Contact Details
- Phone
- +64 3 479 7359
- peter.stockwell@otago.ac.nz
- Position
- Scientific Officer
- Department
- Department of Pathology and Molecular Medicine (Dunedin)
- Qualifications
- BSc(Hons) PhD
- Research summary
- Bioinformatics
- Teaching
- Postgraduate diploma in Clinical Bioinformatics (BINF701) beginning second semester 2023
Research
Peter’s role includes computer analysis of epigenetic data, especially from bisulphite sequencing. He also writes software to support the epigenetics analysis.
Publications
Yassi, M., Ezegbogu, M., Rodger, E. J., Stockwell, P., Chatterjee, A., & Parry, M. (2026). DNAmBERT: A transformer-based model for non-invasive cancer diagnosis using DNA sequence and methylation data. Briefings in Bioinformatics, 27(5), bbag455. doi: 10.1093/bib/bbag455 Journal - Research Article
Ezegbogu, M., Stockwell, P. A., Reid, G., Brockway, B., Kumar, R., Rodger, E., & Chatterjee, A. (2026). Comparison of enzymatic and bisulfite-based methods for sequencing-based cell-free DNA methylation profiling. Frontiers in Epigenetics & Epigenomics, 3, 1693925. doi: 10.3389/freae.2025.1693925 Journal - Research Article
Lynch-Sutherland, C. F., McDougall, L. I., Stockwell, P. A., Chatterjee, A., Gamage, T. K. J. B., James, J. L., Rodger, E. J., Weeks, R. J., Ludgate, J. L., Macaulay, E. C., & Eccles, M. R. (2026). Transcriptional activation of transposable element (TE)-associated genes is frequently associated with altered promoter methylation in placenta and melanoma. International Journal of Molecular Sciences, 27, 5827. doi: 10.3390/ijms27135827 Journal - Research Article
Lynch-Sutherland, C., Stockwell, P., Chatterjee, A., Eccles, M. R., & Macaulay, E. (2026). Epigenetic deregulation of transposable elements links developmental processes and tumorigenesis [Review]. International Journal of Molecular Sciences, 27(6), 2690. doi: 10.3390/ijms27062690 Journal - Research Article
Peppercorn, K., Sharma, S., Edgar, C. D., Stockwell, P. A., Rodger, E. J., Chatterjee, A., & Tate, W. P. (2025). Comparing DNA methylation landscapes in peripheral blood from Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and Long COVID patients. International Journal of Molecular Sciences, 26, 6631. doi: 10.3390/ijms26146631 Journal - Research Article
2026
Journal - Research Article
Yassi, M., Ezegbogu, M., Rodger, E. J., Stockwell, P., Chatterjee, A., & Parry, M. (2026). DNAmBERT: A transformer-based model for non-invasive cancer diagnosis using DNA sequence and methylation data. Briefings in Bioinformatics, 27(5), bbag455. doi: 10.1093/bib/bbag455
Ezegbogu, M., Stockwell, P. A., Reid, G., Brockway, B., Kumar, R., Rodger, E., & Chatterjee, A. (2026). Comparison of enzymatic and bisulfite-based methods for sequencing-based cell-free DNA methylation profiling. Frontiers in Epigenetics & Epigenomics, 3, 1693925. doi: 10.3389/freae.2025.1693925
Lynch-Sutherland, C. F., McDougall, L. I., Stockwell, P. A., Chatterjee, A., Gamage, T. K. J. B., James, J. L., Rodger, E. J., Weeks, R. J., Ludgate, J. L., Macaulay, E. C., & Eccles, M. R. (2026). Transcriptional activation of transposable element (TE)-associated genes is frequently associated with altered promoter methylation in placenta and melanoma. International Journal of Molecular Sciences, 27, 5827. doi: 10.3390/ijms27135827
Lynch-Sutherland, C., Stockwell, P., Chatterjee, A., Eccles, M. R., & Macaulay, E. (2026). Epigenetic deregulation of transposable elements links developmental processes and tumorigenesis [Review]. International Journal of Molecular Sciences, 27(6), 2690. doi: 10.3390/ijms27062690
2025
Journal - Research Article
Peppercorn, K., Sharma, S., Edgar, C. D., Stockwell, P. A., Rodger, E. J., Chatterjee, A., & Tate, W. P. (2025). Comparing DNA methylation landscapes in peripheral blood from Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and Long COVID patients. International Journal of Molecular Sciences, 26, 6631. doi: 10.3390/ijms26146631
Hossain, S. M., Gimenez, G., Stockwell, P., Weeks, R., Almomani, S., Jones, G. T., Ratajska, M., Shuen, M., Bhat, B., … Rodger, E., Jackson, C., Chatterjee, A., & Eccles, M. R. (2025). Pre-treatment DNA methylome and transcriptome profiles correlate with melanoma response to anti-PD1 immunotherapy. Cancer Letters, 618, 217638. doi: 10.1016/j.canlet.2025.217638
2024
Journal - Research Article
Stockwell, P. A., Rodger, E. J., Gimenez, G., Morison, I. M., & Chatterjee, A. (2024). DMAP2: A pipeline for analysis of whole-genome-scale DNA methylation sequencing data. Current Protocols, 4, 370003. doi: 10.1002/cpz1.70003
Ajithkumar, P., Gimenez, G., Stockwell, P. A., Almomani, S., Bowden, S. A., Leichter, A. L., … Pattison, S., … Frizelle, F. A., Eccles, M. R., Purcell, R. V., Rodger, E. J., & Chatterjee, A. (2024). DNA methylome and transcriptome maps of primary colorectal cancer and matched liver metastasis. Data, 9(1), 8. doi: 10.3390/data9010008
Journal - Research Other
Keighley, L. M., Lynch-Sutherland, C. F., McDougall, L., Almomani, S. N., Stockwell, P., & Macaulay, E. C. (2024). Three transposable elements exhibiting differential expression in pre-eclampsia overlap with enhancer regions. Placenta, 158, 10-13. doi: 10.1016/j.placenta.2024.09.010
Conference Contribution - Poster Presentation (not in published proceedings)
Stockwell, P. (2024, August-September). DMAP2: A pipeline for analysis of whole genome-scale DNA methylation sequencing data. Poster session presented at the Queenstown Research Week (QRW) Cancer Meeting, Queenstown, New Zealand.
2023
Chapter in Book - Research
Gimenez, G., Stockwell, P. A., Rodger, E. J., & Chatterjee, A. (2023). Strategy for RNA-seq experimental design and data analysis. In G. J. Seymour, M. P. Cullinan, N. C. K. Heng & P. R. Cooper (Eds.), Oral biology: Molecular techniques and applications: Methods in molecular biology (Vol. 2588). (3rd ed.) (pp. 249-278). New York, NY: Springer. doi: 10.1007/978-1-0716-2780-8_16
Journal - Research Article
Lynch-Sutherland, C. F., McDougall, L. I., Stockwell, P. A., Almomani, S. N., Weeks, R. J., Ludgate, J. L., … Chatterjee, A., … Eccles, M. R., & Macaulay, E. C. (2023). The transposable element-derived transcript of LIN28B has a placental origin and is not specific to tumours. Molecular Genetics & Genomics, 298, 1045-1058. doi: 10.1007/s00438-023-02033-1
Rodger, E. J., Gimenez, G., Ajithkumar, P., Stockwell, P. A., Almomani, S., Bowden, S. A., Leichter, A. L., Ahn, A., Pattison, S., McCall, J. L., … Frizelle, F. A., Eccles, M. R., Purcell, R. V., & Chatterjee, A. (2023). An epigenetic signature of advanced colorectal cancer metastasis. iScience, 26(6), 106986. doi: 10.1016/j.isci.2023.106986
Journal - Research Other
Rodger, E. J., Stockwell, P. A., Almomani, S., Eccles, M. R., & Chatterjee, A. (2023). Protocol for generating high-quality genome-scale DNA methylation sequencing data from human cancer biospecimens. STAR Protocols, 4, 102714. doi: 10.1016/j.xpro.2023.102714
2022
Chapter in Book - Research
Al Momani, S., Rodger, E. J., Stockwell, P. A., Eccles, M. R., & Chatterjee, A. (2022). Generating sequencing-based DNA methylation maps from low DNA input samples. In J. Horsfield & J. Marsman (Eds.), Chromatin: Methods and protocols: Methods in molecular biology (Vol. 2458). (pp. 3-21). New York, NY: Springer. doi: 10.1007/978-1-0716-2140-0_1
Journal - Research Article
Hossain, S. M., Gimenez, G., Stockwell, P. A., Tsai, P., Print, C. G., Rys, J., … Jackson, C., Chatterjee, A., & Eccles, M. R. (2022). Innate immune checkpoint inhibitor resistance is associated with melanoma sub-types exhibiting invasive and de-differentiated gene expression signatures. Frontiers in Immunology, 13, 955063. doi: 10.3389/fimmu.2022.955063
Helliwell, A. M., Stockwell, P. A., Edgar, C. D., Chatterjee, A., & Tate, W. P. (2022). Dynamic epigenetic changes during a relapse and recovery cycle in myalgic encephalomyelitis/chronic fatigue ayndrome. International Journal of Molecular Sciences, 23(19), 11852. doi: 10.3390/ijms231911852
2021
Journal - Research Article
Tschirley, A. M., Stockwell, P. A., Rodger, E. J., Eltherington, O., Morison, I. M., Christensen, N., Chatterjee, A., & Hibma, M. (2021). The mouse papillomavirus epigenetic signature is characterised by DNA hypermethylation after lesion regression. Viruses, 13, 2045. doi: 10.3390/v13102045
Ahn, A., Rodger, E. J., Motwani, J., Gimenez, G., Stockwell, P. A., Parry, M., … Chatterjee, A., & Eccles, M. R. (2021). Transcriptional reprogramming and constitutive PD-L1 expression in melanoma are associated with dedifferentiation and activation of interferon and tumour necrosis factor signalling pathways. Cancers, 13, 4250. doi: 10.3390/cancers13174250
Stockwell, P. A., Lynch-Sutherland, C. F., Chatterjee, A., Macaulay, E. C., & Eccles, M. R. (2021). RepExpress: A novel pipeline for the quantification and characterization of transposable element expression from RNA-seq data. Current Protocols, 1(8), e206. doi: 10.1002/cpz1.206
Voisin, A.-S., Ulloa, V. S., Stockwell, P., Chatterjee, A., & Silvestre, F. (2021). Genome-wide DNA methylation of the liver reveals delayed effects of early-life exposure to 17-α-ethinylestradiol in the self-fertilizing mangrove rivulus. Epigenetics, 17(5), 473-497. doi: 10.1080/15592294.2021.1921337
Motwani, J., Rodger, E. J., Stockwell, P. A., Baguley, B. C., Macaulay, E. C., & Eccles, M. R. (2021). Genome-wide DNA methylation and RNA expression differences correlate with invasiveness in melanoma cell lines. Epigenomics, 13(8), 577-598. doi: 10.2217/epi-2020-0440
2020
Journal - Research Article
Helliwell, A. M., Sweetman, E. C., Stockwell, P. A., Edgar, C. D., Chatterjee, A., & Tate, W. P. (2020). Changes in DNA methylation profiles of myalgic encephalomyelitis/chronic fatigue syndrome patients reflect systemic dysfunctions. Clinical Epigenetics, 12(1), 167. doi: 10.1186/s13148-020-00960-z
Harrop, T. W. R., Guhlin, J., McLaughlin, G. M., Permina, E., Stockwell, P., Gilligan, J., Le Lec, M. F., Gruber, M. A. M., … Lovegrove, M., … Dearden, P. K. (2020). High-quality assemblies for three invasive social wasps from the Vespula genus. Genes Genomes Genetics, 10, 3479-3488. doi: 10.1534/g3.120.401579
Lynch-Sutherland, C. F., Chatterjee, A., Stockwell, P. A., Eccles, M. R., & Macaulay, E. C. (2020). Reawakening the developmental origins of cancer through transposable elements. Frontiers in Oncology, 10, 468. doi: 10.3389/fonc.2020.00468
Bowden, S. A., Stockwell, P. A., Rodger, E. J., Parry, M. F., Eccles, M. R., Stayner, C., & Chatterjee, A. (2020). Extensive inter-cyst DNA methylation variation in autosomal dominant polycystic kidney disease revealed by genome scale sequencing. Frontiers in Genetics, 11, 348. doi: 10.3389/fgene.2020.00348
Conference Contribution - Published proceedings: Abstract
Lynch-Sutherland, C. F., Stockwell, P. A., Eccles, M. R., Chatterjee, A., & Macaulay, E. C. (2020). Reawakening the developmental origins of cancer through transposable elements. Proceedings of the Genetics Otago (GO) Epigenetics User Group (EUG) Symposium. Retrieved from https://blogs.otago.ac.nz/go/2020-3/
Banerjee, R., Smith, J., Stockwell, P., Eccles, M., Weeks, R., & Chatterjee, A. (2020). Investigating DNA methylation as a mechanism for gene activation using gene editing technology. Proceedings of the Genetics Otago (GO) Epigenetics User Group (EUG) Symposium. Retrieved from https://blogs.otago.ac.nz/go/2020-3/
Ahn, A., Rodger, E. J., Stockwell, P. A., Parry, M., Motwani, J., Gallagher, S. J., … Chatterjee, A., & Eccles, M. R. (2020). mRNA and long non-coding RNA expression defines constitutive and inducible PD-L1 expression in melanoma and associated with treatment resistance and response. Proceedings of the Genetics Otago (GO) Epigenetics User Group (EUG) Symposium. Retrieved from https://blogs.otago.ac.nz/go/2020-3/
Stockwell, P. A., & Davies, C. I. (2020). Producing a pipeline for methylation analysis [Invited]. Proceedings of the Genetics Otago (GO) Epigenetics User Group (EUG) Symposium. Retrieved from https://blogs.otago.ac.nz/go/2020-3/
Macaulay, E. C., Almomani, S., Lynch-Sutherland, C. F., Bessemer, B., Chatterjee, A., Alsaleh, A. A., Stockwell, P. A., Ludgate, J. L., Weeks, R. J., Jones, G. T., Day, R. C., Fukazawa, R., Slatter, T. L., Hung, N. A., Devenish, C., Morison, I. M., & Eccles, M. R. (2020). The potential power of placental epigenetics [Invited]. Proceedings of the Genetics Otago (GO) Epigenetics User Group (EUG) Symposium. Retrieved from https://blogs.otago.ac.nz/go/2020-3/
Banerjee, R., Smith, J., Stockwell, P., Eccles, M., Weeks, R., & Chatterjee, A. (2020). Investigating DNA methylation as a mechanism for paradoxical gene activation using epigenomic editing technology. Proceedings of the Genetics Otago (GO) Zoom Symposium. Retrieved from https://blogs.otago.ac.nz/go/2020-3/
2019
Journal - Research Article
Rodger, E. J., Chatterjee, A., Stockwell, P. A., & Eccles, M. R. (2019). Characterisation of DNA methylation changes in EBF3 and TBC1D16 associated with tumour progression and metastasis in multiple cancer types. Clinical Epigenetics, 11, 114. doi: 10.1186/s13148-019-0710-5
Journal - Research Other
Thunders, M., Holley, A., Harding, S., Stockwell, P., & Larsen, P. (2019). Using NGS-methylation profiling to understand the molecular pathogenesis of young MI patients who have subsequent cardiac events [Brief report]. Epigenetics, 14(6), 536-544. doi: 10.1080/15592294.2019.1605815
Conference Contribution - Published proceedings: Full paper
Poulter, R. T. M., Lamont, I., Stockwell, P., Butler, M. I., & Poulter, G. (2019). The completely assembled genome of a strain from the New Zealand Pseudomonas syringae pv. Actinidiae (PSA) outbreak. Acta Horticulturae, 1243, (pp. 23-28). doi: 10.17660/ActaHortic.2019.1243.4
Conference Contribution - Published proceedings: Abstract
Lynch-Sutherland, C., Stockwell, P. A., Eccles, M. R., Chatterjee, A., & Macaulay, E. C. (2019). Good genes gone bad: Are placental genes hijacked by cancer cells to facilitate invasion? Proceedings of the 16th Asian Conference on Transcription. (pp. 77). Retrieved from https://act2019.p.events4you.currinda.com/days/2019-12-02
Motwani, J., Rodger, E. J., Stockwell, P. A., & Eccles, M. R. (2019). Genome-wide DNA methylation and gene expression analysis of non-invasive and invasive melanoma cell lines. Proceedings of the 16th Asian Conference on Transcription. (pp. 68). Retrieved from https://act2019.p.events4you.currinda.com/days/2019-12-02
Chatterjee, A., Rodger, E. J., Ahn, A., Stockwell, P. A., Parry, M., Gallagher, S., … Eccles, M. (2019). Methylome and transcriptome programme segregates PD-L1 expressing and non-expressing melanoma. Proceedings of the 16th Asian Conference on Transcription. (pp. 38-39). Retrieved from http://act2019.p.events4you.currinda.com/days/2019-12-02/
Dearden, P., Duncan, E. J., Gimenez, G., Gruber, M. A. M., Guhlin, J., Harrop, T. W. R., … McLaughlin, G., Permina, E., … Remnant, E. J., Stockwell, P., Quinn, O., & Wilson-Rankin, E. E. (2019). The genomes of three invasive social wasps. Proceedings of the Genetics Society of Australasia (GSA) Conference. Retrieved from https://event.crowdcompass.com/gsa2019
Dearden, P., Duncan, E. J., Gimenez, G., Gruber, M. A. M., Guhlin, J., Harrop, T. W. R., … McLaughlin, G., Permina, E., … Stockwell, P., Quinn, O., & Wilson-Rankin, E. E. (2019). High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing. Proceedings of the Genetics Society of Australasia (GSA) Conference. Retrieved from https://event.crowdcompass.com/gsa2019
Chatterjee, A., Ahn, A., Rodger, E. J., Stockwell, P. A., Parry, M., Motwani, J., … Eccles, M. R. (2019). Global DNA methylation levels regulate PD-L1 expression in melanoma. Cancer Research, 79(13, Suppl.). doi: 10.1158/1538-7445.Am2019-826
Conference Contribution - Verbal presentation and other Conference outputs
Lynch-Sutherland, C. F., Stockwell, P. A., Eccles, M. R., Chatterjee, A., & Macaulay, E. C. (2019, August-September). Good genes gone bad: Are placental genes hijacked by cancer cells to facilitate invasion? Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Macaulay, E. C., Almomani, S., Lynch-Sutherland, C. F., Chatterjee, A. C., Stockwell, P. A., Alsaleh, A. A., Wilson, J. L., Weeks, R. J., Day, R. C., Fukuzawa, R., Slatter, T. L., Hung, N. A., Devenish, C., Morison, I. M., & Eccles, M. R. (2019, August-September). The placental potential: Harnessing insights from placental epigenetics to predict disease. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Helliwell, A. M., Chatterjee, A., Stockwell, P. A., & Tate, W. P. (2019, August-September). DNA methylation changes in myalgic encephalomyelitis/chronic fatigue syndrome. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
2018
Chapter in Book - Research
Chatterjee, A., Ahn, A., Rodger, E. J., Stockwell, P. A., & Eccles, M. R. (2018). A guide for designing and analyzing RNA-Seq data. In N. Raghavachari & N. Garcia-Reyero (Eds.), Gene expression analysis: Methods in molecular biology (Vol. 1783). (pp. 35-80). New York, NY: Humana Press. doi: 10.1007/978-1-4939-7834-2_3
Journal - Research Article
Falisse, E., Ducos, B., Stockwell, P. A., Morison, I. M., Chatterjee, A., & Silvestre, F. (2018). DNA methylation and gene expression alterations in zebrafish early-life stages exposed to the antibacterial agent triclosan. Environmental Pollution, 243(Part B), 1867-1877. doi: 10.1016/j.envpol.2018.10.004
Chatterjee, A., Rodger, E. J., Ahn, A., Stockwell, P. A., Parry, M., Motwani, J., … Eccles, M. R., & Hersey, P. (2018). Marked global DNA hypomethylation is associated with constitutive PD-L1 expression in melanoma. iScience, 4, 312-325. doi: 10.1016/j.isci.2018.05.021
Thunders, M., Chinn, V., Bilewitch, J., & Stockwell, P. (2018). Identification of potential 'lifestyle-responsive' epigenomic biomarkers in healthy women aged 18-40. Biomarkers, 23(5), 453-461. doi: 10.1080/1354750x.2018.1443512
Conference Contribution - Poster Presentation (not in published proceedings)
Ahn, A., Rodger, E. J., Stockwell, P. A., Parry, M., Motwani, J., Gallagher, S. J., … Chatterjee, A., & Eccles, M. R. (2018, August). Investigating the role of DNA methylation, gene expression, long non-coding RNA and transposable elements in constitutive PD-L1 expression in melanoma cell lines. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Eccles, M., Rodger, E., Chatterjee, A., & Stockwell, P. (2018, August). Is EBF3 promotor hypermethylation an oncogenic epi-mutation in multiple cancer types? Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Conference Contribution - Verbal presentation and other Conference outputs
Chatterjee, A., Rodger, E., Ahn, A., Stockwell, P., Parry, M., Motwani, J., … Eccles, M., & Hersey, P. (2018, August). Striking loss of global DNA methylation levels and constitutive PD-L1 expression in melanoma. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
2017
Chapter in Book - Research
Chatterjee, A., Rodger, E. J., Morison, I. M., Eccles, M. R., & Stockwell, P. A. (2017). Tools and strategies for analysis of genome-wide and gene-specific DNA methylation patterns. In G. J. Seymour, M. P. Cullinan & N. C. K. Heng (Eds.), Oral biology: Molecular techniques and applications: Methods in molecular biology (Vol. 1537). (2nd ed.) (pp. 249-277). New York, NY: Springer. doi: 10.1007/978-1-4939-6685-1_15
Chatterjee, A., Rodger, E. J., Stockwell, P. A., Le Mée, G., & Morison, I. M. (2017). Generating multiple base-resolution DNA methylomes using reduced representation bisulfite sequencing. In G. J. Seymour, M. P. Cullinan & N. C. K. Heng (Eds.), Oral biology: Molecular techniques and applications: Methods in molecular biology (Vol. 1537). (2nd ed.) (pp. 279-298). New York, NY: Springer. doi: 10.1007/978-1-4939-6685-1_16
Journal - Research Article
Poulter, R., Taiaroa, G., Sumpter, N., Stockwell, P., & Butler, M. (2017). Complete genome sequence of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae biovar 5, originating from Japan. Genome Announcements, 5(50), e01409-17. doi: 10.1128/genomeA.01409-17
Ludgate, J. L., Wright, J., Stockwell, P. A., Morison, I. M., Eccles, M. R., & Chatterjee, A. (2017). A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA. BMC Medical Genomics, 10, 54. doi: 10.1186/s12920-017-0290-1
Chatterjee, A., Macaulay, E. C., Ahn, A., Ludgate, J. L., Stockwell, P. A., Weeks, R. J., Parry, M. F., Foster, T. J., … Eccles, M. R., & Morison, I. M. (2017). Comparative assessment of DNA methylation patterns between reduced representation bisulfite sequencing and Sequenom EpiTyper methylation analysis. Epigenomics, 9(6), 823-832. doi: 10.2217/epi-2016-0176
Chatterjee, A., Stockwell, P. A., Ahn, A., Rodger, E. J., Leichter, A. L., & Eccles, M. R. (2017). Genome-wide methylation sequencing of paired primary and metastatic cell lines identifies common DNA methylation changes and a role for EBF3 as a candidate epigenetic driver of melanoma metastasis. Oncotarget, 8(4), 6085-6101. doi: 10.18632/oncotarget.14042
Conference Contribution - Poster Presentation (not in published proceedings)
Eccles, M. R., Chatterjee, A., Rodger, E. J., Ahn, A., Leichter, A., Motwani, J., Stockwell, P., & Parry, M. (2017, September). Epigenetic drivers of melanoma metastasis identified by genome-wide reduced-representation bisulphite sequencing (RRBS) analysis. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Eccles, M. R., Chatterjee, A., Rodger, E. J., Ahn, A., Leichter, A., Motwani, J., Stockwell, P., & Parry, M. (2017, September). Epigenetic driver of melanoma metastasis identified by genome-wide analysis. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Leichter, A. L., Day, R. C., Stockwell, P. A., Wilson, M., Guilford, P., Eccles, M. R., & Chatterjee, A. (2017, September). Development of single-cell methodologies to interrogate DNA methylation patterns at a whole genome scale. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Conference Contribution - Verbal presentation and other Conference outputs
Eccles, M. R., Chatterjee, A., Rodger, E. J., Ahn, A., Leichter, A., Motwani, J., Stockwell, P., Parry, M., … Gardner, J., … Sarwar, M., … multiple other members of The Maurice Wilkins Centre. (2017, September). Can research involving NZ melanoma patient participation and extensive networking by researchers help reduce the melanoma burden in NZ? Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Stockwell, P. A., & Chatterjee, A. (2017, September). The DMAP package for DNA methylation analysis. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Chatterjee, A., Stockwell, P. A., Leichter, A. L., Ahn, A., Rodger, E. J., & Eccles, M. R. (2017, September). Epigenetic driver of melanoma metastasis and a clue for novel methylation mediated gene activation mechanism? Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
2016
Journal - Research Article
Chatterjee, A., Stockwell, P. A., Rodger, E. J., Parry, M. F., & Eccles, M. R. (2016). scan_tcga tools for integrated epigenomic and transcriptomic analysis of tumor subgroups. Epigenomics, 8(10), 1315-1330. doi: 10.2217/epi-2016-0063
Chatterjee, A., Lagisz, M., Rodger, E. J., Zhen, L., Stockwell, P. A., Duncan, E. J., Horsfield, J. A., … Nakagawa, S. (2016). Sex differences in DNA methylation and expression in zebrafish brain: A test of an extended ‘male sex drive’ hypothesis. Gene, 590, 307-316. doi: 10.1016/j.gene.2016.05.042
Chatterjee, A., Macaulay, E. C., Rodger, E. J., Stockwell, P. A., Parry, M. F., Roberts, H. E., Slatter, T. L., Hung, N. A., Devenish, C. J., & Morison, I. M. (2016). Placental hypomethylation is more pronounced in genomic loci devoid of retroelements. Genes Genomes Genetics, 6(7), 1911-1921. doi: 10.1534/g3.116.030379
Chatterjee, A., Stockwell, P. A., Rodger, E. J., & Morison, I. M. (2016). Genome-scale DNA methylome and transcriptome profiling of human neutrophils. Scientific Data, 3, 160019. doi: 10.1038/sdata.2016.19
Conference Contribution - Poster Presentation (not in published proceedings)
Macaulay, E. C., Chatterjee, A., Rodger, E. J., Stockwell, P. A., Parry, M. F., Roberts, H. E., Slatter, T. L., Hung, N. A., & Morison, I. M. (2016, March). Placental hypomethylation is more pronounced in genomic loci devoid of retroelements. Poster session presented at the Keystone Symposia on Molecular and Cellular Biology: Chromatin and Epigenetics, Whistler, Canada.
Conference Contribution - Verbal presentation and other Conference outputs
Chatterjee, A., Stockwell, P. A., Ahn, A., Rodger, E. J., Leichter, A., & Eccles, M. R. (2016, August-September). A framework and example for identifying epigenetic drivers of cancer metastasis. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Nelson, New Zealand.
2015
Journal - Research Article
Chatterjee, A., Stockwell, P. A., Rodger, E. J., Duncan, E. J., Parry, M. F., Weeks, R. J., & Morison, I. M. (2015). Genome-wide DNA methylation map of human neutrophils reveals widespread inter-individual epigenetic variation. Scientific Reports, 5, 17328. doi: 10.1038/srep17328
Ha, M., Sabherwal, M., Duncan, E., Stevens, S., Stockwell, P., McConnell, M., Bekhit, A. E.-D., & Carne, A. (2015). In-depth characterization of sheep (Ovis aries) milk whey proteome and comparison with cow (Bos taurus). PLoS ONE, 10(10), e0139774. doi: 10.1371/journal.pone.0139774
Conference Contribution - Published proceedings: Full paper
Gallipoli, L., Butler, M., Mazzaglia, A., Stockwell, P., Lamont, I., Zhu, L., … Poulter, R. T. M. (2015). Genomic diversity of Pseudomonas syringae pv. actinidiae (Psa) in China. Acta Horticulturae, 1095, (pp. 59-64). doi: 10.17660/ActaHortic.2015.1095.6
Butler, M., Jung, J. S., Kim, G. H., Lamont, I., Stockwell, P., Koh, Y. J., & Poulter, R. (2015). Genome features of Pseudomonas syringae pv. actinidiae recently isolated in Korea. Acta Horticulturae, 1095, (pp. 75-79). doi: 10.17660/ActaHortic.2015.1095.8
Conference Contribution - Poster Presentation (not in published proceedings)
Chatterjee, A., Stockwell, P. A., Rodger, E. J., & Eccles, M. R. (2015, August-September). Flexible analysis of TCGA DNA methylation and gene expression data using UNIX tools. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Conference Contribution - Verbal presentation and other Conference outputs
Chatterjee, A., Stockwell, P. A., Ahn, A., Rodger, E. J., Leichter, A. L., & Eccles, M. R. (2015, November). The epigenetic basis of melanoma metastasis. Verbal presentation at the Toxicology Symposium: Toxicology for the Modern Researcher, Dunedin, New Zealand.
Chatterjee, A., Ahn, A., Stockwell, P. A., Rodger, E. J., Leichter, A., & Eccles, M. R. (2015, August-September). Analysis of paired primary and metastatic cell lines identifies common DNA methylation changes in melanoma metastasis. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Poulter, G. T. M., Stockwell, P. A., Lamont, I. L., Poulter, R. T. M., & Butler, M. I. (2015, August-September). The complete genome of PSA - Pseudomonas syringae pv. actinidiae - and the recent emergence of antibiotic resistance in New Zealand. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
2014
Journal - Research Article
Stockwell, P. A., Chatterjee, A., Rodger, E. J., & Morison, I. M. (2014). DMAP: Differential methylation analysis package for RRBS and WGBS data. Bioinformatics, 30(13), 1814-1822. doi: 10.1093/bioinformatics/btu126
Morris, J. N., Crawford, T. S., Jeffs, A., Stockwell, P. A., Eaton-Rye, J. J., & Summerfield, T. C. (2014). Whole genome re-sequencing of two ‘wild-type’ strains of the model cyanobacterium Synechocystis sp. PCC 6803. New Zealand Journal of Botany, 52(1), 36-47. doi: 10.1080/0028825X.2013.846267
Journal - Research Other
Chatterjee, A., Stockwell, P. A., Horsfield, J. A., Morison, I. M., & Nakagawa, S. (2014). Base-resolution DNA methylation landscape of zebrafish brain and liver [Data in brief]. Genomics Data, 2, 342-344. doi: 10.1016/j.gdata.2014.10.008
Conference Contribution - Published proceedings: Abstract
Rodger, E., Chatterjee, A., Stockwell, P., & Morison, I. (2014). DNA methylation markers of myedysplastic syndrome. New Zealand Medical Journal, 127(1398). Retrieved from http://www.nzma.org.nz/journal
2013
Journal - Research Article
Chatterjee, A., Ozaki, Y., Stockwell, P. A., Horsfield, J. A., Morison, I. M., & Nakagawa, S. (2013). Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing. Epigenetics, 8(9), 979-989. doi: 10.4161/epi.25797
Butler, M. I., Stockwell, P. A., Black, M. A., Day, R. C., Lamont, I. L., & Poulter, R. T. M. (2013). Pseudomonas syringae pv. actinidiae from recent outbreaks of kiwifruit bacterial canker belong to different clones that originated in China. PLoS ONE, 8(2), e57464. doi: 10.1371/journal.pone.0057464
Conference Contribution - Verbal presentation and other Conference outputs
Morison, I. M., Chatterjee, A., & Stockwell, P. (2013, August). Epigenetic variation in healthy persons: Where is it and what does it mean? Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
2012
Journal - Research Article
Chatterjee, A., Rodger, E. J., Stockwell, P. A., Weeks, R. J., & Morison, I. M. (2012). Technical considerations for reduced representation bisulfite sequencing with multiplexed libraries. Journal of Biomedicine & Biotechnology, 2012, 741542. doi: 10.1155/2012/741542
Chatterjee, A., Stockwell, P. A., Rodger, E. J., & Morison, I. M. (2012). Comparison of alignment software for genome-wide bisulphite sequence data. Nucleic Acids Research, 40(10), e79. doi: 10.1093/nar/gks150
Conference Contribution - Poster Presentation (not in published proceedings)
Chatterjee, A., Stockwell, P. A., Rodger, E. J., & Morison, I. M. (2012, September). Base-pair resolution DNA methylation map of neutrophils indicates widespread epigenetic variation among normal individuals. Poster session presented at the Division of Health Sciences Research Forum: Health Matters: Research Excellence at Otago, Dunedin, New Zealand.
Chatterjee, A., Stockwell, P. A., Rodger, E. J., & Morison, I. M. (2012, August). Base-pair resolution DNA methylation map of neutrophils indicates widespread epigenetic variation among normal individuals. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Conference Contribution - Verbal presentation and other Conference outputs
Chatterjee, A., Stockwell, P. A., Rodger, E. J., & Morison, I. M. (2012, November). Genome-wide DNA methylation map indicates widespread epigenetic variation in normal individuals. Verbal presentation at the Gravida Annual Science Symposium: What Makes the Best Start for a Healthy Life? Palmerston North, New Zealand.
2011
Journal - Research Article
Kalamorz, F., Keis, S., McMillan, D. G. G., Olsson, K., Stanton, J.-A., Stockwell, P., Black, M. A., … Cook, G. M. (2011). Draft genome sequence of the thermoalkaliphilic Caldalkalibacillus thermarum strain TA2.A1. Journal of Bacteriology, 193(16), 4290-4291. doi: 10.1128/jb.05035-11
Conference Contribution - Verbal presentation and other Conference outputs
Chatterjee, A., Stockwell, P. A., Rodger, E. J., & Morison, I. M. (2011, September). Genome-scale DNA methylation mapping: Unraveling inter-individual variation. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
2010
Journal - Research Article
Simpson, G. G., Laurie, R. E., Dijkwel, P. P., Quesada, V., Stockwell, P. A., Dean, C., & Macknight, R. C. (2010). Noncanonical translation initiation of the Arabidopsis flowering time and alternative polyadenylation regulator FCA. Plant Cell, 22(11), 3764-3777. doi: 10.1105/tpc.110.077990
2009
Journal - Research Article
Jacobs, G. H., Chen, A., Stevens, S. G., Stockwell, P. A., Black, M. A., Tate, W. P., & Brown, C. M. (2009). Transterm: A database to aid the analysis of regulatory sequences in mRNAs. Nucleic Acids Research, 37(Database issue), D72-D76. doi: 10.1093/nar/gkn763
Software
Stockwell, P. A. (2009). SSEdit: Single (Short) Sequence Editor: For MacOS X (Version 6.04) [Computer Software]. Dunedin, New Zealand: Biochemistry Department, University of Otago.
2008
Software
Stockwell, P. A. (2008). HOMED: HOMologous Sequence EDitor: For MacOS X (Version 6.76) [Computer Software]. Dunedin, New Zealand: Department of Biochemistry, University of Otago.
2006
Journal - Research Article
Jacobs, G. H., Stockwell, P. A., Tate, W. P., & Brown, C. M. (2006). Transterm: Extended search facilities and improved integration with other databases. Nucleic Acids Research, 34(Database), D37-D40.
2003
Conference Contribution - Published proceedings: Full paper
Brown, C., Jacobs, G., Stockwell, P., & Schreiber, M. (2003). Detection of signals in mRNAs that influence translation. Applied Bioinformatics. 2(Suppl.3), (pp. S47-S51). [Full Paper]
2002
Journal - Research Article
Jacobs, G. H., Rackham, O., Stockwell, P. A., Tate, W. P., & Brown, C. M. (2002). Transterm: a database of mRNAs and translational control elements. Nucleic Acids Research, 30, 310-311.
2001
Journal - Research Article
Hubbard, M. J., Faught, M. J., Carlisle, B. H., & Stockwell, P. A. (2001). ToothPrint a proteomic database for dental tissues. Proteomics, 1, 132-135.
2000
Journal - Research Article
Jacobs, G. H., Stockwell, P. A., Schreiber, M. J., Tate, W. P., & Brown, C. M. (2000). Transterm: A database of messenger RNA components and signals. Nucleic Acids Research, 28, 293-295.
Sowerby, S. J., Stockwell, P. A., Heckl, W. M., & Petersen, G. B. (2000). Self-programmable, self-assembling, two dimensional genetic matter. Origins of Life & Evolution of the Biosphere, 30, 81-99.
1999
Journal - Research Article
Dalphin, M. E., Stockwell, P. A., Tate, W. P., & Brown, C. M. (1999). TransTerm, the translational signal database, extended to include full coding sequences and untranslated regions. Nucleic Acids Research, 27, 293-294.
Brown, C. M., Jacobs, G. H., Schreiber, M. J., Magnum, J., McNaughton, J. C., Cambray, M., Futschik, M., Major, L. L., Rackham, O., Tate, W. P., … Stockwell, P. A., & Kasabov, N. K. (1999). Using bioinformatics to investigate post-transcriptional control of gene expression. New Zealand BioScience, 7, 11-12.
1998
Journal - Research Article
Dalphin, M. E., Brown, C. M., Stockwell, P. A., & Tate, W. P. (1998). The translational signal database, TransTerm, is now a relational database. Nucleic Acids Research, 26, 335-337.
McNaughton, J. C., Cockburn, D. J., Hughes, G., Jones, W. A., Laing, N. G., Ray, P. N., Stockwell, P. A., & Petersen, G. B. (1998). Is gene deletion in eukaryotes sequence-dependent? A study of nine deletion junctions and nineteen other deletion breakpoints in intron 7 of the human dystrophin gene. Gene, 222, 41-51.
1997
Journal - Research Article
Dalphin, M. E., Brown, C. M., Stockwell, P. A., & Tate, W. P. (1997). The translational signal database, TransTerm: more organisms, complete genomes. Nucleic Acids Research, 25, 246-247.
McNaughton, J. C., Hughes, G., Jones, W. A., Stockwell, P. A., Klamut, H. J., & Petersen, G. B. (1997). The evolution of an intron: analysis of a long, deletion-prone intron in the human dystrophin gene. Genomics, 40(2), 294-304.
1996
Journal - Research Article
Dalphin, M. E., Brown, C., Stockwell, P. A., & Tate, W. P. (1996). TransTerm: a database of translational signals. Nucleic Acids Research, 24, 216-218.