Ylva Ivarsson
@ivarssonlab.bsky.social
Professor of Biochemistry, Uppsala University. Views are my own.
Protein domains, disorder and interactions.
Protein domains, disorder and interactions.
Pinned
Ylva Ivarsson
@ivarssonlab.bsky.social
· Sep 22
Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases
The ubiquitin-specific proteases (USPs) family is the largest family of human deubiquitinating enzymes (DUBs). While most USPs are agnostic to polyubiquitin linkage-type, their substrate specificity i...
www.biorxiv.org
Finally out! Thrilled to share our collaboration with @kulathu.bsky.social, @orafurman.bsky.social, and N Davey. We screened auxiliary domains of USP family #deubiquitinases, revealing short linear motifs (SLiMs), contributing to specificity in complex assembly.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Ylva Ivarsson
US science after a year of Trump
"More than 7,800 research grants terminated or frozen. Some 25,000 scientists and personnel gone from agencies that oversee research." via @nature.com
Dark Age 2.0
"More than 7,800 research grants terminated or frozen. Some 25,000 scientists and personnel gone from agencies that oversee research." via @nature.com
Dark Age 2.0
January 21, 2026 at 7:11 PM
US science after a year of Trump
"More than 7,800 research grants terminated or frozen. Some 25,000 scientists and personnel gone from agencies that oversee research." via @nature.com
Dark Age 2.0
"More than 7,800 research grants terminated or frozen. Some 25,000 scientists and personnel gone from agencies that oversee research." via @nature.com
Dark Age 2.0
Reposted by Ylva Ivarsson
Very much looking forward to the next PMC seminar, featring Benjamin Turk and Giorgia Massacci: www.proteinmodules.org/online-semin...
January 7, 2026 at 12:12 PM
Very much looking forward to the next PMC seminar, featring Benjamin Turk and Giorgia Massacci: www.proteinmodules.org/online-semin...
Not sure if Trump getting the Nobel Prize medal from Machado is more embarrassing for Trump, Machado, the Norwegian Nobel Committee, or the USA as a country.
January 16, 2026 at 6:51 PM
Not sure if Trump getting the Nobel Prize medal from Machado is more embarrassing for Trump, Machado, the Norwegian Nobel Committee, or the USA as a country.
Reposted by Ylva Ivarsson
This is such hard news to process. Such an amazing scientist and inspiration for so many of us.
www.embl.org/news/embl-an...
www.embl.org/news/embl-an...
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
www.embl.org
January 16, 2026 at 6:01 PM
This is such hard news to process. Such an amazing scientist and inspiration for so many of us.
www.embl.org/news/embl-an...
www.embl.org/news/embl-an...
Very much looking forward to the next PMC seminar, featring Benjamin Turk and Giorgia Massacci: www.proteinmodules.org/online-semin...
January 7, 2026 at 12:12 PM
Very much looking forward to the next PMC seminar, featring Benjamin Turk and Giorgia Massacci: www.proteinmodules.org/online-semin...
Reposted by Ylva Ivarsson
Engineered base editors with reduced bystander editing through directed evolution - @geochurch.bsky.social @harvardmed.bsky.social @wyssinstitute.bsky.social go.nature.com/4qmupbv
Engineered base editors with reduced bystander editing through directed evolution - Nature Biotechnology
Base editors are made more precise through deaminase and gRNA engineering.
go.nature.com
December 18, 2025 at 4:35 PM
Engineered base editors with reduced bystander editing through directed evolution - @geochurch.bsky.social @harvardmed.bsky.social @wyssinstitute.bsky.social go.nature.com/4qmupbv
Reposted by Ylva Ivarsson
Last week, we wrapped up our Volkswagen Foundation–funded project with a wonderful final meeting in Uppsala, hosted by Ylva Ivarsson’s group. The photo shows members of our lab together with colleagues from the groups of @ivarssonlab.bsky.social , @hlouchova-lab.bsky.social and Florian Hollfelder.
December 12, 2025 at 10:49 AM
Last week, we wrapped up our Volkswagen Foundation–funded project with a wonderful final meeting in Uppsala, hosted by Ylva Ivarsson’s group. The photo shows members of our lab together with colleagues from the groups of @ivarssonlab.bsky.social , @hlouchova-lab.bsky.social and Florian Hollfelder.
Reposted by Ylva Ivarsson
Don't forget to catch out last seminar of the year on Monday Dec 8!
Catch our last seminar for the year on Dec 8 at 3pm CET! With Dr. Martin Rennie (@martinrennie.bsky.social), Jamal Fahoum (@hebrewuniversity.bsky.social), and Dr. Boglárka Zámbó (@zbobo2.bsky.social)
Register to attend: tinyurl.com/PMCseminar2
Previous seminars: www.youtube.com/@PMCModularity
Register to attend: tinyurl.com/PMCseminar2
Previous seminars: www.youtube.com/@PMCModularity
December 5, 2025 at 4:08 PM
Don't forget to catch out last seminar of the year on Monday Dec 8!
Reposted by Ylva Ivarsson
New paper “Proteome-wide model for human disease genetics” is now live at Nature Genetics: rdcu.be/eRu7K
popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:
popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:
November 24, 2025 at 2:53 PM
New paper “Proteome-wide model for human disease genetics” is now live at Nature Genetics: rdcu.be/eRu7K
popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:
popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:
Reposted by Ylva Ivarsson
Major new direction in the lab: hacking human cell biology with pathogen effectors (eORFs) - amazing collaboration with @miketilapia.bsky.social lab. Huge congrats to first authors Tomas & He & all co-authors! Check out the pre-print on @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...
www.biorxiv.org
November 18, 2025 at 2:51 PM
Major new direction in the lab: hacking human cell biology with pathogen effectors (eORFs) - amazing collaboration with @miketilapia.bsky.social lab. Huge congrats to first authors Tomas & He & all co-authors! Check out the pre-print on @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...
Reposted by Ylva Ivarsson
957 proposals were submitted in the latest round of ERC Synergy applications. They expect to fund 50 which means around 5% success rate. This is really not sustainable and a lot of people are likely avoiding doing this knowing how poor the chances are.
erc.europa.eu/news-events/...
erc.europa.eu/news-events/...
Applications for ERC Synergy Grants 2026: Facts and figures
The ERC Synergy Grants 2026 call closed for applications on 5 November 2025. These are the preliminary data on the submitted proposals:
erc.europa.eu
November 11, 2025 at 1:22 PM
957 proposals were submitted in the latest round of ERC Synergy applications. They expect to fund 50 which means around 5% success rate. This is really not sustainable and a lot of people are likely avoiding doing this knowing how poor the chances are.
erc.europa.eu/news-events/...
erc.europa.eu/news-events/...
Reposted by Ylva Ivarsson
profaff.fr
The new ProfAff database is up and running. Although there are still many things to improve, it is a major upgrade.
The new ProfAff database is up and running. Although there are still many things to improve, it is a major upgrade.
ProfAffv2 - Protein Affinity Database
profaff.fr
October 28, 2025 at 8:04 AM
profaff.fr
The new ProfAff database is up and running. Although there are still many things to improve, it is a major upgrade.
The new ProfAff database is up and running. Although there are still many things to improve, it is a major upgrade.
Reposted by Ylva Ivarsson
I have a PhD opening in my lab for an exiting project using base editor screens to find novel drug targets. Please help spread the word. candidate.hr-manager.net/ApplicationI...
PhD student position in the Cell Signaling and Cell Cycle group at the Danish Cancer Institute.
The Cell Signaling and Cell Cycle group, headed by Prof. Jakob Nilsson, is looking for a highly motivated and enthusiastic PhD student to establish novel CRISPR
candidate.hr-manager.net
October 23, 2025 at 4:18 PM
I have a PhD opening in my lab for an exiting project using base editor screens to find novel drug targets. Please help spread the word. candidate.hr-manager.net/ApplicationI...
Reposted by Ylva Ivarsson
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
Reposted by Ylva Ivarsson
🚨🚨🚨
Two super well-funded PhD grants from our MSCA Doctoral Network @evomg-dn.bsky.social at our lab at @melisupf.bsky.social, @crg.eu and the @evomg-bcn.bsky.social Program.
If you're excited about evolution, genomics and biomedical research, this is your DN! 😃
Further info: www.evomg-dn.eu and 👇
Two super well-funded PhD grants from our MSCA Doctoral Network @evomg-dn.bsky.social at our lab at @melisupf.bsky.social, @crg.eu and the @evomg-bcn.bsky.social Program.
If you're excited about evolution, genomics and biomedical research, this is your DN! 😃
Further info: www.evomg-dn.eu and 👇
EVOMG-DN
EvoMG-DN is a European Doctoral Network funded by the Horizon Europe Marie Skłodowska-Curie Actions (MSCA), composed of 14 beneficiaries and associated partners from both academic and non-academic sectors.
www.evomg-dn.eu
October 15, 2025 at 7:02 AM
🚨🚨🚨
Two super well-funded PhD grants from our MSCA Doctoral Network @evomg-dn.bsky.social at our lab at @melisupf.bsky.social, @crg.eu and the @evomg-bcn.bsky.social Program.
If you're excited about evolution, genomics and biomedical research, this is your DN! 😃
Further info: www.evomg-dn.eu and 👇
Two super well-funded PhD grants from our MSCA Doctoral Network @evomg-dn.bsky.social at our lab at @melisupf.bsky.social, @crg.eu and the @evomg-bcn.bsky.social Program.
If you're excited about evolution, genomics and biomedical research, this is your DN! 😃
Further info: www.evomg-dn.eu and 👇
Reposted by Ylva Ivarsson
new preprint: Ubiquitin is a protein modification linked with degradation but known to regulate other functions. Over 100k ubiquitination sites have been discovered and here we (@julianvangerwen.bsky.social + others) try to prioritize those most critical to the cell www.biorxiv.org/content/10.1...
The functional landscape of the human ubiquitinome
Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme...
www.biorxiv.org
October 9, 2025 at 7:07 AM
new preprint: Ubiquitin is a protein modification linked with degradation but known to regulate other functions. Over 100k ubiquitination sites have been discovered and here we (@julianvangerwen.bsky.social + others) try to prioritize those most critical to the cell www.biorxiv.org/content/10.1...
Reposted by Ylva Ivarsson
Don't forget to catch out next seminar on October 13 at 3pm CEST!
October 10, 2025 at 1:57 PM
Don't forget to catch out next seminar on October 13 at 3pm CEST!
Reposted by Ylva Ivarsson
Can't wait to see you all there!!
🚨🚨The GRC on Intrinsically Disordered Proteins #IDPs is back!! 🍝🧵🏔️Join us for cutting-edge IDP science, great discussions, and mountain views 🌄🍝
📅 June 21-26, 2026 | Les Diablerets, Switzerland
👉 Details & registration: grc.org/intrinsicall...
📅 June 21-26, 2026 | Les Diablerets, Switzerland
👉 Details & registration: grc.org/intrinsicall...
2026 Intrinsically Disordered Proteins Conference GRC
The 2026 Gordon Research Conference on Intrinsically Disordered Proteins will be held in Les Diablerets, Vaud (fr) Switzerland. Apply today to reserve your spot.
grc.org
October 3, 2025 at 1:40 PM
Can't wait to see you all there!!
Never thought I would say this, but I need a Dane.. novonordiskfonden.dk/grant/postdo...
Postdoctoral Fellowships at Uppsala University - 2026 - Novo Nordisk Fonden
novonordiskfonden.dk
October 2, 2025 at 5:11 PM
Never thought I would say this, but I need a Dane.. novonordiskfonden.dk/grant/postdo...
Finally out! Thrilled to share our collaboration with @kulathu.bsky.social, @orafurman.bsky.social, and N Davey. We screened auxiliary domains of USP family #deubiquitinases, revealing short linear motifs (SLiMs), contributing to specificity in complex assembly.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases
The ubiquitin-specific proteases (USPs) family is the largest family of human deubiquitinating enzymes (DUBs). While most USPs are agnostic to polyubiquitin linkage-type, their substrate specificity i...
www.biorxiv.org
September 22, 2025 at 1:28 PM
Finally out! Thrilled to share our collaboration with @kulathu.bsky.social, @orafurman.bsky.social, and N Davey. We screened auxiliary domains of USP family #deubiquitinases, revealing short linear motifs (SLiMs), contributing to specificity in complex assembly.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Ylva Ivarsson
Cool project with the Pless lab on disease-associated variants in a membrane protein, NALCN, that needs to be in complex to function. Most of our computational work was done by PhD student Aleks Panfilova.
After years in making, I am glad to be able to share our attempt on establishing a framework for combined functional and computational assessment of variant pathogenicity in the sodium leak channel NALCN:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
September 18, 2025 at 11:12 AM
Cool project with the Pless lab on disease-associated variants in a membrane protein, NALCN, that needs to be in complex to function. Most of our computational work was done by PhD student Aleks Panfilova.
Reposted by Ylva Ivarsson
Tune in to our next seminar on October 13 at 3pm CEST! We’ll hear from Dr. Cris Viéitez (@crisvieitez.bsky.social) and Dr. Patrick Brunner (@humboldtuni.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
September 15, 2025 at 10:29 AM
Tune in to our next seminar on October 13 at 3pm CEST! We’ll hear from Dr. Cris Viéitez (@crisvieitez.bsky.social) and Dr. Patrick Brunner (@humboldtuni.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
Reposted by Ylva Ivarsson
To protein designers (and others)
The Dept of Chemistry, Lund University & the Wallenberg Initiative for Materials Science for Sustainability is looking for an Assoc Senior Lecturer/Assist Professor in Biomolecular materials with a focus on de novo design and synthesis
lu.varbi.com/en/what:job/...
The Dept of Chemistry, Lund University & the Wallenberg Initiative for Materials Science for Sustainability is looking for an Assoc Senior Lecturer/Assist Professor in Biomolecular materials with a focus on de novo design and synthesis
lu.varbi.com/en/what:job/...
September 8, 2025 at 8:00 PM
To protein designers (and others)
The Dept of Chemistry, Lund University & the Wallenberg Initiative for Materials Science for Sustainability is looking for an Assoc Senior Lecturer/Assist Professor in Biomolecular materials with a focus on de novo design and synthesis
lu.varbi.com/en/what:job/...
The Dept of Chemistry, Lund University & the Wallenberg Initiative for Materials Science for Sustainability is looking for an Assoc Senior Lecturer/Assist Professor in Biomolecular materials with a focus on de novo design and synthesis
lu.varbi.com/en/what:job/...
Reposted by Ylva Ivarsson
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 Ylva Ivarsson
Leo Tianlai Chen and coauthors present PepMLM, an ESM-2–based protein language model that designs target-specific peptide binders from sequence alone, enabling binding and degradation of disease and viral proteins. www.nature.com/articles/s41...
Target sequence-conditioned design of peptide binders using masked language modeling - Nature Biotechnology
PepMLM designs peptide binders against diverse targets using masked language modeling.
www.nature.com
August 16, 2025 at 3:33 PM
Leo Tianlai Chen and coauthors present PepMLM, an ESM-2–based protein language model that designs target-specific peptide binders from sequence alone, enabling binding and degradation of disease and viral proteins. www.nature.com/articles/s41...