We will take a break for February and return on March 9 at 3pm CET. Tune in with Benjamin Maier (@bdmaier.bsky.social), Valeria Bica and Dr Aleksandra Panfilova

Register to attend: tinyurl.com/PMCseminar2

Previous seminars: www.youtube.com/@PMCModularity

Our group has a PhD position open in this Doctoral network. Our topic is around combining proteomics AI and protein structures. Look through the website below to look at all of the projects/groups and apply.

Also don’t miss:
🧬👯 @epetsalaki.bsky.social’s talk “From Data to Digital Twins” (Wed, Digital Twin Models)

📊🧬 My poster P03.14 – Towards Data-Driven Executable Models (Wed)

🧩🤖 @alussana.bsky.social’s poster P18.13 – Data-Driven Inference of Functionally Coherent Gene Modules (Mon)

Excited to present my talk "Data-Driven Mathematical Modelling to Improve Heart Organoid Design" in the Therapeutic Target Discovery module at #ICSB2025 in Dublin tomorrow at 3:20 pm! 🫀💻 @epetsalaki.bsky.social @ebi.embl.org

Check out the recent preprints in #cellbio, selected by the @prelights.bsky.social community.

The featured preLight, from @bdmaier.bsky.social,‬ highlights STEAMBOAT, a ML framework for delineation of cellular interactions from @jianma.bsky.social & team.

journals.biologists.com/jcs/article/...

Postdoctoral Fellow – Bioinformatics & Executable Modelling for Rare Disease Digital Twins We are looking for a motivated and talented postdoctoral-level researcher with experience in executable modelling to join a cutting-edge project developing Digital Twins for rare diseases. This is a u...

I, Rahuman Sheriff @biomodels.bsky.social and Ellie McDonagh from @opentargets.org @ebi.embl.org are looking for an enthusiastic postdoc with skills in executable modelling to create Digital Twins for rare disease (CZI-funded project).

Data-driven extraction of human kinase-substrate relationships from omics datasets Phosphorylation forms an important part of the signalling system that cells use for decision making and regulation of processes such as cell division …

We present SELPHI 2.0 a machine learning model integrating >40 sequence, omics and structural features to predict kinase-substrate interactions between 420 kinases and 240K phosphosites and improve interpretation of global phosphoproteomics data www.sciencedirect.com/science/arti...

If you're looking for a great supervisor, I can't recommend Kristoffer enough. Kristoffer was an outstanding mentor and supervisor for my master's thesis. If you're looking for a PhD position, take a look at his opening!

PhosX: data-driven kinase activity inference from phosphoproteomics experiments AbstractSummary. The inference of kinase activity from phosphoproteomics data can point to causal mechanisms driving signalling processes and potential dru

Kinases play a role in many diseases, making them prime targets for therapeutic intervention.

Enter PhosX, a new tool transforming the way researchers analyse and interpret kinase activity.

Read the full article: academic.oup.com/bioinformati...

@alussana.bsky.social @epetsalaki.bsky.social

Great interview of my postdoc @iguaracy.bsky.social - check it out!

Decoding MASLD Progression: A Molecular Trajectory-Based Framework for Modelling Disease Dynamics Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) has emerged as a silent pandemic, affecting nearly one-third of the global population. This condition encompasses a spectrum of liver d...

New preprint from our group @ebi.embl.org and the Vidal-Puig group! We combined pseudotemporal ordering of cross sectional MASLD patient data with network analysis to describe the disease progression and identify a signature of 24 plasma biomarkers for patient staging www.biorxiv.org/content/10.1...

ARID1A-induced transcriptional reprogramming rewires signalling responses to drug treatment in melanoma Resistance to BRAF and MAPK inhibitors is a significant challenge in melanoma treatment, driven by adaptive and acquired mechanisms that allow tumour cells to evade therapy. Here, we examined early si...

We are proud to present "ARID1A-induced transcriptional reprogramming rewires signalling responses to drug treatment in melanoma" led by Charlie Barker and Sumana Sharma in collaboration with EPIC-XS Utrecht, ProtAvio, @sangerinstitute.bsky.social and UofAthens www.biorxiv.org/content/10.1...

New postdoc program opening soon at SciLifeLab! Feel free to contact me if you are interested in doing a postdoc related to rare RNAs in single-cells, environmental samples or extinct animals 🧬

PhosX is out! doi.org/10.1093/bioi... Leveraging the latest kinase specificity maps by the Cantley, Yaffe, and Turk labs and a rank sum statistic we created PhosX so now we can predict activities for nearly all kinases in your phosphodata, including the understudied ones. Check it out!

Illustration comparing the improvement process in software writing to rock climbing.

🧵 Bioinformatics faces a critical challenge: despite its importance, software quality often falls short due to the lack of proper development practices.

In our latest paper, we advocate for improving software quality in bioinformatics through teamwork.

academic.oup.com/bioinformati...