Publications
All refereed publications and preprints. My name is shown in bold; an asterisk (*) marks equal (co-first) authorship. Titles link to Google Scholar. See also my Google Scholar profile and ORCID record.
2026
- A single-cell spatially-resolved human whole transcriptome atlas of non-small cell lung cancer associates spatial features with clinical response Cell Press Sneak Peek, 2026 Preprint
- Cancer cell-intrinsic inflammasome protein ASC links innate immunity with mitochondrial metabolism in driving pancreatic cancer Nature Communications, 2026
2025
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SpaNorm: spatially-aware normalization for spatial transcriptomics data
Genome Biology, 2025; 26(1):109
Software: SpaNorm
- mastR: an R package for automated identification of tissue-specific gene signatures in multi-group differential expression analysis Bioinformatics, 2025; 41(3):btaf114
- Improved marker detection for rare population in single-cell transcriptomics through text mining-inspired scoring approach bioRxiv, 2025 Preprint
2024
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Library size confounds biology in spatial transcriptomics data
Genome Biology, 2024; 25(1):99
Software: SpaNorm · SubcellularSpatialData
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vissE: a versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis
BMC Bioinformatics, 2024; 25(1)
Software: vissE
- In situ single-cell profiling sheds light on IFI27 localisation during SARS-CoV-2 infection EBioMedicine, 2024; 101
- hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data bioRxiv, 2024 Preprint
2023
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standR: spatial transcriptomic analysis for GeoMx DSP data
Nucleic Acids Research, 2023
Software: standR
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vissE.cloud: a webserver to visualise higher order molecular phenotypes from enrichment analysis
Nucleic Acids Research, 2023
Software: vissE.cloud
- Discovery of a highly potent, selective, orally bioavailable inhibitor of KAT6A/B histone acetyltransferases with efficacy against KAT6A-high ER+ breast cancer Cell Chemical Biology, 2023
- Implementation of DNA methylation array profiling in pediatric central nervous system tumors: the AIM BRAIN project The Journal of Molecular Diagnostics, 2023
- Spatial transcriptomic analysis of Sonic Hedgehog medulloblastoma identifies that the loss of heterogeneity and promotion of differentiation underlies the response to CDK4/6 inhibition Genome Medicine, 2023; 15(1):29
- Transcriptomic profiling of cardiac tissues from SARS-CoV-2 patients identifies DNA damage Immunology, 2023; 168(3):403–419
- Identification of cell types, states and programs by learning gene set representations bioRxiv, 2023 Preprint
2022
- Computational screening of anti-cancer drugs identifies a new BRCA-independent gene expression signature to predict breast cancer sensitivity to cisplatin Cancers, 2022; 14(10):2404
- Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signatures European Respiratory Journal, 2022; 59(6)
- Targeting phenotypic plasticity prevents metastasis and the development of chemotherapy-resistant disease medRxiv, 2022 Preprint
2021
- Systems pharmacogenomics identifies novel targets and clinically actionable therapeutics for medulloblastoma Genome Medicine, 2021; 13(1)
2020
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Stable gene expression for normalisation and single-sample scoring
Nucleic Acids Research, 2020; 48(19):e113
Software: singscore
2019
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Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer
Genome Biology, 2019; 20(1)
Software: dcanr
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Using singscore to predict mutations in acute myeloid leukemia from transcriptomic signatures
F1000Research, 2019; 8
Software: SingscoreAMLMutations
2018
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Single sample scoring of molecular phenotypes
BMC Bioinformatics, 2018; 19(1):404
Software: singscore