Dr Yongxiang Fang BSc, MSc, PhD

Statistican and Bioinformatician Biochemistry & Systems Biology

Publications

2021

Transcriptome and secretome analysis of intra-mammalian life-stages of the emerging helminth pathogen, Calicophoron daubneyi reveals adaptation to a unique host environment. (Journal article)

Huson, K. M., Atcheson, E., Oliver, N. A. M., Best, P., Barley, J. P., Hanna, R. E. B., . . . Robinson, M. W. (2021). Transcriptome and secretome analysis of intra-mammalian life-stages of the emerging helminth pathogen, Calicophoron daubneyi reveals adaptation to a unique host environment.. Molecular & cellular proteomics : MCP, 100055. doi:10.1074/mcp.ra120.002175

DOI: 10.1074/mcp.ra120.002175

Experimental sexual selection reveals rapid divergence in male and female reproductive transcriptomes and their interactions (Journal article)

Veltsos, P., Porcelli, D., Fang, Y., Cossins, A., Ritchie, M., & Snook, R. (2021). Experimental sexual selection reveals rapid divergence in male and female reproductive transcriptomes and their interactions. doi:10.1101/2021.01.29.428831

DOI: 10.1101/2021.01.29.428831

2020

Small Non-Coding RNAome of Ageing Chondrocytes (Journal article)

Balaskas, P., Green, J. A., Haqqi, T. M., Dyer, P., Kharaz, Y. A., Fang, Y., . . . Peffers, M. J. (2020). Small Non-Coding RNAome of Ageing Chondrocytes. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 21(16). doi:10.3390/ijms21165675

DOI: 10.3390/ijms21165675

SnoRNA signatures in cartilage ageing and osteoarthritis (Conference Paper)

Peffers, M. J., Chabronova, A., Balaskas, P., Fang, Y., Dyer, P., Cremers, A., . . . Welting, T. J. M. (2020). SnoRNA signatures in cartilage ageing and osteoarthritis. In SCIENTIFIC REPORTS Vol. 10. doi:10.1038/s41598-020-67446-z

DOI: 10.1038/s41598-020-67446-z

Small RNA signatures of the anterior cruciate ligament from patients with knee joint osteoarthritis (Journal article)

Kharaz, Y., Fang, Y., Welting, T., Peffers, M., & Comerford, E. (2020). Small RNA signatures of the anterior cruciate ligament from patients with knee joint osteoarthritis. doi:10.1101/2020.05.14.20101048

DOI: 10.1101/2020.05.14.20101048

Netazepide Inhibits Expression of Pappalysin 2 in Type 1 Gastric Neuroendocrine Tumors (Journal article)

Lloyd, K. A., Parsons, B. N., Burkitt, M. D., Moore, A. R., Papoutsopoulou, S., Boyce, M., . . . Pritchard, D. M. (2020). Netazepide Inhibits Expression of Pappalysin 2 in Type 1 Gastric Neuroendocrine Tumors. CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY, 10(1), 113-132. doi:10.1016/j.jcmgh.2020.01.010

DOI: 10.1016/j.jcmgh.2020.01.010

Comparison of the myometrial transcriptome from singleton and twin pregnancies by RNA-Seq (Journal article)

Arrowsmith, S., Fang, Y., & Sharp, A. (2020). Comparison of the myometrial transcriptome from singleton and twin pregnancies by RNA-Seq. PLOS ONE, 15(1). doi:10.1371/journal.pone.0227882

DOI: 10.1371/journal.pone.0227882

2019

Characterisation of the NRF2 transcriptional network and its response to chemical insult in primary human hepatocytes: implications for prediction of drug-induced liver injury (Journal article)

Copple, I. M., den Hollander, W., Callegaro, G., Mutter, F. E., Maggs, J. L., Schofield, A. L., . . . Park, B. K. (2019). Characterisation of the NRF2 transcriptional network and its response to chemical insult in primary human hepatocytes: implications for prediction of drug-induced liver injury. Archives of Toxicology, 93, 385-399. doi:10.1007/s00204-018-2354-1

DOI: 10.1007/s00204-018-2354-1

Whole-genome methylation profiling of the retinal pigment epithelium of individuals with age-related macular degeneration reveals differential methylation of the SKI, GTF2H4, and TNXB genes. (Journal article)

Porter, L. F., Saptarshi, N., Fang, Y., Rathi, S., den Hollander, A. I., de Jong, E. K., . . . Paraoan, L. (2019). Whole-genome methylation profiling of the retinal pigment epithelium of individuals with age-related macular degeneration reveals differential methylation of the SKI, GTF2H4, and TNXB genes.. Clinical epigenetics, 11(1), 6. doi:10.1186/s13148-019-0608-2

DOI: 10.1186/s13148-019-0608-2

2018

Genomes of trombidid mites reveal novel predicted allergens and laterally-transferred genes associated with secondary metabolism (Journal article)

Dong, X., Chaisiri, K., Xia, D., Armstrong, S. D., Fang, Y., Donnelly, M. J., . . . Makepeace, B. L. (2018). Genomes of trombidid mites reveal novel predicted allergens and laterally-transferred genes associated with secondary metabolism. GigaScience, 7(12), 33 pages. doi:10.1093/gigascience/giy127

DOI: 10.1093/gigascience/giy127

COMPREHENSIVE EXPRESSION ANALYSIS OF SMALL NON CODING RNAS IN EARLY OSTEOARTHRITIS SYNOVIAL FLUID (Conference Paper)

Peffers, M. J., Balaska, P., Fang, Y., Anderson, J., Burke, K., & Welting, T. (2018). COMPREHENSIVE EXPRESSION ANALYSIS OF SMALL NON CODING RNAS IN EARLY OSTEOARTHRITIS SYNOVIAL FLUID. In OSTEOARTHRITIS AND CARTILAGE Vol. 26 (pp. S186-S187). Retrieved from http://gateway.webofknowledge.com/

Increased socially mediated plasticity in gene expression accompanies rapid adaptive evolution (Journal article)

Pascoal, S., Liu, X., Fang, Y., Paterson, S., Ritchie, M. G., Rockliffe, N., . . . Bailey, N. W. (2018). Increased socially mediated plasticity in gene expression accompanies rapid adaptive evolution. Ecology Letters, 21(4), 546-556. doi:10.1111/ele.12920

DOI: 10.1111/ele.12920

Genomes of trombidid mites reveal novel predicted allergens and laterally-transferred genes associated with secondary metabolism (Journal article)

Dong, X., Chaisiri, K., Xia, D., Armstrong, S., Fang, Y., Donnelly, M., . . . Makepeace, B. (2018). Genomes of trombidid mites reveal novel predicted allergens and laterally-transferred genes associated with secondary metabolism. doi:10.1101/259044

DOI: 10.1101/259044

2017

Mating system manipulation and the evolution of sex-biased gene expression in Drosophila (Journal article)

Veltsos, P., Fang, Y., Cossins, A. R., Snook, R. R., & Ritchie, M. G. (2017). Mating system manipulation and the evolution of sex-biased gene expression in Drosophila. NATURE COMMUNICATIONS, 8. doi:10.1038/s41467-017-02232-6

DOI: 10.1038/s41467-017-02232-6

MicroRNA Profiling in Cartilage Ageing (Journal article)

Balaskas, P., Goljanek-Whysall, K., Clegg, P., Fang, Y., Cremers, A., Emans, P., . . . Peffers, M. (2017). MicroRNA Profiling in Cartilage Ageing. INTERNATIONAL JOURNAL OF GENOMICS, 2017. doi:10.1155/2017/2713725

DOI: 10.1155/2017/2713725

PATHOGEN-SPECIFIC TRADE-OFFS IN HOST TOLERANCE AND SUSCEPTIBILITY PHENOTYPES (Conference Paper)

Antczak, P., Williams, D., Olohan, L., Kay, S., Fang, Y., Gregory, R., . . . Cossins, A. R. (2017). PATHOGEN-SPECIFIC TRADE-OFFS IN HOST TOLERANCE AND SUSCEPTIBILITY PHENOTYPES. In AQUACULTURE Vol. 472 (pp. 145-146). Retrieved from http://gateway.webofknowledge.com/

Serum snoRNAs as biomarkers for joint ageing and post traumatic osteoarthritis (Journal article)

Steinbusch, M. M. F., Fang, Y., Milner, P. I., Clegg, P. D., Young, D. A., Welting, T. J. M., & Peffers, M. J. (2017). Serum snoRNAs as biomarkers for joint ageing and post traumatic osteoarthritis. Scientific reports, 7, 11 pages. doi:10.1038/srep43558

DOI: 10.1038/srep43558

A comparison of host gene expression signatures associated with infection in vitro by the Makona and Ecran (Mayinga) variants of Ebola virus (Journal article)

Bosworth, A., Dowall, S. D., Garcia-Dorival, I., Rickett, N. Y., Bruce, C. B., Matthews, D. A., . . . Hiscox, J. A. (2017). A comparison of host gene expression signatures associated with infection in vitro by the Makona and Ecran (Mayinga) variants of Ebola virus. SCIENTIFIC REPORTS, 7. doi:10.1038/srep43144

DOI: 10.1038/srep43144

Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus (Journal article)

Liu, X., Speranza, E., Muñoz-Fontela, C., Haldenby, S., Rickett, N., Garcia-Dorival, I., . . . Hiscox, J. (2017). Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus. Genome Biology, 18. doi:10.1186/s13059-016-1137-3

DOI: 10.1186/s13059-016-1137-3

2016

A role for small nucleolar RNAs in musculoskeletal ageing and osteoarthritis (Conference Paper)

Peffers, M., Steinbusch, M., Milner, P., Fang, Y., Young, D., Welting, T., & Clegg, P. (2016). A role for small nucleolar RNAs in musculoskeletal ageing and osteoarthritis. In INTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY Vol. 97 (pp. A11). Retrieved from http://gateway.webofknowledge.com/

Decoding the Regulatory Landscape of Ageing in Musculoskeletal Engineered Tissues Using Genome-Wide DNA Methylation and RNASeq (Journal article)

Peffers, M. J., Goljanek-Whysall, K., Collins, J., Fang, Y., Rushton, M., Loughlin, J., . . . Clegg, P. D. (2016). Decoding the Regulatory Landscape of Ageing in Musculoskeletal Engineered Tissues Using Genome-Wide DNA Methylation and RNASeq. PLOS ONE, 11(8). doi:10.1371/journal.pone.0160517

DOI: 10.1371/journal.pone.0160517

Rapid evolution and gene expression: a rapidly evolving Mendelian trait that silences field crickets has widespread effects on mRNA and protein expression (Journal article)

Pascoal, S., Liu, X., Ly, T., Fang, Y., Rockliffe, N., Paterson, S., . . . Bailey, N. W. (2016). Rapid evolution and gene expression: a rapidly evolving Mendelian trait that silences field crickets has widespread effects on mRNA and protein expression. JOURNAL OF EVOLUTIONARY BIOLOGY, 29(6), 1234-1246. doi:10.1111/jeb.12865

DOI: 10.1111/jeb.12865

Rapid evolution and gene expression: a rapidly evolving Mendelian trait that silences field crickets has widespread effects on mRNA and protein expression (Journal article)

Pascoal, S., Liu, X., Ly, T., Fang, Y., Rockliffe, N., Paterson, S., . . . Bailey, N. W. (2016). Rapid evolution and gene expression: a rapidly evolving Mendelian trait that silences field crickets has widespread effects on mRNA and protein expression. JOURNAL OF EVOLUTIONARY BIOLOGY, 29(6), 1234-1246. doi:10.1111/jeb.12865

DOI: 10.1111/jeb.12865

NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap(4)A) and Down-Regulates Immune Response and Cancer Promotion Genes (Journal article)

Marriott, A. S., Vasieva, O., Fang, Y., Copeland, N. A., McLennan, A. G., & Jones, N. J. (2016). NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap(4)A) and Down-Regulates Immune Response and Cancer Promotion Genes. PLOS ONE, 11(5). doi:10.1371/journal.pone.0154674

DOI: 10.1371/journal.pone.0154674

IDENTIFICATION OF SERUM SNORNAS AS BIOMARKERS OF MUSCULOSKELETAL AGEING AND DISEASE (Conference Paper)

Peffers, M. J., Milner, P. M., Fang, Y., Young, D., Whysall, K., & Clegg, P. D. (2016). IDENTIFICATION OF SERUM SNORNAS AS BIOMARKERS OF MUSCULOSKELETAL AGEING AND DISEASE. In OSTEOARTHRITIS AND CARTILAGE Vol. 24 (pp. S41-S42). doi:10.1016/j.joca.2016.01.099

DOI: 10.1016/j.joca.2016.01.099

AGE-RELATED CHANGES IN MESENCHYMAL STEM CELLS IDENTIFIED USING A MULTI-OMICS APPROACH (Journal article)

Peffers, M. J., Collins, J., Fang, Y., Goljanek-Whysall, K., Rushton, M., Loughlin, J., . . . Clegg, P. D. (2016). AGE-RELATED CHANGES IN MESENCHYMAL STEM CELLS IDENTIFIED USING A MULTI-OMICS APPROACH. EUROPEAN CELLS & MATERIALS, 31, 136-159. doi:10.22203/eCM.v031a10

DOI: 10.22203/eCM.v031a10

2015

Integrated transcriptomic and proteomic analyses uncover regulatory roles of Nrf2 in the kidney (Journal article)

Shelton, L. M., Lister, A., Walsh, J., Jenkins, R. E., Wong, M. H. L., Rowe, C., . . . Copple, I. M. (2015). Integrated transcriptomic and proteomic analyses uncover regulatory roles of Nrf2 in the kidney. KIDNEY INTERNATIONAL, 88(06), 1261-1273. doi:10.1038/ki.2015.286

DOI: 10.1038/ki.2015.286

Identification of Potential Biomarkers of Netazepide (YF476) Treatment of Type I Gastric Neuroendocrine Tumours (Conference Paper)

Moore, A. R., Parsons, B. N., Boyce, M. J., Rainbow, L., Fang, Y., Varro, A., . . . Pritchard, D. M. (2015). Identification of Potential Biomarkers of Netazepide (YF476) Treatment of Type I Gastric Neuroendocrine Tumours. In GASTROENTEROLOGY Vol. 148 (pp. S342). Retrieved from http://gateway.webofknowledge.com/

Sa1824 Identification of Potential Biomarkers of Netazepide (YF476) Treatment of Type I Gastric Neuroendocrine Tumours (Journal article)

Moore, A. R., Parsons, B. N., Boyce, M. J., Rainbow, L., Fang, Y., Varro, A., . . . Pritchard, D. M. (2015). Sa1824 Identification of Potential Biomarkers of Netazepide (YF476) Treatment of Type I Gastric Neuroendocrine Tumours. Gastroenterology, 148(4), S-342. doi:10.1016/s0016-5085(15)31140-9

DOI: 10.1016/s0016-5085(15)31140-9

Transcriptome analysis of ageing in uninjured human Achilles tendon (Journal article)

Peffers, M. J., Fang, Y., Cheung, K., Wei, T. K. J., Clegg, P. D., & Birch, H. L. (2015). Transcriptome analysis of ageing in uninjured human Achilles tendon. ARTHRITIS RESEARCH & THERAPY, 17. doi:10.1186/s13075-015-0544-2

DOI: 10.1186/s13075-015-0544-2

2014

Life without Oxygen: Gene Regulatory Responses of the Crucian Carp (Carassius carassius) Heart Subjected to Chronic Anoxia (Journal article)

Stenslokken, K. -O., Ellefsen, S., Vasieva, O., Fang, Y., Farrell, A. P., Olohan, L., . . . Cossins, A. R. (2014). Life without Oxygen: Gene Regulatory Responses of the Crucian Carp (Carassius carassius) Heart Subjected to Chronic Anoxia. PLoS One, 9(11). doi:10.1371/journal.pone.0109978

DOI: 10.1371/journal.pone.0109978

22 Transcriptomic Signatures Of Tendon Ageing (Journal article)

Peffers, M., Fang, Y., Birch, H., Pei, T. K. J., Cheung, K., & Clegg, P. (2014). 22 Transcriptomic Signatures Of Tendon Ageing. British Journal of Sports Medicine, 48(Suppl 2), A14.2-A15. doi:10.1136/bjsports-2014-094114.22

DOI: 10.1136/bjsports-2014-094114.22

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium (Journal article)

Su, Z., Labaj, P. P., Li, S., Thierry-Mieg, J., Thierry-Mieg, D., Shi, W., . . . Shi, L. (2014). A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. NATURE BIOTECHNOLOGY, 32(9), 903-914. doi:10.1038/nbt.2957

DOI: 10.1038/nbt.2957

2013

Article: Transcriptome-wide expression variation associated with environmental plasticity and mating success in cactophilic Drosophila mojavensis. Gilbert Smith, Yongxiang Fang, Xuan Liu, John Kenny, Andrew R Cossins, Cassia Cardoso de Oliveira, William J Etges, Michael G Ritchie (Journal article)

Smith, G., Fang, Y., Liu, X., Kenny, J., Cossins, A. R., Oliveira, C. C. D., . . . Ritchie, M. G. (2013). Article: Transcriptome-wide expression variation associated with environmental plasticity and mating success in cactophilic Drosophila mojavensis. Gilbert Smith, Yongxiang Fang, Xuan Liu, John Kenny, Andrew R Cossins, Cassia Cardoso de Oliveira, William J Etges, Michael G Ritchie. Evolution.

2012

ranscriptomics and in vivo tests reveal novel mechanisms underlying endocrine disruption in an ecological sentinel, Nucella lapillus. (Journal article)

Pascoal, S., Carvalho, G., Vasieva, O., Hughes, R., Cossins, A., Fang, Y., . . . Creer, S. (2012). ranscriptomics and in vivo tests reveal novel mechanisms underlying endocrine disruption in an ecological sentinel, Nucella lapillus.. Molicular Ecology.

2011

Molecular Correlates of Social Dominance: A Novel Role for Ependymin in Aggression (Journal article)

Sneddon, L. U., Schmidt, R., Fang, Y., & Cossins, A. R. (2011). Molecular Correlates of Social Dominance: A Novel Role for Ependymin in Aggression. PLOS ONE, 6(4). doi:10.1371/journal.pone.0018181

DOI: 10.1371/journal.pone.0018181

Molecular Correlates of Social Dominance: A Novel Role for Ependymin in Aggression (Journal article)

Sneddon, L. U., Schmidt, R., Fang, Y., & Cossins, A. R. (n.d.). Molecular Correlates of Social Dominance: A Novel Role for Ependymin in Aggression. PLoS ONE, 6(4), e18181. doi:10.1371/journal.pone.0018181

DOI: 10.1371/journal.pone.0018181

2010

Sesamin as a potential modulator of fatty acid composition in common carp (Cyprinus carpio) (Journal article)

Mraz, J., Schlechtriem, C., Olohan, L. A., Fang, Y., Cossins, A. R., Zlabek, V., . . . Pickova, J. (2010). Sesamin as a potential modulator of fatty acid composition in common carp (Cyprinus carpio). AQUACULTURE RESEARCH, 41(11), e851-e861. doi:10.1111/j.1365-2109.2010.02609.x

DOI: 10.1111/j.1365-2109.2010.02609.x

2008

Microarray analysis of gender- and parasite-specific gene transcription in Strongyloides ratti (Journal article)

Evans, H., Mello, L. V., Fang, Y., Wit, E., Thompson, F. J., Viney, M. E., & Paterson, S. (2008). Microarray analysis of gender- and parasite-specific gene transcription in Strongyloides ratti. INTERNATIONAL JOURNAL FOR PARASITOLOGY, 38(11), 1329-1341. doi:10.1016/j.ijpara.2008.02.004

DOI: 10.1016/j.ijpara.2008.02.004

2006

Hypoxia-inducible myoglobin expression in nonmuscle tissues (Journal article)

Fraser, J., de Mello, L. V., Ward, D., Rees, H. H., Williams, D. R., Fang, Y. C., . . . Cossins, A. R. (2006). Hypoxia-inducible myoglobin expression in nonmuscle tissues. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103(8), 2977-2981. doi:10.1073/pnas.0508270103

DOI: 10.1073/pnas.0508270103

2004

Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate (Journal article)

Gracey, A. Y., Fraser, E. J., Li, W. Z., Fang, Y. X., Taylor, R. R., Rogers, J., . . . Cossins, A. R. (2004). Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 101(48), 16970-16975. doi:10.1073/pnas.0403627101

DOI: 10.1073/pnas.0403627101

2003

A model-based analysis of microarray experimental error and normalisation (Journal article)

Fang, Y. (2003). A model-based analysis of microarray experimental error and normalisation. Nucleic Acids Research, 31(16), 96e-96. doi:10.1093/nar/gng097

DOI: 10.1093/nar/gng097

2001

Model-based scenarios for the epidemiology of HIV/AIDS: the consequences of highly active antiretroviral therapy (Journal article)

Dangerfield, B. C., Fang, Y., & Roberts, C. A. (2001). Model-based scenarios for the epidemiology of HIV/AIDS: the consequences of highly active antiretroviral therapy. System Dynamics Review, 17(2), 119-150. doi:10.1002/sdr.211

DOI: 10.1002/sdr.211