Ylva Ivarsson
Professor at Department of Chemistry for Life Sciences; Biochemistry; Ivarsson group
- Telephone:
- +46 18 471 40 38
- E-mail:
- Ylva.Ivarsson@kemi.uu.se
- Visiting address:
- Husargatan 3
752 37 Uppsala - Postal address:
- Box 576
75123 Uppsala
Short presentation
Ylva Ivarsson is a full professor of Biochemistry with a research team funded by the Swedish Research Council, and EU Marie Curie ETN and others. The research of the group is interdisciplinary and combines biochemical and biophysical methods with bioinformatics and cell-based assays to study motif-based protein-protein interactions.
Biography
Ylva Ivarsson received her PhD in Biochemistry from Uppsala University in 2006, working with Bengt Mannervik. She then joined Maurizio Brunori’s group at the University of Rome “La Sapienza,” where she studied protein folding and misfolding. After two and a half years in Italy, she moved to the Catholic University of Leuven in Belgium to work with Pascale Zimmermann on protein–phospholipid interactions supported by an EMBO long term fellowship.
In 2012, Ylva joined the Donnelly Centre at the University of Toronto in a shared appointment between the groups of Sachdev Sidhu and Philip M. Kim. There, she pioneered proteomic peptide phage display, ProP-PD, a powerful approach for large-scale discovery of protein–peptide interactions. The method opened new possibilities for systematically mapping the short linear motif interactions that shape cellular signaling.
In 2013, Ylva was awarded a Young Investigator grant from the Swedish Research Council and established her independent research group at the Department of Chemistry, Uppsala University. Since then, her group has received several prestigious grants, she was granted tenure in 2017 and promoted to full professor in 2020. Currently, she is also heading the Biochemistry research unit.
Research
The Ivarsson group explores the molecular interaction networks that govern cellular signal transduction, with a particular focus on the intrinsically disordered regions of the proteome. These flexible, motif-rich regions have long been difficult to interpret, yet they encode many of the interaction switches that control cellular behavior. By combining ProP-PD with complementary experimental and computational approaches, and through close collaboration Dr Norman Davey, the group provides functional information for intrinsically disordered regions across both the human and viral proteomes. This work helps reveal how short linear motifs (SLiMs) connect proteins into signaling networks, how viruses hijack host cellular machinery, and how previously uncharacterized disordered regions contribute to biology and disease. The data is made available through the ProP-PD portal: https://slim-tools.org/proppd/
The most recent news from the group of is the release of ASHI: An Atlas of Short Linear Motif-Mediated Human Protein-Protein Interactions, which represent a massive, collaborative work that vastly expands the human SLiM-based interactome: https://www.biorxiv.org/content/10.64898/2026.07.03.735260v1
Prof. Ivarsson is currently coordinating IDPro “Intrinsically disordered proteins in health and disease". IDPro is a Doctoral Network under the Horizon-Europe Marie Skłodowska-Curie Actions focused on aims to deepen our understanding of the molecular principles that govern interactions and regulatory mechanisms within cellular networks. For more information see https://idpro.elte.hu/network

Publications
Recent publications
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Part of Nature Communications, 2026
- DOI for Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases
- Download full text (pdf) of Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases
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The evolving landscape of protein structure and molecular recognition
Part of Trends in Biochemical Sciences (TIBS), p. 525-528, 2026
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Part of Nature Communications, 2026
- DOI for Proviral NUP153 binding to viral proteins and RNA regulates structural-nonstructural protein ratios in orthoflavivirus infection
- Download full text (pdf) of Proviral NUP153 binding to viral proteins and RNA regulates structural-nonstructural protein ratios in orthoflavivirus infection
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A tryptophan-phenylalanine binding motif for the histone methyltransferases MLL4 and MLL3
Part of Journal of Biological Chemistry, 2026
- DOI for A tryptophan-phenylalanine binding motif for the histone methyltransferases MLL4 and MLL3
- Download full text (pdf) of A tryptophan-phenylalanine binding motif for the histone methyltransferases MLL4 and MLL3
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Part of Nucleic Acids Research, 2026
- DOI for NUP98 regulates orthoflavivirus replication through interaction with vRNA and can be targeted for antiviral purposes
- Download full text (pdf) of NUP98 regulates orthoflavivirus replication through interaction with vRNA and can be targeted for antiviral purposes
All publications
Articles in journal
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Part of Nature Communications, 2026
- DOI for Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases
- Download full text (pdf) of Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases
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The evolving landscape of protein structure and molecular recognition
Part of Trends in Biochemical Sciences (TIBS), p. 525-528, 2026
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Part of Nature Communications, 2026
- DOI for Proviral NUP153 binding to viral proteins and RNA regulates structural-nonstructural protein ratios in orthoflavivirus infection
- Download full text (pdf) of Proviral NUP153 binding to viral proteins and RNA regulates structural-nonstructural protein ratios in orthoflavivirus infection
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A tryptophan-phenylalanine binding motif for the histone methyltransferases MLL4 and MLL3
Part of Journal of Biological Chemistry, 2026
- DOI for A tryptophan-phenylalanine binding motif for the histone methyltransferases MLL4 and MLL3
- Download full text (pdf) of A tryptophan-phenylalanine binding motif for the histone methyltransferases MLL4 and MLL3
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Part of Nucleic Acids Research, 2026
- DOI for NUP98 regulates orthoflavivirus replication through interaction with vRNA and can be targeted for antiviral purposes
- Download full text (pdf) of NUP98 regulates orthoflavivirus replication through interaction with vRNA and can be targeted for antiviral purposes
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Part of Archives of Biochemistry and Biophysics, 2025
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Part of Nature Communications, 2025
- DOI for High-throughput investigation of cyclin docking interactions reveals the complexity of motif binding determinants
- Download full text (pdf) of High-throughput investigation of cyclin docking interactions reveals the complexity of motif binding determinants
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Part of Biochimica et Biophysica Acta - Proteins and Proteomics, 2025
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Defining short linear motif binding determinants by phage display-based deep mutational scanning
Part of Protein Science, 2025
- DOI for Defining short linear motif binding determinants by phage display-based deep mutational scanning
- Download full text (pdf) of Defining short linear motif binding determinants by phage display-based deep mutational scanning
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Part of Biology Direct, 2025
- DOI for Elucidation of short linear motif‑based interactions of the MIT and rhodanese domains of the ubiquitin‑specific protease 8
- Download full text (pdf) of Elucidation of short linear motif‑based interactions of the MIT and rhodanese domains of the ubiquitin‑specific protease 8
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Proteome-scale characterisation of motif-based interactome rewiring by disease mutations
Part of Molecular Systems Biology, p. 1025-1048, 2024
- DOI for Proteome-scale characterisation of motif-based interactome rewiring by disease mutations
- Download full text (pdf) of Proteome-scale characterisation of motif-based interactome rewiring by disease mutations
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Exploring the short linear motif-mediated protein-protein interactions of CrkL through ProP-PD
Part of Biochemical and Biophysical Research Communications - BBRC, 2024
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Part of Nature Communications, 2024
- DOI for ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers
- Download full text (pdf) of ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers
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Part of Structure, 2024
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Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
Part of Nature Communications, 2023
- DOI for Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
- Download full text (pdf) of Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
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Part of Current opinion in structural biology, 2023
- DOI for The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome
- Download full text (pdf) of The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome
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Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions
Part of Molecular Systems Biology, 2023
- DOI for Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions
- Download full text (pdf) of Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions
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Part of Analytical Biochemistry, 2023
- DOI for Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions
- Download full text (pdf) of Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions
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Part of Nature Communications, 2023
- DOI for Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets
- Download full text (pdf) of Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets
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Part of Biochemistry, p. 1594-1607, 2023
- DOI for Elucidation of Short Linear Motif-Based Interactions of the FERM Domains of Ezrin, Radixin, Moesin, and Merlin
- Download full text (pdf) of Elucidation of Short Linear Motif-Based Interactions of the FERM Domains of Ezrin, Radixin, Moesin, and Merlin
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Motif-dependent binding on the intervening domain regulates O-GlcNAc transferase
Part of Nature Chemical Biology, p. 1423-1431, 2023
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ProP-PD for proteome-wide motif-mediated interaction discovery
Part of TIBS -Trends in Biochemical Sciences. Regular ed., p. 547-548, 2022
- DOI for ProP-PD for proteome-wide motif-mediated interaction discovery
- Download full text (pdf) of ProP-PD for proteome-wide motif-mediated interaction discovery
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Proteome-scale mapping of binding sites in the unstructured regions of the human proteome
Part of Molecular Systems Biology, 2022
- DOI for Proteome-scale mapping of binding sites in the unstructured regions of the human proteome
- Download full text (pdf) of Proteome-scale mapping of binding sites in the unstructured regions of the human proteome
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A Syntenin Inhibitor Blocks Endosomal Entry of SARS-CoV-2 and a Panel of RNA Viruses
Part of Viruses, 2022
- DOI for A Syntenin Inhibitor Blocks Endosomal Entry of SARS-CoV-2 and a Panel of RNA Viruses
- Download full text (pdf) of A Syntenin Inhibitor Blocks Endosomal Entry of SARS-CoV-2 and a Panel of RNA Viruses
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Part of eLIFE, 2022
- DOI for Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition
- Download full text (pdf) of Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition
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Part of Science Signaling, 2021
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Part of Nature Communications, 2021
- DOI for Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities
- Download full text (pdf) of Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities
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Integrated analysis of Shank1 PDZ interactions with C-terminal and internal binding motifs
Part of Current Research in Structural Biology, p. 41-50, 2021
- DOI for Integrated analysis of Shank1 PDZ interactions with C-terminal and internal binding motifs
- Download full text (pdf) of Integrated analysis of Shank1 PDZ interactions with C-terminal and internal binding motifs
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A High-Affinity Peptide Ligand Targeting Syntenin Inhibits Glioblastoma
Part of Journal of Medicinal Chemistry, p. 1423-1434, 2021
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Part of Biochimica et Biophysica Acta - General Subjects, 2020
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Systematic Discovery of Short Linear Motifs Decodes Calcineurin Phosphatase Signaling
Part of Molecular Cell, p. 342-+, 2020
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Part of Journal of Molecular Biology, p. 5920-5937, 2020
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Genetically Encoded Cyclic Peptide Phage Display Libraries
Part of ACS CENTRAL SCIENCE, p. 336-338, 2020
- DOI for Genetically Encoded Cyclic Peptide Phage Display Libraries
- Download full text (pdf) of Genetically Encoded Cyclic Peptide Phage Display Libraries
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Systematic identification of recognition motifs for the hub protein LC8
Part of Life Science Alliance, 2019
- DOI for Systematic identification of recognition motifs for the hub protein LC8
- Download full text (pdf) of Systematic identification of recognition motifs for the hub protein LC8
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Editorial overview: Folding and binding
Part of Current opinion in structural biology, p. 139-140, 2019
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A Consensus Binding Motif for the PP4 Protein Phosphatase
Part of Molecular Cell, p. 953-964000000, 2019
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Proteome‐wide analysis of phospho‐regulated PDZ domain interactions
Part of Molecular Systems Biology, 2018
- DOI for Proteome‐wide analysis of phospho‐regulated PDZ domain interactions
- Download full text (pdf) of Proteome‐wide analysis of phospho‐regulated PDZ domain interactions
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High-throughput discovery of functional disordered regions
Part of Molecular Systems Biology, 2018
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Part of Biochemistry, p. 66-71, 2018
- DOI for The Sign of Nuclear Magnetic Resonance Chemical Shift Difference as a Determinant of the Origin of Binding Selectivity: Elucidation of the Position Dependence of Phosphorylation in Ligands Binding to Scribble PDZ1
- Download full text (pdf) of The Sign of Nuclear Magnetic Resonance Chemical Shift Difference as a Determinant of the Origin of Binding Selectivity: Elucidation of the Position Dependence of Phosphorylation in Ligands Binding to Scribble PDZ1
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Part of The FEBS Journal, p. 485-498, 2017
- DOI for Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome
- Download full text (pdf) of Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome
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PP2A-B' holoenzyme substrate recognition, regulation and role in cytokinesis
Part of Cell Discovery, 2017
- DOI for PP2A-B' holoenzyme substrate recognition, regulation and role in cytokinesis
- Download full text (pdf) of PP2A-B' holoenzyme substrate recognition, regulation and role in cytokinesis
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Part of Molecular Biology of the Cell, p. 3727-3727, 2017
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A novel role for the Calcineurin phosphatase at the nuclear pore
Part of Molecular Biology of the Cell, p. 3727-3727, 2017
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Part of Molecular Biology of the Cell, p. 3727-3727, 2017
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Uncovering Novel Substrates and Functions for the Calcineurin Phosphatase in Human Cells
Part of The FASEB Journal, 2017
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Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin
Part of FEBS Letters, p. 3-12, 2016
- DOI for Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin
- Download full text (pdf) of Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin
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Pooled screening for antiproliferative inhibitors of protein-protein interactions.
Part of Nature Chemical Biology, p. 275-281, 2016
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Frizzled 7 and PIP2 binding by syntenin PDZ2 domain supports Frizzled 7 trafficking and signalling
Part of Nature Communications, 2016
- DOI for Frizzled 7 and PIP2 binding by syntenin PDZ2 domain supports Frizzled 7 trafficking and signalling
- Download full text (pdf) of Frizzled 7 and PIP2 binding by syntenin PDZ2 domain supports Frizzled 7 trafficking and signalling
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Part of Scientific Reports, 2016
- DOI for Improved affinity at the cost of decreased specificity: a recurring theme in PDZ-peptide interactions.
- Download full text (pdf) of Improved affinity at the cost of decreased specificity: a recurring theme in PDZ-peptide interactions.
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Uncovering novel substrates and functions for the calcineurin phosphatase in human cells.
Part of Molecular Biology of the Cell, 2016
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Selectivity of Aggregation-Determining Interactions
Part of Journal of Molecular Biology, p. 236-247, 2015
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Structural basis of Sorcin-mediated calcium-dependent signal transduction
Part of Scientific Reports, 2015
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Part of Proceedings of the National Academy of Sciences of the United States of America, p. 2542-2547, 2014
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A Structural Portrait of the PDZ Domain Family
Part of Journal of Molecular Biology, p. 3509-3519, 2014
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Part of Journal of Peptide Science, 2014
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Part of PLOS ONE, 2013
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Part of PloS one, 2013
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Part of Journal of Cell Science, p. 1129-1140, 2012
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Part of FEBS Letters, p. 1445-1451, 2012
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Plasticity of PDZ domains in ligand recognition and signaling
Part of FEBS Letters, p. 2638-47, 2012
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Syndecan-syntenin-ALIX regulates the biogenesis of exosomes
Part of Nature cell biology, p. 677-685, 2012
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Part of Journal of Biological Chemistry, p. 44669-78, 2011
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Part of Nature medicine, p. 720-725, 2011
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Structural diversity of PDZ-lipid interactions
Part of ChemBioChem, p. 456-67, 2010
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Part of Nature Structural & Molecular Biology, p. 1431-1437, 2010
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Folding and stability of globular proteins and implications for function
Part of Current opinion in structural biology, p. 3-7, 2009
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Part of Journal of the American Chemical Society, p. 11727-33, 2009
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Part of European Biophysics Journal, p. 721-728, 2008
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Folding and misfolding in a naturally occurring circularly permuted PDZ domain
Part of Journal of Biological Chemistry, p. 8954-60, 2008
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The folding pathway of an engineered circularly permuted PDZ domain
Part of Protein Engineering Design & Selection, p. 155-160, 2008
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Part of Biochimica et Biophysica Acta - General Subjects, p. 1374-1381, 2007
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An on-pathway intermediate in the folding of a PDZ domain
Part of Journal of Biological Chemistry, p. 8568-8572, 2007
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Mechanism of Na(+) binding to thrombin resolved by ultra-rapid kinetics
Part of Biophysical Chemistry, p. 111-114, 2007
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Part of Proceedings of the National Academy of Sciences of the United States of America, p. 4876-4881, 2006
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Part of Protein Engineering Design and Selection, p. 607-616, 2006
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Part of Proceedings of the National Academy of Sciences of the USA, p. 4876-4881, 2006
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Part of FEBS Journal, 2005
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Part of Protein Eng Des Sel, p. 607-16, 2005
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Part of Journal of Biological Chemistry, p. 8733-8738, 2003
Articles, review/survey
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SLiM-binding pockets: an attractive target for broad-spectrum antivirals
Part of TIBS -Trends in Biochemical Sciences. Regular ed., p. 420-427, 2023
- DOI for SLiM-binding pockets: an attractive target for broad-spectrum antivirals
- Download full text (pdf) of SLiM-binding pockets: an attractive target for broad-spectrum antivirals
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How viral proteins bind short linear motifs and intrinsically disordered domains
Part of Essays in Biochemistry, p. 935-944, 2022
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Part of Biochemical Journal, p. 1-22, 2022
- DOI for p Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs
- Download full text (pdf) of p Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs
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Affinity and specificity of motif-based protein-protein interactions
Part of Current opinion in structural biology, p. 26-33, 2019
- DOI for Affinity and specificity of motif-based protein-protein interactions
- Download full text (pdf) of Affinity and specificity of motif-based protein-protein interactions
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Part of Proteomes, 2016
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Part of Cell Communication and Signaling, 2015
- DOI for High-throughput methods for identification of protein-protein interactions involving short linear motifs
- Download full text (pdf) of High-throughput methods for identification of protein-protein interactions involving short linear motifs
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Interaction Analysis through Proteomic Phage Display
Part of BioMed Research International, p. 176172, 2014
- DOI for Interaction Analysis through Proteomic Phage Display
- Download full text (pdf) of Interaction Analysis through Proteomic Phage Display
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Identification and characterization of protein folding intermediates
Part of Biophysical Chemistry, p. 105-113, 2007
Chapters in book
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Identification of PDZ Interactions by Proteomic Peptide Phage Display
Part of PDZ Mediated Interactions, p. 41-60, Springer Nature, 2021
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Identification of Cellular Protein-Protein Interactions
Part of INHIBITORS OF PROTEIN-PROTEIN INTERACTIONS, p. 1-39, Royal Society of Chemistry, 2021
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Part of Toxicology of Glutathione Transferases, p. 47-69, CRC Taylor & Francis, Boca Raton, 2006
Manuscripts (preprints)
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Tick-borne flaviviruses recruits the pro viral factor NUP153 to the replication site
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Systematic discovery of short linear motif binding across human E3 ubiquitin ligases
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Proteome-scale identification of short linear binding motifs for the BTB-KELCH E3 ligase family
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An Atlas of Short Linear Motif Mediated Human Protein-Protein Interactions