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Items: 50

1.

Characterisation of DNA methylation changes in EBF3 and TBC1D16 associated with tumour progression and metastasis in multiple cancer types.

Rodger EJ, Chatterjee A, Stockwell PA, Eccles MR.

Clin Epigenetics. 2019 Aug 5;11(1):114. doi: 10.1186/s13148-019-0710-5.

2.

DNA methylation and gene expression alterations in zebrafish early-life stages exposed to the antibacterial agent triclosan.

Falisse E, Ducos B, Stockwell PA, Morison IM, Chatterjee A, Silvestre F.

Environ Pollut. 2018 Dec;243(Pt B):1867-1877. doi: 10.1016/j.envpol.2018.10.004. Epub 2018 Oct 3.

PMID:
30408875
3.

Marked Global DNA Hypomethylation Is Associated with Constitutive PD-L1 Expression in Melanoma.

Chatterjee A, Rodger EJ, Ahn A, Stockwell PA, Parry M, Motwani J, Gallagher SJ, Shklovskaya E, Tiffen J, Eccles MR, Hersey P.

iScience. 2018 Jun 29;4:312-325. doi: 10.1016/j.isci.2018.05.021. Epub 2018 Jun 28.

4.

A Guide for Designing and Analyzing RNA-Seq Data.

Chatterjee A, Ahn A, Rodger EJ, Stockwell PA, Eccles MR.

Methods Mol Biol. 2018;1783:35-80. doi: 10.1007/978-1-4939-7834-2_3.

PMID:
29767357
5.

A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA.

Ludgate JL, Wright J, Stockwell PA, Morison IM, Eccles MR, Chatterjee A.

BMC Med Genomics. 2017 Aug 31;10(1):54. doi: 10.1186/s12920-017-0290-1.

6.

Comparative assessment of DNA methylation patterns between reduced representation bisulfite sequencing and Sequenom EpiTyper methylation analysis.

Chatterjee A, Macaulay EC, Ahn A, Ludgate JL, Stockwell PA, Weeks RJ, Parry MF, Foster TJ, Knarston IM, Eccles MR, Morison IM.

Epigenomics. 2017 Jun;9(6):823-832. doi: 10.2217/epi-2016-0176. Epub 2017 May 19.

7.

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.

Chatterjee A, Stockwell PA, Ahn A, Rodger EJ, Leichter AL, Eccles MR.

Oncotarget. 2017 Jan 24;8(4):6085-6101. doi: 10.18632/oncotarget.14042.

8.

Generating Multiple Base-Resolution DNA Methylomes Using Reduced Representation Bisulfite Sequencing.

Chatterjee A, Rodger EJ, Stockwell PA, Le Mée G, Morison IM.

Methods Mol Biol. 2017;1537:279-298.

PMID:
27924600
9.

Tools and Strategies for Analysis of Genome-Wide and Gene-Specific DNA Methylation Patterns.

Chatterjee A, Rodger EJ, Morison IM, Eccles MR, Stockwell PA.

Methods Mol Biol. 2017;1537:249-277. Review.

PMID:
27924599
10.

scan_tcga tools for integrated epigenomic and transcriptomic analysis of tumor subgroups.

Chatterjee A, Stockwell PA, Rodger EJ, Parry MF, Eccles MR.

Epigenomics. 2016 Oct;8(10):1315-1330. Epub 2016 Sep 14.

11.

Sex differences in DNA methylation and expression in zebrafish brain: a test of an extended 'male sex drive' hypothesis.

Chatterjee A, Lagisz M, Rodger EJ, Zhen L, Stockwell PA, Duncan EJ, Horsfield JA, Jeyakani J, Mathavan S, Ozaki Y, Nakagawa S.

Gene. 2016 Sep 30;590(2):307-16. doi: 10.1016/j.gene.2016.05.042. Epub 2016 May 31.

12.

Placental Hypomethylation Is More Pronounced in Genomic Loci Devoid of Retroelements.

Chatterjee A, Macaulay EC, Rodger EJ, Stockwell PA, Parry MF, Roberts HE, Slatter TL, Hung NA, Devenish CJ, Morison IM.

G3 (Bethesda). 2016 Jul 7;6(7):1911-21. doi: 10.1534/g3.116.030379.

13.

Genome-scale DNA methylome and transcriptome profiling of human neutrophils.

Chatterjee A, Stockwell PA, Rodger EJ, Morison IM.

Sci Data. 2016 Mar 15;3:160019. doi: 10.1038/sdata.2016.19.

14.

Genome-wide DNA methylation map of human neutrophils reveals widespread inter-individual epigenetic variation.

Chatterjee A, Stockwell PA, Rodger EJ, Duncan EJ, Parry MF, Weeks RJ, Morison IM.

Sci Rep. 2015 Nov 27;5:17328. doi: 10.1038/srep17328.

15.

Base-resolution DNA methylation landscape of zebrafish brain and liver.

Chatterjee A, Stockwell PA, Horsfield JA, Morison IM, Nakagawa S.

Genom Data. 2014 Oct 16;2:342-4. doi: 10.1016/j.gdata.2014.10.008. eCollection 2014 Dec.

16.

DMAP: differential methylation analysis package for RRBS and WGBS data.

Stockwell PA, Chatterjee A, Rodger EJ, Morison IM.

Bioinformatics. 2014 Jul 1;30(13):1814-22. doi: 10.1093/bioinformatics/btu126. Epub 2014 Mar 7.

PMID:
24608764
17.

Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing.

Chatterjee A, Ozaki Y, Stockwell PA, Horsfield JA, Morison IM, Nakagawa S.

Epigenetics. 2013 Sep;8(9):979-89. doi: 10.4161/epi.25797. Epub 2013 Jul 24.

18.

Pseudomonas syringae pv. actinidiae from recent outbreaks of kiwifruit bacterial canker belong to different clones that originated in China.

Butler MI, Stockwell PA, Black MA, Day RC, Lamont IL, Poulter RT.

PLoS One. 2013;8(2):e57464. doi: 10.1371/journal.pone.0057464. Epub 2013 Feb 27.

19.

Technical considerations for reduced representation bisulfite sequencing with multiplexed libraries.

Chatterjee A, Rodger EJ, Stockwell PA, Weeks RJ, Morison IM.

J Biomed Biotechnol. 2012;2012:741542. doi: 10.1155/2012/741542. Epub 2012 Oct 10.

20.

Comparison of alignment software for genome-wide bisulphite sequence data.

Chatterjee A, Stockwell PA, Rodger EJ, Morison IM.

Nucleic Acids Res. 2012 May;40(10):e79. doi: 10.1093/nar/gks150. Epub 2012 Feb 16.

21.

Noncanonical translation initiation of the Arabidopsis flowering time and alternative polyadenylation regulator FCA.

Simpson GG, Laurie RE, Dijkwel PP, Quesada V, Stockwell PA, Dean C, Macknight RC.

Plant Cell. 2010 Nov;22(11):3764-77. doi: 10.1105/tpc.110.077990. Epub 2010 Nov 12.

22.

Transterm: a database to aid the analysis of regulatory sequences in mRNAs.

Jacobs GH, Chen A, Stevens SG, Stockwell PA, Black MA, Tate WP, Brown CM.

Nucleic Acids Res. 2009 Jan;37(Database issue):D72-6. doi: 10.1093/nar/gkn763. Epub 2008 Nov 4.

23.

Transterm--extended search facilities and improved integration with other databases.

Jacobs GH, Stockwell PA, Tate WP, Brown CM.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D37-40.

24.

Transterm: a database of mRNAs and translational control elements.

Jacobs GH, Rackham O, Stockwell PA, Tate W, Brown CM.

Nucleic Acids Res. 2002 Jan 1;30(1):310-1.

25.

ToothPrint, a proteomic database for dental tissues.

Hubbard MJ, Faught MJ, Carlisle BH, Stockwell PA.

Proteomics. 2001 Jan;1(1):132-5.

PMID:
11680893
26.

Self-programmable, self-assembling two-dimensional genetic matter.

Sowerby SJ, Stockwell PA, Heckl WM, Petersen GB.

Orig Life Evol Biosph. 2000 Feb;30(1):81-99.

PMID:
10836266
27.

Transterm: a database of messenger RNA components and signals.

Jacobs GH, Stockwell PA, Schrieber MJ, Tate WP, Brown CM.

Nucleic Acids Res. 2000 Jan 1;28(1):293-5.

28.

TransTerm, the translational signal database, extended to include full coding sequences and untranslated regions.

Dalphin ME, Stockwell PA, Tate WP, Brown CM.

Nucleic Acids Res. 1999 Jan 1;27(1):293-4.

29.

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.

McNaughton JC, Cockburn DJ, Hughes G, Jones WA, Laing NG, Ray PN, Stockwell PA, Petersen GB.

Gene. 1998 Nov 5;222(1):41-51.

PMID:
9813236
30.

The translational signal database, TransTerm, is now a relational database.

Dalphin ME, Brown CM, Stockwell PA, Tate WP.

Nucleic Acids Res. 1998 Jan 1;26(1):335-7.

31.

The evolution of an intron: analysis of a long, deletion-prone intron in the human dystrophin gene.

McNaughton JC, Hughes G, Jones WA, Stockwell PA, Klamut HJ, Petersen GB.

Genomics. 1997 Mar 1;40(2):294-304.

PMID:
9119397
32.

The translational signal database, TransTerm: more organisms, complete genomes.

Dalphin ME, Brown CM, Stockwell PA, Tate WP.

Nucleic Acids Res. 1997 Jan 1;25(1):246-7.

33.

TransTerm: a database of translational signals.

Dalphin ME, Brown CM, Stockwell PA, Tate WP.

Nucleic Acids Res. 1996 Jan 1;24(1):216-8.

34.

Phylogenetic relationships among transposon-like elements in human and primate DNA.

McNaughton JC, Marshall CJ, Broom JE, Hughes G, Jones WA, Stockwell PA, Petersen GB.

J Mol Evol. 1995 Feb;40(2):127-35.

PMID:
7699719
35.

Sequence of a transposon identified as Tn1000 (gamma delta).

Broom JE, Hill DF, Hughes G, Jones WA, McNaughton JC, Stockwell PA, Petersen GB.

DNA Seq. 1995;5(3):185-9.

PMID:
7612932
36.

The translational termination signal database (TransTerm) now also includes initiation contexts.

Brown CM, Stockwell PA, Dalphin ME, Tate WP.

Nucleic Acids Res. 1994 Sep;22(17):3620-4.

37.

A cluster of transposon-like repetitive sequences in intron 7 of the human dystrophin gene.

McNaughton JC, Broom JE, Hill DF, Jones WA, Marshall CJ, Renwick NM, Stockwell PA, Petersen GB.

J Mol Biol. 1993 Jul 5;232(1):314-21.

PMID:
8392588
38.

The translational termination signal database.

Brown CM, Dalphin ME, Stockwell PA, Tate WP.

Nucleic Acids Res. 1993 Jul 1;21(13):3119-23.

39.

The putative single-stranded DNA-binding protein of the filamentous bacteriophage, Ifl. Amino acid sequence of the protein and structure of the gene.

Carne A, Hill DF, Stockwell PA, Hughes G, Petersen GB.

Proc Biol Sci. 1991 Jul 22;245(1312):23-30.

PMID:
1682927
40.

Sequence analysis suggests that tetra-nucleotides signal the termination of protein synthesis in eukaryotes.

Brown CM, Stockwell PA, Trotman CN, Tate WP.

Nucleic Acids Res. 1990 Nov 11;18(21):6339-45.

41.

The signal for the termination of protein synthesis in procaryotes.

Brown CM, Stockwell PA, Trotman CN, Tate WP.

Nucleic Acids Res. 1990 Apr 25;18(8):2079-86.

42.

A homologue of retroviral pseudoproteases in the parapoxvirus, orf virus.

Mercer AA, Fraser KM, Stockwell PA, Robinson AJ.

Virology. 1989 Oct;172(2):665-8.

PMID:
2678731
43.

Laser excitation of fluorescent-labeled polypeptides in polyacrylamide gels.

Duffy VE, Stockwell PA, Warrington DM, Monk BC.

Anal Biochem. 1989 Jun;179(2):291-8.

PMID:
2505638
44.

GELENT: a sequence gel entry program for keyboard and sonic digitizer input.

Broom JE, Stockwell PA, Hill DF.

Comput Appl Biosci. 1989 Apr;5(2):155-7.

PMID:
2720465
45.
46.

HOMED: a homologous sequence editor.

Stockwell PA.

Trends Biochem Sci. 1988 Aug;13(8):322-4. No abstract available.

PMID:
3154284
47.

HOMED: a homologous sequence editor.

Stockwell PA, Petersen GB.

Comput Appl Biosci. 1987 Mar;3(1):37-43.

PMID:
3453212
48.

VTUTIN: a full screen gel management editor.

Stockwell PA.

Comput Appl Biosci. 1985 Dec;1(4):253-9.

PMID:
3880348
49.
50.

Gene duplication in tetraploid fish: model for gene silencing at unlinked duplicated loci.

Bailey GS, Poulter RT, Stockwell PA.

Proc Natl Acad Sci U S A. 1978 Nov;75(11):5575-9.

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