Author

James Smith

Institute of Cancer Research

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

Same name, identified by ORCID

Biology Disciplines

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Bioengineering· 1 Bioinformatics· 1 Biophysics· 1 Developmental Biology· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 3 Organism:human· 3 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Research Focus:clustering· 1 Research Focus:database / resource· 1 Approach:deep learning· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Ahmed M. Ibrahim· 1 shared Ahsan TanweeriD· 1 shared Alan BrowniD· 1 shared Ardan PatwardhaniD· 1 shared Benjamin J. WalkeriD· 1 shared Blanca Sanchez Paya· 1 shared Cécile FortiD· 1 shared Daniel Holder· 1 shared

Activity by Year

2017-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 9 mutual co-author links

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1 shared paperBioengineering

Ahmed M. Ibrahim

Author profile →

5 papers

Recent·Most cited

Enhancer-gene regulatory interactions in colorectal cancer revealed through genome-wide CRISPRi perturbations

Philip Law, Jayaram Vijayakrishnan, James Smith, Timothy Barry, Maria Mandelia, Eugene Katsevich, Richard S. Houlston

The paper uses CRISPRi Perturb-seq to identify 238 enhancer-gene regulatory associations in colorectal cancer and integrates chromatin data to understand their spatial organization.

Wellcome Open Research · Jul 30, 2026Peer-reviewedGenomics

Extracellular matrix defects destabilise apical cytoarchitecture and mechanical properties during early Down syndrome neurodevelopment

Teresa P. Silva, Ekaterina R. Iijima, Ioakeim Ampartzidis, Grace Cooksley, Blanca Sanchez Paya, Ekin Ucuncu, Daniel Holder, Imogen Smith, James Smith, Giovanni Giuseppe Giobbe, Paolo De Coppi, Kathleen J. Millen, Jonathan D. W. Clarke, Frederick J. Livesey, Nicholas D. E. Greene, , Paula Alexandre

This study shows that ECM defects in Down syndrome neurodevelopment cause apical cytoarchitecture and mechanical property instability in neural stem cell models.

bioRxiv · Jun 23, 2026 · PreprintDevelopmental Biology

Axonemal dynein contributions to flagellar beat types and waveforms

Sophia Fochler, Matthew H. Doran, Tom Beneke, James Smith, Cécile Fort, Benjamin J. Walker, Alan Brown, Eva Gluenz, Richard John Wheeler

This study identifies specific dynein contributions to flagellar beat types in Leishmania, challenging the existing model of dynein function in flagellar beating.

bioRxiv · Nov 6, 2025 · PreprintBiophysics

PDB NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank

Preeti Choudhary, Zukang Feng, John M. Berrisford, Henry Chao, Yasuyo Ikegawa, Ezra Peisach, Dennis W. Piehl, James Smith, Ahsan Tanweer, Mihály Váradi, John Westbrook, Jasmine Y. Young, Ardan Patwardhan, Kyle L. Morris, Jeffrey C. Hoch, , Stephen Kevin Burley

The PDB NextGen Archive centralizes and streamlines access to integrated structural annotations and enriched data from wwPDB partners and external sources.

Database · Jan 1, 2024Peer-reviewedBioinformatics

Game theoretic consideration of transgenic bacteria in the human gut microbiota as a pro-biotic prophylactic for metabolic syndrome

Ahmed M. Ibrahim, James Smith

This paper uses game theory to model the coexistence of transgenic and indigenous gut bacteria as a potential prophylactic for metabolic syndrome by altering omega-3 to omega-6 fat ratios.

bioRxiv · Nov 3, 2017 · PreprintBioengineering