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Items: 1 to 20 of 34

1.

Predicting the functional impact of protein mutations: application to cancer genomics.

Reva B, Antipin Y, Sander C.

Nucleic Acids Res. 2011 Sep 1;39(17):e118. doi: 10.1093/nar/gkr407. Epub 2011 Jul 3.

2.

Integrated genomic analyses of ovarian carcinoma.

Cancer Genome Atlas Research Network.

Nature. 2011 Jun 29;474(7353):609-15. doi: 10.1038/nature10166. Erratum in: Nature. 2012 Oct 11;490(7419):298.

3.

PathScan: a tool for discerning mutational significance in groups of putative cancer genes.

Wendl MC, Wallis JW, Lin L, Kandoth C, Mardis ER, Wilson RK, Ding L.

Bioinformatics. 2011 Jun 15;27(12):1595-602. doi: 10.1093/bioinformatics/btr193. Epub 2011 Apr 14.

4.

A decade's perspective on DNA sequencing technology.

Mardis ER.

Nature. 2011 Feb 10;470(7333):198-203. doi: 10.1038/nature09796.

PMID:
21307932
5.

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.

Wang K, Li M, Hakonarson H.

Nucleic Acids Res. 2010 Sep;38(16):e164. doi: 10.1093/nar/gkq603. Epub 2010 Jul 3.

6.

Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM).

Carter H, Samayoa J, Hruban RH, Karchin R.

Cancer Biol Ther. 2010 Sep 15;10(6):582-7. Epub 2010 Oct 1.

7.

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.

Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM.

Bioinformatics. 2010 Jun 15;26(12):i237-45. doi: 10.1093/bioinformatics/btq182.

8.

A method and server for predicting damaging missense mutations.

Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR.

Nat Methods. 2010 Apr;7(4):248-9. doi: 10.1038/nmeth0410-248. No abstract available.

9.

Driver mutations in TP53 are ubiquitous in high grade serous carcinoma of the ovary.

Ahmed AA, Etemadmoghadam D, Temple J, Lynch AG, Riad M, Sharma R, Stewart C, Fereday S, Caldas C, Defazio A, Bowtell D, Brenton JD.

J Pathol. 2010 May;221(1):49-56. doi: 10.1002/path.2696.

10.

Forkhead box M1 transcription factor: a novel target for cancer therapy.

Wang Z, Ahmad A, Li Y, Banerjee S, Kong D, Sarkar FH.

Cancer Treat Rev. 2010 Apr;36(2):151-6. doi: 10.1016/j.ctrv.2009.11.006. Epub 2009 Dec 22. Review.

11.

The Pfam protein families database.

Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A.

Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22. doi: 10.1093/nar/gkp985. Epub 2009 Nov 17.

12.

PROSITE, a protein domain database for functional characterization and annotation.

Sigrist CJ, Cerutti L, de Castro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N.

Nucleic Acids Res. 2010 Jan;38(Database issue):D161-6. doi: 10.1093/nar/gkp885. Epub 2009 Oct 25.

13.

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.

Kumar P, Henikoff S, Ng PC.

Nat Protoc. 2009;4(7):1073-81. doi: 10.1038/nprot.2009.86. Epub 2009 Jun 25.

PMID:
19561590
14.

The Sequence Alignment/Map format and SAMtools.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup.

Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8.

15.

SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.

Wilson D, Pethica R, Zhou Y, Talbot C, Vogel C, Madera M, Chothia C, Gough J.

Nucleic Acids Res. 2009 Jan;37(Database issue):D380-6. doi: 10.1093/nar/gkn762. Epub 2008 Nov 26.

16.

A novel signaling pathway impact analysis.

Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim JS, Kim CJ, Kusanovic JP, Romero R.

Bioinformatics. 2009 Jan 1;25(1):75-82. doi: 10.1093/bioinformatics/btn577. Epub 2008 Nov 5.

17.

Somatic mutations affect key pathways in lung adenocarcinoma.

Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K, Metcalf GA, Ng B, Milosavljevic A, Gonzalez-Garay ML, Osborne JR, Meyer R, Shi X, Tang Y, Koboldt DC, Lin L, Abbott R, Miner TL, Pohl C, Fewell G, Haipek C, Schmidt H, Dunford-Shore BH, Kraja A, Crosby SD, Sawyer CS, Vickery T, Sander S, Robinson J, Winckler W, Baldwin J, Chirieac LR, Dutt A, Fennell T, Hanna M, Johnson BE, Onofrio RC, Thomas RK, Tonon G, Weir BA, Zhao X, Ziaugra L, Zody MC, Giordano T, Orringer MB, Roth JA, Spitz MR, Wistuba II, Ozenberger B, Good PJ, Chang AC, Beer DG, Watson MA, Ladanyi M, Broderick S, Yoshizawa A, Travis WD, Pao W, Province MA, Weinstock GM, Varmus HE, Gabriel SB, Lander ES, Gibbs RA, Meyerson M, Wilson RK.

Nature. 2008 Oct 23;455(7216):1069-75. doi: 10.1038/nature07423.

18.

Ryanodine receptor expression correlates with tumor grade in breast cancer.

Abdul M, Ramlal S, Hoosein N.

Pathol Oncol Res. 2008 Jun;14(2):157-60. doi: 10.1007/s12253-008-9045-9. Epub 2008 Apr 23.

PMID:
18431693
19.

The Catalogue of Somatic Mutations in Cancer (COSMIC).

Forbes SA, Bhamra G, Bamford S, Dawson E, Kok C, Clements J, Menzies A, Teague JW, Futreal PA, Stratton MR.

Curr Protoc Hum Genet. 2008 Apr;Chapter 10:Unit 10.11. doi: 10.1002/0471142905.hg1011s57.

20.

The mutations and potential targets of the forkhead transcription factor FOXL2.

Moumné L, Batista F, Benayoun BA, Nallathambi J, Fellous M, Sundaresan P, Veitia RA.

Mol Cell Endocrinol. 2008 Jan 30;282(1-2):2-11. Epub 2007 Nov 19. Review.

PMID:
18155828

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