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Items: 1 to 50 of 123

1.

Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data.

Chkhaidze K, Heide T, Werner B, Williams MJ, Huang W, Caravagna G, Graham TA, Sottoriva A.

PLoS Comput Biol. 2019 Jul 29;15(7):e1007243. doi: 10.1371/journal.pcbi.1007243. eCollection 2019 Jul.

2.

NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline.

Schenck RO, Lakatos E, Gatenbee C, Graham TA, Anderson ARA.

BMC Bioinformatics. 2019 May 22;20(1):264. doi: 10.1186/s12859-019-2876-4.

3.

Quantification of Crypt and Stem Cell Evolution in the Normal and Neoplastic Human Colon.

Baker AM, Cereser B, Melton S, Fletcher AG, Rodriguez-Justo M, Tadrous PJ, Humphries A, Elia G, McDonald SAC, Wright NA, Simons BD, Jansen M, Graham TA.

Cell Rep. 2019 May 21;27(8):2524. doi: 10.1016/j.celrep.2019.05.035. No abstract available.

4.

Measuring Clonal Evolution in Cancer with Genomics.

Williams MJ, Sottoriva A, Graham TA.

Annu Rev Genomics Hum Genet. 2019 Aug 31;20:309-329. doi: 10.1146/annurev-genom-083117-021712. Epub 2019 May 5.

PMID:
31059289
5.

Correction: Genomic profiling reveals spatial intra-tumor heterogeneity in follicular lymphoma.

Araf S, Wang J, Korfi K, Pangault C, Kotsiou E, Rio-Machin A, Rahim T, Heward J, Clear A, Iqbal S, Davies JK, Johnson P, Calaminici M, Montoto S, Auer R, Chelala C, Gribben JG, Graham TA, Fest T, Fitzgibbon J, Okosun J.

Leukemia. 2019 Jun;33(6):1540. doi: 10.1038/s41375-019-0425-9.

PMID:
30903015
6.

Crypt fusion as a homeostatic mechanism in the human colon.

Baker AM, Gabbutt C, Williams MJ, Cereser B, Jawad N, Rodriguez-Justo M, Jansen M, Barnes CP, Simons BD, McDonald SA, Graham TA, Wright NA.

Gut. 2019 Nov;68(11):1986-1993. doi: 10.1136/gutjnl-2018-317540. Epub 2019 Mar 14.

7.

Multiregion human bladder cancer sequencing reveals tumour evolution, bladder cancer phenotypes and implications for targeted therapy.

Heide T, Maurer A, Eipel M, Knoll K, Geelvink M, Veeck J, Knuechel R, van Essen J, Stoehr R, Hartmann A, Altmueller J, Graham TA, Gaisa NT.

J Pathol. 2019 Jun;248(2):230-242. doi: 10.1002/path.5250. Epub 2019 Mar 18.

PMID:
30719704
8.

From Colitis to Cancer: An Evolutionary Trajectory That Merges Maths and Biology.

Al Bakir I, Curtius K, Graham TA.

Front Immunol. 2018 Oct 16;9:2368. doi: 10.3389/fimmu.2018.02368. eCollection 2018. Review.

9.

Reply to 'Neutral tumor evolution?'

Heide T, Zapata L, Williams MJ, Werner B, Caravagna G, Barnes CP, Graham TA, Sottoriva A.

Nat Genet. 2018 Dec;50(12):1633-1637. doi: 10.1038/s41588-018-0256-z. No abstract available.

PMID:
30374073
10.

Reply to 'Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution'.

Werner B, Williams MJ, Barnes CP, Graham TA, Sottoriva A.

Nat Genet. 2018 Dec;50(12):1624-1626. doi: 10.1038/s41588-018-0235-4. No abstract available.

PMID:
30374070
11.

Emergency Physician Use of the Alberta Netcare Portal, a Province-Wide Interoperable Electronic Health Record: Multi-Method Observational Study.

Graham TA, Ballermann M, Lang E, Bullard MJ, Parsons D, Mercuur G, San Agustin P, Ali S.

JMIR Med Inform. 2018 Sep 25;6(3):e10184. doi: 10.2196/10184.

12.

Reply to 'Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data'.

Williams MJ, Werner B, Heide T, Barnes CP, Graham TA, Sottoriva A.

Nat Genet. 2018 Dec;50(12):1628-1630. doi: 10.1038/s41588-018-0210-0. No abstract available.

PMID:
30250125
13.

The evolutionary landscape of colorectal tumorigenesis.

Cross W, Kovac M, Mustonen V, Temko D, Davis H, Baker AM, Biswas S, Arnold R, Chegwidden L, Gatenbee C, Anderson AR, Koelzer VH, Martinez P, Jiang X, Domingo E, Woodcock DJ, Feng Y, Kovacova M, Maughan T; S:CORT Consortium, Jansen M, Rodriguez-Justo M, Ashraf S, Guy R, Cunningham C, East JE, Wedge DC, Wang LM, Palles C, Heinimann K, Sottoriva A, Leedham SJ, Graham TA, Tomlinson IPM.

Nat Ecol Evol. 2018 Oct;2(10):1661-1672. doi: 10.1038/s41559-018-0642-z. Epub 2018 Aug 31.

14.

Detecting repeated cancer evolution from multi-region tumor sequencing data.

Caravagna G, Giarratano Y, Ramazzotti D, Tomlinson I, Graham TA, Sanguinetti G, Sottoriva A.

Nat Methods. 2018 Sep;15(9):707-714. doi: 10.1038/s41592-018-0108-x. Epub 2018 Aug 31.

15.

Author Correction: Quantification of subclonal selection in cancer from bulk sequencing data.

Williams MJ, Werner B, Heide T, Curtis C, Barnes CP, Sottoriva A, Graham TA.

Nat Genet. 2018 Sep;50(9):1342. doi: 10.1038/s41588-018-0169-x.

PMID:
30022114
16.

Evolutionary history of human colitis-associated colorectal cancer.

Baker AM, Cross W, Curtius K, Al Bakir I, Choi CR, Davis HL, Temko D, Biswas S, Martinez P, Williams MJ, Lindsay JO, Feakins R, Vega R, Hayes SJ, Tomlinson IPM, McDonald SAC, Moorghen M, Silver A, East JE, Wright NA, Wang LM, Rodriguez-Justo M, Jansen M, Hart AL, Leedham SJ, Graham TA.

Gut. 2019 Jun;68(6):985-995. doi: 10.1136/gutjnl-2018-316191. Epub 2018 Jul 10.

17.

Transmission of diffuse large B-cell lymphoma by an allogeneic stem-cell transplant.

Araf S, Wang J, Ashton-Key M, Korfi K, Di Bella D, Rio-Machin A, Odabashian M, Foria V, Du MQ, Cucco F, Barrans S, Johnson P, Laird SR, Fisher AM, Cullis JO, Graham TA, Okosun J, Fitzgibbon J, Chiecchio L.

Haematologica. 2019 Apr;104(4):e174-e177. doi: 10.3324/haematol.2018.196907. Epub 2018 Jul 5. No abstract available.

18.

A HIF-LIMD1 negative feedback mechanism mitigates the pro-tumorigenic effects of hypoxia.

Foxler DE, Bridge KS, Foster JG, Grevitt P, Curry S, Shah KM, Davidson KM, Nagano A, Gadaleta E, Rhys HI, Kennedy PT, Hermida MA, Chang TY, Shaw PE, Reynolds LE, McKay TR, Wang HW, Ribeiro PS, Plevin MJ, Lagos D, Lemoine NR, Rajan P, Graham TA, Chelala C, Hodivala-Dilke KM, Spendlove I, Sharp TV.

EMBO Mol Med. 2018 Aug;10(8). pii: e8304. doi: 10.15252/emmm.201708304.

19.

Quantification of subclonal selection in cancer from bulk sequencing data.

Williams MJ, Werner B, Heide T, Curtis C, Barnes CP, Sottoriva A, Graham TA.

Nat Genet. 2018 Jun;50(6):895-903. doi: 10.1038/s41588-018-0128-6. Epub 2018 May 28. Erratum in: Nat Genet. 2018 Sep;50(9):1342.

20.

The effects of mutational processes and selection on driver mutations across cancer types.

Temko D, Tomlinson IPM, Severini S, Schuster-Böckler B, Graham TA.

Nat Commun. 2018 May 10;9(1):1857. doi: 10.1038/s41467-018-04208-6.

21.

Somatic POLE exonuclease domain mutations are early events in sporadic endometrial and colorectal carcinogenesis, determining driver mutational landscape, clonal neoantigen burden and immune response.

Temko D, Van Gool IC, Rayner E, Glaire M, Makino S, Brown M, Chegwidden L, Palles C, Depreeuw J, Beggs A, Stathopoulou C, Mason J, Baker AM, Williams M, Cerundolo V, Rei M, Taylor JC, Schuh A, Ahmed A, Amant F, Lambrechts D, Smit VT, Bosse T, Graham TA, Church DN, Tomlinson I.

J Pathol. 2018 Jul;245(3):283-296. doi: 10.1002/path.5081. Epub 2018 Apr 30.

22.

Genomic profiling reveals spatial intra-tumor heterogeneity in follicular lymphoma.

Araf S, Wang J, Korfi K, Pangault C, Kotsiou E, Rio-Machin A, Rahim T, Heward J, Clear A, Iqbal S, Davies JK, Johnson P, Calaminici M, Montoto S, Auer R, Chelala C, Gribben JG, Graham TA, Fest T, Fitzgibbon J, Okosun J.

Leukemia. 2018 May;32(5):1261-1265. doi: 10.1038/s41375-018-0043-y. Epub 2018 Feb 8. No abstract available. Erratum in: Leukemia. 2019 Jun;33(6):1540.

23.

Evolution of Barrett's esophagus through space and time at single-crypt and whole-biopsy levels.

Martinez P, Mallo D, Paulson TG, Li X, Sanchez CA, Reid BJ, Graham TA, Kuhner MK, Maley CC.

Nat Commun. 2018 Feb 23;9(1):794. doi: 10.1038/s41467-017-02621-x.

24.

Robust RNA-based in situ mutation detection delineates colorectal cancer subclonal evolution.

Baker AM, Huang W, Wang XM, Jansen M, Ma XJ, Kim J, Anderson CM, Wu X, Pan L, Su N, Luo Y, Domingo E, Heide T, Sottoriva A, Lewis A, Beggs AD, Wright NA, Rodriguez-Justo M, Park E, Tomlinson I, Graham TA.

Nat Commun. 2017 Dec 8;8(1):1998. doi: 10.1038/s41467-017-02295-5.

25.

An evolutionary perspective on field cancerization.

Curtius K, Wright NA, Graham TA.

Nat Rev Cancer. 2018 Jan;18(1):19-32. doi: 10.1038/nrc.2017.102. Epub 2017 Dec 8. Review.

PMID:
29217838
26.

Cumulative burden of inflammation predicts colorectal neoplasia risk in ulcerative colitis: a large single-centre study.

Choi CR, Al Bakir I, Ding NJ, Lee GH, Askari A, Warusavitarne J, Moorghen M, Humphries A, Ignjatovic-Wilson A, Thomas-Gibson S, Saunders BP, Rutter MD, Graham TA, Hart AL.

Gut. 2017 Nov 17. pii: gutjnl-2017-314190. doi: 10.1136/gutjnl-2017-314190. [Epub ahead of print]

27.

Insights Into the Pathophysiology of Esophageal Adenocarcinoma.

Quante M, Graham TA, Jansen M.

Gastroenterology. 2018 Jan;154(2):406-420. doi: 10.1053/j.gastro.2017.09.046. Epub 2017 Oct 14. Review.

PMID:
29037468
28.

Classifying the evolutionary and ecological features of neoplasms.

Maley CC, Aktipis A, Graham TA, Sottoriva A, Boddy AM, Janiszewska M, Silva AS, Gerlinger M, Yuan Y, Pienta KJ, Anderson KS, Gatenby R, Swanton C, Posada D, Wu CI, Schiffman JD, Hwang ES, Polyak K, Anderson ARA, Brown JS, Greaves M, Shibata D.

Nat Rev Cancer. 2017 Oct;17(10):605-619. doi: 10.1038/nrc.2017.69. Epub 2017 Sep 15. Review.

29.

Reply: Uncertainties in tumor allele frequencies limit power to infer evolutionary pressures.

Williams MJ, Werner B, Barnes CP, Graham TA, Sottoriva A.

Nat Genet. 2017 Aug 30;49(9):1289-1291. doi: 10.1038/ng.3877. No abstract available.

PMID:
28854180
30.

A single amino acid in MRGPRX2 necessary for binding and activation by pruritogens.

Reddy VB, Graham TA, Azimi E, Lerner EA.

J Allergy Clin Immunol. 2017 Dec;140(6):1726-1728. doi: 10.1016/j.jaci.2017.05.046. Epub 2017 Jul 6. No abstract available.

31.

Transdiagnostic emotional vulnerabilities linking obsessive-compulsive and depressive symptoms in a community-based sample of adolescents.

Chasson GS, Bello MS, Luxon AM, Graham TAA, Leventhal AM.

Depress Anxiety. 2017 Aug;34(8):761-769. doi: 10.1002/da.22669. Epub 2017 Jun 29.

32.

Quantification of within-sample genetic heterogeneity from SNP-array data.

Martinez P, Kimberley C, BirkBak NJ, Marquard A, Szallasi Z, Graham TA.

Sci Rep. 2017 Jun 12;7(1):3248. doi: 10.1038/s41598-017-03496-0.

33.

Between-region genetic divergence reflects the mode and tempo of tumor evolution.

Sun R, Hu Z, Sottoriva A, Graham TA, Harpak A, Ma Z, Fischer JM, Shibata D, Curtis C.

Nat Genet. 2017 Jul;49(7):1015-1024. doi: 10.1038/ng.3891. Epub 2017 Jun 5.

34.

Evolution of Premalignant Disease.

Curtius K, Wright NA, Graham TA.

Cold Spring Harb Perspect Med. 2017 Dec 1;7(12). pii: a026542. doi: 10.1101/cshperspect.a026542. Review.

35.

High stakes and high emotions: providing safe care in Canadian emergency departments.

Ali S, Thomson D, Graham TA, Rickard SE, Stang AS.

Open Access Emerg Med. 2017 Jan 19;9:23-26. doi: 10.2147/OAEM.S122646. eCollection 2017.

36.

Clonal evolution of colorectal cancer in IBD.

Choi CR, Bakir IA, Hart AL, Graham TA.

Nat Rev Gastroenterol Hepatol. 2017 Apr;14(4):218-229. doi: 10.1038/nrgastro.2017.1. Epub 2017 Feb 8. Review.

PMID:
28174420
37.

Multiple keratoacanthomas occurring in surgical margins and de novo treated with intralesional methotrexate.

Veerula VL, Ezra N, Aouthmany M, Graham TA, Wolverton SE, Somani AK.

Cutis. 2016 Dec;98(6):E12-E15.

PMID:
28099546
38.

PIK3CA mutations are common in lobular carcinoma in situ, but are not a biomarker of progression.

Shah V, Nowinski S, Levi D, Shinomiya I, Kebaier Ep Chaabouni N, Gillett C, Grigoriadis A, Graham TA, Roylance R, Simpson MA, Pinder SE, Sawyer EJ.

Breast Cancer Res. 2017 Jan 17;19(1):7. doi: 10.1186/s13058-016-0789-y.

39.

Catch my drift? Making sense of genomic intra-tumour heterogeneity.

Sottoriva A, Barnes CP, Graham TA.

Biochim Biophys Acta Rev Cancer. 2017 Apr;1867(2):95-100. doi: 10.1016/j.bbcan.2016.12.003. Epub 2017 Jan 7. Review.

40.

Measuring cancer evolution from the genome.

Graham TA, Sottoriva A.

J Pathol. 2017 Jan;241(2):183-191. doi: 10.1002/path.4821. Epub 2016 Nov 18. Review.

PMID:
27741350
41.

Functional versus non-functional intratumor heterogeneity in cancer.

Williams MJ, Werner B, Graham TA, Sottoriva A.

Mol Cell Oncol. 2016 Apr 22;3(4):e1162897. doi: 10.1080/23723556.2016.1162897. eCollection 2016 Jul.

42.

Dynamic clonal equilibrium and predetermined cancer risk in Barrett's oesophagus.

Martinez P, Timmer MR, Lau CT, Calpe S, Sancho-Serra Mdel C, Straub D, Baker AM, Meijer SL, Kate FJ, Mallant-Hent RC, Naber AH, van Oijen AH, Baak LC, Scholten P, Böhmer CJ, Fockens P, Bergman JJ, Maley CC, Graham TA, Krishnadath KK.

Nat Commun. 2016 Aug 19;7:12158. doi: 10.1038/ncomms12158.

43.

New paradigms in clonal evolution: punctuated equilibrium in cancer.

Cross WCh, Graham TA, Wright NA.

J Pathol. 2016 Oct;240(2):126-36. doi: 10.1002/path.4757. Epub 2016 Aug 24. Review.

PMID:
27282810
44.

Differential clonal evolution in oesophageal cancers in response to neo-adjuvant chemotherapy.

Findlay JM, Castro-Giner F, Makino S, Rayner E, Kartsonaki C, Cross W, Kovac M, Ulahannan D, Palles C, Gillies RS, MacGregor TP, Church D, Maynard ND, Buffa F, Cazier JB, Graham TA, Wang LM, Sharma RA, Middleton M, Tomlinson I.

Nat Commun. 2016 Apr 5;7:11111. doi: 10.1038/ncomms11111.

45.

Tumour Cell Heterogeneity.

Gay L, Baker AM, Graham TA.

F1000Res. 2016 Feb 29;5. pii: F1000 Faculty Rev-238. doi: 10.12688/f1000research.7210.1. eCollection 2016. Review.

46.

A Computational Modeling Approach for Deriving Biomarkers to Predict Cancer Risk in Premalignant Disease.

Dhawan A, Graham TA, Fletcher AG.

Cancer Prev Res (Phila). 2016 Apr;9(4):283-95. doi: 10.1158/1940-6207.CAPR-15-0248. Epub 2016 Feb 5.

47.

Identification of neutral tumor evolution across cancer types.

Williams MJ, Werner B, Barnes CP, Graham TA, Sottoriva A.

Nat Genet. 2016 Mar;48(3):238-244. doi: 10.1038/ng.3489. Epub 2016 Jan 18.

48.

Evolution of oesophageal adenocarcinoma from metaplastic columnar epithelium without goblet cells in Barrett's oesophagus.

Lavery DL, Martinez P, Gay LJ, Cereser B, Novelli MR, Rodriguez-Justo M, Meijer SL, Graham TA, McDonald SA, Wright NA, Jansen M.

Gut. 2016 Jun;65(6):907-13. doi: 10.1136/gutjnl-2015-310748. Epub 2015 Dec 23.

49.

Quantifying human intestinal stem cell and crypt dynamics: the implications for cancer screening and prevention.

Baker AM, Graham TA.

Expert Rev Gastroenterol Hepatol. 2016;10(3):277-9. doi: 10.1586/17474124.2016.1134314. Epub 2016 Jan 20. No abstract available.

PMID:
26690852
50.

Pan-cancer analysis of the extent and consequences of intratumor heterogeneity.

Andor N, Graham TA, Jansen M, Xia LC, Aktipis CA, Petritsch C, Ji HP, Maley CC.

Nat Med. 2016 Jan;22(1):105-13. doi: 10.1038/nm.3984. Epub 2015 Nov 30.

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