Mr John Cole

  • Research Scientist (Immunology & Infection)

telephone: 0141 330 6267
email: John.Cole@glasgow.ac.uk

Import to contacts

Biography

I completed a B.Sci (Hons) in Molecular Genetics at University of Glasgow in 2009, modelling cultural and genetic coevolution for the project. I received a Research Assistant post under Dr Richard Wilson writing tools to detect mutability at the clinically important ADRB2 gene. In 2012 I completed an MRes in Bioinformatics at University of Glasgow, writing tools that detected over 200,000 new high frequency human STR alleles in the 1,000 genome project data. In 2013, I joined the Beatson Institute under Professor Peter Adams, working on the epigenetics of cancer, ageing and cellular senescence. 

In 2016, I joined Professor Carl Goodyear's group in the Infection, Immunity and Inflammation (now School of Infection & Immunity), under the industry-academia collaboration The GLAZgo Discovery Centre, focussing on the omics of rheumatology and respiratory disease. In this time, I developed Searchlight - a tool for automating the data analysis step of bulk RNA-seq. I grew to appreciate that the wider Immunology groups needed additional bioinformatic support and started several initiatives - support drop-ins, training courses and introductory lectures. I also founded the Glasgow Bioinformatic Community - now the Glasgow Computational Biology Community. During the COVID-19 pandemic, I set up the Bioinformatic Support for Dry Masters Projects programme alongside Glasgow Polyomics, which has remained popular, and saved 100s of students from the tedium of a literature review. 

The new Bioinformatics Facility - The Bioinformatic Core which I now manage, as a pay-for-use service - was launched in 2021. I provide bioinformatic support to the School on all levels, including omic data analysis, assistance with grant bids and manuscripts, and general advice in abundance. During this time, I have recognised the global demand for affordable, high quality bioinformatic training for PhD students and Post-Docs and have developed the Bioinformatics for Wet-Lab Biologists programme in response. This has been popular with over 200 attendees a year, from across Europe and Africa, and a median rating of 10/10 for content and delivery. We are now a formal training partner for the British Society of Immunology and its members. 

My most recent work involves new methods for the analysis of Spatial Transcriptomics, combining image information with RNA-seq, as part of the Glasgow-Lilly collaboration. I am also developing new methods for assessing transcriptome aligners and the impact of misaligned reads on research.  

 

Publications

List by: Type | Date

Jump to: 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2017 | 2016 | 2015 | 2014 | 2010
Number of items: 39.

2024

Nair, R., Lannagan, T. R.M., Jackstadt, R., Andrusaite, A., Cole, J., Boyne, C., Nibbs, R. J.B. , Sansom, O. J. and Milling, S. (2024) Co-inhibition of TGF-β and PD-L1 pathways in a metastatic colorectal cancer mouse model triggers interferon responses, innate cells and T cells, alongside metabolic changes and tumor resistance. OncoImmunology, 13(1), 2330194. (doi: 10.1080/2162402X.2024.2330194)

Nair, R., Lannagan, T. R.M., Jackstadt, R., Andrusaite, A., Cole, J., Boyne, C., Nibbs, R. J.B., Sansom, O. J. and Milling, S. (2024) Cancer cell metabolic reprogramming by co-inhibition of TGF-β and PD-L1 may lead to tumour resistance in a metastatic colorectal cancer mouse model. OncoImmunology, (Accepted for Publication)

2023

Jaffery, H. et al. (2023) IĸB Protein BCL3 as a controller of osteogenesis and bone health. Arthritis and Rheumatology, 75(12), 2148-2160-2148-2160. (doi: 10.1002/art.42639) (PMID:37410754)

Thümmler, K. et al. (2023) Fibroblast growth factor 9 (FGF9) mediated neurodegeneration: implications for progressive multiple sclerosis? Neuropathology and Applied Neurobiology, 49(5), e12935. (doi: 10.1111/nan.12935) (PMID:37705188)

Cole, S. et al. (2023) Differential regulation of IL-17A and IL-17F via STAT5 contributes to psoriatic disease. Journal of Allergy and Clinical Immunology, 152(3), pp. 783-798. (doi: 10.1016/j.jaci.2023.03.035) (PMID:37244461)

Ormsby, M. J. et al. (2023) An intact S-layer is advantageous to Clostridioides difficile within the host. PLoS Pathogens, 19(6), e1011015. (doi: 10.1371/journal.ppat.1011015) (PMID:37384772) (PMCID:PMC10310040)

Johnsson, H., Cole, J., McInnes, I. B. , Graham, G. and Siebert, S. (2023) Differences in transcriptional changes in psoriasis and psoriatic arthritis skin with immunoglobulin gene enrichment in psoriatic arthritis. Rheumatology, (doi: 10.1093/rheumatology/kead195) (PMID:37137278) (Early Online Publication)

Johnsson, H., Cole, J., Siebert, S. , McInnes, I. B. and Graham, G. (2023) Cutaneous lesions in psoriatic arthritis are enriched in chemokine transcriptomic pathways. Arthritis Research and Therapy, 25, 73. (doi: 10.1186/s13075-023-03034-6) (PMID:37131254) (PMCID:PMC10152590)

Orchard, K. J.A., Akbar, M., Crower, L. A.N., Cole, J., Millar, N. L. and Raleigh, S. M. (2023) Characterization of histone modifications in late-stage rotator cuff tendinopathy. Genes, 14(2), 496. (doi: 10.3390/genes14020496) (PMID:36833423) (PMCID:PMC9956879)

2022

Thümmler, K. , Williams, M. T.S., Kitson, S., Sood, S., Akbar, M., Cole, J. J., Goodyear, C. S. , Hunter, E. and Soutar, R. (2022) Targeting 3D chromosomal architecture at the RANK loci to suppress myeloma-driven osteoclastogenesis. OncoImmunology, 11(1), 2104070. (doi: 10.1080/2162402X.2022.2104070) (PMID:35936985) (PMCID:PMC9348127)

Prendergast, C. T., Benson, R. A. , Scales, H. E. , Bonilha, C. S., Cole, J. J., McInnes, I. , Brewer, J. M. and Garside, P. (2022) Dissecting the molecular control of immune cell accumulation in the inflamed joint. JCI Insight, 7(7), e151281. (doi: 10.1172/jci.insight.151281) (PMID:35192549) (PMCID:PMC9057592)

2021

Suzuki, M., Cole, J. J., Konno, S., Makita, H., Kimura, H., Nishimura, M. and Maciewicz, R. A. (2021) Large‐scale plasma proteomics can reveal distinct endotypes in chronic obstructive pulmonary disease and severe asthma. Clinical and Translational Allergy, 11(10), e12091. (doi: 10.1002/clt2.12091)

Cole, J. J., Faydaci, B. A., Mcguinness, D. , Shaw, R., Maciewicz, R. A., Robertson, N. A. and Goodyear, C. S. (2021) Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts. BMC Bioinformatics, 22(1), 411. (doi: 10.1186/s12859-021-04321-2)

Cole, J. J. et al. (2021) No evidence for differential gene expression in major depressive disorder PBMCs, but robust evidence of elevated biological ageing. Translational Psychiatry, 11, 404. (doi: 10.1038/s41398-021-01506-4) (PMID:34294682) (PMCID:PMC8298604)

Ansalone, C. , Cole, J., Chilaka, S., Sunzini, F., Sood, S., Robertson, J., Siebert, S. , McInnes, I. B. and Goodyear, C. (2021) TNF is a homeostatic regulator of distinct epigenetically primed human osteoclast precursors. Annals of the Rheumatic Diseases, 80(6), pp. 748-757. (doi: 10.1136/annrheumdis-2020-219262) (PMID:33692019) (PMCID:PMC8142443)

Kästele, V. et al. (2021) Intestinal-derived ILCs migrating in lymph increase IFNγ production in response to Salmonella Typhimurium infection. Mucosal Immunology, 14(3), pp. 717-727. (doi: 10.1038/s41385-020-00366-3) (PMID:33414524) (PMCID:PMC8075955)

Baer, H. M. et al. (2021) P83 Understanding Differences in Serum and Mucosal Immunopathotypes in Crohn’s Disease. BSG Campus, 21-29 Jan 2021. (doi: 10.1136/gutjnl-2020-bsgcampus.158)

Latif, A.-L. et al. (2021) BRD4-mediated repression of p53 is a target for combination therapy in AML. Nature Communications, 12, 241. (doi: 10.1038/s41467-020-20378-8) (PMID:33431824) (PMCID:PMC7801601)

2020

Li, S. et al. (2020) A Synthetic Lethal Approach to Eradicate AML via Synergistic Activation of Pro-Apoptotic p53 By MDM2 and BET Inhibitors. 62nd ASH Annual Meeting and Exposition, 5-8 Dec 2020. (doi: 10.1182/blood-2020-143079)

Li, S. et al. (2020) 3102 – A Synthetic Lethality Approach to Eradicate AML via Synergistic Activation of Pro-Apoptotic p53 By MDM2 and BET Inhibitors. 49th Annual Scientific Meeting of the ISEH (International Society for Experimental Hematology), 19-21 Aug 2020. (doi: 10.1016/j.exphem.2020.09.115)

Johnsson, H., Cole, J., Wilson, G., Pingen, M., Mcmonagle, F., Holmes, S., Mcinnes, I., Siebert, S. and Graham, G. (2020) SAT0351 Chemokine Pathways Are Enriched in Psoriatic Arthritis (Psa) Skin Lesions with Increased Expression of Atypical Chemokine Receptor 2 (ACKR2). EULAR 2021, 2-5 June 2020. (doi: 10.1136/annrheumdis-2020-eular.2980)

Rodgers, L. C., Cole, J., Rattigan, K. M., Barrett, M. P. , Kurian, N., McInnes, I. B. and Goodyear, C. S. (2020) The rheumatoid synovial environment alters fatty acid metabolism in human monocytes and enhances CCL20 secretion. Rheumatology, 59(4), pp. 869-878. (doi: 10.1093/rheumatology/kez378) (PMID:31497857)

Baer, H.M. et al. (2020) P014 Identification of Crohn’s Disease Immunopathotypes. 15th Congress of ECCO, Vienna, Austria, 12–15 Feb 2020. (doi: 10.1093/ecco-jcc/jjz203.143)

2019

Thümmler, K. et al. (2019) Polarizing receptor activation dissociates Fibroblast Growth Factor 2 mediated inhibition of myelination from its neuroprotective potential. Acta Neuropathologica Communications, 7, 212. (doi: 10.1186/s40478-019-0864-6) (PMID:31856924) (PMCID:PMC6923900)

Smith, E. L., Somma, D. , Kerrigan, D., McIntyre, Z., Cole, J. J., Liang, K. L., Kiely, P. A., Keeshan, K. and Carmody, R. J. (2019) The regulation of sequence specific NF-ĸB DNA binding and transcription by IKKβ Phosphorylation of NF-ĸB p50 at Serine 80. Nucleic Acids Research, 47(21), pp. 11151-11161. (doi: 10.1093/nar/gkz873) (PMID:31598684) (PMCID:PMC6868378)

Asghar, S., Litherland, G., Meek, D., Cole, J., Lockhart, J., Goodyear, C. S. and Crilly, A. (2019) Differential Effects of Exosomes Derived from Separate Osteoarthritis Synovial Compartments: Implications for Erosive Cartilage Disease. 2019 OARSI World Congress on Osteoarthritis, Toronto, Canada, 2-5 May 2019. (doi: 10.1016/j.joca.2019.02.295)

Rodgers, L.C., Cole, J., Rattigan, K., Barrett, M.P., Kurian, N., McInnes, I.B. and Goodyear, C.S. (2019) P108/O28 Fatty Acid Oxidation Can Drive Human Monocyte Derived CCL20 in the RA Synovial Environment. 39th European Workshop for Rheumatology Research, Lyon, France, 28 Feb-2 March 2019. (doi: 10.1136/annrheumdis-2018-EWRR2019.96)

2017

Rai, T. S., Glass, M., Cole, J. J., Rather, M., Marsden, M., Neilson, M., Brock, C., Humphreys, I. R., Everett, R. D. and Adams, P. D. (2017) Histone chaperone HIRA deposits histone H3.3 onto foreign viral DNA and contributes to anti-viral intrinsic immunity. Nucleic Acids Research, 45(20), pp. 11673-11683. (doi: 10.1093/nar/gkx771) (PMID:28981850) (PMCID:PMC5691367)

van Tuyn, J. et al. (2017) Oncogene-expressing senescent melanocytes upregulate MhC class II, a candidate melanoma suppressor function. Journal of Investigative Dermatology, 137(10), pp. 2197-2207. (doi: 10.1016/j.jid.2017.05.030) (PMID:28647344) (PMCID:PMC5613751)

Cole, J. J. et al. (2017) Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions. Genome Biology, 18, 58. (doi: 10.1186/s13059-017-1185-3) (PMID:28351383) (PMCID:PMC5370462)

2016

Nelson, D. M. et al. (2016) Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability. Genome Biology, 17, 158. (doi: 10.1186/s13059-016-1017-x) (PMID:27457071) (PMCID:PMC4960804)

Correia-Melo, C. et al. (2016) Mitochondria are required for pro-ageing features of the senescent phenotype. EMBO Journal, 35, pp. 724-742. (doi: 10.15252/embj.201592862) (PMID:26848154) (PMCID:PMC4818766)

2015

Latif, A.-L., Cole, J. J., Monteiro Campos, J., Clark, W., McGarry, L., Brock, C., Newcombe, A., Keeshan, K. , Copland, M. and Adams, P. D. (2015) Dual inhibition of MDM2 and BET cooperate to eradicate acute myeloid leukemia. Blood, 126(23), p. 674. (doi: 10.1182/blood.V126.23.674.674)

MacKenzie, D. J., Robertson, N. A., Cole, J. and Adams, P. (2015) Su1996 oncogenic BRAFV600e downregulates DNMT3B and does not directly induce the CpG island hypermethylator phenotype in human colorectal adenocarcinoma. Gastroenterology, 148(4), S570. (doi: 10.1016/S0016-5085(15)31925-9)

Dikovskaya, D. et al. (2015) Mitotic stress is an integral part of the oncogene-induced senescence program that promotes multinucleation and cell cycle arrest. Cell Reports, 12(9), pp. 1483-1496. (doi: 10.1016/j.celrep.2015.07.055) (PMID:26299965) (PMCID:PMC4562906)

2014

Lund, K., Cole, J., VanderKraats, N. D., McBryan, T., Pchelintsev, N. A., Clark, W., Copland, M. , Edwards, J. R. and Adams, P. (2014) DNMT inhibitors reverse a specific signature of aberrant promoter DNA methylation and associated gene silencing in AML. Genome Biology, 15(7), p. 406. (doi: 10.1186/s13059-014-0406-2)

Lund, K., Cole, J., McBryan, T., Copland, M. and Adams, P. (2014) Investigating effects of epigenetic modulation in acute myeloid leukaemia. Lancet, 383(Supl 1), S70. (doi: 10.1016/S0140-6736(14)60333-0) (PMID:19345831) (PMCID:PMC2866651)

Rai, T. S. et al. (2014) HIRA orchestrates a dynamic chromatin landscape in senescence and is required for suppression of neoplasia. Genes and Development, 28(24), pp. 2712-2725. (doi: 10.1101/gad.247528.114) (PMID:25512559) (PMCID:PMC4265675)

2010

Wilson, R.H., Moran, C.N., Cole, J., Pitsiladis, Y.P. and Bailey, M.E.S. (2010) Evolutionary history of the ADRB2 gene in humans. American Journal of Human Genetics, 86(3), pp. 490-493. (doi: 10.1016/j.ajhg.2010.01.031) (PMID:20215008) (PMCID:PMC2833374)

This list was generated on Fri Apr 19 15:36:13 2024 BST.
Jump to: Articles | Conference or Workshop Item
Number of items: 39.

Articles

Nair, R., Lannagan, T. R.M., Jackstadt, R., Andrusaite, A., Cole, J., Boyne, C., Nibbs, R. J.B. , Sansom, O. J. and Milling, S. (2024) Co-inhibition of TGF-β and PD-L1 pathways in a metastatic colorectal cancer mouse model triggers interferon responses, innate cells and T cells, alongside metabolic changes and tumor resistance. OncoImmunology, 13(1), 2330194. (doi: 10.1080/2162402X.2024.2330194)

Nair, R., Lannagan, T. R.M., Jackstadt, R., Andrusaite, A., Cole, J., Boyne, C., Nibbs, R. J.B., Sansom, O. J. and Milling, S. (2024) Cancer cell metabolic reprogramming by co-inhibition of TGF-β and PD-L1 may lead to tumour resistance in a metastatic colorectal cancer mouse model. OncoImmunology, (Accepted for Publication)

Jaffery, H. et al. (2023) IĸB Protein BCL3 as a controller of osteogenesis and bone health. Arthritis and Rheumatology, 75(12), 2148-2160-2148-2160. (doi: 10.1002/art.42639) (PMID:37410754)

Thümmler, K. et al. (2023) Fibroblast growth factor 9 (FGF9) mediated neurodegeneration: implications for progressive multiple sclerosis? Neuropathology and Applied Neurobiology, 49(5), e12935. (doi: 10.1111/nan.12935) (PMID:37705188)

Cole, S. et al. (2023) Differential regulation of IL-17A and IL-17F via STAT5 contributes to psoriatic disease. Journal of Allergy and Clinical Immunology, 152(3), pp. 783-798. (doi: 10.1016/j.jaci.2023.03.035) (PMID:37244461)

Ormsby, M. J. et al. (2023) An intact S-layer is advantageous to Clostridioides difficile within the host. PLoS Pathogens, 19(6), e1011015. (doi: 10.1371/journal.ppat.1011015) (PMID:37384772) (PMCID:PMC10310040)

Johnsson, H., Cole, J., McInnes, I. B. , Graham, G. and Siebert, S. (2023) Differences in transcriptional changes in psoriasis and psoriatic arthritis skin with immunoglobulin gene enrichment in psoriatic arthritis. Rheumatology, (doi: 10.1093/rheumatology/kead195) (PMID:37137278) (Early Online Publication)

Johnsson, H., Cole, J., Siebert, S. , McInnes, I. B. and Graham, G. (2023) Cutaneous lesions in psoriatic arthritis are enriched in chemokine transcriptomic pathways. Arthritis Research and Therapy, 25, 73. (doi: 10.1186/s13075-023-03034-6) (PMID:37131254) (PMCID:PMC10152590)

Orchard, K. J.A., Akbar, M., Crower, L. A.N., Cole, J., Millar, N. L. and Raleigh, S. M. (2023) Characterization of histone modifications in late-stage rotator cuff tendinopathy. Genes, 14(2), 496. (doi: 10.3390/genes14020496) (PMID:36833423) (PMCID:PMC9956879)

Thümmler, K. , Williams, M. T.S., Kitson, S., Sood, S., Akbar, M., Cole, J. J., Goodyear, C. S. , Hunter, E. and Soutar, R. (2022) Targeting 3D chromosomal architecture at the RANK loci to suppress myeloma-driven osteoclastogenesis. OncoImmunology, 11(1), 2104070. (doi: 10.1080/2162402X.2022.2104070) (PMID:35936985) (PMCID:PMC9348127)

Prendergast, C. T., Benson, R. A. , Scales, H. E. , Bonilha, C. S., Cole, J. J., McInnes, I. , Brewer, J. M. and Garside, P. (2022) Dissecting the molecular control of immune cell accumulation in the inflamed joint. JCI Insight, 7(7), e151281. (doi: 10.1172/jci.insight.151281) (PMID:35192549) (PMCID:PMC9057592)

Suzuki, M., Cole, J. J., Konno, S., Makita, H., Kimura, H., Nishimura, M. and Maciewicz, R. A. (2021) Large‐scale plasma proteomics can reveal distinct endotypes in chronic obstructive pulmonary disease and severe asthma. Clinical and Translational Allergy, 11(10), e12091. (doi: 10.1002/clt2.12091)

Cole, J. J., Faydaci, B. A., Mcguinness, D. , Shaw, R., Maciewicz, R. A., Robertson, N. A. and Goodyear, C. S. (2021) Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts. BMC Bioinformatics, 22(1), 411. (doi: 10.1186/s12859-021-04321-2)

Cole, J. J. et al. (2021) No evidence for differential gene expression in major depressive disorder PBMCs, but robust evidence of elevated biological ageing. Translational Psychiatry, 11, 404. (doi: 10.1038/s41398-021-01506-4) (PMID:34294682) (PMCID:PMC8298604)

Ansalone, C. , Cole, J., Chilaka, S., Sunzini, F., Sood, S., Robertson, J., Siebert, S. , McInnes, I. B. and Goodyear, C. (2021) TNF is a homeostatic regulator of distinct epigenetically primed human osteoclast precursors. Annals of the Rheumatic Diseases, 80(6), pp. 748-757. (doi: 10.1136/annrheumdis-2020-219262) (PMID:33692019) (PMCID:PMC8142443)

Kästele, V. et al. (2021) Intestinal-derived ILCs migrating in lymph increase IFNγ production in response to Salmonella Typhimurium infection. Mucosal Immunology, 14(3), pp. 717-727. (doi: 10.1038/s41385-020-00366-3) (PMID:33414524) (PMCID:PMC8075955)

Latif, A.-L. et al. (2021) BRD4-mediated repression of p53 is a target for combination therapy in AML. Nature Communications, 12, 241. (doi: 10.1038/s41467-020-20378-8) (PMID:33431824) (PMCID:PMC7801601)

Rodgers, L. C., Cole, J., Rattigan, K. M., Barrett, M. P. , Kurian, N., McInnes, I. B. and Goodyear, C. S. (2020) The rheumatoid synovial environment alters fatty acid metabolism in human monocytes and enhances CCL20 secretion. Rheumatology, 59(4), pp. 869-878. (doi: 10.1093/rheumatology/kez378) (PMID:31497857)

Thümmler, K. et al. (2019) Polarizing receptor activation dissociates Fibroblast Growth Factor 2 mediated inhibition of myelination from its neuroprotective potential. Acta Neuropathologica Communications, 7, 212. (doi: 10.1186/s40478-019-0864-6) (PMID:31856924) (PMCID:PMC6923900)

Smith, E. L., Somma, D. , Kerrigan, D., McIntyre, Z., Cole, J. J., Liang, K. L., Kiely, P. A., Keeshan, K. and Carmody, R. J. (2019) The regulation of sequence specific NF-ĸB DNA binding and transcription by IKKβ Phosphorylation of NF-ĸB p50 at Serine 80. Nucleic Acids Research, 47(21), pp. 11151-11161. (doi: 10.1093/nar/gkz873) (PMID:31598684) (PMCID:PMC6868378)

Rai, T. S., Glass, M., Cole, J. J., Rather, M., Marsden, M., Neilson, M., Brock, C., Humphreys, I. R., Everett, R. D. and Adams, P. D. (2017) Histone chaperone HIRA deposits histone H3.3 onto foreign viral DNA and contributes to anti-viral intrinsic immunity. Nucleic Acids Research, 45(20), pp. 11673-11683. (doi: 10.1093/nar/gkx771) (PMID:28981850) (PMCID:PMC5691367)

van Tuyn, J. et al. (2017) Oncogene-expressing senescent melanocytes upregulate MhC class II, a candidate melanoma suppressor function. Journal of Investigative Dermatology, 137(10), pp. 2197-2207. (doi: 10.1016/j.jid.2017.05.030) (PMID:28647344) (PMCID:PMC5613751)

Cole, J. J. et al. (2017) Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions. Genome Biology, 18, 58. (doi: 10.1186/s13059-017-1185-3) (PMID:28351383) (PMCID:PMC5370462)

Nelson, D. M. et al. (2016) Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability. Genome Biology, 17, 158. (doi: 10.1186/s13059-016-1017-x) (PMID:27457071) (PMCID:PMC4960804)

Correia-Melo, C. et al. (2016) Mitochondria are required for pro-ageing features of the senescent phenotype. EMBO Journal, 35, pp. 724-742. (doi: 10.15252/embj.201592862) (PMID:26848154) (PMCID:PMC4818766)

Latif, A.-L., Cole, J. J., Monteiro Campos, J., Clark, W., McGarry, L., Brock, C., Newcombe, A., Keeshan, K. , Copland, M. and Adams, P. D. (2015) Dual inhibition of MDM2 and BET cooperate to eradicate acute myeloid leukemia. Blood, 126(23), p. 674. (doi: 10.1182/blood.V126.23.674.674)

MacKenzie, D. J., Robertson, N. A., Cole, J. and Adams, P. (2015) Su1996 oncogenic BRAFV600e downregulates DNMT3B and does not directly induce the CpG island hypermethylator phenotype in human colorectal adenocarcinoma. Gastroenterology, 148(4), S570. (doi: 10.1016/S0016-5085(15)31925-9)

Dikovskaya, D. et al. (2015) Mitotic stress is an integral part of the oncogene-induced senescence program that promotes multinucleation and cell cycle arrest. Cell Reports, 12(9), pp. 1483-1496. (doi: 10.1016/j.celrep.2015.07.055) (PMID:26299965) (PMCID:PMC4562906)

Lund, K., Cole, J., VanderKraats, N. D., McBryan, T., Pchelintsev, N. A., Clark, W., Copland, M. , Edwards, J. R. and Adams, P. (2014) DNMT inhibitors reverse a specific signature of aberrant promoter DNA methylation and associated gene silencing in AML. Genome Biology, 15(7), p. 406. (doi: 10.1186/s13059-014-0406-2)

Lund, K., Cole, J., McBryan, T., Copland, M. and Adams, P. (2014) Investigating effects of epigenetic modulation in acute myeloid leukaemia. Lancet, 383(Supl 1), S70. (doi: 10.1016/S0140-6736(14)60333-0) (PMID:19345831) (PMCID:PMC2866651)

Rai, T. S. et al. (2014) HIRA orchestrates a dynamic chromatin landscape in senescence and is required for suppression of neoplasia. Genes and Development, 28(24), pp. 2712-2725. (doi: 10.1101/gad.247528.114) (PMID:25512559) (PMCID:PMC4265675)

Wilson, R.H., Moran, C.N., Cole, J., Pitsiladis, Y.P. and Bailey, M.E.S. (2010) Evolutionary history of the ADRB2 gene in humans. American Journal of Human Genetics, 86(3), pp. 490-493. (doi: 10.1016/j.ajhg.2010.01.031) (PMID:20215008) (PMCID:PMC2833374)

Conference or Workshop Item

Baer, H. M. et al. (2021) P83 Understanding Differences in Serum and Mucosal Immunopathotypes in Crohn’s Disease. BSG Campus, 21-29 Jan 2021. (doi: 10.1136/gutjnl-2020-bsgcampus.158)

Li, S. et al. (2020) A Synthetic Lethal Approach to Eradicate AML via Synergistic Activation of Pro-Apoptotic p53 By MDM2 and BET Inhibitors. 62nd ASH Annual Meeting and Exposition, 5-8 Dec 2020. (doi: 10.1182/blood-2020-143079)

Li, S. et al. (2020) 3102 – A Synthetic Lethality Approach to Eradicate AML via Synergistic Activation of Pro-Apoptotic p53 By MDM2 and BET Inhibitors. 49th Annual Scientific Meeting of the ISEH (International Society for Experimental Hematology), 19-21 Aug 2020. (doi: 10.1016/j.exphem.2020.09.115)

Johnsson, H., Cole, J., Wilson, G., Pingen, M., Mcmonagle, F., Holmes, S., Mcinnes, I., Siebert, S. and Graham, G. (2020) SAT0351 Chemokine Pathways Are Enriched in Psoriatic Arthritis (Psa) Skin Lesions with Increased Expression of Atypical Chemokine Receptor 2 (ACKR2). EULAR 2021, 2-5 June 2020. (doi: 10.1136/annrheumdis-2020-eular.2980)

Baer, H.M. et al. (2020) P014 Identification of Crohn’s Disease Immunopathotypes. 15th Congress of ECCO, Vienna, Austria, 12–15 Feb 2020. (doi: 10.1093/ecco-jcc/jjz203.143)

Asghar, S., Litherland, G., Meek, D., Cole, J., Lockhart, J., Goodyear, C. S. and Crilly, A. (2019) Differential Effects of Exosomes Derived from Separate Osteoarthritis Synovial Compartments: Implications for Erosive Cartilage Disease. 2019 OARSI World Congress on Osteoarthritis, Toronto, Canada, 2-5 May 2019. (doi: 10.1016/j.joca.2019.02.295)

Rodgers, L.C., Cole, J., Rattigan, K., Barrett, M.P., Kurian, N., McInnes, I.B. and Goodyear, C.S. (2019) P108/O28 Fatty Acid Oxidation Can Drive Human Monocyte Derived CCL20 in the RA Synovial Environment. 39th European Workshop for Rheumatology Research, Lyon, France, 28 Feb-2 March 2019. (doi: 10.1136/annrheumdis-2018-EWRR2019.96)

This list was generated on Fri Apr 19 15:36:13 2024 BST.

Grants

Grants and Awards listed are those received whilst working with the University of Glasgow.

  • Identification of novel drug targets for large vessel vasculitis
    Vasculitis UK
    2023 - 2025
     

Teaching

Undergraduate Teaching

  • Level 4 bioinformatics and R for biologists (coordinator)
  • Level 4: Personalised medicine and clinical trials (lecturer)
  • Level 4: Genetics (lecturer)

 

Postgraduate Teaching

  • R and data analysis for bioinformatics (coordinator)
  • Bioinformatics using R for biologists (coordinator)
  • Introduction to omics for precision medicine (coordinator)
  • Statistics and data analysis for bioinformatics (deputy coordinator)
    Bioinformatics support for wet-lab masters summer projects (coordinator)
  • RNA and Next Generation Sequencing (lecturer)

 

PhD student and Postdoc Training

I set up and run the Bioinformatics for Wet-Lab Biologists programme, which aims to equip wet-lab scientists who have no prior experience of omics or coding, with all the skills they need to perform their own analysis unaided. This is an entirely entry level and skills-based programme. Covering R and command line programming, omic tools and technologies, parsing, omic plots and data analysis (PCA, heatmaps, volcano plots, violin, fold vs fold, signature analysis, pathway analysis etc). 

The full programme is split into four logical blocks, the first being essential, the others optional as required:

  • Block 1 - Omic data analysis and visualisation using R (2 weeks)
  • Block 2 - Complex experiments, signatures, and biomarkers (1 week)
  • Block 3 - Command line omics (2 weeks)
  • Block 4 - Single cell RNA-seq (1 week)

All blocks are run via zoom, five days a week, 9.30am to 12.30pm (allowing for regular wet-lab work in the afternoon) and run several times a year. They cost £125 per week for Glasgow members and £150 per week for external. For dates and to sign up please fill out this form (this form), or email John for further information.

 

Professional activities & recognition

Editorial boards

  • 2022 - present: Discover Immunology

Selected international presentations

  • 2019: NGS & Single Cell Analysis Congress (London, UK)
  • 2020: NGS & Single Cell Analysis Congress (London, UK)
  • 2021: BSI Congress (Edinburgh, UK)
  • 2022: BSI Summer School (Coventry, UK)
  • 2022: BSI Congress (Liverpool, UK)

Supplementary

  • Reviewer 2018 - 2021: Immunology Conference Committees 2020: NGS & Single Cell Analysis Congress 2021 - present: Glasgow Computational Biology Conference

A head and shoulders shot of Mr John Cole