Author

Javier Espinoza-Herrera

University of California San DiegoORCID 0009-0004-8644-5867Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Biophysics· 1

Signature Assays, Organisms & Methods

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Research Focus:database / resource· 2 Approach:large language model· 1 Assay:protein sequence· 1 Assay:proteomics· 1 Approach:statistical model· 1

Frequent Co-Authors

Adrián JinichiD· 2 shared Adriana Siordia· 2 shared Sarah Marta VeskimägiiD· 2 shared Ailyn López Jasso· 1 shared Akshay Uppal· 1 shared Andy SpenceriD· 1 shared Erika GarayiD· 1 shared Joaquin Trevilla Santa AnaiD· 1 shared

Activity by Year

2026-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 35 mutual co-author links

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2 shared papersBiophysics

Adrián JinichORCID

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2 papers

Recent·Most cited

ProtoPure: Literature Mining and Analysis of Protein Purification Protocols at Proteome Scale

Ricardo Almada‐Monter, Jose Martinez-Lomeli, Erika Garay, Joaquin Trevilla Santa Ana, Andy Spencer, Adriana Siordia, Param Chordiya, Sofia Luna Armijo, Joel Maya Herrera, Nathaniel Roethler, Sarah Marta Veskimägi, Akshay Uppal, Melina Shamshoum, Adrián Jinich

ProtoPure automates the extraction and analysis of protein purification protocols from literature, revealing trends in recombinant expression practices and diverse downstream purification strategies.

bioRxiv · Oct 30, 2026 · PreprintBiophysics

Protein Language Visualizer: A Repository for Homology Exploration with Language Model Embeddings

Javier Espinoza-Herrera, María F. Manríquez-García, Sofía Medina-Bermejo, Ailyn López Jasso, Juan P. Ruiz-Alcocer, Adriana Siordia, Sarah Marta Veskimägi, Nate Roethler, Adrián Jinich

The paper introduces PLVis, a framework using protein language model embeddings to visualize and explore protein homology, validated through case studies on Mycobacterium and Plasmodium proteomes.

Digital Discovery · Jan 1, 2026Peer-reviewedBioinformatics