Publications
Selected publications
- Osteoarthritis year in review: genetics, genomics, epigenetics. (Journal article - 2022)
- OATargets: a knowledge base of genes associated with osteoarthritis joint damage in animals (Journal article - 2021)
- SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data. (Journal article - 2019)
- Stratification of knee osteoarthritis: two major patient subgroups identified by genome-wide expression analysis of articular cartilage. (Journal article - 2018)
- PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations. (Journal article - 2016)
- Gene expression changes in damaged osteoarthritic cartilage identify a signature of non-chondrogenic and mechanical responses. (Journal article - 2016)
- Tissue gene expression profiles and communication networks inform candidate blood biomarker identification in psoriasis and atopic dermatitis. (Journal article - 2024)
- The methylomic landscape of human articular cartilage development contains epigenetic signatures of osteoarthritis risk. (Journal article - 2024)
2024
The methylomic landscape of human articular cartilage development contains epigenetic signatures of osteoarthritis risk.
McDonnell, E., Orr, S. E., Barter, M. J., Rux, D., Brumwell, A., Wrobel, N., . . . Rice, S. J. (2024). The methylomic landscape of human articular cartilage development contains epigenetic signatures of osteoarthritis risk.. American journal of human genetics, 111(12), 2756-2772. doi:10.1016/j.ajhg.2024.10.017
HPB SO33 - Transcriptomic characterisation of the diabetogenic pancreatic ductal adenocarcinoma phenotype
Stott, M., Hasoon, M., Oldfield, L., Soul, J., Halloran, C., & Costello, E. (2024). HPB SO33 - Transcriptomic characterisation of the diabetogenic pancreatic ductal adenocarcinoma phenotype. British Journal of Surgery, 111(Supplement_9). doi:10.1093/bjs/znae271.266
Comparative transcriptomic analysis of articular cartilage of post-traumatic osteoarthritis models.
Gilbert, S. J., Soul, J., Hao, Y., Lin, H., Piróg, K. A., Coxhead, J., . . . Blain, E. J. (2024). Comparative transcriptomic analysis of articular cartilage of post-traumatic osteoarthritis models.. Disease models & mechanisms, 17(10), dmm050583. doi:10.1242/dmm.050583
Systems analysis of miR-199a/b-5p and multiple miR-199a/b-5p targets during chondrogenesis.
Patel, K., Barter, M., Soul, J., Clark, P., Proctor, C., Clark, I., . . . Shanley, D. P. (2024). Systems analysis of miR-199a/b-5p and multiple miR-199a/b-5p targets during chondrogenesis.. eLife, 12, RP89701. doi:10.7554/elife.89701
microRNA-324 mediates bone homeostasis and the regulation of osteoblast and osteoclast differentiation and activity.
Hayman, D. J., Johnson de Sousa Brito, F. M., Lin, H., Prior, A., Charlesworth, G., Hao, Y., . . . Young, D. A. (2024). microRNA-324 mediates bone homeostasis and the regulation of osteoblast and osteoclast differentiation and activity.. Bone, 117273. doi:10.1016/j.bone.2024.117273
SERPINA3 is a marker of cartilage differentiation and is essential for the expression of extracellular matrix genes during early chondrogenesis.
Barter, M. J., Turner, D. A., Rice, S. J., Hines, M., Lin, H., Falconer, A. M. D., . . . Wilkinson, D. J. (2024). SERPINA3 is a marker of cartilage differentiation and is essential for the expression of extracellular matrix genes during early chondrogenesis.. Matrix biology : journal of the International Society for Matrix Biology, S0945-053X(24)00095-7. doi:10.1016/j.matbio.2024.07.004
Tissue gene expression profiles and communication networks inform candidate blood biomarker identification in psoriasis and atopic dermatitis.
Soul, J., Carlsson, E., Hofmann, S. R., Russ, S., Hawkes, J., Schulze, F., . . . Hedrich, C. M. (2024). Tissue gene expression profiles and communication networks inform candidate blood biomarker identification in psoriasis and atopic dermatitis.. Clinical immunology (Orlando, Fla.), 265, 110283. doi:10.1016/j.clim.2024.110283
Epigenomic landscape across human articular cartilage development
McDonnell, E., Brumwell, A., Wrobel, N., Murphy, L., Overmann, L. M., Lisgo, S. N., . . . Rice, S. J. (2024). Epigenomic landscape across human articular cartilage development. Osteoarthritis and Cartilage, 32, S14-S15. doi:10.1016/j.joca.2024.02.023
2023
Mesenchymal Stromal Cell Secretome Is Affected by Tissue Source and Donor Age.
Turlo, A. J., Hammond, D. E., Ramsbottom, K. A., Soul, J., Gillen, A., McDonald, K., & Peffers, M. J. (2023). Mesenchymal Stromal Cell Secretome Is Affected by Tissue Source and Donor Age.. Stem cells (Dayton, Ohio), 41(11), 1047-1059. doi:10.1093/stmcls/sxad060
2022
Osteoarthritis year in review: genetics, genomics, epigenetics.
Young, D. A., Barter, M. J., & Soul, J. (2022). Osteoarthritis year in review: genetics, genomics, epigenetics.. Osteoarthritis and cartilage, 30(2), 216-225. doi:10.1016/j.joca.2021.11.004
2021
Increased hippocampal excitability in miR-324-null mice.
Hayman, D. J., Modebadze, T., Charlton, S., Cheung, K., Soul, J., Lin, H., . . . Young, D. A. (2021). Increased hippocampal excitability in miR-324-null mice.. Scientific reports, 11(1), 10452. doi:10.1038/s41598-021-89874-1
Identification and characterization of two consistent osteoarthritis subtypes by transcriptome and clinical data integration.
Coutinho de Almeida, R., Mahfouz, A., Mei, H., Houtman, E., den Hollander, W., Soul, J., . . . Meulenbelt, I. (2021). Identification and characterization of two consistent osteoarthritis subtypes by transcriptome and clinical data integration.. Rheumatology (Oxford, England), 60(3), 1166-1175. doi:10.1093/rheumatology/keaa391
The angiogenic potential of CD271+ human adipose tissue-derived mesenchymal stem cells.
Smith, R. J. P., Faroni, A., Barrow, J. R., Soul, J., & Reid, A. J. (2021). The angiogenic potential of CD271+ human adipose tissue-derived mesenchymal stem cells.. Stem cell research & therapy, 12(1), 160. doi:10.1186/s13287-021-02177-0
OATargets: a knowledge base of genes associated with osteoarthritis joint damage in animals
Soul, J., Barter, M. J., Little, C. B., & Young, D. A. (2021). OATargets: a knowledge base of genes associated with osteoarthritis joint damage in animals. ANNALS OF THE RHEUMATIC DISEASES, 80(3), 376-383. doi:10.1136/annrheumdis-2020-218344
Transgenic inhibition of interleukin-6 trans-signaling does not prevent skeletal pathologies in mucolipidosis type II mice.
Westermann, L. M., Baranowsky, A., Di Lorenzo, G., Danyukova, T., Soul, J., Schwartz, J. -M., . . . Pohl, S. (2021). Transgenic inhibition of interleukin-6 trans-signaling does not prevent skeletal pathologies in mucolipidosis type II mice.. Scientific reports, 11(1), 3556. doi:10.1038/s41598-021-82802-3
2020
Imbalanced cellular metabolism compromises cartilage homeostasis and joint function in a mouse model of mucolipidosis type III gamma.
Westermann, L. M., Fleischhauer, L., Vogel, J., Jenei-Lanzl, Z., Ludwig, N. F., Schau, L., . . . Danyukova, T. (2020). Imbalanced cellular metabolism compromises cartilage homeostasis and joint function in a mouse model of mucolipidosis type III gamma.. Disease models & mechanisms, 13(11), dmm046425. doi:10.1242/dmm.046425
microRNA-seq of cartilage reveals an overabundance of miR-140-3p which contains functional isomiRs.
Woods, S., Charlton, S., Cheung, K., Hao, Y., Soul, J., Reynard, L. N., . . . Young, D. A. (2020). microRNA-seq of cartilage reveals an overabundance of miR-140-3p which contains functional isomiRs.. RNA (New York, N.Y.), 26(11), 1575-1588. doi:10.1261/rna.075176.120
2019
Cartilage endoplasmic reticulum stress may influence the onset but not the progression of experimental osteoarthritis.
Kung, L. H. W., Mullan, L., Soul, J., Wang, P., Mori, K., Bateman, J. F., . . . Boot-Handford, R. P. (2019). Cartilage endoplasmic reticulum stress may influence the onset but not the progression of experimental osteoarthritis.. Arthritis research & therapy, 21(1), 206. doi:10.1186/s13075-019-1988-6
SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data.
Soul, J., Hardingham, T. E., Boot-Handford, R. P., & Schwartz, J. -M. (2019). SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data.. Bioinformatics (Oxford, England), 35(13), 2283-2290. doi:10.1093/bioinformatics/bty947
XBP1 signalling is essential for alleviating mutant protein aggregation in ER-stress related skeletal disease.
Piróg, K. A., Dennis, E. P., Hartley, C. L., Jackson, R. M., Soul, J., Schwartz, J. -M., . . . Briggs, M. D. (2019). XBP1 signalling is essential for alleviating mutant protein aggregation in ER-stress related skeletal disease.. PLoS genetics, 15(7), e1008215. doi:10.1371/journal.pgen.1008215
Identification of long non-coding RNAs expressed in knee and hip osteoarthritic cartilage.
Ajekigbe, B., Cheung, K., Xu, Y., Skelton, A. J., Panagiotopoulos, A., Soul, J., . . . Young, D. A. (2019). Identification of long non-coding RNAs expressed in knee and hip osteoarthritic cartilage.. Osteoarthritis and cartilage, 27(4), 694-702. doi:10.1016/j.joca.2018.12.015
2018
Stratification of knee osteoarthritis: two major patient subgroups identified by genome-wide expression analysis of articular cartilage.
Soul, J., Dunn, S. L., Anand, S., Serracino-Inglott, F., Schwartz, J. -M., Boot-Handford, R. P., & Hardingham, T. E. (2018). Stratification of knee osteoarthritis: two major patient subgroups identified by genome-wide expression analysis of articular cartilage.. Annals of the rheumatic diseases, 77(3), 423. doi:10.1136/annrheumdis-2017-212603
2016
PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations.
Soul, J., Dunn, S. L., Hardingham, T. E., Boot-Handford, R. P., & Schwartz, J. -M. (2016). PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations.. Bioinformatics (Oxford, England), 32(24), 3847-3849. doi:10.1093/bioinformatics/btw545
Gene expression changes in damaged osteoarthritic cartilage identify a signature of non-chondrogenic and mechanical responses.
Dunn, S. L., Soul, J., Anand, S., Schwartz, J. -M., Boot-Handford, R. P., & Hardingham, T. E. (2016). Gene expression changes in damaged osteoarthritic cartilage identify a signature of non-chondrogenic and mechanical responses.. Osteoarthritis and cartilage, 24(8), 1431-1440. doi:10.1016/j.joca.2016.03.007
2015
PhenomeExpress: a refined network analysis of expression datasets by inclusion of known disease phenotypes.
Soul, J., Hardingham, T. E., Boot-Handford, R. P., & Schwartz, J. -M. (2015). PhenomeExpress: a refined network analysis of expression datasets by inclusion of known disease phenotypes.. Scientific reports, 5, 8117. doi:10.1038/srep08117
2011
Quantitative proteomic analysis of the adipocyte plasma membrane.
Prior, M. J., Larance, M., Lawrence, R. T., Soul, J., Humphrey, S., Burchfield, J., . . . James, D. E. (2011). Quantitative proteomic analysis of the adipocyte plasma membrane.. Journal of proteome research, 10(11), 4970-4982. doi:10.1021/pr200446r