Ylva Ivarsson

Can't wait to see you all there!!

Postdoctoral Fellowships at Uppsala University - 2026 - Novo Nordisk Fonden

Never thought I would say this, but I need a Dane.. novonordiskfonden.dk/grant/postdo...

Fabulous work by Aimiliani Konstantinou, together with three other #UBIMOTIF members Alicia Córdova-Pérez, Julia K. Varga & Maximilian Vieler. #CYLD, #USP7, #USP11, #USP20, #USP22, #USP33

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...

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...

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.

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

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/...

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

Target sequence-conditioned design of peptide binders using masked language modeling - Nature Biotechnology PepMLM designs peptide binders against diverse targets using masked language modeling.

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...

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 👇

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

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/...

Predicting the protein interaction landscape of a free-living bacterium with pooled-AlphaFold3 https://www.biorxiv.org/content/10.1101/2025.07.01.662654v1

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.

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...

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/...

.. more information about the IDPro network here: idpro.elte.hu

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.

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

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/...

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!)

It's June 20 in New Zealand, which means it's the last day to have your abstract considered for oral presentations at the IUBMB Focussed Meeting on kinases and pseudokinases!

Sequence-based prediction of condensate composition reveals that specificity can emerge from multivalent interactions among disordered regions https://www.biorxiv.org/content/10.1101/2025.06.13.659429v1

Characterizing protein sequence determinants of nuclear condensates by high-throughput pooled imaging with CondenSeq Nature Methods - CondenSeq is an imaging-based, high-throughput platform for characterizing condensate formation within the nuclear environment, uncovering the protein sequence features that...

In the nucleus, many intrinsically disordered proteins (IDPs) form condensates. What IDP sequence features drive this behavior? We developed CondenSeq, a high-throughput approach to measure nuclear condensate formation, and applied it to ~14,000 IDPs to find out!

rdcu.be/eq975

“The search is on for 25 researchers from around the world in Lund University’s largest ever international recruitment drive. The main focus will be on AI research and other areas in which the University has a strategic focus.”

www.lunduniversity.lu.se/article/lund...

AlphaFold models of host-pathogen interactions elucidate the prevalence and structural modes of molecular mimicry Pathogens exploit host cellular machinery through protein-protein interactions (PPIs), often using molecular mimicry to hijack host cellular processes. While there have been thousands of host-pathogen...

New lab preprint - Delora Baptista tested AlphaFold 2 and 3 for the prediction of structures of host-pathogen interactions and then applied these to study convergence of binding and molecular mimicry in host-pathogen vs. host-host interactions.
www.biorxiv.org/content/10.1...

"Journal name : POSITIF JOURNAL - we can publish papers of all subjects." Very positive indeed.

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)

Sarah Shammas (University of Oxford):Opportunities in DNA binding provided by protein disorder Sonia Longhi (AFMB Marseille): Intrinsic disorder, phase transitions and fibril formation by the Henipavirus V and W proteins: a new hallmark of viral pathogenesis?

IDPSeminars is back with another seminar this week from @sarahshammas.bsky.social and @sonia-longhi.bsky.social!

Come hear about transcriptional regulation and viral pathogenesis!

Thursday June 5th!
PST 10 am EST 1 pm CET 7 pm!

Info: idpseminars.com
Signup form: forms.gle/3yCHeYvuuqLh...

When you ask ChatGTP for advices on what not to do you get honest advices 😂 "Avoid becoming a dean or high-level university administrator, it could reduce the ability to do research and publish. While these roles bring influence, they often pull scientists away from the bench and their networks."

Tiselius Symposium 28 August 2025, Uppsala

Happy to announce the 2025 Tiselius symposium in Uppsala, August 28. Excellent line up of speakers including Lori Passmore @lapassmore.bsky.social, Katja Luck @katjaluck.bsky.social, Markku Varjosalo @varjosal.bsky.social and Arne Elofsson. No fee & short talk slots available tiseliussymposium.org

The genetic architecture of an allosteric hormone receptor Many proteins function as switches, detecting chemicals and transducing their concentrations into cellular responses. Receptor switches are key to the integration of environmental signals, yet it is n...

1 plant hormone receptor ☘️
3,500 mutants, to single-site saturation 🧬
>45,000 binding and abundance measurements 📶

Very happy to present our latest work – where deep mutational scanning meets the world of small molecules.



www.biorxiv.org/content/10.1...



With @benlehner.bsky.social

[1/7]