Author

David Berman

Cambridge Consultants (United Kingdom)

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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Bioinformatics· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Assay:protein sequence· 2 Approach:deep learning· 1 Research Focus:drug response / drug discovery· 1 Organism:E. coli· 1 Research Focus:gene regulatory network inference· 1 Approach:machine learning (classical)· 1 Research Focus:perturbation response prediction· 1 Research Focus:protein design· 1

Frequent Co-Authors

Anna Schooneveld· 2 shared Kotryna Bloznelyte· 2 shared Shafiat Dewan· 2 shared Will Addison· 2 shared Akash Kumar GuptaiD· 1 shared Ece Ibrahimi· 1 shared Fikayo Adepoju· 1 shared Frances Patricia Jones· 1 shared

Activity by Year

2024-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersSystems Biology

Anna Schooneveld

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2 papers

Recent·Most cited

An Improved Systematic Method for Constructing ecGEMs using a Protein-Chemical Transformer

Anna Schooneveld, Shafiat Dewan, Navot Arad, Sam Genway, Sonya Kaur Kalsi, Kotryna Bloznelyte, Will Addison, David Berman

The paper introduces a transformer-based method to predict kcat values for E. coli enzymes, improving ecGEMs with fewer calibrations and better performance than existing models.

bioRxiv · Oct 29, 2025 · PreprintSystems Biology

Protein Language Models in Directed Evolution

Russell G. Maguire, Kotryna Bloznelyte, Fikayo Adepoju, Matthew Armean-Jones, Shafiat Dewan, Stella Fozzard, Sophie E. Goddard, Akash Kumar Gupta, Ece Ibrahimi, Frances Patricia Jones, Preet Lalli, Anna Schooneveld, Sean Thompson, David Berman, Will Addison, , Ian Taylor

This paper demonstrates how protein language models can guide directed evolution to improve PET degradation enzyme variants.

bioRxiv · Aug 20, 2024 · PreprintBioinformatics