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
On circuit topology of knots!
Circuit topology for bottom-up engineering of molecular knots
doi.org/10.3390/sym1...
A tile model of circuit topology for entangled biopolymers
www.nature.com/articles/s41...
Polynomial invariant of molecular circuit topology
doi.org/10.3390/sym1...
#ChemSky #knot
Circuit topology for bottom-up engineering of molecular knots
doi.org/10.3390/sym1...
A tile model of circuit topology for entangled biopolymers
www.nature.com/articles/s41...
Polynomial invariant of molecular circuit topology
doi.org/10.3390/sym1...
#ChemSky #knot
November 21, 2025 at 3:38 PM
On circuit topology of knots!
Circuit topology for bottom-up engineering of molecular knots
doi.org/10.3390/sym1...
A tile model of circuit topology for entangled biopolymers
www.nature.com/articles/s41...
Polynomial invariant of molecular circuit topology
doi.org/10.3390/sym1...
#ChemSky #knot
Circuit topology for bottom-up engineering of molecular knots
doi.org/10.3390/sym1...
A tile model of circuit topology for entangled biopolymers
www.nature.com/articles/s41...
Polynomial invariant of molecular circuit topology
doi.org/10.3390/sym1...
#ChemSky #knot
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
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
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
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
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
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...
"Substance P: From Pain to Cancer" is now in print!
We contributed a chapter on immunobiology and pharmacology of neuropeptide substance P!
www.sciencedirect.com/science/arti...
#immunology #neurology #neuropeptide #pharmacology #ChemSky
We contributed a chapter on immunobiology and pharmacology of neuropeptide substance P!
www.sciencedirect.com/science/arti...
#immunology #neurology #neuropeptide #pharmacology #ChemSky
December 4, 2024 at 8:11 PM
"Substance P: From Pain to Cancer" is now in print!
We contributed a chapter on immunobiology and pharmacology of neuropeptide substance P!
www.sciencedirect.com/science/arti...
#immunology #neurology #neuropeptide #pharmacology #ChemSky
We contributed a chapter on immunobiology and pharmacology of neuropeptide substance P!
www.sciencedirect.com/science/arti...
#immunology #neurology #neuropeptide #pharmacology #ChemSky
Inspiring talk by Evan Spruijt at NWO Chain 2024! He shared exciting insights into how coacervate-based and liposome-based #protocells come together to facilitate complex chemistry related to the origin of life on Earth!
#Evolution #OriginofLife #Biomolecular #Condensate #ChemSky
#Evolution #OriginofLife #Biomolecular #Condensate #ChemSky
December 3, 2024 at 2:10 PM
Inspiring talk by Evan Spruijt at NWO Chain 2024! He shared exciting insights into how coacervate-based and liposome-based #protocells come together to facilitate complex chemistry related to the origin of life on Earth!
#Evolution #OriginofLife #Biomolecular #Condensate #ChemSky
#Evolution #OriginofLife #Biomolecular #Condensate #ChemSky
While human #proteins span a wide range of molecular weights, from approximately 0.26 to 4000 kDa, human chemokines are restricted to a narrow range of about 8 to 14 kDa. We asked whether there might be an optimality in #cellular #communications.
arxiv.org/abs/2412.00771
#Immunology #Chemokine
arxiv.org/abs/2412.00771
#Immunology #Chemokine
December 3, 2024 at 9:19 AM
While human #proteins span a wide range of molecular weights, from approximately 0.26 to 4000 kDa, human chemokines are restricted to a narrow range of about 8 to 14 kDa. We asked whether there might be an optimality in #cellular #communications.
arxiv.org/abs/2412.00771
#Immunology #Chemokine
arxiv.org/abs/2412.00771
#Immunology #Chemokine
Our work on the cover of Materials Advances!
Single-cell analysis of innate immune cell mechanics: an application to cancer immunology
pubs.rsc.org/en/content/a...
#immunology #innateimmunity #immunomechanics #mechanobiology #SingleCell
Single-cell analysis of innate immune cell mechanics: an application to cancer immunology
pubs.rsc.org/en/content/a...
#immunology #innateimmunity #immunomechanics #mechanobiology #SingleCell
December 1, 2024 at 12:22 PM
Our work on the cover of Materials Advances!
Single-cell analysis of innate immune cell mechanics: an application to cancer immunology
pubs.rsc.org/en/content/a...
#immunology #innateimmunity #immunomechanics #mechanobiology #SingleCell
Single-cell analysis of innate immune cell mechanics: an application to cancer immunology
pubs.rsc.org/en/content/a...
#immunology #innateimmunity #immunomechanics #mechanobiology #SingleCell
On catalytic microswimmers: the motion of catalytically active colloids approaching a surface
arxiv.org/abs/2411.11656
#Colloids #ActiveMatter #ChemSky #Catalysis
arxiv.org/abs/2411.11656
#Colloids #ActiveMatter #ChemSky #Catalysis
November 29, 2024 at 12:11 PM
On catalytic microswimmers: the motion of catalytically active colloids approaching a surface
arxiv.org/abs/2411.11656
#Colloids #ActiveMatter #ChemSky #Catalysis
arxiv.org/abs/2411.11656
#Colloids #ActiveMatter #ChemSky #Catalysis
Celebrating 40 years of Biopharmaceutical Sciences at the Leiden Academic Centre for Drug Research! Douwe Breimer reminded us that multidisciplinarity has been a key element of this program since Day 1.
#LeidenUniversity #LACDR #Pharmacy #PharmaSky #MedSky #ChemSky #PharmaFab
#LeidenUniversity #LACDR #Pharmacy #PharmaSky #MedSky #ChemSky #PharmaFab
November 28, 2024 at 3:12 PM
Celebrating 40 years of Biopharmaceutical Sciences at the Leiden Academic Centre for Drug Research! Douwe Breimer reminded us that multidisciplinarity has been a key element of this program since Day 1.
#LeidenUniversity #LACDR #Pharmacy #PharmaSky #MedSky #ChemSky #PharmaFab
#LeidenUniversity #LACDR #Pharmacy #PharmaSky #MedSky #ChemSky #PharmaFab
Towards single-cell immunometabolomics:
Machine Learning-aided Direct Infusion Mass Spectrometry (DI-MS) enables single cell metabolic analysis of human cells
analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/...
#immunology #innateimmunity #MassSpectrometry #AnalyticalChemistry
Machine Learning-aided Direct Infusion Mass Spectrometry (DI-MS) enables single cell metabolic analysis of human cells
analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/...
#immunology #innateimmunity #MassSpectrometry #AnalyticalChemistry
November 22, 2024 at 11:07 PM
Towards single-cell immunometabolomics:
Machine Learning-aided Direct Infusion Mass Spectrometry (DI-MS) enables single cell metabolic analysis of human cells
analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/...
#immunology #innateimmunity #MassSpectrometry #AnalyticalChemistry
Machine Learning-aided Direct Infusion Mass Spectrometry (DI-MS) enables single cell metabolic analysis of human cells
analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/...
#immunology #innateimmunity #MassSpectrometry #AnalyticalChemistry
Insights into the conformational dynamics of Glucocorticoid Receptor AF1 region - a circuit topology analysis of disordered compact regions
www.biorxiv.org/content/10.1...
#nuclearreceptors #IDP #IDR #topology #glucocorticoid
www.biorxiv.org/content/10.1...
#nuclearreceptors #IDP #IDR #topology #glucocorticoid
November 21, 2024 at 3:52 PM
Insights into the conformational dynamics of Glucocorticoid Receptor AF1 region - a circuit topology analysis of disordered compact regions
www.biorxiv.org/content/10.1...
#nuclearreceptors #IDP #IDR #topology #glucocorticoid
www.biorxiv.org/content/10.1...
#nuclearreceptors #IDP #IDR #topology #glucocorticoid