Author

P. Matsudaira

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 3 Cell Biology· 1 Physiology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 4 Assay:imaging· 2 Research Focus:protein folding & dynamics· 2 Research Focus:cell signaling & trafficking· 1 Research Focus:cell type annotation· 1 Approach:comparative / phylogenetic analysis· 1 Research Focus:development & morphogenesis· 1 Organism:mouse· 1

Frequent Co-Authors

A. Krah· 2 shared A. T. Shivgan· 2 shared C. S. Verma· 2 shared J. K. Marzinek· 2 shared P. J. Bond· 2 shared A. Kabla· 1 shared B. P. Nguyen· 1 shared D. Bhattacharya· 1 shared

Activity by Year

2018-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 12 mutual co-author links

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2 shared papersBiophysics

A. Krah

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

A coarse-grained model of glycosaminoglycans for biomolecular simulation

A. T. Shivgan, J. K. Marzinek, A. Krah, P. Matsudaira, C. S. Verma, P. J. Bond

This paper develops a coarse-grained model for glycosaminoglycans compatible with Martini forcefields, enabling simulation of their conformational and thermodynamic properties.

bioRxiv · Oct 6, 2023Biophysics

Contributions of individual satellite cells to muscle regeneration assessed using a confetti mouse model

H. Heemskerk, N. S. Jagannathan, N. J. M. Nasir, B. P. Nguyen, K. Sacadevan, P. Matsudaira, P. T. So, L. Tucker-Kellogg

The paper uses a confetti mouse model to assess fiber-crossing by satellite cells during muscle regeneration, finding that 26-33% of SCs contribute to multiple adjacent fibers.

bioRxiv · Aug 25, 2023 · PreprintPhysiology

Extending the Martini coarse-grained forcefield to N-glycans

A. T. Shivgan, J. K. Marzinek, R. G. Huber, A. Krah, R. H. Henchman, P. Matsudaira, C. S. Verma, P. J. Bond

This paper extends the Martini forcefield to model N-glycans by optimizing coarse-grained parameters and validating them against experimental data on lectin binding and solvation properties.

Journal of Chemical Information and Modeling · Jul 6, 2020Peer-reviewedBiophysics

The Degradation-promoting Roles of Deubiquitinases Ubp6 and Ubp3 in Cytosolic and ER Protein Quality Control

H. Wu, D. T. W. Ng, I. Cheong, P. Matsudaira

This study identifies Ubp6 and Ubp3 as deubiquitinases that regulate protein quality control by modulating ubiquitin levels and degradation pathways in yeast.

bioRxiv · Jan 22, 2020Cell Biology

Strain maps characterize the symmetry of convergence and extension patterns during Zebrafish gastrulation

D. Bhattacharya, J. Zhong, S. Tavakoli, A. Kabla, P. Matsudaira

The paper maps strain patterns during zebrafish gastrulation to understand convergence and extension movements, identifying symmetric and rotational strain features.

bioRxiv · Sep 4, 2018Biophysics