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Recent papers

Listed here are the laboratory's most recent papers. Links to previous years are provided in the side menu.

2015

  • Josephidou M, Lynch AG and Tavaré S.
    multiSNV: a probabilistic approach for improving detection of somatic point mutations from multiple related tumour samples. Nucleic Acids Research doi:10.1093/nar/gkv135 

  • Massie CE, Spiteri I, Ross-Adams H, Luxton H, Kay J, Whitaker HC, Dunning MJ, Lamb AD, Ramos-Montoya A, Brewer DS, Cooper CS, Eeles R, Warren AY, Tavare ́ S, Neal DE, and Lynch AG.
    Hes5 silencing is an early and recurrent change in prostate tumourigenesis. Endocr Relat Cancer [Epub ahead of print]

  • Modelska A, Turro E, Russell RJB, Sbarrato T, Spriggs K, Miller J, Gräf S, Provenzano E, Blows F, Pharoah P, Caldas C, and Le Quesne J.  
    The malignant phe- notype in breast cancer is driven by eIF4A1-mediated changes in the translational landscape. Cell Death & Disease 6, e1603
     
  • Piccirillo SGM, Spiteri I, Sottoriva A, Touloumis A, Ber S, Price SJ, Heywood R, Francis N-J, Howarth KD, Collins VP, Venkitaraman AR, Curtis C, Marioni JC, Tavaré S, and Watts C.
    Contributions to drug resistance in glioblastoma derived from malignant cells in the sub-ependymal zone. Cancer Res 75, 194–202

  • Gubernator M, Slater SC, Spencer HL, Spiteri I, Sottoriva A, Riu F, Rowlinson J, Avolio E, Katare R, Mangialardi G.  Oikawa A, Reni C, Campagnolo P, Spinetti G, Touloumis A, Tavaré S, Prandi F, Pesce M, Hofner M, Klemens V, Emanueli C, Angelini G and Madeddu P 
    Epigenetic profile of human adventitial progenitor cells correlates with therapeutic outcomes in a mouse model of limb ischemia. Arterioscler Thromb Vasc Biol [Epub ahead of print]

  • Aravinthan A, Challis B, Shannon N, Hoare M, Heaney J and Alexander GJM.
    Selective insulin resistance in hepatocyte senescence. Exp Cell Res. 331, 38-45

  • Vollan HKM, Rueda OM, Chin S-F, Curtis C, Turashvili G, Shah S, Lingjærde OC, Yuan Y, Ng CK, Dunning MJ et al.
    A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer. Mol Oncol 9, 115-27

2014 

  • Cairns J, Lynch AG, and Tavaré S
    Quantifying the impact of inter-site hetero- geneity on the distribution of ChIP-seq data. Front Genet 5, 399. 29

  • Jauhiainen A, Madhu B, Narita M, Narita M, Griffiths J, and Tavaré S
    Normalization of metabolomics data with applications to correlation maps. Bioinformatics 30, 2155–61

  • Ju YS, Alexandrov LB, Gerstung M, Martincorena I, Nik-Zainal S, Ramakrishna M, Davies HR, Papaemmanuil E, Gundem G, Shlien A et al.
    Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer. Elife 10.7554/eLife.02935

  • Samarajiwa SA, Mangan NE, Hardy MP, Najdovska M, Dubach D, Braniff S-J, Owczarek CM and Hertzog PJ
    Soluble IFN receptor potentiates in vivo type I IFN signaling and exacerbates TLR4-mediated septic shock. J Immunol 192, 4425–35. 

  • Sanchez-Garcia F, Villagrasa P, Matsui J, Kotliar D, Castro V, Akavia U-D, Chen B-J, Saucedo-Cuevas L, Rodriguez Barrueco R, Llobet-Navas D, Silva JM, and Pe’er D.
    Integration of genomic data enables selective discovery of breast cancer drivers. Cell 159, 1461–1475.

  • Tubio JMC, Li Y, Ju YS, Martincorena I, Cooke SL, Tojo M, Gundem G, Pipinikas CP, Zamora J, Raine K. et al.
    Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science 345, 1251343.  

  • Turro E, Astle WJ and Tavaré S.
    Flexible analysis of RNA-seq data using mixed effects models. Bioinformatics 30, 180–8. 

  • Weaver JMJ, Ross-Innes CS, Shannon N, Lynch AG, Forshew T, Barbera M, Murtaza M, Ong C-AJ, Lao-Sirieix P, Dunning MJ et al.
    Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis. Nat Genet 46, 837–43. 

  • Aravinthan A, Shannon N, Heaney J, Hoare M, Marshall A and Alexander GJM
    The senescent hepatocyte gene signature in chronic liver disease. Exp Gerontol 60, 37–45. 

  • Llobet-Navas D, Rodrıguez-Barrueco R, Castro V, Ugalde AP, Sumazin P, Jacob-Sendler D, Demircan B, Castillo-Martın M, Putcha P, Marshall N et al.
    The mir-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland. Genes Dev 28, 765–82. 

  • Shen SQ, Turro E and Corbo JC
    Hybrid mice reveal parent-of-origin and cis- and trans-regulatory effects in the retina. PLoS One 9, e109382. 

  • Silva A-L, Dawson SN, Arends MJ, Guttula K, Hall N, Cameron EA, Huang TH-M, Brenton JD, Tavaré S, Bienz M and Ibrahim AE
    Boosting Wnt activity during colorectal cancer progression through selective hypermethylation of Wnt signaling antagonists. BMC Cancer 14, 891.  

2013

 

  • Sottoriva A, Spiteri I, Piccirillo SG, Touloumis A, Collins VP, Marioni JC, Curtis C, Watts C, Tavaré S. Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics. Proc Natl Acad Sci U S A. 2013 Feb 14. [Epub ahead of print]
  • Sottoriva A, Spiteri I, Shibata D, Curtis C, Tavaré S. Single-molecule genomic data delineate patient-specific tumor profiles and cancer stem cell organization. Cancer Res. 2013 Jan 1;73(1):41-9.

 

2012

 

  • Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Graf S, Ha G, Haari G, Bashashati A, Russell R, McKinney S, METABRIC Group, Langerd A, Green A, Provenzano E, Wishart G, Pinder S, Watson P, Markowetz F, Murphy L, Ellis I, Purushotham A, Borresen-Dale A-L, Brenton J, Tavaré S, Caldas C & Aparicio S. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 2012; 486: 346-352.
  • Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom DT and Marioni JC. Extensive compensatory cis-trans regulation in the evolution of mouse gene expression. Genome Res. 2012; 22: 2376-2384
  • Bidwell BN, Slaney CY, Withana NP, Forster S, Cao Y, Mikeska T, Loi S, Andrews D, Mangan NE, Samarajiwa SA, de Weerd NA, Argani P, Möller A , Smyth MJ , Anderson RL, Hertzog PJ and Parker BS Silencing of Irf7 pathways in breast cancer cells promotes bone metastasis through immune escape mechanisms. Nature Medicine 2012; 18: 1224–1231
  • Chandra T, Kirschner K, Thuret J-Y, Pope BD, Ryba T, Newman S, Ahmed K, Samarajiwa SA, Salama R, Carroll T, Stark R, Rekin's Janky, Narita M, Xue L, Chicas A, Nũnez S, Janknecht R, Hayashi-Takanaka Y, Wilson MD, Marshall A, Odom DT, Madan Babu M, Bazett-Jones DP, Tavaré S, Edwards PAW, Lowe S, Kimura H, Gilbert DM, Narita M.  Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation. Molecular Cell 2012; 47(2):203-14
  • Maia AT, Antoniou AC, O'Reilly M, Samarajiwa S, Dunning M, Kartsonaki C, Chin SF, Curtis CN, McGuffog L, Domchek SM, Embrace E, Easton DF, Peock S, Frost D, Evans DG, Eeles R, Izatt L, Adlard J, Eccles D, Gemo G, Sinilnikova OM, Mazoyer S, Stoppa-Lyonnet D, Gauthier-Villars M, Faivre L, Venat-Bouvet L, Delnatte C, Nevanlinna H, Couch FJ, Godwin AK, Caligo MA, Swe-Brca SB, Barkardottir RB, Kconfab K, Chen X, Beesley J, Healey S, Caldas C, Chenevix-Trench G, Ponder BA. Effects of BRCA2 cis-regulation in normal breast and cancer risk amongst BRCA2 mutation carriers. Breast Cancer Res. 2012; 14(2):R63