Yinyin Yuan

Yinyin is interested in dissecting heterogeneity in complex diseases with tightly connected computational methods and biological experiments. Specifically, she is interested in developing methods that systematically combine cellular image processing and integrative molecular data mining, to generate a more comprehensive understanding of cancer. In close collaboration with several other experimental groups at CRI and abroad, she has been working on characterising the genomic landscape of breast cancer.

My new lab website: www.yuanlab.org

I will soon move to the Institute of Cancer Research (ICR) in London to start my own lab in June 2012. I have the following open positions: ICR is one of the most influential cancer research institutes in the world. You will be working with some of the best scientific minds as well as having access to plenty of resources and funding for conferences. Please send me an email if you are interested.

Vita

04/2009 - 05/2012
Postdoctoral research at Cancer Research UK Cambridge Research Institute

01/2005 - 03/2009
Ph.D. student at the Department of Computer Science, University of Warwick, UK.

10/2003 - 12/2004
Master student at the Department of Computer Science, University of Warwick, UK.

09/1999 - 07/2003
Undergraduate study at the University of Science and Technology of China (USTC).

Degrees

Ph D, Department of Computer Science, University of Warwick, UK, 2009

M.Sc., Department of Computer Science, University of Warwick, UK, 2005

B.Sc., Department of Computer Science, University of Science and Technology of China (USTC)

Awards and fellowship

  • Junior Research Fellowship 2010, Wolfson College, Cambridge
  • Best poster award at CRI symposium 2011
  • Best paper award at BIBM 2010
    • Yinyin Yuan

    Yinyin Yuan
    CR UK - CRI
    Li Ka Shing Centre
    Robinson Way
    Cambridge, CB2 0RE, UK
    e: first.last@cancer.org.uk
    p: +44 (0) 1223 40 4317

    Funded by CRUK logo Affiliated with Cambridge University

    Talks online

    videolectures.net
    Differential regulation of gene expression by copy-number alterations in cancer sub-types

    Wet lab training

    Software

    1. PSDF Patient-specific data fusion for cancer subtype discovery
    2. DANCE Deregulation Analysis in Networks of Copy-number-driven Expressions
    3. lol Lots Of Lasso, various optimization methods for lasso inference
    4. CRImage Tumour image analysis
    5. DPC Directed Partial Correlation for efficient large-scale gene network inference

    Recent talks and teaching

    1. Invited talk at Tsinghua University, Beijing, China, Dec 2011
    2. Presentation at CSHL-Asia Bioinformatics, Suzhou, China, Nov 2011
    3. Presentation at EMBO|EMBL Symposium: Cancer Genomics in Heidelberg, Sep 2011.
    4. Two presentations at ISMB 2011 in Vienna, Jul 2011.
    5. Presentation at CFM Canceromatics II: Multilevel Interpretation of Cancer Genome in Madrid, Mar 2011
    6. Lecturing and supervision for Mphil Network Biology, Cambridge, Lent term 2011&2012.
    7. Presentation at the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2010), Hong Kong, Dec 2010.
    8. Teaching a two-day course on Analysis of Globally Coherent Data for GlaxoSmithKline, Stevenage, Oct 2010.
    9. Presentation at the Cancer Bioinformatics Workshop at CRI, Sept 2010.
    10. Presentation at RECOMB 2010 satellite meeting on Computational Cancer Biology in Oslo, June 2010.

    Publications

    Journal papers

    1. Y. Yuan, et al., Quantitative image analysis of cellular heterogeneity in primary breast tumors, in preparation.
    2. C. Curtis, et al., The integrative genomic and transcriptomic landscape of 1000 breast tumours, Nature, to appear.
    3. Y. Yuan*, R. S. Savage*, F. Markowetz, Patient-specific data fusion defines prognostic cancer subtypes, PLoS Comput Biol. 2011 Oct;7(10):e1002227.
    4. Y. Yuan, O. M. Rueda, C. Curtis, F. Markowetz, Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer, Bioinformatics, doi:10.1093/bioinformatics/btr450, 2011. [ Preprint, R package ]
    5. Y. Yuan, C. Curtis, C. Caldas, F. Markowetz, A sparse regulatory network of copy-number driven expression reveals putative breast cancer oncogenes, IEEE/ACM Trans Comput Biol Bioinform, 2011.[ Preprint, R package ]
    6. Y. Yuan, C.-T. Li, and Oliver Windram, Directed partial correlation: inferring large-scale gene regulatory network through induced topology disruptions, PLoS ONE 6(4): e16835. doi:10.1371/journal.pone.0016835, 2011. [ Paper, R package ]
    7. C.-T. Li, Y. Yuan and R. Wilson, Conditional Random Fields for Gene Expression Data Analysis, Bioinformatics, 24(21):2467-2473, 2008.
    8. Y. Yuan and C.-T. Li, A Bayes Random Field Approach for Integrative Large-Scale Regulatory Network Analysis, Journal of Integrative Bioinformatics, 5(2):99, 2008.
    9. Y. Yuan, C.-T. Li and R.Wilson, Partial Mixture Model for Gene Expression Tight Clustering, BMC Bioinformatics, 9:287, 2008.
    10. Y. Yuan and C.-T. Li, Understanding Gene Clusters: An Investigation into Quantitative Assessment, in review, 2008.
    11. C.-T. Li and Y. Yuan, Digital Watermarking Scheme Exploiting Non-deterministic Dependence for Image Authentication, Optical Engineering, 45(12):127001-1-127001-6, 2006.
    12. S. Wu, Y. Yuan, J. Lu and L. Huang, Applying Markov Chain to Text Steganography, Journal of Computer Research and Development, China, 2002.

    Conference papers

    1. Y. Yuan, C. Curtis, C. Caldas, F. Markowetz, "A sparse regulatory network of copy-number driven expression reveals putative breast cancer oncogenes," IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2010 Best Paper).
    2. Y. Yuan and C.-T. Li, “Inferring Causal Relations from Large-Scale Multivariate Time Series: A Fast Method for Gene Expression Data,” IEEE Symposium on ComputationalIntelligence in Bioinformatics and Computational Biology (CIBCB), US, 2009.
    3. Y. Yuan and C.-T. Li, “Probabilistic Framework for Gene Expression Clustering Validation Based on Gene Ontology and Graph Theory,” in Proc. of International Conference of Acoustics, Speech, and Signal Processing (ICASSP), pp. 625-628, Las Vegas, US, 2008.
    4. Y. Yuan and C.-T. Li, “Partial Mixture Model for Tight Clustering in Exploratory Gene Expression Analysis,” in Proc. of International Symposium on BioInformatics and BioEngineering (BIBE), 1061-1065, Boston, US, 2007.
    5. Y. Yuan and C.-T. Li, “Unsupervised Clustering of Gene Expression Time Series with Conditional Random Fields,” in Proc. of IEEE Workshop on Biomedical Applications for Digital Ecosystems (BADS), Cairns, Australia, 2007.
    6. Y. Yuan and C.-T. Li, “Fragile Watermarking Scheme Exploiting Non-deterministic Block-wise Dependency,” in Proc. of International Conference on Pattern Recognition (ICPR), 4:23-26, Cambridge, UK, 2004.

    Personal development

    Outside work she enjoys travelling, sports, and dancing. Her favourite sports include tennis, climbing, hiking, diving (PADI advanced), and skiing. She is a committee member of the Cambridge University Contemporary Dance Workshop.