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Items: 1 to 20 of 110

1.

Computational genomics tools for dissecting tumour-immune cell interactions.

Hackl H, Charoentong P, Finotello F, Trajanoski Z.

Nat Rev Genet. 2016 Jul 4;17(8):441-58. doi: 10.1038/nrg.2016.67. Review.

PMID:
27376489
2.

Tumour-immune cell interactions modulated by chemokines.

Jöhrer K, Pleyer L, Olivier A, Maizner E, Zelle-Rieser C, Greil R.

Expert Opin Biol Ther. 2008 Mar;8(3):269-90. doi: 10.1517/14712598.8.3.269 . Review.

PMID:
18294099
3.

Bioinformatics for cancer immunology and immunotherapy.

Charoentong P, Angelova M, Efremova M, Gallasch R, Hackl H, Galon J, Trajanoski Z.

Cancer Immunol Immunother. 2012 Nov;61(11):1885-903. doi: 10.1007/s00262-012-1354-x. Epub 2012 Sep 18. Review.

4.

A comparison of tools for the simulation of genomic next-generation sequencing data.

Escalona M, Rocha S, Posada D.

Nat Rev Genet. 2016 Aug;17(8):459-69. doi: 10.1038/nrg.2016.57. Epub 2016 Jun 20. Review. Erratum in: Nat Rev Genet. 2018 Nov;19(11):733.

5.

Computational Methods for Identification of T Cell Neoepitopes in Tumors.

Jurtz VI, Olsen LR.

Methods Mol Biol. 2019;1878:157-172. doi: 10.1007/978-1-4939-8868-6_9.

PMID:
30378075
6.

From cancer genomes to cancer models: bridging the gaps.

Baudot A, Real FX, Izarzugaza JM, Valencia A.

EMBO Rep. 2009 Apr;10(4):359-66. doi: 10.1038/embor.2009.46. Epub 2009 Mar 20. Review.

7.

Dissecting the molecular mechanisms of cancer through bioinformatics-based experimental approaches.

Rivenbark AG, Coleman WB.

J Cell Biochem. 2007 Aug 1;101(5):1074-86. Review.

PMID:
17372928
8.

Exploring TCGA Pan-Cancer data at the UCSC Cancer Genomics Browser.

Cline MS, Craft B, Swatloski T, Goldman M, Ma S, Haussler D, Zhu J.

Sci Rep. 2013 Oct 2;3:2652. doi: 10.1038/srep02652.

9.

An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples.

Yadav VK, De S.

Brief Bioinform. 2015 Mar;16(2):232-41. doi: 10.1093/bib/bbu002. Epub 2014 Feb 20. Review.

10.

Computational biology for ageing.

Wieser D, Papatheodorou I, Ziehm M, Thornton JM.

Philos Trans R Soc Lond B Biol Sci. 2011 Jan 12;366(1561):51-63. doi: 10.1098/rstb.2010.0286. Review.

11.

Expanding the computational toolbox for mining cancer genomes.

Ding L, Wendl MC, McMichael JF, Raphael BJ.

Nat Rev Genet. 2014 Aug;15(8):556-70. doi: 10.1038/nrg3767. Epub 2014 Jul 8. Review.

12.

Genomics and proteomics in process development: opportunities and challenges.

Gupta P, Lee KH.

Trends Biotechnol. 2007 Jul;25(7):324-30. Epub 2007 May 1. Review.

PMID:
17475353
13.

Principles and methods of integrative genomic analyses in cancer.

Kristensen VN, Lingjærde OC, Russnes HG, Vollan HK, Frigessi A, Børresen-Dale AL.

Nat Rev Cancer. 2014 May;14(5):299-313. doi: 10.1038/nrc3721. Review.

PMID:
24759209
14.

Genomics pipelines and data integration: challenges and opportunities in the research setting.

Davis-Turak J, Courtney SM, Hazard ES, Glen WB Jr, da Silveira WA, Wesselman T, Harbin LP, Wolf BJ, Chung D, Hardiman G.

Expert Rev Mol Diagn. 2017 Mar;17(3):225-237. doi: 10.1080/14737159.2017.1282822. Epub 2017 Jan 25. Review.

15.

Challenges in exome analysis by LifeScope and its alternative computational pipelines.

Pranckevičiene E, Rančelis T, Pranculis A, Kučinskas V.

BMC Res Notes. 2015 Sep 7;8:421. doi: 10.1186/s13104-015-1385-4.

16.

A Practical Guide to The Cancer Genome Atlas (TCGA).

Wang Z, Jensen MA, Zenklusen JC.

Methods Mol Biol. 2016;1418:111-41. doi: 10.1007/978-1-4939-3578-9_6.

PMID:
27008012
17.

Immunoinformatics and epitope prediction in the age of genomic medicine.

Backert L, Kohlbacher O.

Genome Med. 2015 Nov 20;7:119. doi: 10.1186/s13073-015-0245-0. Review.

18.

TIminer: NGS data mining pipeline for cancer immunology and immunotherapy.

Tappeiner E, Finotello F, Charoentong P, Mayer C, Rieder D, Trajanoski Z.

Bioinformatics. 2017 Oct 1;33(19):3140-3141. doi: 10.1093/bioinformatics/btx377.

19.

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

Afgan E, Sloggett C, Goonasekera N, Makunin I, Benson D, Crowe M, Gladman S, Kowsar Y, Pheasant M, Horst R, Lonie A.

PLoS One. 2015 Oct 26;10(10):e0140829. doi: 10.1371/journal.pone.0140829. eCollection 2015.

20.

Applications of systems biology in cancer immunotherapy: from target discovery to biomarkers of clinical outcome.

Guhathakurta D, Sheikh NA, Meagher TC, Letarte S, Trager JB.

Expert Rev Clin Pharmacol. 2013 Jul;6(4):387-401. doi: 10.1586/17512433.2013.811814. Review.

PMID:
23927667

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