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

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

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

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

Chapter in Book - Research

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

Chapter in Book - Research

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. Advance online publication. doi: 10.1007/s00438-023-02033-1

Journal - Research Article

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 Article

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

Journal - Research Article

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

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 Article

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

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

Journal - Research Article

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

Journal - Research Article

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 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

Journal - Research Article

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

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

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

Journal - Research Article

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

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

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

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

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.

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.

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.

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.

Journal - Research Article

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.

Journal - Research Article

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.

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.

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.

Journal - Research Article

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.

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.

Journal - Research Article

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.

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.

Journal - Research Article

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

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

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

Journal - Research Other