Alireza Mashaghi
@alirezamashaghi.bsky.social
Scientist, Physician, University Professor (UHD) at Leiden University, Scientist at Harvard, ETH Zürich Alumni; Views my own.
Website: https://www.mashaghilab.org
Website: https://www.mashaghilab.org
Our protocol on "Scanning probe microscopy for rheological analysis of biomolecular condensates" is now available for interested users!
doi.org/10.1016/j.xp...
#ChemSky #Biphysics #Biomolecular_Condensates #IDP #Rheology #AFM
doi.org/10.1016/j.xp...
#ChemSky #Biphysics #Biomolecular_Condensates #IDP #Rheology #AFM
November 10, 2025 at 5:22 PM
Our protocol on "Scanning probe microscopy for rheological analysis of biomolecular condensates" is now available for interested users!
doi.org/10.1016/j.xp...
#ChemSky #Biphysics #Biomolecular_Condensates #IDP #Rheology #AFM
doi.org/10.1016/j.xp...
#ChemSky #Biphysics #Biomolecular_Condensates #IDP #Rheology #AFM
Vasily from our team was invited to present at the #NRRN meeting on “Conformational Dynamics and Chromatin Assembly of #Glucocorticoid Receptor Using Topological Modeling and Single-Molecule Analysis.” Looking forward to connecting with researchers on advances in nuclear receptor research.
#ChemSky
#ChemSky
November 6, 2025 at 5:42 PM
Vasily from our team was invited to present at the #NRRN meeting on “Conformational Dynamics and Chromatin Assembly of #Glucocorticoid Receptor Using Topological Modeling and Single-Molecule Analysis.” Looking forward to connecting with researchers on advances in nuclear receptor research.
#ChemSky
#ChemSky
We discovered that the "orphan" nuclear receptor Nur77 binds DNA under regulation by #glucocorticoid receptor & glucocorticoids. The synthetic glucocorticoid dexamethasone directly interacts with Nur77, revealing a new function for this drug & a potential ligand for Nur77.
doi.org/10.1101/2025...
doi.org/10.1101/2025...
October 29, 2025 at 8:08 AM
We discovered that the "orphan" nuclear receptor Nur77 binds DNA under regulation by #glucocorticoid receptor & glucocorticoids. The synthetic glucocorticoid dexamethasone directly interacts with Nur77, revealing a new function for this drug & a potential ligand for Nur77.
doi.org/10.1101/2025...
doi.org/10.1101/2025...
We’re excited to share our new #PyMOL plugin for protein topology analysis, now available!
doi.org/10.1101/2025...
Link to the report and the GitHub repository:
We’d appreciate your feedback — please try it out in PyMOL and report any bugs or suggestions!
#ChemSky #IDP #Topology #Bioinformatics
doi.org/10.1101/2025...
Link to the report and the GitHub repository:
We’d appreciate your feedback — please try it out in PyMOL and report any bugs or suggestions!
#ChemSky #IDP #Topology #Bioinformatics
October 23, 2025 at 7:09 AM
We’re excited to share our new #PyMOL plugin for protein topology analysis, now available!
doi.org/10.1101/2025...
Link to the report and the GitHub repository:
We’d appreciate your feedback — please try it out in PyMOL and report any bugs or suggestions!
#ChemSky #IDP #Topology #Bioinformatics
doi.org/10.1101/2025...
Link to the report and the GitHub repository:
We’d appreciate your feedback — please try it out in PyMOL and report any bugs or suggestions!
#ChemSky #IDP #Topology #Bioinformatics
An interview with Stanford scientist Jonathan Chen on Medical #AI!
Also, see the piece we co-authored on Statistical #Physics and its applications in #Medicine:
pubmed.ncbi.nlm.nih.gov/33228143/
Also, see the piece we co-authored on Statistical #Physics and its applications in #Medicine:
pubmed.ncbi.nlm.nih.gov/33228143/
October 15, 2025 at 4:24 PM
An interview with Stanford scientist Jonathan Chen on Medical #AI!
Also, see the piece we co-authored on Statistical #Physics and its applications in #Medicine:
pubmed.ncbi.nlm.nih.gov/33228143/
Also, see the piece we co-authored on Statistical #Physics and its applications in #Medicine:
pubmed.ncbi.nlm.nih.gov/33228143/
Our postdoctoral researcher Aida Naghilou presented our lab’s development of SPM-based technology for biomolecular condensate analysis at the Erwin Schrödinger Institute during the workshop “Charged Soft Matter: Bridging Theory and Experiment”!
www.youtube.com/playlist?lis...
#ChemSky #SoftMatter
www.youtube.com/playlist?lis...
#ChemSky #SoftMatter
October 14, 2025 at 1:13 PM
Our postdoctoral researcher Aida Naghilou presented our lab’s development of SPM-based technology for biomolecular condensate analysis at the Erwin Schrödinger Institute during the workshop “Charged Soft Matter: Bridging Theory and Experiment”!
www.youtube.com/playlist?lis...
#ChemSky #SoftMatter
www.youtube.com/playlist?lis...
#ChemSky #SoftMatter
We recently had some fun with protamine, which we used to model the Aggregate-to-Condensate transition in polyelectrolyte systems!
pubs.acs.org/doi/10.1021/...
#ChemSky #Bioengineering
pubs.acs.org/doi/10.1021/...
#ChemSky #Bioengineering
Protamine Drives Liquid and Solid Condensation of DNA and Glycosaminoglycans
Phase-separated biomolecular condensates play a crucial role in cellular organization. In the nucleus, phase separation regulates the assembly and function of nuclear proteins and the genome. Here, we...
pubs.acs.org
September 23, 2025 at 7:32 AM
We recently had some fun with protamine, which we used to model the Aggregate-to-Condensate transition in polyelectrolyte systems!
pubs.acs.org/doi/10.1021/...
#ChemSky #Bioengineering
pubs.acs.org/doi/10.1021/...
#ChemSky #Bioengineering
We recently carried out the first single-molecule analysis of protein folding & unfolding in a cytosolic environment using optical tweezers—moving beyond simplistic buffer conditions to study proteins where they actually function.
advanced.onlinelibrary.wiley.com/doi/10.1002/...
#ChemSky #Biophysics
advanced.onlinelibrary.wiley.com/doi/10.1002/...
#ChemSky #Biophysics
Cytosolic Interactome Protects Against Protein Unfolding in a Single Molecule Experiment
Single molecule experiments aimed at probing protein folding are typically performed in buffer conditions and cannot therefore be representative of the multi-faceted and complex cooperative interacti...
advanced.onlinelibrary.wiley.com
September 11, 2025 at 5:51 AM
We recently carried out the first single-molecule analysis of protein folding & unfolding in a cytosolic environment using optical tweezers—moving beyond simplistic buffer conditions to study proteins where they actually function.
advanced.onlinelibrary.wiley.com/doi/10.1002/...
#ChemSky #Biophysics
advanced.onlinelibrary.wiley.com/doi/10.1002/...
#ChemSky #Biophysics
PhD student Vasily Akulov from our group is presenting our collaborative research with Eva Estébanez-Perpiñá’s group at the EMBO Workshop in Palermo, Italy!
meetings.embo.org/event/25-str...
#EMBO #StructuralBiology #IDP #Topology
meetings.embo.org/event/25-str...
#EMBO #StructuralBiology #IDP #Topology
September 9, 2025 at 8:24 PM
PhD student Vasily Akulov from our group is presenting our collaborative research with Eva Estébanez-Perpiñá’s group at the EMBO Workshop in Palermo, Italy!
meetings.embo.org/event/25-str...
#EMBO #StructuralBiology #IDP #Topology
meetings.embo.org/event/25-str...
#EMBO #StructuralBiology #IDP #Topology
On extracellular #biomolecular condensates!
We demonstrate that phase-separated #condensate #droplets can form and function in the #extracellular environment and may interact with cells!
www.sciencedirect.com/science/arti...
#CellBiology #Biophysics #ChemicalEngineering #SyntheticBiology #ChemSky
We demonstrate that phase-separated #condensate #droplets can form and function in the #extracellular environment and may interact with cells!
www.sciencedirect.com/science/arti...
#CellBiology #Biophysics #ChemicalEngineering #SyntheticBiology #ChemSky
July 31, 2025 at 9:36 AM
On extracellular #biomolecular condensates!
We demonstrate that phase-separated #condensate #droplets can form and function in the #extracellular environment and may interact with cells!
www.sciencedirect.com/science/arti...
#CellBiology #Biophysics #ChemicalEngineering #SyntheticBiology #ChemSky
We demonstrate that phase-separated #condensate #droplets can form and function in the #extracellular environment and may interact with cells!
www.sciencedirect.com/science/arti...
#CellBiology #Biophysics #ChemicalEngineering #SyntheticBiology #ChemSky
Check out our research on Semantic Topology at the 63rd Annual Meeting of the Association for Computational Linguistics (ACL 2025) in Vienna next week!
#ACL2025 #Interdisciplinary #Semantics
#ACL2025 #Interdisciplinary #Semantics
July 26, 2025 at 5:08 PM
Check out our research on Semantic Topology at the 63rd Annual Meeting of the Association for Computational Linguistics (ACL 2025) in Vienna next week!
#ACL2025 #Interdisciplinary #Semantics
#ACL2025 #Interdisciplinary #Semantics
Semantic Topology: a New Perspective for Communication Style Characterization
aclanthology.org/2025.finding...
#Linguistics #NLProc #ACL2025NLP #ACL2025
aclanthology.org/2025.finding...
#Linguistics #NLProc #ACL2025NLP #ACL2025
July 25, 2025 at 2:04 PM
Semantic Topology: a New Perspective for Communication Style Characterization
aclanthology.org/2025.finding...
#Linguistics #NLProc #ACL2025NLP #ACL2025
aclanthology.org/2025.finding...
#Linguistics #NLProc #ACL2025NLP #ACL2025
On disordered topologically compact states in intrinsically disordered proteins! We explored this concept in the context of the human Glucocorticoid Receptor.
pubs.acs.org/doi/10.1021/...
#ChemSky #IDP #Protein #Biophysics #Topology #CompChem
pubs.acs.org/doi/10.1021/...
#ChemSky #IDP #Protein #Biophysics #Topology #CompChem
July 19, 2025 at 8:29 AM
On disordered topologically compact states in intrinsically disordered proteins! We explored this concept in the context of the human Glucocorticoid Receptor.
pubs.acs.org/doi/10.1021/...
#ChemSky #IDP #Protein #Biophysics #Topology #CompChem
pubs.acs.org/doi/10.1021/...
#ChemSky #IDP #Protein #Biophysics #Topology #CompChem
New Boltzmann Medalist Mehran Kardar at StatPhys29 in Florence, showing the first handmade slide that led to the #KPZ equation. #StatisticalPhysics #Physics Photo: Andrea Gabrielli
July 17, 2025 at 5:07 AM
New Boltzmann Medalist Mehran Kardar at StatPhys29 in Florence, showing the first handmade slide that led to the #KPZ equation. #StatisticalPhysics #Physics Photo: Andrea Gabrielli
Team snapshot after our regular group meeting — this time with a great talk by Muriel Hammond on intrinsically disordered proteins!
June 3, 2025 at 2:25 PM
Team snapshot after our regular group meeting — this time with a great talk by Muriel Hammond on intrinsically disordered proteins!
For those interested in topological analysis of biomolecular condensates!
Article 1: link.springer.com/article/10.1...
Article 2: www.sciencedirect.com/science/arti...
#Topology #Condensate #PhaseSeparation #Aggregation #ChemSky #Biophysics #Polymer #Nanoscience
Article 1: link.springer.com/article/10.1...
Article 2: www.sciencedirect.com/science/arti...
#Topology #Condensate #PhaseSeparation #Aggregation #ChemSky #Biophysics #Polymer #Nanoscience
May 25, 2025 at 10:49 AM
For those interested in topological analysis of biomolecular condensates!
Article 1: link.springer.com/article/10.1...
Article 2: www.sciencedirect.com/science/arti...
#Topology #Condensate #PhaseSeparation #Aggregation #ChemSky #Biophysics #Polymer #Nanoscience
Article 1: link.springer.com/article/10.1...
Article 2: www.sciencedirect.com/science/arti...
#Topology #Condensate #PhaseSeparation #Aggregation #ChemSky #Biophysics #Polymer #Nanoscience
The first model of full length human androgen receptor and its polyQ expanded variant!
onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com/doi/full/10....
#endocrinology #androgen #hormone #receptor #SBMA #polyglutamine #prostate
onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com/doi/full/10....
#endocrinology #androgen #hormone #receptor #SBMA #polyglutamine #prostate
Polyglutamine expansion induced dynamic misfolding of androgen receptor
Spinal bulbar muscular atrophy (SBMA) is caused by a polyglutamine expansion (pQe) in the N-terminal transactivation domain of the human androgen receptor (AR-NTD), resulting in a combination of toxi...
onlinelibrary.wiley.com
May 15, 2025 at 1:09 PM
The first model of full length human androgen receptor and its polyQ expanded variant!
onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com/doi/full/10....
#endocrinology #androgen #hormone #receptor #SBMA #polyglutamine #prostate
onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com/doi/full/10....
#endocrinology #androgen #hormone #receptor #SBMA #polyglutamine #prostate
PhD student Laurens Heling from my laboratory will be presenting a the #LACDR Spring Symposium!
"Single Molecule Analysis Reveals Allosteric Regulation of #Androgen #Receptor DNA Binding"
#SingleMolecule #Biophysics #Endocrinology
"Single Molecule Analysis Reveals Allosteric Regulation of #Androgen #Receptor DNA Binding"
#SingleMolecule #Biophysics #Endocrinology
May 11, 2025 at 8:42 AM
PhD student Laurens Heling from my laboratory will be presenting a the #LACDR Spring Symposium!
"Single Molecule Analysis Reveals Allosteric Regulation of #Androgen #Receptor DNA Binding"
#SingleMolecule #Biophysics #Endocrinology
"Single Molecule Analysis Reveals Allosteric Regulation of #Androgen #Receptor DNA Binding"
#SingleMolecule #Biophysics #Endocrinology
Reposted by Alireza Mashaghi
Researchers at Leiden University have created a unique model that mimics how disease develops after a dengue infection. This 'dengue-on-a-chip' model helps them study the virus more effectively. The timing is crucial, as climate change is causing dengue to spread worldwide.
Read more:
Read more:
Leiden scientists create first-ever dengue-on-a-chip to study this deadly virus
Researchers at Leiden University have created a unique model that mimics how disease develops after a dengue infection. This 'dengue-on-a-chip' model helps them study the virus more effectively. The t...
www.universiteitleiden.nl
April 10, 2025 at 1:31 PM
Researchers at Leiden University have created a unique model that mimics how disease develops after a dengue infection. This 'dengue-on-a-chip' model helps them study the virus more effectively. The timing is crucial, as climate change is causing dengue to spread worldwide.
Read more:
Read more:
Research update from our lab: Dengue-on-a-chip and single-cell rheology reveal that Dengue is a "disease of mechanics"!
#Bioengineering #Virology #Infection #Mechanobiology
pubs.acs.org/doi/10.1021/...
#Bioengineering #Virology #Infection #Mechanobiology
pubs.acs.org/doi/10.1021/...
Revealing Mechanopathology Induced by Dengue NS1 Using Organ Chips and Single-Cell Force Spectroscopy
Capillary leakage is a hallmark of severe dengue, yet its precise mechanisms remain elusive. Emerging evidence highlights the dengue virus’s targeting of mechanically active endothelial cells as a key contributor to dengue shock syndrome. The viral nonstructural protein 1 (NS1) has been identified as a central player, disrupting endothelial integrity and inducing vascular hyperpermeability independently of pro-inflammatory cytokines. This study provides a direct assessment of NS1-induced endothelial pathology by combining single-cell force spectroscopy and a microvessel-on-a-chip platform. We demonstrate that NS1 significantly alters endothelial cell mechanics, reducing cell stiffness and compromising junctional integrity, thereby directly linking these mechanical alterations to vascular dysfunction. These findings establish a framework for understanding the mechano-pathology of dengue and offer a platform for developing targeted therapeutic strategies to mitigate severe disease outcomes.
pubs.acs.org
March 25, 2025 at 8:30 PM
Research update from our lab: Dengue-on-a-chip and single-cell rheology reveal that Dengue is a "disease of mechanics"!
#Bioengineering #Virology #Infection #Mechanobiology
pubs.acs.org/doi/10.1021/...
#Bioengineering #Virology #Infection #Mechanobiology
pubs.acs.org/doi/10.1021/...
Research update from our lab:
We reported the first use of Scanning Probe Microscopy in biomolecular condensate research!
#ChemSky #Interdisciplinary #Biophysics #Mechanics #Rheology
www.universiteitleiden.nl/en/news/2025...
We reported the first use of Scanning Probe Microscopy in biomolecular condensate research!
#ChemSky #Interdisciplinary #Biophysics #Mechanics #Rheology
www.universiteitleiden.nl/en/news/2025...
From liquid to solid: revolutionary technique uncovers disease-related changes in tiny droplets within our cells
Understanding the behaviour of tiny droplets in our cells could aid the search for new treatments. A team of Leiden researchers has developed a groundbreaking method to study how these droplets transi...
www.universiteitleiden.nl
February 14, 2025 at 5:26 AM
Research update from our lab:
We reported the first use of Scanning Probe Microscopy in biomolecular condensate research!
#ChemSky #Interdisciplinary #Biophysics #Mechanics #Rheology
www.universiteitleiden.nl/en/news/2025...
We reported the first use of Scanning Probe Microscopy in biomolecular condensate research!
#ChemSky #Interdisciplinary #Biophysics #Mechanics #Rheology
www.universiteitleiden.nl/en/news/2025...
At NWO Physics conference in Veldhoven! Our team presented on biomolecular condensates and circuit topology!
#NWO #Physics #NWOPhysics #SoftMatter #Topology #Materials
#NWO #Physics #NWOPhysics #SoftMatter #Topology #Materials
January 22, 2025 at 8:26 AM
At NWO Physics conference in Veldhoven! Our team presented on biomolecular condensates and circuit topology!
#NWO #Physics #NWOPhysics #SoftMatter #Topology #Materials
#NWO #Physics #NWOPhysics #SoftMatter #Topology #Materials
A glimpse into our research at the exciting intersection of physical sciences and medicine/pharmacy!
www.youtube.com/watch?v=a4jR...
#interdisciplinary #Medicine #Physics #Chemistry #Engineering #Mathematics #Computational #SocialScience
www.youtube.com/watch?v=a4jR...
#interdisciplinary #Medicine #Physics #Chemistry #Engineering #Mathematics #Computational #SocialScience
The Mashaghi Lab for Interdisciplinary Medical Innovations
YouTube video by Alireza Mashaghi Lab
www.youtube.com
December 15, 2024 at 4:23 PM
A glimpse into our research at the exciting intersection of physical sciences and medicine/pharmacy!
www.youtube.com/watch?v=a4jR...
#interdisciplinary #Medicine #Physics #Chemistry #Engineering #Mathematics #Computational #SocialScience
www.youtube.com/watch?v=a4jR...
#interdisciplinary #Medicine #Physics #Chemistry #Engineering #Mathematics #Computational #SocialScience
On topological analysis of single-cell HiC data!
#genome #chromatin #bioinformatics #SingleCell
link.springer.com/protocol/10....
www.sciencedirect.com/science/arti...
#genome #chromatin #bioinformatics #SingleCell
link.springer.com/protocol/10....
www.sciencedirect.com/science/arti...
December 11, 2024 at 10:06 PM
On topological analysis of single-cell HiC data!
#genome #chromatin #bioinformatics #SingleCell
link.springer.com/protocol/10....
www.sciencedirect.com/science/arti...
#genome #chromatin #bioinformatics #SingleCell
link.springer.com/protocol/10....
www.sciencedirect.com/science/arti...