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Results: 1 to 20 of 99

1.

EMu: probabilistic inference of mutational processes and their localization in the cancer genome.

Fischer A, Illingworth CJ, Campbell PJ, Mustonen V.

Genome Biol. 2013 Apr 29;14(4):R39. doi: 10.1186/gb-2013-14-4-r39.

PMID:
23628380
[PubMed - in process]
Free PMC Article
2.

Deciphering signatures of mutational processes operative in human cancer.

Alexandrov LB, Nik-Zainal S, Wedge DC, Campbell PJ, Stratton MR.

Cell Rep. 2013 Jan 31;3(1):246-59. doi: 10.1016/j.celrep.2012.12.008. Epub 2013 Jan 10.

PMID:
23318258
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Patterns and processes of somatic mutations in nine major cancers.

Jia P, Pao W, Zhao Z.

BMC Med Genomics. 2014 Feb 19;7:11. doi: 10.1186/1755-8794-7-11.

PMID:
24552141
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Mutation signatures of carcinogen exposure: genome-wide detection and new opportunities for cancer prevention.

Poon SL, McPherson JR, Tan P, Teh BT, Rozen SG.

Genome Med. 2014 Mar 31;6(3):24. doi: 10.1186/gm541. eCollection 2014. Review.

PMID:
25031618
[PubMed]
5.

Signatures of mutational processes in human cancer.

Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, Bignell GR, Bolli N, Borg A, Børresen-Dale AL, Boyault S, Burkhardt B, Butler AP, Caldas C, Davies HR, Desmedt C, Eils R, Eyfjörd JE, Foekens JA, Greaves M, Hosoda F, Hutter B, Ilicic T, Imbeaud S, Imielinski M, Jäger N, Jones DT, Jones D, Knappskog S, Kool M, Lakhani SR, López-Otín C, Martin S, Munshi NC, Nakamura H, Northcott PA, Pajic M, Papaemmanuil E, Paradiso A, Pearson JV, Puente XS, Raine K, Ramakrishna M, Richardson AL, Richter J, Rosenstiel P, Schlesner M, Schumacher TN, Span PN, Teague JW, Totoki Y, Tutt AN, Valdés-Mas R, van Buuren MM, van 't Veer L, Vincent-Salomon A, Waddell N, Yates LR; Australian Pancreatic Cancer Genome Initiative; ICGC Breast Cancer Consortium; ICGC MMML-Seq Consortium; ICGC PedBrain, Zucman-Rossi J, Futreal PA, McDermott U, Lichter P, Meyerson M, Grimmond SM, Siebert R, Campo E, Shibata T, Pfister SM, Campbell PJ, Stratton MR.

Nature. 2013 Aug 22;500(7463):415-21. doi: 10.1038/nature12477. Epub 2013 Aug 14. Erratum in: Nature. 2013 Oct 10;502(7470):258. Imielinsk, Marcin [corrected to Imielinski, Marcin].

PMID:
23945592
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Mutational processes molding the genomes of 21 breast cancers.

Nik-Zainal S, Alexandrov LB, Wedge DC, Van Loo P, Greenman CD, Raine K, Jones D, Hinton J, Marshall J, Stebbings LA, Menzies A, Martin S, Leung K, Chen L, Leroy C, Ramakrishna M, Rance R, Lau KW, Mudie LJ, Varela I, McBride DJ, Bignell GR, Cooke SL, Shlien A, Gamble J, Whitmore I, Maddison M, Tarpey PS, Davies HR, Papaemmanuil E, Stephens PJ, McLaren S, Butler AP, Teague JW, Jönsson G, Garber JE, Silver D, Miron P, Fatima A, Boyault S, Langerød A, Tutt A, Martens JW, Aparicio SA, Borg Å, Salomon AV, Thomas G, Børresen-Dale AL, Richardson AL, Neuberger MS, Futreal PA, Campbell PJ, Stratton MR; Breast Cancer Working Group of the International Cancer Genome Consortium.

Cell. 2012 May 25;149(5):979-93. doi: 10.1016/j.cell.2012.04.024. Epub 2012 May 17.

PMID:
22608084
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Joint genotype inference with germline and somatic mutations.

Bareke E, Saillour V, Spinella JF, Vidal R, Healy J, Sinnett D, Csűrös M.

BMC Bioinformatics. 2013;14 Suppl 5:S3. doi: 10.1186/1471-2105-14-S5-S3. Epub 2013 Apr 10.

PMID:
23734724
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

TITAN: Inference of copy number architectures in clonal cell populations from tumor whole genome sequence data.

Ha G, Roth A, Khattra J, Ho J, Yap D, Prentice LM, Melnyk N, McPherson A, Bashashati A, Laks E, Biele J, Ding J, Le A, Rosner J, Shumansky K, Marra MA, Gilks CB, Huntsman DG, McAlpine JN, Aparicio S, Shah SP.

Genome Res. 2014 Jul 24. pii: gr.180281.114. [Epub ahead of print]

PMID:
25060187
[PubMed - as supplied by publisher]
Free Article
9.

Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities.

Sanguinetti G, Lawrence ND, Rattray M.

Bioinformatics. 2006 Nov 15;22(22):2775-81. Epub 2006 Sep 11.

PMID:
16966362
[PubMed - indexed for MEDLINE]
Free Article
10.

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer.

Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D, Jia M, Shepherd R, Leung K, Menzies A, Teague JW, Campbell PJ, Stratton MR, Futreal PA.

Nucleic Acids Res. 2011 Jan;39(Database issue):D945-50. doi: 10.1093/nar/gkq929. Epub 2010 Oct 15.

PMID:
20952405
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.

Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP.

Bioinformatics. 2010 Mar 15;26(6):730-6. doi: 10.1093/bioinformatics/btq040. Epub 2010 Feb 3.

PMID:
20130035
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Genome-wide mutational analyses of breast and colorectal cancers.

Lin J, Sjöblom T.

Discov Med. 2007 Feb;7(37):13-9.

PMID:
17343800
[PubMed - indexed for MEDLINE]
Free Article
13.

Genome destabilizing mutator alleles drive specific mutational trajectories in Saccharomyces cerevisiae.

Stirling PC, Shen Y, Corbett R, Jones SJ, Hieter P.

Genetics. 2014 Feb;196(2):403-12. doi: 10.1534/genetics.113.159806. Epub 2013 Dec 13.

PMID:
24336748
[PubMed - in process]
Free PMC Article
14.

Global mutational profiling of formalin-fixed human colon cancers from a pathology archive.

Adams MD, Veigl ML, Wang Z, Molyneux N, Sun S, Guda K, Yu X, Markowitz SD, Willis J.

Mod Pathol. 2012 Dec;25(12):1599-608. doi: 10.1038/modpathol.2012.121. Epub 2012 Aug 10.

PMID:
22878650
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Genome-wide mutational signatures of aristolochic acid and its application as a screening tool.

Poon SL, Pang ST, McPherson JR, Yu W, Huang KK, Guan P, Weng WH, Siew EY, Liu Y, Heng HL, Chong SC, Gan A, Tay ST, Lim WK, Cutcutache I, Huang D, Ler LD, Nairismägi ML, Lee MH, Chang YH, Yu KJ, Chan-On W, Li BK, Yuan YF, Qian CN, Ng KF, Wu CF, Hsu CL, Bunte RM, Stratton MR, Futreal PA, Sung WK, Chuang CK, Ong CK, Rozen SG, Tan P, Teh BT.

Sci Transl Med. 2013 Aug 7;5(197):197ra101. doi: 10.1126/scitranslmed.3006086.

PMID:
23926199
[PubMed - indexed for MEDLINE]
Free Article
16.

Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature.

Doughty E, Kertesz-Farkas A, Bodenreider O, Thompson G, Adadey A, Peterson T, Kann MG.

Bioinformatics. 2011 Feb 1;27(3):408-15. doi: 10.1093/bioinformatics/btq667. Epub 2010 Dec 7.

PMID:
21138947
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Mutational pattern and frequency of induced nucleotide changes in mouse ENU mutagenesis.

Takahasi KR, Sakuraba Y, Gondo Y.

BMC Mol Biol. 2007 Jun 20;8:52.

PMID:
17584492
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Identification of cancer genes by mutational profiling of tumor genomes.

Benvenuti S, Arena S, Bardelli A.

FEBS Lett. 2005 Mar 21;579(8):1884-90. Review.

PMID:
15763568
[PubMed - indexed for MEDLINE]
Free Article
19.

REAPR: a universal tool for genome assembly evaluation.

Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD.

Genome Biol. 2013 May 27;14(5):R47. doi: 10.1186/gb-2013-14-5-r47.

PMID:
23710727
[PubMed - in process]
Free PMC Article
20.

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.

Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA.

Bioinformatics. 2012 Feb 15;28(4):464-9. doi: 10.1093/bioinformatics/btr703. Epub 2011 Dec 22.

PMID:
22199388
[PubMed - indexed for MEDLINE]
Free PMC Article

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