All Stories

  1. SpatialRNA: a Python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset

    Article • Bioinformatics, December 2025, Oxford University Press (OUP)

    Dr Davis J McCarthy

  2. Denoising image-based spatial transcriptomics data with DenoIST

    Article • November 2025, openRxiv

    Dr Davis J McCarthy

  3. simPIC:flexible simulation of paired-insertion counts for single-cell ATAC sequencing data

    Article • September 2025, openRxiv

    Dr Davis J McCarthy

  4. Flexible and efficient count-distribution and mixed-model methods for eQTL mapping with quasar

    Article • July 2025, openRxiv

    Dr Davis J McCarthy

  5. Bayesian inference for copy number intra-tumoral heterogeneity from single-cell RNA-sequencing data

    Article • Biometrics, July 2025, Oxford University Press (OUP)

    Dr Davis J McCarthy

  6. Orchestrating multi-state QTL analysis with Bioconductor

    Article • April 2025, openRxiv

    Dr Davis J McCarthy

  7. SpatialRNA: a python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset

    Article • March 2025, openRxiv

    Dr Davis J McCarthy

  8. Spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis

    Article • Nature Genetics, February 2025, Springer Science + Business Media

    Dr Davis J McCarthy

  9. A high-resolution meiotic crossover map from single-nucleus ATAC-seq reveals insights into the recombination landscape in mammalian sperm

    Article • December 2024, openRxiv

    Dr Davis J McCarthy

  10. Going beyond cell clustering and feature aggregation: Is there single cell level information in single-cell ATAC-seq data?

    Article • December 2024, openRxiv

    Dr Davis J McCarthy

  11. Profiling genetically driven alternative splicing across the Indonesian archipelago

    Article • The American Journal of Human Genetics, November 2024, Elsevier

    Dr Davis J McCarthy

  12. Comparison of AI-integrated pathways with human-AI interaction in population mammographic screening for breast cancer

    Article • Nature Communications, August 2024, Springer Science + Business Media

    Dr Davis J McCarthy

  13. BRAIxDet: Learning to detect malignant breast lesion with incomplete annotations

    Article • Medical Image Analysis, August 2024, Elsevier

    Dr Davis J McCarthy

  14. Profiling genetically driven alternative splicing across the Indonesian Archipelago

    Article • May 2024, openRxiv

    Dr Davis J McCarthy

  15. De novo transcriptome assembly and genome annotation of the fat-tailed dunnart (Sminthopsis crassicaudata)

    Article • Gigabyte, May 2024, GigaScience Press

    Dr Davis J McCarthy

  16. Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods

    Article • Genome Biology, April 2024, Springer Science + Business Media

    Dr Davis J McCarthy

  17. Cell-type-specific and disease-associated expression quantitative trait loci in the human lung

    Article • Nature Genetics, March 2024, Springer Science + Business Media

    Dr Davis J McCarthy

  18. MAssively-Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massively-Parallel Cytometry Experiments

    Article • March 2024, openRxiv

    Dr Davis J McCarthy

  19. A comparison of marker gene selection methods for single-cell RNA sequencing data

    Article • Genome Biology, February 2024, Springer Science + Business Media

    Dr Davis J McCarthy

  20. An Interpretable and Accurate Deep-Learning Diagnosis Framework Modeled With Fully and Semi-Supervised Reciprocal Learning

    Article • IEEE Transactions on Medical Imaging, January 2024, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Davis J McCarthy

  21. Fancm has dual roles in the limiting of meiotic crossovers and germ cell maintenance in mammals

    Article • Cell Genomics, August 2023, Elsevier

    Dr Andrew J Deans, Dr Davis J McCarthy

  22. ADMANI: Annotated Digital Mammograms and Associated Non-Image Datasets

    Article • Radiology Artificial Intelligence, March 2023, Radiological Society of North America (RSNA)

    Dr Davis J McCarthy

  23. Trade-off between conservation of biological variation and batch effect removal in deep generative modeling for single-cell transcriptomics

    Article • BMC Bioinformatics, November 2022, Springer Science + Business Media

    Dr Davis J McCarthy

  24. SSNIP-seq: A simple and rapid method for isolation of single-sperm nucleic acid for high-throughput sequencing

    Article • PLOS One, September 2022, PLOS

    Dr Davis J McCarthy

  25. sgcocaller and comapr: personalised haplotype assembly and comparative crossover map analysis using single-gamete sequencing data

    Article • Nucleic Acids Research, September 2022, Oxford University Press (OUP)

    Dr Davis J McCarthy

  26. Proliferation drives quorum sensing of microbial products in human macrophage populations

    Article • May 2022, openRxiv

    Dr Davis J McCarthy

  27. A comparison of marker gene selection methods for single-cell RNA sequencing data

    Article • May 2022, Cold Spring Harbor Laboratory Press

    Dr Davis J McCarthy

  28. Demuxafy: Improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods

    Article • March 2022, Cold Spring Harbor Laboratory Press

    Dr Davis J McCarthy

  29. sgcocaller and comapr: personalised haplotype assembly and comparative crossover map analysis using single-gamete sequencing data

    Article • February 2022, Cold Spring Harbor Laboratory Press

    Dr Davis J McCarthy

  30. splatPop: simulating population scale single-cell RNA sequencing data

    Article • Genome Biology, December 2021, Springer Science + Business Media

    Dr Davis J McCarthy

  31. Key signaling networks are dysregulated in patients with the adipose tissue disorder, lipedema

    Article • International Journal of Obesity, November 2021, Springer Science + Business Media

    Dr Davis J McCarthy

  32. splatPop: simulating population scale single-cell RNA sequencing data

    Article • June 2021, Cold Spring Harbor Laboratory Press

    Dr Davis J McCarthy

  33. Personalized genome structure via single gamete sequencing

    Article • Genome Biology, April 2021, Springer Science + Business Media

    Dr Davis J McCarthy

  34. Optimising expression quantitative trait locus mapping workflows for single-cell studies

    Article • January 2021, Cold Spring Harbor Laboratory Press

    Dr Davis J McCarthy

  35. Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data

    Article • Nature Protocols, December 2020, Springer Science + Business Media

    Dr Davis J McCarthy

  36. Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

    Article • Nature Biotechnology, April 2020, Springer Science + Business Media

    Dr Davis J McCarthy

  37. Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes

    Article • Nature Chemical Biology, March 2020, Springer Science + Business Media

    Dr Davide Danovi, Dr Davis J McCarthy

  38. Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

    Article • Nature Communications, February 2020, Springer Science + Business Media

    Dr Davis J McCarthy, Professor Fiona M Watt

  39. Eleven grand challenges in single-cell data science

    Article • February 2020, Springer Science + Business Media

    Dr Davis J McCarthy

  40. Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference

    Article • December 2019, Springer Science + Business Media

    Dr Davis J McCarthy

  41. 12 Grand Challenges in Single-Cell Data Science

    Article • August 2019, PeerJ

    Dr Davis J McCarthy

  42. 12 Grand Challenges in Single-Cell Data Science

    Article • August 2019, PeerJ

    Dr Davis J McCarthy

  43. 12 Grand challenges in single-cell data science

    Article • August 2019, PeerJ

    Dr Davis J McCarthy

  44. Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

    Article • May 2019, Cold Spring Harbor Laboratory Press

    Dr Davis J McCarthy

  45. Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference

    Article • April 2019, Cold Spring Harbor Laboratory Press

    Dr Davis J McCarthy

  46. Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

    Article • February 2019, Springer Science + Business Media

    Dr Davis J McCarthy

  47. Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants

    Article • September 2018, Cold Spring Harbor Laboratory Press

    Dr Davis J McCarthy

  48. Visualization of Biomedical Data

    Article • Annual Review of Biomedical Data Science, July 2018, Annual Reviews

    Dr Davis J McCarthy

  49. Combined single cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

    Article • May 2018, Cold Spring Harbor Laboratory Press

    Dr Davis J McCarthy

  50. Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

    Article • Scientific Data, December 2017, Nature

    Dr Davis J McCarthy, Annemari Käräjämäki

  51. f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq

    Article • November 2017, Springer Science + Business Media

    Dr Davis J McCarthy

  52. NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease

    Article • Mucosal Immunology, November 2017, Nature

    Dr Davis J McCarthy

  53. Erratum: Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs

    Article • Nature, June 2017, Springer Science + Business Media

    Professor Fiona M Watt, Dr Davis J McCarthy, Dr Davide Danovi

  54. Common genetic variation drives molecular heterogeneity in human iPSCs

    Article • Nature, May 2017, Nature

    Dr Angela Goncalves, Dr Davis J McCarthy, Professor Fiona M Watt, Dr Davide Danovi

  55. Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R

    Article • Bioinformatics, January 2017, Oxford University Press (OUP)

    Dr Davis J McCarthy

  56. A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor

    Article • F1000Research, October 2016, Faculty of 1000, Ltd.

    Dr Davis J McCarthy

  57. A step-by-step workflow for low-level analysis of single-cell RNA-seq data

    Article • F1000Research, August 2016, Faculty of 1000, Ltd.

    Dr Davis J McCarthy

  58. The genetic architecture of type 2 diabetes

    Article • Nature, July 2016, Nature

    Dr Davis J McCarthy, Annemari Käräjämäki

  59. Classification of low quality cells from single-cell RNA-seq data

    Article • February 2016, Springer Science + Business Media

    Dr Davis J McCarthy

  60. Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders

    Article • Clinical Immunology, October 2015, Elsevier

    Dr Davis J McCarthy

  61. Gain-of-Function Mutations in ZIC1 Are Associated with Coronal Craniosynostosis and Learning Disability

    Article • The American Journal of Human Genetics, September 2015, Elsevier

    Dr Davis J McCarthy

  62. Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

    Article • Nature Genetics, May 2015, Nature

    Dr Davis J McCarthy

  63. MOZ and BMI1 play opposing roles during Hox gene activation in ES cells and in body segment identity specification in vivo

    Article • Proceedings of the National Academy of Sciences, April 2015, Proceedings of the National Academy of Sciences

    Dr Davis J McCarthy

  64. Erythrocytosis associated with a novel missense mutation in the BPGM gene

    Article • Haematologica, July 2014, Ferrata Storti Foundation (Haematologica)

    Dr Davis J McCarthy

  65. Whole-genome sequencing of bladder cancers reveals somatic CDKN1A mutations and clinicopathological associations with mutation burden

    Article • Nature Communications, April 2014, Nature

    Dr Davis J McCarthy

  66. Choice of transcripts and software has a large effect on variant annotation

    Article • Genome Medicine, January 2014, Springer Science + Business Media

    Dr Davis J McCarthy

  67. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

    Article • Nature Protocols, August 2013, Nature

    Dr Davis J McCarthy

  68. Homozygous mutations in a predicted endonuclease are a novel cause of congenital dyserythropoietic anemia type I

    Article • Haematologica, May 2013, Ferrata Storti Foundation (Haematologica)

    Dr Davis J McCarthy

  69. Mutations in TCF12, encoding a basic helix-loop-helix partner of TWIST1, are a frequent cause of coronal craniosynostosis

    Article • Nature Genetics, January 2013, Nature

    Dr Davis J McCarthy

  70. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

    Article • Nucleic Acids Research, January 2012, Oxford University Press (OUP)

    Dr Davis J McCarthy

  71. Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates

    Article • Statistical Applications in Genetics and Molecular Biology, January 2012, De Gruyter

    Dr Davis J McCarthy

  72. Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design

    Article • September 2011, Springer Science + Business Media

    Dr Davis J McCarthy

  73. Aliskiren increases bradykinin and tissue kallikrein mRNA levels in the heart

    Article • Clinical and Experimental Pharmacology and Physiology, August 2011, Wiley

    Dr Davis J McCarthy

  74. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

    Article • Bioinformatics, November 2009, Oxford University Press (OUP)

    Dr Davis J McCarthy

  75. Testing significance relative to a fold-change threshold is a TREAT

    Article • Bioinformatics, January 2009, Oxford University Press (OUP)

    Dr Davis J McCarthy