Published in:

Dan MacLean, Kentaro Yoshida, Anne Edwards, Lisa Crossman, Bernardo Clavijo, Matt Clark, David Swarbreck, Matthew Bashton, Patrick Chapman, Mark Gijzen, Mario Caccamo, Allan Downie, Sophien Kamoun and Diane GO Saunders (2013) Crowdsourcing genomic analyses of ash and ash dieback — power to the people. GigaScience 2:2. doi:10.1186/2047-217X-2-2

Phillip Lord, Simon Cockell and Robert Stevens (2012) Three Steps to Heaven: Semantic Publishing in a Real-World Workflow. Future Internet 4(4): 1004-1015. doi:10.3390/fi4041004

Ka Cheong Lee, Kay Padget, Hannah Curtis, Ian G. Cowell, Davide Moiani, Zbyslaw Sondka, Nicholas J. Morris, Graham H. Jackson, Simon J. Cockell, John A. Tainer, and Caroline A. Austin (2012) MRE11 facilitates the removal of human topoisomerase II complexes from genomic DNA. Biology Open; Advance Online Publication July 16, 2012. doi: 10.1242/bio.20121834

Y. Xu, M.J. Barter, D.C. Swan, K.S. Rankin, A.D. Rowan, M. Santibanez-Koref, J. Loughlin, D.A. Young (2012) Identification of the pathogenic pathways in osteoarthritic hip cartilage: commonality and discord between hip and knee OA. Osteoarthritis and Cartilage, Available online 31 May 2012. doi: 10.1016/j.joca.2012.05.006

Patience Cole-Ezea, Dan Swan, Daryl Shanley, John Hesketh (2012) Glutathione peroxidase 4 has a major role in protecting mitochondria from oxidative damage and maintaining oxidative phosphorylation complexes in gut epithelial cells. Free Radical Biology and Medicine. Available online 25th May 2012. doi: 10.1016/j.freeradbiomed.2012.05.029

Arthur G Pratt, Daniel C Swan, Sarah Richardson, Gillian Wilson, Catharien MU Hilkens, David A Young, John D Issacs (2012) A CD4 T cell gene signature for early rheumatoid arthritis implicates interleukin 6-mediated STAT3 signalling, particularly in anti-citrullinated peptide antibody-negative disease. Annals of the Rhumatic Diseases. First published online April 24th 2012. doi: 10.1136/annrheumdis-2011-200968.

Jochen Weile, Katherine James, Jennifer Hallinan, Simon J Cockell, Phillip Lord, Anil Wipat and Darren Wilkinson (2012) Bayesian integration of networks without gold standards. Bioinformatics 28(11) 1495-1500. doi: 10.1093/bioinformatics/bts154.

Caroline L. Relton, Alexandra Groom, Beate St. Pourcain, Adrian E. Sayers, Daniel C. Swan, Nicholas D. Embleton, Mark S. Pearce, Susan M. Ring, Kate Northstone, Jon H. Tobias, Joseph Trakalo, Andy R. Ness, Seif O. Shaheen, George Davey Smith (2012) DNA Methylation Patterns in Cord Blood DNA and Body Size in Childhood. PLoS One 7(3): e31821. doi:10.1371/journal.pone.0031821

Valérie Turcot, Alexandra Groom, James C. McConnell, Mark S. Pearce, Catherine Potter, Nicholas D. Embleton, Daniel C. Swan, Caroline L. Relton (2012) Bioinformatic selection of putative epigenetically regulated loci associated with obesity using gene expression data. Gene 2012 Mar 9. doi: 10.1016/j.gene.2012.02.001

Alexandra Groom, Catherine Potter, Daniel C Swan, Ghazaleh Fatemifar, David M Evans, Susan M Ring, Valerie Turcot, Mark S Pearce, Nicholas D Embleton, George Davey Smith, John C Mathers, Caroline L Relton (2011) Postnatal growth and DNA methylation are associated with differential gene expression of the TACSTD2 gene and childhood fat mass. Diabetes 2011 Dec 21. doi: 10.2337/db11-1039

Andrew C Browning, Eugene P Halligan, Elizabeth A Stewart, Daniel C Swan, Rosamund Dove, Govindi J Samaranayake, Winfried M Amoaku (2011) Comparative gene expression profiling of human umbilical vein endothelial cells and ocular vascular endothelial cells. Br J Ophthalmol. 2011 Oct 25. doi:10.1136/bjophthalmol-2011-300572.

Laurence D Parnell, Pierre Lindenbaum, Khader Shameer, Giovanni Marco Dall’Olio, Daniel C. Swan, Lars Juhl Jensen, Simon J. Cockell, Brent S Pedersen, Mary E. Mangan, Christopher A. Miller, Istvan Albert (2011) BioStar: An Online Question & Answer Resource for the Bioinformatics Community. PLoS Comput Biol 7(10): e1002216. doi:10.1371/journal.pcbi.1002216.

Stadler L, Hoffmann T, Tomlinson D, Song Q, Lee T, Busby M, Nyathi Y, Gendra E, Tiede C, Flanagan K, Cockell SJ, Wipat A, Harwood C, Wagner S, Knowles M, Davis J, Ko Ferrigno P (2011) Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and Applications of the SQT variant Protein Engineering Design and Selection 24(9): 751-63 doi: 10.1093/protein/gzr019.

Weile J, Pocock M, Cockell SJ, Lord P, Dewar JM, Holstein E, Wilkinson D, Lydall D, Hallinan J, Wipat A (2011) Customisable views on semantically integrated networks for systems biology Bioinformatics first published online March 16, 2011 doi:10.1093/bioinformatics/btr134 PubMed

Werner A, Swan D (2010) What are natural antisense transcripts good for? Biochem Soc Trans. 2010 Aug 1;38(4):1144-9. PubMed

Daniels DJ, Clothier C, Swan DC, Saretzki G (2010)  Immediate and gradual gene expression changes in telomerase over-expressing fibroblasts. Biochem Biophys Res Commun. 2010 Jul 15 PubMed

Christine Hoogland, Martin O’Gorman, Philippe Bogard, Frank Gibson, Matthias Berth, Simon J Cockell, Andreas Ekefjärd, Ola Forsstrom-Olsson, Anna Kapferer, Mattias Nilsson, Salvador Martínez-Bartolomé, Juan Pablo Albar, Sira Echevarría-Zomeño, Montserrat Martínez-Gomariz, Johann Joets, Pierre-Alain Binz, Chris F Taylor, Andrew Dowsey, Andrew R Jones. (2010) Guidelines for reporting the use of gel image informatics in proteomics. Nature Biotechnology 28:655-6 PubMed

Varanasi SS, Olstad OK, Swan DC, Sanderson P, Gautvik VT, Reppe S, Francis RM, Gautvik KM, and Datta HK (2010) Skeletal site-related variation in human trabecular bone transcriptome and signaling. PLoS One 2010 May 18; 5(5) PubMed

Andrews E, Armstrong M, Tugwood J, Swan D, Glaves P, Pirmohamed M, Aithal GP, Wright MC, Day CP, Daly AK (2010) A role for the pregnane X receptor in flucloxacillin-induced liver injury. Hepatology. 51: 1656-1664. PubMed

Kaveh Emami, Nicholas J. Morris, Simon J. Cockell, Gabriela Golebiowska, Qing-Yao Shu, Angharad M.R. Gatehouse (2010) 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. Journal of Agricultural and Food Chemistry 58(11):6912-22 PubMed

Simon J Cockell, Jochen Weile, Phillip Lord, Claire Wipat, Dmytro Andriychenko, Matthew Pocock, Darren Wilkinson, Malcolm Young and Anil Wipat (2010) An integrated dataset for in silico drug discovery. Journal of Integrative Bioinformatics 7(3):116. PubMed

Ince RA, Petersen RS, Swan DC, Panzeri S. (2009) Python for information theoretic analysis of neural data. Front Neuroinformatics. 3: 4. PubMed

Mark Carlile, Daniel Swan, Kelly Jackson, Keziah Preston-Fayers, Benoit Ballester, Paul Flicek and Andreas Werner (2009) Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues Nucleic Acids Research, February 23, doi:10.1093/nar/gkp088 PubMed

M Hong, K R Ryan, P D Arkwright, A R Gennery, C Costigan, M Dominguez, D W Denning, V McConnell, A J Cant, M Abinun, G P Spickett, D C Swan, C S Gillespie, D A Young, D Lilic (2009) Pattern recognition receptor expression is not impaired in patients with chronic mucocutanous candidiasis with or without autoimmune polyendocrinopathy candidiasis ectodermal dystrophy. Clinical and experimental immunology (22 January) PubMed

Werner A, Carlile M, Swan D. (2009) What do natural antisense transcripts regulate? RNA Biol. 2;6(1) PubMed

Jackson KA, Valentine RA, McKay JA, Swan DC, Mathers JC, Ford D. (2008) Analysis of differential gene-regulatory responses to zinc in human intestinal and placental cell lines. Br J Nutr. : 1-10. PubMed

Greenall A, Lei G, Swan DC, James K, Wang L, Peters H, Wipat A, Wilkinson DJ, Lydall D. (2008) A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2 in chromosome end protection. Genome Biol. 9: R146. PubMed

Waterhouse JC, Swan DC, Russell RR. (2007) Comparative genome hybridization of Streptococcus mutans strains. Oral Microbiol Immunol. 22: 103-110. PubMed

S.J. Cockell, B. Oliva, and R. M. Jackson. (2007)  Evaluating in silico predictions of protein-protein interactions using Comparative Docking Bioinformatics 23, 573-581  PubMed

Field D, Tiwari B, Booth T, Houten S, Swan D, Bertrand N, Thurston M. (2006) Open software for biologists: from famine to feast. Nat Biotechnol. 24: 801-803. PubMed

Acknowledged in:

Müjdat Zeybel, Timothy Hardy, Yi K Wong, John C Mathers, Christopher R Fox, Agata Gackowska, Fiona Oakley, Alastair D Burt, Caroline L Wilson, Quentin M Anstee, Matt J Barter, Steven Masson, Ahmed M Elsharkawy, Derek A Mann and Jelena Mann (2012) Multigenerational epigenetic adaptation of the hepatic wound-healing response. Nature Medicine Published online 02 September 2012. doi: 10.1038/nm.2893

Christophe J. Noël, Nicia Diaz, Thomas Sicheritz-Ponten, Lucie Safarikova, Jan Tachezy, Petrus Tang, Pier-Luigi Fiori and Robert P. Hirt (2010) Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics. BMC Genomics 11:99 PubMed

Leaver M, Domínguez-Cuevas P, Coxhead JM, Daniel RA, Errington J (2009) Life without a wall or division machine in Bacillus subtilis. Nature. 2009 Feb 12;457(7231):849-53 PubMed

Lister A, Charoensawan V, De S, James K, Janga SC and Huppert J (2009) Interfacing systems biology and synthetic biology. Genome Biology 10:309 PubMed

MH Karavolos, H Spencer, DM Bulmer, A Thompson, K Winzer, P Williams, JCD Hinton, and CM Anjam Khan (2008) Adrenaline modulates the global transcriptional profile of Salmonella revealing a role in the antimicrobial peptide and oxidative stress resistance responses. BMC Genomics. 2008 Oct 6;9:458. PubMed

Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM. (2008) The archaebacterial origin of eukaryotes. Proc Natl Acad Sci U S A. Dec 10 PubMed

Booth T, Gilbert J, Neufeld JD, Ball J, Thurston M, Chipman K Joint I, Field D (2007) Handlebar: a flexible, web-based inventory manager for handling barcoded samples.  Biotechniques.  Mar;42(3):300-02  PubMed

David Hancock, Michael Wilson, Giles Velarde, Norman Morrison, Andrew Hayes, Helen Hulme, A Joseph Wood, Karim Nashar, Douglas B Kell and Andy Brass  (2005) maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination. BMC Bioinformatics. Nov 3;6:264. PubMed

Conference papers:

A CD4+T-Cell Gene Expression Signature Predicts Drug Survival On Methotrexate Monotherapy in Early Rheumatoid Arthritis. (Pratt AG, Brown PM, Cockell SJ, Wilson G, Isaacs JD) – Annual Scientific Meeting of the American College of Rheumatology (ACR) (November 9th-14th 2012)

The Medical Research Council Neuromuscular Centre for Translational Research Mitochondrial Disease Patient Cohort Study UK: from conceptualisation to utilisation (Nesbitt V, Pitceathly R, Cockell S, Poulton J, Rahman S, Hanna M, Turnbull D, McFarland R) – United Kingdom Neuromuscular Translational Research Conference (March 22nd-23rd 2012)

Three Steps to Heaven (Phillip Lord, Simon Cockell and Robert Stevens) – Sepublica Workshop at 9th Extended Semantic Web Conference 2012 (May 27th-31st, 2012) – awarded ‘best paper’.

Comparative Genome Hybridisation of Streptococcus mutans strains (J.C. Waterhouse, D. C. Swan, and R.R.B. Russell) – International Association for Dental Research Pan European Federation 2006 (September 13-16, 2006)