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Items: 45

1.

Androgen-regulated transcription of ESRP2 drives alternative splicing patterns in prostate cancer.

Munkley J, Ling L, Krishnan SRG, Hysenaj G, Scott E, Dalgliesh C, Oo HZ, Maia TM, Cheung K, Ehrmann I, Livermore KE, Zielinska H, Thompson O, Knight B, McCullagh P, McGrath J, Crundwell M, Harries LW, Daugaard M, Cockell S, Barbosa-Morais NL, Oltean S, Elliott DJ.

Elife. 2019 Sep 3;8. pii: e47678. doi: 10.7554/eLife.47678. [Epub ahead of print]

2.

Pax9 is required for cardiovascular development and interacts with Tbx1 in the pharyngeal endoderm to control 4th pharyngeal arch artery morphogenesis.

Phillips HM, Stothard CA, Qureshi WMS, Kousa AI, Briones-Leon JA, Khasawneh RR, O'Loughlin C, Sanders R, Mazzotta S, Dodds R, Seidel K, Bates T, Nakatomi M, Cockell SJ, Schneider JE, Mohun TJ, Maehr R, Kist R, Peters H, Bamforth SD.

Development. 2019 Aug 23. pii: dev.177618. doi: 10.1242/dev.177618. [Epub ahead of print]

3.

An ancient germ cell-specific RNA-binding protein protects the germline from cryptic splice site poisoning.

Ehrmann I, Crichton JH, Gazzara MR, James K, Liu Y, Grellscheid SN, Curk T, de Rooij D, Steyn JS, Cockell S, Adams IR, Barash Y, Elliott DJ.

Elife. 2019 Jan 24;8. pii: e39304. doi: 10.7554/eLife.39304.

4.

High-throughput sequencing identifies aetiology-dependent differences in ductular reaction in human chronic liver disease.

Govaere O, Cockell S, Van Haele M, Wouters J, Van Delm W, Van den Eynde K, Bianchi A, van Eijsden R, Van Steenbergen W, Monbaliu D, Nevens F, Roskams T.

J Pathol. 2019 May;248(1):66-76. doi: 10.1002/path.5228. Epub 2019 Jan 30.

PMID:
30584802
5.

Deconstructing Retinal Organoids: Single Cell RNA-Seq Reveals the Cellular Components of Human Pluripotent Stem Cell-Derived Retina.

Collin J, Queen R, Zerti D, Dorgau B, Hussain R, Coxhead J, Cockell S, Lako M.

Stem Cells. 2019 May;37(5):593-598. doi: 10.1002/stem.2963. Epub 2019 Jan 12.

6.

RRAD, IL4I1, CDKN1A, and SERPINE1 genes are potentially co-regulated by NF-κB and p53 transcription factors in cells exposed to high doses of ionizing radiation.

Szołtysek K, Janus P, Zając G, Stokowy T, Walaszczyk A, Widłak W, Wojtaś B, Gielniewski B, Cockell S, Perkins ND, Kimmel M, Widlak P.

BMC Genomics. 2018 Nov 12;19(1):813. doi: 10.1186/s12864-018-5211-y.

7.

B-cell activity markers are associated with different disease activity domains in primary Sjögren's syndrome.

James K, Chipeta C, Parker A, Harding S, Cockell SJ, Gillespie CS, Hallinan J, Barone F, Bowman SJ, Ng WF, Fisher BA; UK Primary Sjögren’s Syndrome Registry.

Rheumatology (Oxford). 2018 Mar 28. doi: 10.1093/rheumatology/key063. [Epub ahead of print]

8.

Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes.

Janus P, Szołtysek K, Zając G, Stokowy T, Walaszczyk A, Widłak W, Wojtaś B, Gielniewski B, Iwanaszko M, Braun R, Cockell S, Perkins ND, Kimmel M, Widlak P.

Cell Signal. 2018 Jun;46:23-31. doi: 10.1016/j.cellsig.2018.02.011. Epub 2018 Feb 21.

PMID:
29476964
9.

Cross platform analysis of transcriptomic data identifies ageing has distinct and opposite effects on tendon in males and females.

Pease LI, Clegg PD, Proctor CJ, Shanley DJ, Cockell SJ, Peffers MJ.

Sci Rep. 2017 Oct 31;7(1):14443. doi: 10.1038/s41598-017-14650-z.

10.

Influence of Genetic Variations in Selenoprotein Genes on the Pattern of Gene Expression after Supplementation with Brazil Nuts.

Donadio JLS, Rogero MM, Cockell S, Hesketh J, Cozzolino SMF.

Nutrients. 2017 Jul 11;9(7). pii: E739. doi: 10.3390/nu9070739.

11.

Abundant and equipotent founder cells establish and maintain acute lymphoblastic leukaemia.

Elder A, Bomken S, Wilson I, Blair HJ, Cockell S, Ponthan F, Dormon K, Pal D, Heidenreich O, Vormoor J.

Leukemia. 2017 Dec;31(12):2577-2586. doi: 10.1038/leu.2017.140. Epub 2017 May 10.

12.

Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics.

James K, Cockell SJ, Zenkin N.

Methods. 2017 May 1;120:76-84. doi: 10.1016/j.ymeth.2017.04.016. Epub 2017 Apr 21. Review.

PMID:
28434904
13.

Misincorporation by RNA polymerase is a major source of transcription pausing in vivo.

James K, Gamba P, Cockell SJ, Zenkin N.

Nucleic Acids Res. 2017 Feb 17;45(3):1105-1113. doi: 10.1093/nar/gkw969.

14.

Analysis of primary visual cortex in dementia with Lewy bodies indicates GABAergic involvement associated with recurrent complex visual hallucinations.

Khundakar AA, Hanson PS, Erskine D, Lax NZ, Roscamp J, Karyka E, Tsefou E, Singh P, Cockell SJ, Gribben A, Ramsay L, Blain PG, Mosimann UP, Lett DJ, Elstner M, Turnbull DM, Xiang CC, Brownstein MJ, O'Brien JT, Taylor JP, Attems J, Thomas AJ, McKeith IG, Morris CM.

Acta Neuropathol Commun. 2016 Jun 30;4(1):66. doi: 10.1186/s40478-016-0334-3.

15.

An Integrated Data Driven Approach to Drug Repositioning Using Gene-Disease Associations.

Mullen J, Cockell SJ, Woollard P, Wipat A.

PLoS One. 2016 May 19;11(5):e0155811. doi: 10.1371/journal.pone.0155811. eCollection 2016.

16.

Transcriptomics and proteomics show that selenium affects inflammation, cytoskeleton, and cancer pathways in human rectal biopsies.

Méplan C, Johnson IT, Polley AC, Cockell S, Bradburn DM, Commane DM, Arasaradnam RP, Mulholland F, Zupanic A, Mathers JC, Hesketh J.

FASEB J. 2016 Aug;30(8):2812-25. doi: 10.1096/fj.201600251R. Epub 2016 Apr 21.

17.

A RelA(p65) Thr505 phospho-site mutation reveals an important mechanism regulating NF-κB-dependent liver regeneration and cancer.

Moles A, Butterworth JA, Sanchez A, Hunter JE, Leslie J, Sellier H, Tiniakos D, Cockell SJ, Mann DA, Oakley F, Perkins ND.

Oncogene. 2016 Sep 1;35(35):4623-32. doi: 10.1038/onc.2015.526. Epub 2016 Feb 8.

18.

Mining integrated semantic networks for drug repositioning opportunities.

Mullen J, Cockell SJ, Tipney H, Woollard PM, Wipat A.

PeerJ. 2016 Jan 19;4:e1558. doi: 10.7717/peerj.1558. eCollection 2016.

19.

Zinc sensing by metal-responsive transcription factor 1 (MTF1) controls metallothionein and ZnT1 expression to buffer the sensitivity of the transcriptome response to zinc.

Hardyman JE, Tyson J, Jackson KA, Aldridge C, Cockell SJ, Wakeling LA, Valentine RA, Ford D.

Metallomics. 2016 Mar;8(3):337-43. doi: 10.1039/c5mt00305a.

PMID:
26824222
20.

A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren's Syndrome.

James K, Al-Ali S, Tarn J, Cockell SJ, Gillespie CS, Hindmarsh V, Locke J, Mitchell S, Lendrem D, Bowman S, Price E, Pease CT, Emery P, Lanyon P, Hunter JA, Gupta M, Bombardieri M, Sutcliffe N, Pitzalis C, McLaren J, Cooper A, Regan M, Giles I, Isenberg D, Saravanan V, Coady D, Dasgupta B, McHugh N, Young-Min S, Moots R, Gendi N, Akil M, Griffiths B; UK Primary Sjögren’s Syndrome registry, Wipat A, Newton J, Jones DE, Isaacs J, Hallinan J, Ng WF.

PLoS One. 2015 Dec 22;10(12):e0143970. doi: 10.1371/journal.pone.0143970. eCollection 2015.

21.

The NF-κB subunit c-Rel regulates Bach2 tumour suppressor expression in B-cell lymphoma.

Hunter JE, Butterworth JA, Zhao B, Sellier H, Campbell KJ, Thomas HD, Bacon CM, Cockell SJ, Gewurz BE, Perkins ND.

Oncogene. 2016 Jun 30;35(26):3476-84. doi: 10.1038/onc.2015.399. Epub 2015 Nov 2.

22.

Genome-wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells.

Manville CM, Smith K, Sondka Z, Rance H, Cockell S, Cowell IG, Lee KC, Morris NJ, Padget K, Jackson GH, Austin CA.

Biol Open. 2015 Oct 12;4(11):1436-47. doi: 10.1242/bio.014308.

23.

Genetic Networks Required to Coordinate Chromosome Replication by DNA Polymerases α, δ, and ε in Saccharomyces cerevisiae.

Dubarry M, Lawless C, Banks AP, Cockell S, Lydall D.

G3 (Bethesda). 2015 Aug 21;5(10):2187-97. doi: 10.1534/g3.115.021493.

24.

Epigenetic landscape correlates with genetic subtype but does not predict outcome in childhood acute lymphoblastic leukemia.

Gabriel AS, Lafta FM, Schwalbe EC, Nakjang S, Cockell SJ, Iliasova A, Enshaei A, Schwab C, Rand V, Clifford SC, Kinsey SE, Mitchell CD, Vora A, Harrison CJ, Moorman AV, Strathdee G.

Epigenetics. 2015;10(8):717-26. doi: 10.1080/15592294.2015.1061174.

25.

SIRT1 affects DNA methylation of polycomb group protein target genes, a hotspot of the epigenetic shift observed in ageing.

Wakeling LA, Ions LJ, Escolme SM, Cockell SJ, Su T, Dey M, Hampton EV, Jenkins G, Wainwright LJ, McKay JA, Ford D.

Hum Genomics. 2015 Jun 24;9:14. doi: 10.1186/s40246-015-0036-0.

26.

The zinc finger protein ZNF658 regulates the transcription of genes involved in zinc homeostasis and affects ribosome biogenesis through the zinc transcriptional regulatory element.

Ogo OA, Tyson J, Cockell SJ, Howard A, Valentine RA, Ford D.

Mol Cell Biol. 2015 Mar;35(6):977-87. doi: 10.1128/MCB.01298-14. Epub 2015 Jan 12.

27.

Regulation of p53 and Rb links the alternative NF-κB pathway to EZH2 expression and cell senescence.

Iannetti A, Ledoux AC, Tudhope SJ, Sellier H, Zhao B, Mowla S, Moore A, Hummerich H, Gewurz BE, Cockell SJ, Jat PS, Willmore E, Perkins ND.

PLoS Genet. 2014 Sep 25;10(9):e1004642. doi: 10.1371/journal.pgen.1004642. eCollection 2014 Sep.

28.

A distributed computational search strategy for the identification of diagnostics targets: application to finding aptamer targets for methicillin-resistant staphylococci.

Flanagan K, Cockell S, Harwood C, Hallinan J, Nakjang S, Lawry B, Wipat A.

J Integr Bioinform. 2014 Jun 30;11(2):242. doi: 10.2390/biecoll-jib-2014-242.

PMID:
24980620
29.

Contribution of natural antisense transcription to an endogenous siRNA signature in human cells.

Werner A, Cockell S, Falconer J, Carlile M, Alnumeir S, Robinson J.

BMC Genomics. 2014 Jan 13;15:19. doi: 10.1186/1471-2164-15-19.

30.

Utility of B-13 progenitor-derived hepatocytes in hepatotoxicity and genotoxicity studies.

Probert PM, Chung GW, Cockell SJ, Agius L, Mosesso P, White SA, Oakley F, Brown CD, Wright MC.

Toxicol Sci. 2014 Feb;137(2):350-70. doi: 10.1093/toxsci/kft258. Epub 2013 Nov 14.

31.

MRE11 facilitates the removal of human topoisomerase II complexes from genomic DNA.

Lee KC, Padget K, Curtis H, Cowell IG, Moiani D, Sondka Z, Morris NJ, Jackson GH, Cockell SJ, Tainer JA, Austin CA.

Biol Open. 2012 Sep 15;1(9):863-73. doi: 10.1242/bio.20121834. Epub 2012 Jul 11.

32.

Bayesian integration of networks without gold standards.

Weile J, James K, Hallinan J, Cockell SJ, Lord P, Wipat A, Wilkinson DJ.

Bioinformatics. 2012 Jun 1;28(11):1495-500. doi: 10.1093/bioinformatics/bts154. Epub 2012 Apr 6.

33.

BioStar: an online question & answer resource for the bioinformatics community.

Parnell LD, Lindenbaum P, Shameer K, Dall'Olio GM, Swan DC, Jensen LJ, Cockell SJ, Pedersen BS, Mangan ME, Miller CA, Albert I.

PLoS Comput Biol. 2011 Oct;7(10):e1002216. doi: 10.1371/journal.pcbi.1002216. Epub 2011 Oct 27. No abstract available.

34.

Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and applications of the SQT variant.

Stadler LK, Hoffmann T, Tomlinson DC, Song Q, Lee T, Busby M, Nyathi Y, Gendra E, Tiede C, Flanagan K, Cockell SJ, Wipat A, Harwood C, Wagner SD, Knowles MA, Davis JJ, Keegan N, Ferrigno PK.

Protein Eng Des Sel. 2011 Sep;24(9):751-63. doi: 10.1093/protein/gzr019. Epub 2011 May 25.

PMID:
21616931
35.

Customizable views on semantically integrated networks for systems biology.

Weile J, Pocock M, Cockell SJ, Lord P, Dewar JM, Holstein EM, Wilkinson D, Lydall D, Hallinan J, Wipat A.

Bioinformatics. 2011 May 1;27(9):1299-306. doi: 10.1093/bioinformatics/btr134. Epub 2011 Mar 16.

36.

Emotional experiences of caregivers of patients with a ventricular assist device.

Kaan A, Young QR, Cockell S, Mackay M.

Prog Transplant. 2010 Jun;20(2):142-7.

PMID:
20642172
37.

Guidelines for reporting the use of gel image informatics in proteomics.

Hoogland C, O'Gorman M, Bogard P, Gibson F, Berth M, Cockell SJ, Ekefjärd A, Forsstrom-Olsson O, Kapferer A, Nilsson M, Martínez-Bartolomé S, Albar JP, Echevarría-Zomeño S, Martínez-Gomariz M, Joets J, Binz PA, Taylor CF, Dowsey A, Jones AR; Minimum Information About a Proteomics Experiment (MIAPE).

Nat Biotechnol. 2010 Jul;28(7):655-6. doi: 10.1038/nbt0710-655. No abstract available.

PMID:
20622830
38.

Changes in protein expression profiles between a low phytic acid rice ( Oryza sativa L. Ssp. japonica) line and its parental line: a proteomic and bioinformatic approach.

Emami K, Morris NJ, Cockell SJ, Golebiowska G, Shu QY, Gatehouse AM.

J Agric Food Chem. 2010 Jun 9;58(11):6912-22. doi: 10.1021/jf904082b.

PMID:
20441221
39.

An integrated dataset for in silico drug discovery.

Cockell SJ, Weile J, Lord P, Wipat C, Andriychenko D, Pocock M, Wilkinson D, Young M, Wipat A.

J Integr Bioinform. 2010 Mar 25;7(3). doi: 10.2390/biecoll-jib-2010-116.

PMID:
20375448
40.

Structure-based evaluation of in silico predictions of protein-protein interactions using Comparative Docking.

Cockell SJ, Oliva B, Jackson RM.

Bioinformatics. 2007 Mar 1;23(5):573-81. Epub 2007 Jan 18.

PMID:
17237047
41.

Postpartum flatal and Fecal Incontinence Quality-of-Life Scale: a disease- and population-specific measure.

Cockell SJ, Oates-Johnson T, Gilmour DT, Vallis TM, Turnbull GK.

Qual Health Res. 2003 Oct;13(8):1132-44.

PMID:
14556423
42.
43.

Assessment of shape- and weight-based self-esteem in adolescents.

Geller J, Srikameswaran S, Cockell SJ, Zaitsoff SL.

Int J Eat Disord. 2000 Nov;28(3):339-45.

PMID:
10942921
44.

Psychiatric comorbidity associated with eating disorder symptomatology among adolescents in the community.

Zaider TI, Johnson JG, Cockell SJ.

Int J Eat Disord. 2000 Jul;28(1):58-67.

PMID:
10800014
45.

Inhibited expression of negative emotions and interpersonal orientation in anorexia nervosa.

Geller J, Cockell SJ, Hewitt PL, Goldner EM, Flett GL.

Int J Eat Disord. 2000 Jul;28(1):8-19. Erratum in: Int J Eat Disord 2000 Dec;28(4):481.

PMID:
10800009

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