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Integrative cancer genomics: models, algorithms and analysis

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Abstract

In the past decade, the remarkable development of high-throughput sequencing technology accelerates the generation of large amount of multiple dimensional data such as genomic, epigenomic, transcriptomic and proteomic data. The comprehensive data make it possible to understand the underlying mechanisms of biology and disease such as cancer systematically. It also provides great challenges for computational cancer genomics due to the complexity, scale and noise of data. In this article, we aim to review the recent developments and progresses of computational models, algorithms and analysis of complex data in cancer genomics. These topics of this paper include the identification of driver mutations, the genetic heterogeneity analysis, genomic markers discovery of drug response, pan-cancer scale analysis and so on.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (Grant Nos. 61379092, 61422309, 61621003 and 11131009), the Strategic Priority Research Program of the Chinese Academy of Sciences (CAS) (XDB13040600), the Outstanding Young Scientist Program of CAS, Key Research Program of Frontier Sciences, CAS (QYZDB-SSW-SYS008), and the Key Laboratory of Random Complex Structures and Data Science, CAS (2008DP173182).

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  1. National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China

    Jinyu Chen & Shihua Zhang

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  1. Jinyu Chen
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  2. Shihua Zhang
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Correspondence to Shihua Zhang.

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Jinyu Chen is a PhD student at Academy of Mathematics and Systems Science, Chinese Academy of Sciences, China. Her research interests are mainly in bioinformatics, cancer genomics, pattern recognition and data mining.

Shihua Zhang received the PhD degree in applied mathematics and bioinformatics from the Academy of Mathematics and Systems Science, Chinese Academy of Sciences, China in 2008 with the highest honor. He has been in the same institute and worked as an assistant professor since 2008. His research interests are mainly in pattern recognition and bioinformatics. He has won various honors including Outstanding Young Scientist Program of CAS (2014) and Youth Science and Technology Award of China (2013). He is the awardee of the NSFC Excellent Young Scholars Program in 2014. Now he serves as an Editorial Board Member of Scientific Reports, Current Bioinformatics and an Associate Editor of BMC Genomics, Frontiers in Bioinformatics and Computational Biology, respectively. He is also a member of the IEEE, ISCB and SIAM.

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Chen, J., Zhang, S. Integrative cancer genomics: models, algorithms and analysis. Front. Comput. Sci. 11, 392–406 (2017). https://doi.org/10.1007/s11704-016-5568-5

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