Lightnews — Scholar-powered news

Benjamin Maier

@bdmaier.bsky.social

170 followers 330 following 3 posts

SysBio PhD Student in the Petsalaki Group (Whole Cell Signalling) at EMBL-EBI and Cambridge University (Churchill College) | 🇩🇪 BS | 🇸🇪 MS | https://benjamindominikmaier.github.io/. Highlighting preprints for preLights: https://shorturl.at/8MPdH

benjamindominikmaier.github.io

Posts Media Videos Starter Packs

Reposted by Benjamin Maier

Pedro Beltrao @pedrobeltrao.bsky.social · 1d

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.

protaiomics.bsky.social @protaiomics.bsky.social · 1d

🌟Ready to apply?
16 fully funded PhD positions are open in ProtAIomics Doctoral Network!
Join 16 labs across Europe to advance AI-powered proteomics and drive discoveries in health & biotechnology.
👉 Apply here: www.protaiomics.eu
#Proteomics #ArtificialIntelligence #MSCA #PhDOpportunities

6 8

Benjamin Maier @bdmaier.bsky.social · 3d

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)

2 2

Benjamin Maier @bdmaier.bsky.social · 3d

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

1 2 6

Reposted by Benjamin Maier

Journal of Cell Science @jcellsci.bsky.social · Jun 20

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/...

preLights in cell biology (June 2025) | Journal of Cell Science | The Company of Biologists

journals.biologists.com

4 5

Reposted by Benjamin Maier

Evangelia Petsalaki @epetsalaki.bsky.social · Jun 13

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).

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...

embl.wd103.myworkdayjobs.com

1 5 5

Reposted by Benjamin Maier

Evangelia Petsalaki @epetsalaki.bsky.social · May 16

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...

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 …

www.sciencedirect.com

1 13 24

Benjamin Maier @bdmaier.bsky.social · Mar 28

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!

Kristoffer Sahlin @ksahlin.bsky.social · Mar 26

As for my project (Project 1 in the list), please help spread the word to students interested in doing a PhD in Computational Biology/Bioinformatics. Note that PhD students here are employed with a salary, that the position comes with benefits, and that there are no tuition fees. (2/3)

Reposted by Benjamin Maier

EMBL-EBI @ebi.embl.org · Jan 27

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

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

academic.oup.com

1 14 21

Reposted by Benjamin Maier

Evangelia Petsalaki @epetsalaki.bsky.social · Feb 4

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

EMBL-EBI @ebi.embl.org · Feb 4

Organoids have incredible potential in drug discovery and disease modelling.

In this Scientific Computing World interview, @iguaracy.bsky.social discusses organoid construction, nanobots, and how bioinformatics is transforming biomedical research.

www.scientific-computing.com/article/usin...

1 3

Reposted by Benjamin Maier

Evangelia Petsalaki @epetsalaki.bsky.social · Jan 19

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...

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...

www.biorxiv.org

1 3 13

Reposted by Benjamin Maier

Evangelia Petsalaki @epetsalaki.bsky.social · Dec 10

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...

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...

www.biorxiv.org

1 6 13

Reposted by Benjamin Maier

Marc Friedländer @marcfriedlander.bsky.social · Nov 29

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 🧬

SciLifeLab @scilifelab.se · Nov 26

Calling Recent PhDs! The PULSE postdoc program at SciLifeLab is opening soon, matchmaking portfolio now published! 🧪🌍🖥️🧬

The program welcomes researchers from all over the world – 48 in total, in an academic and an entrepreneurial track.

#MolBiol #AcademicSky #PlantSciJobs

The face and upper body of a young scientist in bright laboratory environment. In the foreground: a blurry out of focus vial with red liquid.

8 10

Reposted by Benjamin Maier

Evangelia Petsalaki @epetsalaki.bsky.social · Nov 21

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!

3 38 110

Reposted by Benjamin Maier

Anthony Mathelier @amathelier.bsky.social · Nov 18

🧵 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...

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

4 39 120