Helsinki 🌈🌥🇫🇮

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Mariike Kuijjer @mkuijjer.bsky.social · Jul 28

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...

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

academic.oup.com

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Mariike Kuijjer @mkuijjer.bsky.social · Jul 7

Looking for something to read over the summer 📖? Check out our latest publication in Briefings in Bioinformatics: academic.oup.com/bib/article/...

Gene regulatory network integration with multi-omics data enhances survival predictions in cancer

Abstract. The emergence of high-throughput omics technologies has resulted in their wide application to cancer studies, greatly increasing our understandin

academic.oup.com

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Mariike Kuijjer @mkuijjer.bsky.social · Jul 1

Beautiful halo on my ride home 🇫🇮🌥

Reposted by Mariike Kuijjer

Norwegian Centre for Molecular Biosciences and Medicine (NCMBM) @ncmbm.bsky.social · Jun 30

📣 We’re recruiting 1-2 Group Leaders! NCMBM is looking for early-career researchers ready to establish their independent research groups!

🧬 With an attractive start-up package, help us shape the future of molecular biosciences and medicine in 🇳🇴 and be part of the @nordicembl.bsky.social!

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Mariike Kuijjer @mkuijjer.bsky.social · May 26

Join us tomorrow at noon to learn more on spatial tumor ecosystems from @afarkkila.bsky.social from @farkkilab.bsky.social ! The talk will be at Forum, @forskningsparken.bsky.social

Mariike Kuijjer @mkuijjer.bsky.social · May 23

Happy to host @afarkkila.bsky.social at next week's @ncmbm.bsky.social international seminar! Join us Tuesday May 27 at 12 in Forskningsparken to learn more on spatial biology of ovarian cancer. Info 👇
www.med.uio.no/ncmbm/englis...

NCMBM International Seminar: Anniina Färkkilä - NCMBM - Norwegian Centre for Molecular Biosciences and Medicine

Anniina Färkkilä, MD PhD, is an Assistant professor in translational gynecologic oncology and a Specialist in gynecology at the University of Helsinki, Finland. The title of her talk is:

www.med.uio.no

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