Author

Robert S James

Quadram Institute

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· 4 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Assay:metagenomics· 4 Assay:long-read sequencing· 3 Approach:statistical model· 3 Research Focus:benchmarking· 2 Approach:experimental assay· 2 Research Focus:genome assembly· 2 Organism:bacteria (other)· 1 Approach:Bayesian inference· 1

Frequent Co-Authors

Christopher QuinceiD· 4 shared Sébastien RaguideauiD· 4 shared Rayan ChikhiiD· 3 shared Gaëtan Benoit· 2 shared A. Murat EreniD· 1 shared Aaron E. DarlingiD· 1 shared Adam M. PhillippyiD· 1 shared Andrew D. MillardiD· 1 shared

Activity by Year

2019-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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4 shared papersBioinformatics

Christopher QuinceORCID

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Author profile →

5 papers

Recent·Most cited

REMAG: recovery of eukaryotic genomes from metagenomic data using non-contrastive self-supervised learning

Daniel Gómez‐Pérez, Sébastien Raguideau, Sally D. Warring, Robert S James, Falk Hildebrand, Christopher Quince

REMAG improves eukaryotic genome recovery from metagenomic data by using non-contrastive self-supervised learning, outperforming existing tools in producing near-complete genomes.

bioRxiv · Oct 13, 2026 · PreprintBioinformatics

High-quality metagenome assembly from nanopore reads with nanoMDBG

Gaëtan Benoit, Robert S James, Sébastien Raguideau, Georgina Alabone, Tim Goodall, Rayan Chikhi, Christopher Quince

nanoMDBG improves metagenome assembly from ONT reads, producing more high-quality MAGs with less computational resources than existing assemblers.

Nature Communications · Mar 6, 2026Peer-reviewedBioinformatics

Efficient High-Quality Metagenome Assembly from Long Accurate Reads using Minimizer-space de Bruijn Graphs

Gaëtan Benoit, Sébastien Raguideau, Robert S James, Adam M. Phillippy, Rayan Chikhi, Christopher Quince

The paper introduces a metagenomics assembler that improves efficiency and assembly quality for long reads, achieving faster performance and better recovery of MAGs and viral/plasmid sequences.

bioRxiv · Jul 7, 2023 · PreprintBioinformatics

Metagenomics Strain Resolution on Assembly Graphs

Christopher Quince, Sergey Nurk, Sébastien Raguideau, Robert S James, Orkun S. Soyer, Joanna Kimberley Summers, Antoine Limasset, A. Murat Eren, Rayan Chikhi, Aaron E. Darling

STRONG identifies strains de novo from metagenome samples using coassembly, binning, and a Bayesian algorithm to resolve haplotypes and abundances.

bioRxiv · Sep 6, 2020 · PreprintBioinformatics

LAMBDR: Long-range amplification and Nanopore sequencing of Mycobacterium bovis direct-repeat region. A novel method for in-silico spoligotyping of M. bovis directly from badger faeces.

Robert S James, Emma Rachel Travis, Andrew D. Millard, P.C. Hewlett, Lidija Kravar‐Garde, Elizabeth M. H. Wellington

bioRxiv · Oct 3, 2019 · PreprintMolecular Biology