Author

J. Vargas

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· 4 Biochemistry· 2 Bioengineering· 1 Cancer Biology· 1

Signature Assays, Organisms & Methods

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Assay:cryo-EM· 5 Approach:experimental assay· 4 Approach:deep learning· 3 Approach:statistical model· 3 Organism:human· 2 Research Focus:protein structure prediction· 2 Research Focus:cell signaling & trafficking· 1 Research Focus:cell type annotation· 1

Frequent Co-Authors

K. H. Bui· 3 shared C. O. S. Sorzano· 2 shared D. Dai· 2 shared J. M. Carazo· 2 shared M. Ichikawa· 2 shared A. A. Khalifa· 1 shared A. A. Z. Khalifa· 1 shared A. Ballandras-Colas· 1 shared

Activity by Year

2018-2022 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 12 mutual co-author links

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3 shared papersBiophysics

K. H. Bui

Mutual co-authors in cluster

Author profile →

8 papers

Recent·Most cited

Multivalent interactions essential for lentiviral integrase function

A. Ballandras-Colas, V. Chivukula, D. T. Gruszka, Z. Shan, P. K. Singh, V. E. Pye, R. K. McLean, G. J. Bedwell, W. Li, A. Nans, N. J. Cook, H. J. Fadel, E. M. Poeschla, D. J. Griffiths, J. Vargas, , P. Cherepanov

This study reports cryo-EM structures of the lentiviral intasome and shows that multivalent interactions are essential for integrase function and virus infectivity.

bioRxiv · Jan 26, 2022Biochemistry

IFN-{lambda}4 may contribute to HCV persistence by increasing ER stress and enhancing IRF1 signaling

O. O. Onabajo, F. Wang, M.-H. Lee, O. Florez-Vargas, A. Obajemu, M. A. A. Castro, C. Tanikawa, J. Vargas, S.-F. Liao, C. Song, Y.-H. Huang, C.-Y. Shen, A. R. Banday, T. R. O'Brien, Z. Hu, , L. Prokunina-Olsson

This study investigates the association between IFNL4 genetic variants and HCV-related cirrhosis and HCC risk, finding protective effects against cirrhosis and increased HCC risk in specific populations.

bioRxiv · Oct 28, 2020 · PreprintCancer Biology

Local computational methods to improve the interpretability and analysis of cryo-EM maps

S. Kaur, J. Gomez-Blanco, S. Adinarayanan, A. Khalifa, R. Sanchez-Garcia, D. Wrapp, J. S. McLellan, K. H. Bui, J. Vargas

The paper introduces local computational methods to improve cryo-EM map interpretability by avoiding over-sharpening and providing local B-factors and occupancy maps.

bioRxiv · May 11, 2020Biophysics

The interdomain helix between the kinase and RNase domains of IRE1α transmits the conformational change that underlies ER stress-induced activation.

D. Ricci, S. Tutton, I. Marrocco, M. Ying, D. Blumenthal, D. Eletto, J. Vargas, S. Boyle, H. Fazelinia, J. C. Paton, A. W. Paton, C.-H. A. Tang, C.-C. A. Hu, T. Gidalevitz, Y. Argon

This study identifies the interdomain helix between IRE1α kinase and RNase domains as critical for transmitting conformational changes during ER stress, revealing its role in regulating oligomerization, RNase activity, and kinase function.

bioRxiv · Jan 14, 2020 · PreprintBiochemistry

The inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications

A. A. Z. Khalifa, M. Ichikawa, D. Dai, C. Black, K. Peri, T. S. McAlear, S. Kubo, S. Veyron, S. K. Yang, J. Vargas, J.-F. Trempe, S. Bechstedt, K. H. Bui

The paper identifies new inner junction proteins in cilia and shows they form an interaction hub involving tubulin post-translational modifications.

bioRxiv · Oct 10, 2019Biophysics

Tubulin Lattice in Cilia is in a Stressed Form Regulated by Microtubule Inner Proteins

M. Ichikawa, A. A. Khalifa, K. Basu, D. Dai, M. A. Faghfor Maghrebi, J. Vargas, K. H. Bui

This study presents the near-atomic structure of Tetrahymena doublet microtubules, showing that microtubule inner proteins stabilize the tubulin lattice and contribute to the intrinsic stress in cilia.

bioRxiv · Apr 2, 2019Biophysics

Automatic local resolution-based sharpening of cryo-EM maps.

E. Ramirez-Aportela, J. L. Vilas, R. Melero, P. Conesa, M. Martinez, D. Maluenda, J. Mota, A. Jimenez, J. Vargas, R. Marabini, J. M. Carazo, C. O. S. Sorzano

This paper introduces a new automatic method for sharpening cryo-EM maps based on local resolution, improving map quality and interpretability.

bioRxiv · Oct 2, 2018Biophysics

ENRICH: a fast method to improve the quality of flexible macromolecular reconstructions

M. Kazemi, C. O. S. Sorzano, A. Des Georges, J. M. Carazo, J. Vargas

ENRICH improves 3D map quality from small, heterogeneous cryo-EM datasets by merging particles across conformations using optical flow.

bioRxiv · Aug 26, 2018Bioengineering