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Publications

2018

  • Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease. Kinchen J, Chen HH, Parikh K, Antanaviciute A, Jagielowicz M, Fawkner-Corbett D, Ashley N, Cubitt L, Mellado-Gomez E, Attar M, Sharma E, Wills Q, Bowden R, Richter FC, Ahern D, Puri KD, Henault J, Gervais F, Koohy H, Simmons A. Cell. 2018 Sep 25. pii: S0092-8674(18)31168-1. doi: 10.1016/j.cell.2018.08.067. PMID: 30270042
  • Reproducibility of Molecular Phenotypes after Long-Term Differentiation to Human iPSC-Derived Neurons: A Multi-Site Omics Study. Volpato V, Smith J, Sandor C, Ried JS, Baud A, Handel A, Newey SE, Wessely F, Attar M, Whiteley E, Chintawar S, Verheyen A, Barta T, Lako M, Armstrong L, Muschet C, Artati A, Cusulin C, Christensen K, Patsch C, Sharma E, Nicod J, Brownjohn P, Stubbs V, Heywood WE, Gissen P, De Filippis R, Janssen K, Reinhardt P, Adamski J, Royaux I, Peeters PJ, Terstappen GC, Graf M, Livesey FJ, Akerman CJ, Mills K, Bowden R, Nicholson G, Webber C, Cader MZ, Lakics V. Stem Cell Reports. 2018 Sep 6. pii: S2213-6711(18)30357-6. doi: 10.1016/j.stemcr.2018.08.013. PMID: 30245212
  • A Requirement for Zic2 in the Regulation of Nodal Expression Underlies the Establishment of Left-Sided Identity. Dykes IM, Szumska D, Kuncheria L, Puliyadi R, Chen CM, Papanayotou C, Lockstone H, Dubourg C, David V, Schneider JE, Keane TM, Adams DJ, Brown SDM, Mercier S, Odent S, Collignon J, Bhattacharya S. Sci Rep. 2018 Jul 11;8(1):10439. doi: 10.1038/s41598-018-28714-1. PMID: 29992973
  • Impact of spliceosome mutations on RNA splicing in myelodysplasia: dysregulated genes/pathways and clinical associations. Pellagatti A, Armstrong RN, Steeples V, Sharma E, Repapi E, Singh S, Sanchi A, Radujkovic A, Horn P, Dolatshad H, Roy S, Broxholme J, Lockstone H, Taylor S, Giagounidis A, Vyas P, Schuh A, Hamblin A, Papaemmanuil E, Killick S, Malcovati L, Hennrich ML, Gavin AC, Ho AD, Luft T, Hellström-Lindberg E, Cazzola M, Smith CWJ, Smith S, Boultwood J. Blood. 2018 Jun 21. doi: 10.1182/blood-2018-04-843771. PMID: 29930011
  • A practical solution for preserving single cells for RNA sequencing. Attar M, Sharma E, Li S, Bryer C, Cubitt L, Broxholme J, Lockstone H, Kinchen J, Simmons A, Piazza P, Buck D, Livak KJ, Bowden R. Sci Rep. 2018 Feb 1;8(1):2151. doi: 10.1038/s41598-018-20372-7. PMID: 29391536

2017

  • Variability of genome-wide DNA methylation and mRNA expression profiles in reproductive and endocrine disease related tissues. Rahmioglu N, Drong AW, Lockstone H, Tapmeier T, Hellner K, Saare M, Laisk-Podar T, Dew C, Tough E, Nicholson G, Peters M, Morris AP, Lindgren CM, Becker CM, Zondervan KT. Epigenetics. 2017;12(10):897-908. doi: 10.1080/15592294.2017.1367475. PMID: 29099281
  • A Novel Strategy Combining Array-CGH, Whole-exome Sequencing and In Utero Electroporation in Rodents to Identify Causative Genes for Brain Malformations. Conti V, Carabalona A, Pallesi-Pocachard E, Leventer RJ, Schaller F, Parrini E, Deparis AA, Watrin F, Buhler E, Novara F, Lise S, Pagnamenta AT, Kini U, Taylor JC, Zuffardi O, Represa A, Keays DA, Guerrini R, Falace A, Cardoso C. J Vis Exp. 2017 Dec 1;(130). doi: 10.3791/53570. PMID: 29286390
  • Mammalian γ2 AMPK regulates intrinsic heart rate. Yavari A, Bellahcene M, Bucchi A, Sirenko S, Pinter K, Herring N, Jung JJ, Tarasov KV, Sharpe EJ, Wolfien M, Czibik G, Steeples V, Ghaffari S, Nguyen C, Stockenhuber A, Clair JRS, Rimmbach C, Okamoto Y, Yang D, Wang M, Ziman BD, Moen JM, Riordon DR, Ramirez C, Paina M, Lee J, Zhang J, Ahmet I, Matt MG, Tarasova YS, Baban D, Sahgal N, Lockstone H, Puliyadi R, de Bono J, Siggs OM, Gomes J, Muskett H, Maguire ML, Beglov Y, Kelly M, Dos Santos PPN, Bright NJ, Woods A, Gehmlich K, Isackson H, Douglas G, Ferguson DJP, Schneider JE, Tinker A, Wolkenhauer O, Channon KM, Cornall RJ, Sternick EB, Paterson DJ, Redwood CS, Carling D, Proenza C, David R, Baruscotti M, DiFrancesco D, Lakatta EG, Watkins H, Ashrafian H. Nat Commun. 2017 Nov 2;8(1):1258. doi: 10.1038/s41467-017-01342-5. PMID: 29097735
  • NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease. Schwerd T, Bryant RV, Pandey S, Capitani M, Meran L, Cazier JB, Jung J, Mondal K, Parkes M, Mathew CG, Fiedler K, McCarthy DJ; WGS500 Consortium; Oxford IBD cohort study investigators; COLORS in IBD group investigators; UK IBD Genetics Consortium, Sullivan PB, Rodrigues A, Travis SPL, Moore C, Sambrook J, Ouwehand WH, Roberts DJ, Danesh J; INTERVAL Study, Russell RK, Wilson DC, Kelsen JR, Cornall R, Denson LA, Kugathasan S, Knaus UG, Serra EG, Anderson CA, Duerr RH, McGovern DP, Cho J, Powrie F, Li VS, Muise AM, Uhlig HH. Mucosal Immunol. 2017 Nov 1. doi: 10.1038/mi.2017.74. PMID: 29091079
  • BrowseVCF: a web-based application and workflow to quickly prioritize disease-causative variants in VCF files. Salatino S, Ramraj V. Brief Bioinform. 2017 Sep 1;18(5):774-779. doi: 10.1093/bib/bbw054. PMID: 27373737
  • MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry. Jain M, Tyson JR, Loose M, Ip CLC, Eccles DA, O'Grady J, Malla S, Leggett RM, Wallerman O, Jansen HJ, Zalunin V, Birney E, Brown BL, Snutch TP, Olsen HE; MinION Analysis and Reference Consortium. F1000Res. 2017 May 31;6:760. doi: 10.12688/f1000research.11354.1. eCollection 2017. PMID: 28794860
  • Epigenetic pathway inhibitors represent potential drugs for treating pancreatic and bronchial neuroendocrine tumors. Lines KE, Stevenson M, Filippakopoulos P, Müller S, Lockstone HE, Wright B, Grozinsky-Glasberg S, Grossman AB, Knapp S, Buck D, Bountra C, Thakker RV. Oncogenesis. 2017 May 15;6(5):e332. doi: 10.1038/oncsis.2017.30. PMID: 28504695
  • The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq. Wills QF, Mellado-Gomez E, Nolan R, Warner D, Sharma E, Broxholme J, Wright B, Lockstone H, James W, Lynch M, Gonzales M, West J, Leyrat A, Padilla-Parra S, Filippi S, Holmes C, Moore MD, Bowden R. BMC Genomics. 2017 Jan 7;18(1):53. doi: 10.1186/s12864-016-3445-0. PMID: 28061811
  • Making the most of RNA-seq: Pre-processing sequencing data with Opossum for reliable SNP variant detection. Oikkonen L, Lise S. Wellcome Open Res. 2017 Jan 17;2:6. doi: 10.12688/wellcomeopenres.10501.2. PMID: 28239666
  • Repo-Man/PP1 regulates heterochromatin formation in interphase. de Castro IJ, Budzak J, Di Giacinto ML, Ligammari L, Gokhan E, Spanos C, Moralli D, Richardson C, de Las Heras JI, Salatino S, Schirmer EC, Ullman KS, Bickmore WA, Green C, Rappsilber J, Lamble S, Goldberg MW, Vinciotti V, Vagnarelli P. Nat Commun. 2017 Jan 16;8:14048. doi: 10.1038/ncomms14048. PMID: 28091603

2016

  • Impact of IL-27 on hepatocyte antiviral gene expression and function. Ramamurthy N, Boninsegna S, Adams R, Sahgal N, Lockstone H, Baban D, Marchi E, Klenerman P. Wellcome Open Res. 2016 Nov 17;1:17. doi: 10.12688/wellcomeopenres.9917.1. PMID: 28058287
  • Autosomal dominant osteopetrosis associated with renal tubular acidosis is due to a CLCN7 mutation. Piret SE, Gorvin CM, Trinh A, Taylor J, Lise S, Taylor JC, Ebeling PR, Thakker RV. Am J Med Genet A. 2016 Nov;170(11):2988-2992. doi: 10.1002/ajmg.a.37755. PMID: 27540713
  • Expression of Idh1R132H in the Murine Subventricular Zone Stem Cell Niche Recapitulates Features of Early Gliomagenesis. Bardella C, Al-Dalahmah O, Krell D, Brazauskas P, Al-Qahtani K, Tomkova M, Adam J, Serres S, Lockstone H, Freeman-Mills L, Pfeffer I, Sibson N, Goldin R, Schuster-Böeckler B, Pollard PJ, Soga T, McCullagh JS, Schofield CJ, Mulholland P, Ansorge O, Kriaucionis S, Ratcliffe PJ, Szele FG, Tomlinson I. Cancer Cell. 2016 Oct 10;30(4):578-594. doi: 10.1016/j.ccell.2016.08.017. PMID: 27693047
  • 53BP1 Integrates DNA Repair and p53-Dependent Cell Fate Decisions via Distinct Mechanisms. Cuella-Martin R, Oliveira C, Lockstone HE, Snellenberg S, Grolmusova N, Chapman JR. Mol Cell. 2016 Oct 6;64(1):51-64. doi: 10.1016/j.molcel.2016.08.002. PMID: 27546791
  • Comparison of Next-Generation Sequencing Technologies for Comprehensive Assessment of Full-Length Hepatitis C Viral Genomes. Thomson E, Ip CL, Badhan A, Christiansen MT, Adamson W, Ansari MA, Bibby D, Breuer J, Brown A, Bowden R, Bryant J, Bonsall D, Da Silva Filipe A, Hinds C, Hudson E, Klenerman P, Lythgow K, Mbisa JL, McLauchlan J, Myers R, Piazza P, Roy S, Trebes A, Sreenu VB, Witteveldt J; STOP-HCV Consortium, Barnes E, Simmonds P. J Clin Microbiol. 2016 Oct;54(10):2470-84. doi: 10.1128/JCM.00330-16. PMID: 27385709
  • Combination of Whole Genome Sequencing, Linkage, and Functional Studies Implicates a Missense Mutation in Titin as a Cause of Autosomal Dominant Cardiomyopathy With Features of Left Ventricular Noncompaction. Hastings R, de Villiers CP, Hooper C, Ormondroyd L, Pagnamenta A, Lise S, Salatino S, Knight SJ, Taylor JC, Thomson KL, Arnold L, Chatziefthimiou SD, Konarev PV, Wilmanns M, Ehler E, Ghisleni A, Gautel M, Blair E, Watkins H, Gehmlich K. Circ Cardiovasc Genet. 2016 Oct;9(5):426-435. PMID: 27625337
  • Premalignant SOX2 overexpression in the fallopian tubes of ovarian cancer patients: Discovery and validation studies. Hellner K, Miranda F, Fotso Chedom D, Herrero-Gonzalez S, Hayden DM, Tearle R, Artibani M, KaramiNejadRanjbar M, Williams R, Gaitskell K, Elorbany S, Xu R, Laios A, Buiga P, Ahmed K, Dhar S, Zhang RY, Campo L, Myers KA, Lozano M, Ruiz-Miró M, Gatius S, Mota A, Moreno-Bueno G, Matias-Guiu X, Benítez J, Witty L, McVean G, Leedham S, Tomlinson I, Drmanac R, Cazier JB, Klein R, Dunne K, Bast RC Jr, Kennedy SH, Hassan B, Lise S, Garcia MJ, Peters BA, Yau C, Sauka-Spengler T, Ahmed AA. EBioMedicine. 2016 Aug;10:137-49. doi: 10.1016/j.ebiom.2016.06.048. PMID: 27492892
  • Negative autoregulation of BMP dependent transcription by SIN3B splicing reveals a role for RBM39. Faherty N, Benson M, Sharma E, Lee A, Howarth A, Lockstone H, Ebner D, Bhattacharya S. Sci Rep. 2016 Jun 21;6:28210. doi: 10.1038/srep28210. PMID: 27324164
  • Evaluation of Viremia Frequencies of a Novel Human Pegivirus by Using Bioinformatic Screening and PCR. Bonsall D, Gregory WF, Ip CL, Donfield S, Iles J, Ansari MA, Piazza P, Trebes A, Brown A, Frater J, Pybus OG, Goulder P, Klenerman P, Bowden R, Gomperts ED, Barnes E, Kapoor A, Sharp CP, Simmonds P. Emerg Infect Dis. 2016 Apr;22(4):671-8. doi: 10.3201/eid2204.151812. PMID: 26982117
  • Evolutionary dynamics of Enterococcus faecium reveals complex genomic relationships between isolates with independent emergence of vancomycin resistance. van Hal SJ, Ip CL, Ansari MA, Wilson DJ, Espedido BA, Jensen SO, Bowden R. Microb Genom. 2016 Jan 19;2(1). doi: 10.1099/mgen.0.000048. PMID: 27713836

2015

  • Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders. van Schouwenburg PA, Davenport EE, Kienzler AK, Marwah I, Wright B, Lucas M, Malinauskas T, Martin HC; WGS500 Consortium, Lockstone HE, Cazier JB, Chapel HM, Knight JC, Patel SY. Clin Immunol. 2015 Oct;160(2):301-14. doi: 10.1016/j.clim.2015.05.020. PMID: 26122175
  • MinION Analysis and Reference Consortium: Phase 1 data release and analysis. Ip CLC, Loose M, Tyson JR, de Cesare M, Brown BL, Jain M, Leggett RM, Eccles DA, Zalunin V, Urban JM, Piazza P, Bowden RJ, Paten B, Mwaigwisya S, Batty EM, Simpson JT, Snutch TP, Birney E, Buck D, Goodwin S, Jansen HJ, O'Grady J, Olsen HE; MinION Analysis and Reference Consortium. F1000Res. 2015 Oct 15;4:1075. doi: 10.12688/f1000research.7201.1. eCollection 2015. PMID: 26834992
  • ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens. Bonsall D, Ansari MA, Ip C, Trebes A, Brown A, Klenerman P, Buck D; STOP-HCV Consortium, Piazza P, Barnes E, Bowden R. F1000Res. 2015 Oct 13;4:1062. doi: 10.12688/f1000research.7111.1. eCollection 2015. PMID: 27092241
  • Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study. Walker TM, Kohl TA, Omar SV, Hedge J, Del Ojo Elias C, Bradley P, Iqbal Z, Feuerriegel S, Niehaus KE, Wilson DJ, Clifton DA, Kapatai G, Ip CLC, Bowden R, Drobniewski FA, Allix-Béguec C, Gaudin C, Parkhill J, Diel R, Supply P, Crook DW, Smith EG, Walker AS, Ismail N, Niemann S, Peto TEA; Modernizing Medical Microbiology (MMM) Informatics Group. Lancet Infect Dis. 2015 Oct;15(10):1193-1202. doi: 10.1016/S1473-3099(15)00062-6. PMID: 26116186
  • Gain-of-Function Mutations in ZIC1 Are Associated with Coronal Craniosynostosis and Learning Disability. Twigg SR, Forecki J, Goos JA, Richardson IC, Hoogeboom AJ, van den Ouweland AM, Swagemakers SM, Lequin MH, Van Antwerp D, McGowan SJ, Westbury I, Miller KA, Wall SA; WGS500 Consortium, van der Spek PJ, Mathijssen IM, Pauws E, Merzdorf CS, Wilkie AO. Am J Hum Genet. 2015 Sep 3;97(3):378-88. doi: 10.1016/j.ajhg.2015.07.007. PMID: 26340333
  • Disruption of SF3B1 results in deregulated expression and splicing of key genes and pathways in myelodysplastic syndrome hematopoietic stem and progenitor cells. Dolatshad H, Pellagatti A, Fernandez-Mercado M, Yip BH, Malcovati L, Attwood M, Przychodzen B, Sahgal N, Kanapin AA, Lockstone H, Scifo L, Vandenberghe P, Papaemmanuil E, Smith CW, Campbell PJ, Ogawa S, Maciejewski JP, Cazzola M, Savage KI, Boultwood J. Leukemia. 2015 Aug;29(8):1798. doi: 10.1038/leu.2015.178. PMID: 26242354
  • Factors influencing success of clinical genome sequencing across a broad spectrum of disorders. Taylor JC, Martin HC, Lise S, Broxholme J, Cazier JB, Rimmer A, Kanapin A, Lunter G, Fiddy S, Allan C, Aricescu AR, Attar M, Babbs C, Becq J, Beeson D, Bento C, Bignell P, Blair E, Buckle VJ, Bull K, Cais O, Cario H, Chapel H, Copley RR, Cornall R, Craft J, Dahan K, Davenport EE, Dendrou C, Devuyst O, Fenwick AL, Flint J, Fugger L, Gilbert RD, Goriely A, Green A, Greger IH, Grocock R, Gruszczyk AV, Hastings R, Hatton E, Higgs D, Hill A, Holmes C, Howard M, Hughes L, Humburg P, Johnson D, Karpe F, Kingsbury Z, Kini U, Knight JC, Krohn J, Lamble S, Langman C, Lonie L, Luck J, McCarthy D, McGowan SJ, McMullin MF, Miller KA, Murray L, Németh AH, Nesbit MA, Nutt D, Ormondroyd E, Oturai AB, Pagnamenta A, Patel SY, Percy M, Petousi N, Piazza P, Piret SE, Polanco-Echeverry G, Popitsch N, Powrie F, Pugh C, Quek L, Robbins PA, Robson K, Russo A, Sahgal N, van Schouwenburg PA, Schuh A, Silverman E, Simmons A, Sørensen PS, Sweeney E, Taylor J, Thakker RV, Tomlinson I, Trebes A, Twigg SR, Uhlig HH, Vyas P, Vyse T, Wall SA, Watkins H, Whyte MP, Witty L, Wright B, Yau C, Buck D, Humphray S, Ratcliffe PJ, Bell JI, Wilkie AO, Bentley D, Donnelly P, McVean G. Nat Genet. 2015 Jul;47(7):717-726. doi: 10.1038/ng.3304. PMID: 25985138