About me

Shi Yu
Postdoctoral Scholar
Institute for Genomics and Systems Biology
Department of Medicine
University of Chicago

Knapp Center for Biomedical Discovery
900 E. 57th St. Room 10148
Chicago, IL 60637, US
Tel: 773-702-6799

I obtained Ph.D in Electrical Engineering at Katholieke Universiteit Leuven in Nov 2009. My old website at K.U.Leuven.

Research

My main interests are cloud computing, biomedical text mining, multiple kernel learning methods, data integration and fusion.

I am currently working with Andrey Rzhetsky and Robert Grossman

I also collaborate with computational biologist at K.U.Leuven, my Alma Mater, on disease gene prioritization. I was the developer of MerKator, a kernel based platform for cross-species computational disease gene prioritization.

It was a very nice experience working with Yves Moreau, Johan Suykens, and Bart De Moor during my Ph.D.

Publications

Full book
Yu S., Tranchevent L.C., De Moor B., Moreau Y., Kernel-based Data Fusion for Machine Learning, vol. 345 of Studies in Computational Intelligence, Springer, Heidelberg, 2011.

International journal
Yu S., Van Vooren S., Tranchevent L., De Moor B., Moreau Y. Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining, Bioinformatics, 24(16), i119-i125, 2008.
Yu S., Tranchevent L., De Moor B., Moreau Y. Gene prioritization and clustering by multi-view text mining, BMC Bioinformatics, vol. 11, no. 28, Jan. 2010, pp. 1-48.
Tranchevent L., Barriot R, Yu S., Van Vooren S., Van Loo P., Coessens B., De Moor B., Moreau Y. ENDEAVOUR update: a web resource for gene prioritization in multiple species. Nucleic Acids Research, 36(1): W377-W384, 2008.
Liu X., Yu S., Janssens F., Glanzel W., De Moor B., Moreau Y. Weighted hybrid clustering by combining text mining and bibliometrics on large scale journal database. Journal of American Information and Science Technology, Jun. 2010, pp. 1105-1119.
Yu S., Falck T., Daemen A., Tranchevent L.C., Suykens J., De Moor B., Moreau Y., L2-norm multiple kernel learning and its application to biomedical data fusion, BMC Bioinformatics, vol. 11, no. 309, Jun. 2010, pp. 1-53.
Yu S., Liu X., Tranchevent L., Glanzel W., Suykens J., De Moor B., Moreau Y., Optimized data fusion for K-means Laplacian Clustering, Bioinformatics, vol. 27, no. 21, Jan. 2011, pp. 118-126.
Yu S., Tranchevent L., Liu X., Glanzel W., Suykens J., De Moor B., Moreau Y., Optimized data fusion for kernel k-menas clustering, accepted by IEEE Transactions on Pattern Analysis and Machine Intelligence, in publication.
See full list ...

Professional Service

I am a reviewer of several international journals and machine learning conferences

ACM Transactions on Computational Biology and Bioinformatics
Briefings in Bioinformatics
BMC Bioinformatics
PLOS Computational Biology
BMC Medical Genomics
IEEE Transactions on Knowledge and Data Engineering

IJCNN 2008 (International Joint Conference on Neural Networks)
AAAI 2009 (Twenty-Fourth AAAI Conference on Artificial Intelligence)
NIPS 2010 (Twenty-Fourth Annual Conference on Neural Information Processing Systems)
AMIA 2012 (AMIA Summit on Translational Bioinformatics)

Hobbies

Sometimes I am escorted by music and passion. I play Epiphone Les Paul Custom and Seagull S6 Slim

I am also a video game lover from 1998. There are two games on which I spent amazing amount of time: Myst and Might and Magic Heros. However, my favourite video game producer is Blizzard.

I play tennis, my favourite racquet is Prince Triple Threat Bandit and I have been using it for more than 10 years. My favourite tennis player is Gustavo Kuerten.

I love travelling. I have travelled many countries in Asia, Europe, now I am saving money to explore North America. :)

I am also studying French at the Department of Roman Languages @ University of Chicago. When I was in Leuven, I stuided at CLT Language Centre. They both offer very very good French programs!