Julian van Gerwen
@julianvangerwen.bsky.social
Computational biologist studying protein signalling | PhD candidate in Beltrao group at IMSB in ETH Zürich
Reposted by Julian van Gerwen
Catch our next seminar on November 10 at 3pm CET! You'll see presentations from Prof. Gideon Schreiber (@weizmanninstitute.bsky.social) and Alessandro Lussana (@alussana.bsky.social).
Register to attend: tinyurl.com/PMCseminar2
Recordings of previous seminars: www.youtube.com/@PMCModularity
Register to attend: tinyurl.com/PMCseminar2
Recordings of previous seminars: www.youtube.com/@PMCModularity
October 21, 2025 at 12:58 PM
Catch our next seminar on November 10 at 3pm CET! You'll see presentations from Prof. Gideon Schreiber (@weizmanninstitute.bsky.social) and Alessandro Lussana (@alussana.bsky.social).
Register to attend: tinyurl.com/PMCseminar2
Recordings of previous seminars: www.youtube.com/@PMCModularity
Register to attend: tinyurl.com/PMCseminar2
Recordings of previous seminars: www.youtube.com/@PMCModularity
Check out our approach for adding covalent bonds to AlphaFold3, which we apply to ubiquitin. Watch this space!
You may have noticed that AlphaFold3 does not allow covalent bonds between/within polymer chains (protein, DNA, RNA) but allows it for ligands. We tried to go around this limitation by simply treating one of residues/nucleic acids as a ligand.
October 17, 2025 at 12:57 AM
Check out our approach for adding covalent bonds to AlphaFold3, which we apply to ubiquitin. Watch this space!
Reposted by Julian van Gerwen
You may have noticed that AlphaFold3 does not allow covalent bonds between/within polymer chains (protein, DNA, RNA) but allows it for ligands. We tried to go around this limitation by simply treating one of residues/nucleic acids as a ligand.
October 16, 2025 at 10:47 AM
You may have noticed that AlphaFold3 does not allow covalent bonds between/within polymer chains (protein, DNA, RNA) but allows it for ligands. We tried to go around this limitation by simply treating one of residues/nucleic acids as a ligand.
Excited to share some of my PhD work on ubiquitin www.biorxiv.org/content/10.1...!
Huge collaborative effort from many people
Check out the whole story here
Huge collaborative effort from many people
Check out the whole story here
October 9, 2025 at 7:15 AM
Excited to share some of my PhD work on ubiquitin www.biorxiv.org/content/10.1...!
Huge collaborative effort from many people
Check out the whole story here
Huge collaborative effort from many people
Check out the whole story here
Reposted by Julian van Gerwen
We are back with an exciting seminar on September 8 at 3pm CEST! We’ll hear from Prof. Birthe Kragelund and Maximilian Vieler (@uu.se).
Register to attend:
tinyurl.com/PMCseminar2
Recordings of previous seminars: www.youtube.com/@PMCModularity
Register to attend:
tinyurl.com/PMCseminar2
Recordings of previous seminars: www.youtube.com/@PMCModularity
August 15, 2025 at 3:36 PM
We are back with an exciting seminar on September 8 at 3pm CEST! We’ll hear from Prof. Birthe Kragelund and Maximilian Vieler (@uu.se).
Register to attend:
tinyurl.com/PMCseminar2
Recordings of previous seminars: www.youtube.com/@PMCModularity
Register to attend:
tinyurl.com/PMCseminar2
Recordings of previous seminars: www.youtube.com/@PMCModularity
Reposted by Julian van Gerwen
Check out our latest preprint where we show synergistic interactions between bacteria for the degradation of complex polysaccharides 🌊🦠🔺
@envsysmicro.at @akshitg.bsky.social
#MicroSky
www.biorxiv.org/content/10.1...
@envsysmicro.at @akshitg.bsky.social
#MicroSky
www.biorxiv.org/content/10.1...
A division of labor controls the degradation of fucoidans in the ocean
Fucoidans, complex polysaccharides produced by brown algae and diatoms, contribute to long-term carbon sequestration due to their resistance to microbial degradation1,2. While individual microbes can ...
www.biorxiv.org
August 14, 2025 at 11:32 AM
Check out our latest preprint where we show synergistic interactions between bacteria for the degradation of complex polysaccharides 🌊🦠🔺
@envsysmicro.at @akshitg.bsky.social
#MicroSky
www.biorxiv.org/content/10.1...
@envsysmicro.at @akshitg.bsky.social
#MicroSky
www.biorxiv.org/content/10.1...
Reposted by Julian van Gerwen
New blog post: Why do we still publish in scientific journals ? What is holding us back from letting go of traditional publishing? No major insight here but I am curious what others think. www.evocellnet.com/2025/07/why-...
Why do we still publish in scientific journals ?
We publish in scientific journals to disclose our discoveries, such that others can build upon them. But we now have preprint servers and we...
www.evocellnet.com
July 23, 2025 at 7:36 AM
New blog post: Why do we still publish in scientific journals ? What is holding us back from letting go of traditional publishing? No major insight here but I am curious what others think. www.evocellnet.com/2025/07/why-...
Reposted by Julian van Gerwen
Unexpectedly, @jurgjn.bsky.social found that running Alphafold3 predictions for protein interactions can yield ipTM scores that are more predictive of true interactions when run in pools of proteins instead of pairwise predictions. Presumably, this reflects some sort of "competition effect".
July 22, 2025 at 2:13 PM
Unexpectedly, @jurgjn.bsky.social found that running Alphafold3 predictions for protein interactions can yield ipTM scores that are more predictive of true interactions when run in pools of proteins instead of pairwise predictions. Presumably, this reflects some sort of "competition effect".
Reposted by Julian van Gerwen
TIME CHANGE - Because of a public holiday, we have moved the next seminar to Monday June 16 at 3pm CET. Tune in to hear from Dr. Lucía Chemes (@unsamoficial.bsky.social) and Julian van Gerwen (@julianvangerwen.bsky.social).
Register to attend:
tinyurl.com/PMCseminar2
(1/2)
Register to attend:
tinyurl.com/PMCseminar2
(1/2)
June 6, 2025 at 3:19 PM
TIME CHANGE - Because of a public holiday, we have moved the next seminar to Monday June 16 at 3pm CET. Tune in to hear from Dr. Lucía Chemes (@unsamoficial.bsky.social) and Julian van Gerwen (@julianvangerwen.bsky.social).
Register to attend:
tinyurl.com/PMCseminar2
(1/2)
Register to attend:
tinyurl.com/PMCseminar2
(1/2)
Reposted by Julian van Gerwen
Increasing the time limits post PhD for ERC starting grant applications is a bad idea. It will mean fewer junior PIs getting an ERC at the start of the group. Those complaining about the previous time limits will not really benefit. The competition will be higher.
erc.europa.eu/news-events/...
erc.europa.eu/news-events/...
Changes to the 2026 and 2027 Work Programmes
With the launch of the competitions for grants under ERC Work Programme 2026 in July of this year, several changes to the submission of applications and the evaluation of proposals will apply. The mai...
erc.europa.eu
June 2, 2025 at 11:36 AM
Increasing the time limits post PhD for ERC starting grant applications is a bad idea. It will mean fewer junior PIs getting an ERC at the start of the group. Those complaining about the previous time limits will not really benefit. The competition will be higher.
erc.europa.eu/news-events/...
erc.europa.eu/news-events/...
Reposted by Julian van Gerwen
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...
Excited to share some of our work on ubiquitin at this seminar!
May 16, 2025 at 6:15 PM
Excited to share some of our work on ubiquitin at this seminar!
Reposted by Julian van Gerwen
We utilized protein kinases to probe substrate protein structures. The phosphate groups enabled selective extraction of labeled sites.
Detecting Protein Higher-Order Structural Changes Using Kinase as a Phospho-Labeler www.biorxiv.org/content/10.1...
Detecting Protein Higher-Order Structural Changes Using Kinase as a Phospho-Labeler www.biorxiv.org/content/10.1...
Detecting Protein Higher-Order Structural Changes Using Kinase as a Phospho-Labeler
We developed an approach to detect protein conformational changes on a proteome-wide scale by labeling proteins with phosphate groups through in vitro kinase reactions. This structural proteomics appr...
www.biorxiv.org
May 13, 2025 at 1:38 AM
We utilized protein kinases to probe substrate protein structures. The phosphate groups enabled selective extraction of labeled sites.
Detecting Protein Higher-Order Structural Changes Using Kinase as a Phospho-Labeler www.biorxiv.org/content/10.1...
Detecting Protein Higher-Order Structural Changes Using Kinase as a Phospho-Labeler www.biorxiv.org/content/10.1...
It was a pleasure to attend this amazing meeting! Huge thanks to the organisers
Ready & EXCITED to kick off two exciting days of #Ubiquitin & Friends! #ubfriends2025
May 10, 2025 at 2:05 PM
It was a pleasure to attend this amazing meeting! Huge thanks to the organisers
Reposted by Julian van Gerwen
Join us at 6pm CET April 14 for the next seminar in our series with Prof. Anne-Claude Gingras (@uoft.bsky.social) and Dr. Veronica Venafra.
Register to attend: tinyurl.com/register-pmc-seminar
(1/2)
Register to attend: tinyurl.com/register-pmc-seminar
(1/2)
March 25, 2025 at 2:53 PM
Join us at 6pm CET April 14 for the next seminar in our series with Prof. Anne-Claude Gingras (@uoft.bsky.social) and Dr. Veronica Venafra.
Register to attend: tinyurl.com/register-pmc-seminar
(1/2)
Register to attend: tinyurl.com/register-pmc-seminar
(1/2)
Reposted by Julian van Gerwen
New blog post - State of the lab 12, yearly series on being a group leader in academia. This one reflects back on the transition from junior PI to a more established scientist www.evocellnet.com/2025/03/stat...
State of the lab 12 - Becoming an established scientist
This blog post is part of a (nearly) yearly series on running a research group in academia. This post summarizes year 12, the 3rd year afte...
www.evocellnet.com
March 16, 2025 at 1:37 PM
New blog post - State of the lab 12, yearly series on being a group leader in academia. This one reflects back on the transition from junior PI to a more established scientist www.evocellnet.com/2025/03/stat...