Benjamin Maier
@bdmaier.bsky.social
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
Highlighting preprints for preLights: https://shorturl.at/8MPdH
Reposted by Benjamin Maier
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.
🌟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
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
October 8, 2025 at 9:45 AM
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.
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
October 5, 2025 at 5:57 PM
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
Reposted by Benjamin Maier
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/...
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
June 20, 2025 at 9:51 AM
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/...
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/...
Reposted by Benjamin Maier
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
June 13, 2025 at 3:45 PM
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).
Reposted by Benjamin Maier
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
May 16, 2025 at 9:09 AM
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!
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)
March 28, 2025 at 8:15 AM
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!
Reposted by Benjamin Maier
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
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
January 27, 2025 at 11:57 AM
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
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
Reposted by Benjamin Maier
Great interview of my postdoc @iguaracy.bsky.social - check it out!
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...
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...
February 4, 2025 at 12:42 PM
Great interview of my postdoc @iguaracy.bsky.social - check it out!
Reposted by Benjamin Maier
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
January 19, 2025 at 11:18 AM
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...
Reposted by Benjamin Maier
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
December 10, 2024 at 9:44 AM
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...
Reposted by Benjamin Maier
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 🧬
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 program welcomes researchers from all over the world – 48 in total, in an academic and an entrepreneurial track.
#MolBiol #AcademicSky #PlantSciJobs
November 29, 2024 at 12:27 PM
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 🧬
Reposted by Benjamin Maier
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!
November 21, 2024 at 6:33 AM
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!
Reposted by Benjamin Maier
🧵 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...
In our latest paper, we advocate for improving software quality in bioinformatics through teamwork.
academic.oup.com/bioinformati...
November 18, 2024 at 2:48 PM
🧵 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...
In our latest paper, we advocate for improving software quality in bioinformatics through teamwork.
academic.oup.com/bioinformati...