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Items: 1 to 50 of 169

1.

Loss of the interleukin-6 receptor causes immunodeficiency, atopy, and abnormal inflammatory responses.

Spencer S, Köstel Bal S, Egner W, Lango Allen H, Raza SI, Ma CA, Gürel M, Zhang Y, Sun G, Sabroe RA, Greene D, Rae W, Shahin T, Kania K, Ardy RC, Thian M, Staples E, Pecchia-Bekkum A, Worrall WPM, Stephens J, Brown M, Tuna S, York M, Shackley F, Kerrin D, Sargur R, Condliffe A, Tipu HN, Kuehn HS, Rosenzweig SD, Turro E, Tavaré S, Thrasher AJ, Jodrell DI, Smith KGC, Boztug K, Milner JD, Thaventhiran JED.

J Exp Med. 2019 Sep 2;216(9):1986-1998. doi: 10.1084/jem.20190344. Epub 2019 Jun 24.

2.

The landscape of selection in 551 esophageal adenocarcinomas defines genomic biomarkers for the clinic.

Frankell AM, Jammula S, Li X, Contino G, Killcoyne S, Abbas S, Perner J, Bower L, Devonshire G, Ococks E, Grehan N, Mok J, O'Donovan M, MacRae S, Eldridge MD, Tavaré S; Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Fitzgerald RC.

Nat Genet. 2019 Mar;51(3):506-516. doi: 10.1038/s41588-018-0331-5. Epub 2019 Feb 4.

3.

Introduction to the Paul Joyce special issue.

Tavaré S, Buzbas EO.

Theor Popul Biol. 2018 Jul;122:1-2. doi: 10.1016/j.tpb.2018.07.001. No abstract available.

PMID:
30025565
4.

Fixation and Spread of Somatic Mutations in Adult Human Colonic Epithelium.

Nicholson AM, Olpe C, Hoyle A, Thorsen AS, Rus T, Colombé M, Brunton-Sim R, Kemp R, Marks K, Quirke P, Malhotra S, Ten Hoopen R, Ibrahim A, Lindskog C, Myers MB, Parsons B, Tavaré S, Wilkinson M, Morrissey E, Winton DJ.

Cell Stem Cell. 2018 Jun 1;22(6):909-918.e8. doi: 10.1016/j.stem.2018.04.020. Epub 2018 May 17.

5.

Ancestral inference from haplotypes and mutations.

Griffiths RC, Tavaré S.

Theor Popul Biol. 2018 Jul;122:12-21. doi: 10.1016/j.tpb.2018.04.006. Epub 2018 Apr 25.

PMID:
29704515
6.

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets.

Wedge DC, Gundem G, Mitchell T, Woodcock DJ, Martincorena I, Ghori M, Zamora J, Butler A, Whitaker H, Kote-Jarai Z, Alexandrov LB, Van Loo P, Massie CE, Dentro S, Warren AY, Verrill C, Berney DM, Dennis N, Merson S, Hawkins S, Howat W, Lu YJ, Lambert A, Kay J, Kremeyer B, Karaszi K, Luxton H, Camacho N, Marsden L, Edwards S, Matthews L, Bo V, Leongamornlert D, McLaren S, Ng A, Yu Y, Zhang H, Dadaev T, Thomas S, Easton DF, Ahmed M, Bancroft E, Fisher C, Livni N, Nicol D, Tavaré S, Gill P, Greenman C, Khoo V, Van As N, Kumar P, Ogden C, Cahill D, Thompson A, Mayer E, Rowe E, Dudderidge T, Gnanapragasam V, Shah NC, Raine K, Jones D, Menzies A, Stebbings L, Teague J, Hazell S, Corbishley C; CAMCAP Study Group, de Bono J, Attard G, Isaacs W, Visakorpi T, Fraser M, Boutros PC, Bristow RG, Workman P, Sander C; TCGA Consortium, Hamdy FC, Futreal A, McDermott U, Al-Lazikani B, Lynch AG, Bova GS, Foster CS, Brewer DS, Neal DE, Cooper CS, Eeles RA.

Nat Genet. 2018 May;50(5):682-692. doi: 10.1038/s41588-018-0086-z. Epub 2018 Apr 16.

7.

Division-independent differentiation mandates proliferative competition among stem cells.

Reilein A, Melamed D, Tavaré S, Kalderon D.

Proc Natl Acad Sci U S A. 2018 Apr 3;115(14):E3182-E3191. doi: 10.1073/pnas.1718646115. Epub 2018 Mar 19.

8.

Simulating the component counts of combinatorial structures.

Arratia R, Barbour AD, Ewens WJ, Tavaré S.

Theor Popul Biol. 2018 Jul;122:5-11. doi: 10.1016/j.tpb.2018.02.002. Epub 2018 Feb 9.

PMID:
29432792
9.

Corrigendum: A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy.

Noorani A, Bornschein J, Lynch AG, Secrier M, Achilleos A, Eldridge M, Bower L, Weaver JMJ, Crawte J, Ong CA, Shannon N, MacRae S, Grehan N, Nutzinger B, O'Donovan M, Hardwick R, Tavaré S, Fitzgerald RC; Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium.

Genome Res. 2017 Oct;27(10):1782. doi: 10.1101/gr.229153.117. No abstract available.

10.

Synthetic lethality between androgen receptor signalling and the PARP pathway in prostate cancer.

Asim M, Tarish F, Zecchini HI, Sanjiv K, Gelali E, Massie CE, Baridi A, Warren AY, Zhao W, Ogris C, McDuffus LA, Mascalchi P, Shaw G, Dev H, Wadhwa K, Wijnhoven P, Forment JV, Lyons SR, Lynch AG, O'Neill C, Zecchini VR, Rennie PS, Baniahmad A, Tavaré S, Mills IG, Galanty Y, Crosetto N, Schultz N, Neal D, Helleday T.

Nat Commun. 2017 Aug 29;8(1):374. doi: 10.1038/s41467-017-00393-y.

11.

New Model for Estimating Glomerular Filtration Rate in Patients With Cancer.

Janowitz T, Williams EH, Marshall A, Ainsworth N, Thomas PB, Sammut SJ, Shepherd S, White J, Mark PB, Lynch AG, Jodrell DI, Tavaré S, Earl H.

J Clin Oncol. 2017 Aug 20;35(24):2798-2805. doi: 10.1200/JCO.2017.72.7578. Epub 2017 Jul 7.

12.

A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy.

Noorani A, Bornschein J, Lynch AG, Secrier M, Achilleos A, Eldridge M, Bower L, Weaver JMJ, Crawte J, Ong CA, Shannon N, MacRae S, Grehan N, Nutzinger B, O'Donovan M, Hardwick R, Tavaré S, Fitzgerald RC; Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium.

Genome Res. 2017 Jun;27(6):902-912. doi: 10.1101/gr.214296.116. Epub 2017 May 2. Erratum in: Genome Res. 2017 Oct;27(10 ):1782.

13.

Corrigendum: Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance.

Secrier M, Li X, de Silva N, Eldridge MD, Contino G, Bornschein J, MacRae S, Grehan N, O'Donovan M, Miremadi A, Yang TP, Bower L, Chettouh H, Crawte J, Galeano-Dalmau N, Grabowska A, Saunders J, Underwood T, Waddell N, Barbour AP, Nutzinger B, Achilleos A, Edwards PA, Lynch AG, Tavaré S, Fitzgerald RC; Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium.

Nat Genet. 2017 Jan 31;49(2):317. doi: 10.1038/ng0217-317a. No abstract available.

PMID:
28138154
14.

Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance.

Secrier M, Li X, de Silva N, Eldridge MD, Contino G, Bornschein J, MacRae S, Grehan N, O'Donovan M, Miremadi A, Yang TP, Bower L, Chettouh H, Crawte J, Galeano-Dalmau N, Grabowska A, Saunders J, Underwood T, Waddell N, Barbour AP, Nutzinger B, Achilleos A, Edwards PA, Lynch AG, Tavaré S, Fitzgerald RC; Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium.

Nat Genet. 2016 Oct;48(10):1131-41. doi: 10.1038/ng.3659. Epub 2016 Sep 5. Erratum in: Nat Genet. 2017 Jan 31;49(2):317.

15.

HDTD: analyzing multi-tissue gene expression data.

Touloumis A, Marioni JC, Tavaré S.

Bioinformatics. 2016 Jul 15;32(14):2193-5. doi: 10.1093/bioinformatics/btw224. Epub 2016 Jun 7.

16.

Erratum to: Transcriptional profiling of MnSOD-mediated lifespan extension in Drosophila reveals a species-general network of aging and metabolic genes.

Curtis C, Landis GN, Folk D, Wehr NB, Hoe N, Waskar M, Abdueva D, Skvortsov D, Ford D, Luu A, Badrinath A, Levine RL, Bradley TJ, Tavaré S, Tower J.

Genome Biol. 2016 May 6;17(1):93. No abstract available.

17.

Choline Kinase Alpha as an Androgen Receptor Chaperone and Prostate Cancer Therapeutic Target.

Asim M, Massie CE, Orafidiya F, Pértega-Gomes N, Warren AY, Esmaeili M, Selth LA, Zecchini HI, Luko K, Qureshi A, Baridi A, Menon S, Madhu B, Escriu C, Lyons S, Vowler SL, Zecchini VR, Shaw G, Hessenkemper W, Russell R, Mohammed H, Stefanos N, Lynch AG, Grigorenko E, D'Santos C, Taylor C, Lamb A, Sriranjan R, Yang J, Stark R, Dehm SM, Rennie PS, Carroll JS, Griffiths JR, Tavaré S, Mills IG, McEwan IJ, Baniahmad A, Tilley WD, Neal DE.

J Natl Cancer Inst. 2015 Dec 11;108(5). doi: 10.1093/jnci/djv371. Print 2016 May.

18.

Metabolomic changes during cellular transformation monitored by metabolite-metabolite correlation analysis and correlated with gene expression.

Madhu B, Narita M, Jauhiainen A, Menon S, Stubbs M, Tavaré S, Narita M, Griffiths JR.

Metabolomics. 2015;11(6):1848-1863. Epub 2015 Aug 11.

19.

Mobile element insertions are frequent in oesophageal adenocarcinomas and can mislead paired-end sequencing analysis.

Paterson AL, Weaver JM, Eldridge MD, Tavaré S, Fitzgerald RC, Edwards PA; OCCAMs Consortium.

BMC Genomics. 2015 Jul 10;16:473. doi: 10.1186/s12864-015-1685-z.

20.

Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53.

Kirschner K, Samarajiwa SA, Cairns JM, Menon S, Pérez-Mancera PA, Tomimatsu K, Bermejo-Rodriguez C, Ito Y, Chandra T, Narita M, Lyons SK, Lynch AG, Kimura H, Ohbayashi T, Tavaré S, Narita M.

PLoS Genet. 2015 Mar 19;11(3):e1005053. doi: 10.1371/journal.pgen.1005053. eCollection 2015 Mar.

21.

multiSNV: a probabilistic approach for improving detection of somatic point mutations from multiple related tumour samples.

Josephidou M, Lynch AG, Tavaré S.

Nucleic Acids Res. 2015 May 19;43(9):e61. doi: 10.1093/nar/gkv135. Epub 2015 Feb 26.

22.

Genetic mapping of natural variation in schooling tendency in the threespine stickleback.

Greenwood AK, Ardekani R, McCann SR, Dubin ME, Sullivan A, Bensussen S, Tavaré S, Peichel CL.

G3 (Bethesda). 2015 Feb 25;5(5):761-9. doi: 10.1534/g3.114.016519.

23.

Testing the mean matrix in high-dimensional transposable data.

Touloumis A, Tavaré S, Marioni JC.

Biometrics. 2015 Mar;71(1):157-166. doi: 10.1111/biom.12257. Epub 2015 Jan 23.

PMID:
25615804
24.

Epigenetic profile of human adventitial progenitor cells correlates with therapeutic outcomes in a mouse model of limb ischemia.

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, Madeddu P.

Arterioscler Thromb Vasc Biol. 2015 Mar;35(3):675-88. doi: 10.1161/ATVBAHA.114.304989. Epub 2015 Jan 8.

PMID:
25573856
25.

HES5 silencing is an early and recurrent change in prostate tumourigenesis.

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; UK Prostate ICGC Group, Warren AY, Tavaré S, Neal DE, Lynch AG.

Endocr Relat Cancer. 2015 Apr;22(2):131-44. doi: 10.1530/ERC-14-0454. Epub 2015 Jan 5.

26.

Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data.

Cairns J, Lynch AG, Tavaré S.

Front Genet. 2014 Nov 14;5:399. doi: 10.3389/fgene.2014.00399. eCollection 2014.

27.

Boosting Wnt activity during colorectal cancer progression through selective hypermethylation of Wnt signaling antagonists.

Silva AL, Dawson SN, Arends MJ, Guttula K, Hall N, Cameron EA, Huang TH, Brenton JD, Tavaré S, Bienz M, Ibrahim AE.

BMC Cancer. 2014 Nov 29;14:891. doi: 10.1186/1471-2407-14-891.

28.

Contributions to drug resistance in glioblastoma derived from malignant cells in the sub-ependymal zone.

Piccirillo SG, Spiteri I, Sottoriva A, Touloumis A, Ber S, Price SJ, Heywood R, Francis NJ, Howarth KD, Collins VP, Venkitaraman AR, Curtis C, Marioni JC, Tavaré S, Watts C.

Cancer Res. 2015 Jan 1;75(1):194-202. doi: 10.1158/0008-5472.CAN-13-3131. Epub 2014 Nov 18.

29.

Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis.

Weaver JMJ, Ross-Innes CS, Shannon N, Lynch AG, Forshew T, Barbera M, Murtaza M, Ong CJ, Lao-Sirieix P, Dunning MJ, Smith L, Smith ML, Anderson CL, Carvalho B, O'Donovan M, Underwood TJ, May AP, Grehan N, Hardwick R, Davies J, Oloumi A, Aparicio S, Caldas C, Eldridge MD, Edwards PAW, Rosenfeld N, Tavaré S, Fitzgerald RC; OCCAMS consortium.

Nat Genet. 2014 Aug;46(8):837-843. doi: 10.1038/ng.3013. Epub 2014 Jun 22.

30.

Normalization of metabolomics data with applications to correlation maps.

Jauhiainen A, Madhu B, Narita M, Narita M, Griffiths J, Tavaré S.

Bioinformatics. 2014 Aug 1;30(15):2155-61. doi: 10.1093/bioinformatics/btu175. Epub 2014 Apr 7.

PMID:
24711654
31.

Fkh1 and Fkh2 bind multiple chromosomal elements in the S. cerevisiae genome with distinct specificities and cell cycle dynamics.

Ostrow AZ, Nellimoottil T, Knott SR, Fox CA, Tavaré S, Aparicio OM.

PLoS One. 2014 Feb 4;9(2):e87647. doi: 10.1371/journal.pone.0087647. eCollection 2014.

32.

Flexible analysis of RNA-seq data using mixed effects models.

Turro E, Astle WJ, Tavaré S.

Bioinformatics. 2014 Jan 15;30(2):180-8. doi: 10.1093/bioinformatics/btt624. Epub 2013 Nov 26.

PMID:
24281695
33.

Defining stem cell dynamics in models of intestinal tumor initiation.

Vermeulen L, Morrissey E, van der Heijden M, Nicholson AM, Sottoriva A, Buczacki S, Kemp R, Tavaré S, Winton DJ.

Science. 2013 Nov 22;342(6161):995-8. doi: 10.1126/science.1243148.

34.

Continuous clonal labeling reveals small numbers of functional stem cells in intestinal crypts and adenomas.

Kozar S, Morrissey E, Nicholson AM, van der Heijden M, Zecchini HI, Kemp R, Tavaré S, Vermeulen L, Winton DJ.

Cell Stem Cell. 2013 Nov 7;13(5):626-33. doi: 10.1016/j.stem.2013.08.001. Epub 2013 Sep 12.

35.

The relative timing of mutations in a breast cancer genome.

Newman S, Howarth KD, Greenman CD, Bignell GR, Tavaré S, Edwards PA.

PLoS One. 2013 Jun 10;8(6):e64991. doi: 10.1371/journal.pone.0064991. Print 2013.

36.

The level of origin firing inversely affects the rate of replication fork progression.

Zhong Y, Nellimoottil T, Peace JM, Knott SR, Villwock SK, Yee JM, Jancuska JM, Rege S, Tecklenburg M, Sclafani RA, Tavaré S, Aparicio OM.

J Cell Biol. 2013 Apr 29;201(3):373-83. doi: 10.1083/jcb.201208060.

37.

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics.

Sottoriva A, Spiteri I, Piccirillo SG, Touloumis A, Collins VP, Marioni JC, Curtis C, Watts C, Tavaré S.

Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):4009-14. doi: 10.1073/pnas.1219747110. Epub 2013 Feb 14.

38.

Transcriptional dynamics elicited by a short pulse of notch activation involves feed-forward regulation by E(spl)/Hes genes.

Housden BE, Fu AQ, Krejci A, Bernard F, Fischer B, Tavaré S, Russell S, Bray SJ.

PLoS Genet. 2013;9(1):e1003162. doi: 10.1371/journal.pgen.1003162. Epub 2013 Jan 3.

39.

Assessing senescence in Drosophila using video tracking.

Ardekani R, Tavaré S, Tower J.

Methods Mol Biol. 2013;965:501-16. doi: 10.1007/978-1-62703-239-1_33.

PMID:
23296680
40.

A Bayesian approach to phylogeographic clustering.

Manolopoulou I, Legarreta L, Emerson BC, Brooks S, Tavaré S.

Interface Focus. 2011 Dec 6;1(6):909-21. doi: 10.1098/rsfs.2011.0054. Epub 2011 Oct 5.

41.

Single-molecule genomic data delineate patient-specific tumor profiles and cancer stem cell organization.

Sottoriva A, Spiteri I, Shibata D, Curtis C, Tavaré S.

Cancer Res. 2013 Jan 1;73(1):41-9. doi: 10.1158/0008-5472.CAN-12-2273. Epub 2012 Oct 22.

42.

Three-dimensional tracking and behaviour monitoring of multiple fruit flies.

Ardekani R, Biyani A, Dalton JE, Saltz JB, Arbeitman MN, Tower J, Nuzhdin S, Tavaré S.

J R Soc Interface. 2013 Jan 6;10(78):20120547. doi: 10.1098/rsif.2012.0547. Epub 2012 Oct 3.

43.

Calling sample mix-ups in cancer population studies.

Lynch AG, Chin SF, Dunning MJ, Caldas C, Tavaré S, Curtis C.

PLoS One. 2012;7(8):e41815. doi: 10.1371/journal.pone.0041815. Epub 2012 Aug 9.

44.

Using GFP video to track 3D movement and conditional gene expression in free-moving flies.

Ardekani R, Huang YM, Sancheti P, Stanciauskas R, Tavaré S, Tower J.

PLoS One. 2012;7(7):e40506. doi: 10.1371/journal.pone.0040506. Epub 2012 Jul 19.

45.

Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation.

Chandra T, Kirschner K, Thuret JY, Pope BD, Ryba T, Newman S, Ahmed K, Samarajiwa SA, Salama R, Carroll T, Stark R, Janky R, Narita M, Xue L, Chicas A, Nũnez S, Janknecht R, Hayashi-Takanaka Y, Wilson MD, Marshall A, Odom DT, Babu MM, Bazett-Jones DP, Tavaré S, Edwards PA, Lowe SW, Kimura H, Gilbert DM, Narita M.

Mol Cell. 2012 Jul 27;47(2):203-14. doi: 10.1016/j.molcel.2012.06.010. Epub 2012 Jul 12.

46.

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.

Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Gräf S, Ha G, Haffari G, Bashashati A, Russell R, McKinney S; METABRIC Group, Langerød A, Green A, Provenzano E, Wishart G, Pinder S, Watson P, Markowetz F, Murphy L, Ellis I, Purushotham A, Børresen-Dale AL, Brenton JD, Tavaré S, Caldas C, Aparicio S.

Nature. 2012 Apr 18;486(7403):346-52. doi: 10.1038/nature10983.

47.

Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae.

Knott SR, Peace JM, Ostrow AZ, Gan Y, Rex AE, Viggiani CJ, Tavaré S, Aparicio OM.

Cell. 2012 Jan 20;148(1-2):99-111. doi: 10.1016/j.cell.2011.12.012.

48.

High DNA methylation pattern intratumoral diversity implies weak selection in many human colorectal cancers.

Siegmund KD, Marjoram P, Tavaré S, Shibata D.

PLoS One. 2011;6(6):e21657. doi: 10.1371/journal.pone.0021657. Epub 2011 Jun 28.

49.

Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors.

Sottoriva A, Vermeulen L, Tavaré S.

PLoS Comput Biol. 2011 May;7(5):e1001132. doi: 10.1371/journal.pcbi.1001132. Epub 2011 May 5.

50.

Spatial coupling of mTOR and autophagy augments secretory phenotypes.

Narita M, Young AR, Arakawa S, Samarajiwa SA, Nakashima T, Yoshida S, Hong S, Berry LS, Reichelt S, Ferreira M, Tavaré S, Inoki K, Shimizu S, Narita M.

Science. 2011 May 20;332(6032):966-70. doi: 10.1126/science.1205407. Epub 2011 Apr 21.

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