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
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...
Reposted by Ylva Ivarsson
We’re looking for curious, innovative science leaders at EMBL Heidelberg! 🔬🧬🦠
Join a vibrant, interdisciplinary community where collaboration and innovation are nurtured at all levels.
Take a look at these four open positions 👇
Join a vibrant, interdisciplinary community where collaboration and innovation are nurtured at all levels.
Take a look at these four open positions 👇
August 7, 2025 at 8:28 AM
We’re looking for curious, innovative science leaders at EMBL Heidelberg! 🔬🧬🦠
Join a vibrant, interdisciplinary community where collaboration and innovation are nurtured at all levels.
Take a look at these four open positions 👇
Join a vibrant, interdisciplinary community where collaboration and innovation are nurtured at all levels.
Take a look at these four open positions 👇
Reposted by Ylva Ivarsson
We are looking for a PhD student in (mostly )wet-lab biochemistry to work on short linear motifs, intrinsically disordered regions, in the context of the Marie Curie network "IDPro". More info an apply here: www.uu.se/en/about-uu/...
PhD student in Biochemistry - Uppsala University
PhD student in Biochemistry, Disciplinary Domain of Science and Technology, Faculty of Chemistry, Department of Chemistry - BMC, Uppsala University
www.uu.se
June 30, 2025 at 8:39 AM
We are looking for a PhD student in (mostly )wet-lab biochemistry to work on short linear motifs, intrinsically disordered regions, in the context of the Marie Curie network "IDPro". More info an apply here: www.uu.se/en/about-uu/...
Reposted by Ylva Ivarsson
Predicting the protein interaction landscape of a free-living bacterium with pooled-AlphaFold3 https://www.biorxiv.org/content/10.1101/2025.07.01.662654v1
July 5, 2025 at 4:07 AM
Predicting the protein interaction landscape of a free-living bacterium with pooled-AlphaFold3 https://www.biorxiv.org/content/10.1101/2025.07.01.662654v1
Reposted by Ylva Ivarsson
And of course, we could not have done this without NIH funding that has been critical for supporting my students’ training and my career, and for giving us the resources to shed light on some aspects of the molecular basis of human diseases.
Excited to see this paper out in its final form, and huge congrats to first author Ziyuan (Jason) Jiang just a week before his thesis defense. This work has become an invaluable resource in our lab for SHP2 projects, and we hope it resonates with the whole field.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
July 1, 2025 at 1:05 PM
And of course, we could not have done this without NIH funding that has been critical for supporting my students’ training and my career, and for giving us the resources to shed light on some aspects of the molecular basis of human diseases.
Reposted by Ylva Ivarsson
Variant characterization in the intrinsically disordered human proteome - here is how we did it using short linear motif prediction, AlphaFold, and experimentation. Check out our preprint: www.biorxiv.org/cgi/content/...
Variant characterization in the intrinsically disordered human proteome
Variant effect prediction remains a key challenge to resolve in precision medicine. Sophisticated computational models that exploit sequence conservation and structure are increasingly successful in t...
www.biorxiv.org
July 1, 2025 at 5:34 AM
Variant characterization in the intrinsically disordered human proteome - here is how we did it using short linear motif prediction, AlphaFold, and experimentation. Check out our preprint: www.biorxiv.org/cgi/content/...
Reposted by Ylva Ivarsson
Do you have experience in mechanistic modelling of biological systems and want to do a postdoc with an interdisciplinary team on developing Digital Twins for rare disease? We have the job for you! Check it out below - deadline July 13th, online interviews 24th July.
Your weekly reminder that there is a really fun post @ebi.embl.org in our group in collaboration with Sheriff Rahuman (@biomodels) and Ellie McDonagh (@opentargets) to create Digital Twins for rare disease using multiomics, executable modelling and AI. Join our interdisciplinary team! Deadline 13/07
Exciting opportunity at the forefront of network biology, multiomics, AI and DT. Deadline 13th July! embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
June 30, 2025 at 1:47 PM
Do you have experience in mechanistic modelling of biological systems and want to do a postdoc with an interdisciplinary team on developing Digital Twins for rare disease? We have the job for you! Check it out below - deadline July 13th, online interviews 24th July.
We are looking for a PhD student in (mostly )wet-lab biochemistry to work on short linear motifs, intrinsically disordered regions, in the context of the Marie Curie network "IDPro". More info an apply here: www.uu.se/en/about-uu/...
PhD student in Biochemistry - Uppsala University
PhD student in Biochemistry, Disciplinary Domain of Science and Technology, Faculty of Chemistry, Department of Chemistry - BMC, Uppsala University
www.uu.se
June 30, 2025 at 8:39 AM
We are looking for a PhD student in (mostly )wet-lab biochemistry to work on short linear motifs, intrinsically disordered regions, in the context of the Marie Curie network "IDPro". More info an apply here: www.uu.se/en/about-uu/...
Reposted by Ylva Ivarsson
A major KI initiative to recruit new assistant professors with outstanding proposals in all areas of medicine, biomedicine and public health. We offer an amazing research environment, great colleagues and generous startup packages. Check it out and get working on your applications! (repost please!)
Applications are now open! We are recruiting 20 Assistant Professors in a wide range of subject areas. We're looking for early-career researchers with strong scientific merits and future potential.
🔗 All positions: ki.se/en/about-ki/...
🔗 All positions: ki.se/en/about-ki/...
June 25, 2025 at 10:08 AM
A major KI initiative to recruit new assistant professors with outstanding proposals in all areas of medicine, biomedicine and public health. We offer an amazing research environment, great colleagues and generous startup packages. Check it out and get working on your applications! (repost please!)