期刊论文详细信息
BMC Cancer
Computational cancer biology: education is a natural key to many locks
Frank Emmert-Streib1  Shu-Dong Zhang2  Peter Hamilton2 
[1] Computational Biology and Machine Learning Laboratory, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Faculty of Medicine, Health and Life Sciences, Queen’s University Belfast, Belfast, Lisburn Road, Belfast, UK
[2] Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Faculty of Medicine, Health and Life Sciences, Queen’s University Belfast, Lisburn Road, Belfast, UK
关键词: Systems medicine;    Statistical genomics;    Computational genomics;    Computational oncology;    Genomics data;    Computational biology;    Cancer;   
Others  :  1106757
DOI  :  10.1186/s12885-014-1002-2
 received in 2014-07-05, accepted in 2014-12-22,  发布年份 2015
PDF
【 摘 要 】

Background

Oncology is a field that profits tremendously from the genomic data generated by high-throughput technologies, including next-generation sequencing. However, in order to exploit, integrate, visualize and interpret such high-dimensional data efficiently, non-trivial computational and statistical analysis methods are required that need to be developed in a problem-directed manner.

Discussion

For this reason, computational cancer biology aims to fill this gap. Unfortunately, computational cancer biology is not yet fully recognized as a coequal field in oncology, leading to a delay in its maturation and, as an immediate consequence, an under-exploration of high-throughput data for translational research.

Summary

Here we argue that this imbalance, favoring ’wet lab-based activities’, will be naturally rectified over time, if the next generation of scientists receives an academic education that provides a fair and competent introduction to computational biology and its manifold capabilities. Furthermore, we discuss a number of local educational provisions that can be implemented on university level to help in facilitating the process of harmonization.

【 授权许可】

   
2015 Emmert-Streib et al.; licensee BioMed Central.

【 预 览 】
附件列表
Files Size Format View
20150202012355752.pdf 923KB PDF download
Figure 1. 83KB Image download
【 图 表 】

Figure 1.

【 参考文献 】
  • [1]Stehelin D, Varmus HE, Bishop JM, Vogt PK: Dna related to the transforming gene(s) of avian sarcoma viruses is present in normal avian dna. Nature 1976, 260:170-3.
  • [2]Weinberg RA: The Biology of Cancer. Garland Science, New York; 2007.
  • [3]Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al.: Initial sequencing and analysis of the human genome. Nature 2001, 409(6822):860-921.
  • [4]Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, et al.: The sequence of the human genome. Science 2001, 291(5507):1304-51.
  • [5]Quackenbush J: The Human Genome: The Book of Essential Knowledge. Curiosity Guides. Imagine Publishing, New York; 2011.
  • [6]Dehmer M, Emmert-Streib F, Graber A: Salvador A (eds.): Applied Statistics for Network Biology: Methods for Systems Biology. Wiley-Blackwell, Weinheim; 2011.
  • [7]Ma H, Goryanin I: Human metabolic network reconstruction and its impact on drug discovery and development. Drug Discov Today 2008, 13(9-10):402-8.
  • [8]Sechi S (ed.): Quantitative Proteomics by Mass Spectrometry. Humana Press, Totowa, NJ; 2007.
  • [9]Wang Z, Gerstein M, Snyder M: RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63.
  • [10]Yates JRR: Mass spectral analysis in proteomics. Annu Rev Biophys Biomol Struct 2004, 33:297-316.
  • [11]Beißbarth T, Speed TP: Gostat: find statistically overrepresented gene ontologies within a group of genes. Bioinformatics 2004, 20(9):1464-5. doi:10.1093/bioinformatics/bth088
  • [12]Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, et al.: Classification of human lung carcinomas by mrna expression profiling reveals distinct adenocarcinoma subclasses. Proc Nat Acad Sci 2001, 98(24):13790-5. doi:10.1073/pnas.191502998
  • [13]Sadanandam A, Lyssiotis CA, Homicsko K, Collisson EA, Gibb WJ, Wullschleger S, et al.: A colorectal cancer classification system that associates cellular phenotype and responses to therapy. Nat Med 2013, 19(5):619-25.
  • [14]Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, et al.: Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Nat Acad Sci 2001, 98(19):10869-74. doi:10.1073/pnas.191367098
  • [15]Storey JD, Tibshirani R: Statistical significance for genomewide studies. Proc Natl Acad Sci USA 2003, 100(16):9440-5.
  • [16]Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98(18):5116-21.
  • [17]Akavia UD, Litvin O, Kim J, Sanchez-Garcia F, Kotliar D, Causton HC, et al.: An integrated approach to uncover drivers of cancer. Cell 2010, 143(6):1005-17. doi:10.1016/j.cell.2010.11.013
  • [18]Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, et al.Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013:1–5.
  • [19]Segal E, Friedman N, Koller D, Regev A: A module map showing conditional activity of expression modules in cancer. Nat Genet 2004, 36(3):1090-8.
  • [20]Marx V: Biology: The big challenges of big data. Nature 2013, 498(7453):255-60.
  • [21]Costa FF: Big data in biomedicine. Drug Discov Today 2014, 19(4):433-40. doi:10.1016/j.drudis.2013.10.012
  • [22]Mias G, Snyder M: Personal genomes, quantitative dynamic omics and personalized medicine. Quant Biol 2013, 1(1):71-90. doi:10.1007/s40484-013-0005-3
  • [23]Lynch C: Big data: How do your data grow? Nature 2008, 455(7209):28-9.
  • [24]Irizarry RA, Wu Z, Jaffee HA: Comparison of Affymetrix GeneChip expression measures. Bioinformatics 2006, 22(7):789-94.
  • [25]Shmulevich I, Dougherty ER, Kim S, Zhang W: Probabilistic boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 2002, 18(2):261-74.
  • [26]R Development Core Team: R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria; 2008.
  • [27]Service RF: Biology’s dry future. Science 2013, 342(6155):186-9.
  文献评价指标  
  下载次数:17次 浏览次数:35次