Methods that seem similar may estimate different quantities, distinct approaches can be closely related. In our new preprint, we analyze single-sample network inference methods in a common framework to reveal key similarities, differences, and benchmarking pitfalls:
www.biorxiv.org/content/10.6...
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)
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 ๐๐๐ฅ๐ฉ๐ช
This work was led by ๐๐จ๐ฅ๐๐ง, with contributions from ๐๐๐ญ๐ข๐๐ง๐. Thanks also to many group members for testing and providing feedback on the method. Funding from Kreftforeningen, NFR, Familien Blix Fond, and iCAN ๐
๐ 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. ๐
Would you like to model and analyze sample-specific regulatory networks? Check out our latest BioRxiv pre-print in which we present ๐๐ข๐๐๐๐, a command line workflow that makes modeling and analysis of single-sample networks really easy, transparent, and reproducible ๐ช: www.biorxiv.org/content/10.1...
This work was led by ๐๐จ๐ฅ๐๐ง, with contributions from ๐๐๐ญ๐ข๐๐ง๐. Thanks also to many group members for testing and providing feedback on the method. Funding from Kreftforeningen, NFR, Familien Blix Fond, and iCAN ๐
๐ 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. ๐
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 ๐คฉ
www.embl.org/about/info/c...
Read their side-by-side Q&A on how international mobility builds both skills and community:
๐ 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 ๐ Code is available in Snakemake ๐ 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, ๐), 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 ๐), 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. ๐)
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...
October welcomes 2 new group members in the Kuijjer group! Welcome Samantha Martin and Turan Koรง! More info: www.kuijjerlab.org/blog/new-gro...
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 ๐
Nice location for the iCAN 2025 symposium!
Great spot for a pause and outdoor dinner in between work and dance, in beautiful Copenhagen ๐งโโ๏ธ๐ฉ๐ฐ
Touring the Nordics and Europe for science in early fall brings sundogs, rainbows, and beautiful clouds ๐ธ๐ช๐ซ๐ฎ๐ฉ๐ช๐ณ๐ด๐ฉ๐ฐ Also good to have packed rain gear ๐ฒ๐ฆ
We are growing the wet-lab ๐งช Welcome Atefeh to the Oslo group! More info ๐ www.kuijjerlab.org/blog/atefeh-...
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 theyโll drive in the years ahead! Info ๐
www.kuijjerlab.org/blog/new-gro...
Back from a wonderful joint group retreat in Fornebu ๐๐ณ๐ด We had lots of pork neck, ๐ถ๏ธ gossip, and fruitful discussions. Hope to do this again soon to keep connections strong ๐ช So lucky to be part of this brilliant team of scientists ๐ซ Read more here: www.kuijjerlab.org/blog/group-r...
At the Meilahti campus bus stop, on my way to the group retreat in Fornebu ๐
Iโm 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
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 ๐ซ๐ฎ๐งโ๐ More info: ican.fi/icandoc/
Sundog above Helsinki ๐๐ฅ๐ซ๐ฎ