Machine Learning for Personalized Medicine

Marie-Curie Action: "Initial Training Networks"

Project: Functional annotation of genomic variation explaining phenotypes

Yi Zhong
Gunnar Rätsch
Memorial Sloan-Kettering Cancer Center
New York City, USA


Yi Zhong was born in Deyang, China, in 1981. He studied microbial genomics at the Shanghai Jiao Tong University (China), and obtained his MSc in 2007 working on comparative genomics and proteomics.

Project description

I study protein translation profiles of human normal and cancer cells and how they are affected by using different drugs. I use transcriptome-scale ribosome footprint data to investigate the eIF4A-dependent mechanism of translational control that contributes to oncogenesis and underlies the anticancer effects of drugs. I am also developing analysis tools to identify the genes featuring either one of the two changes in different physiologic or pathologic conditions:
1) translational efficiency and
2) distribution profile of ribosome occupancy on mRNA.
By combining observation of translation profile changes with cancer genome data, I am aiming to estimate the drug effects on the tumor for patients with different germline and somatic variants.

Motivation for participating in the network

In recent years, tremendous progress has been made in biomedical research. This is spurred by not only the advent of new biological technologies, but also through the application of interdisciplinary methods to biomedical problem contexts. In particular, machine learning and statistical methods have enabled the analysis and interpretation of large datasets generated from sequencing experiments. The future of personalized medicine relies on the intersection of high-quality data with state of the art analytical methods. I believe the advantage of participating in ITN will provide me the opportunity to work at the frontier of personalized medicine together with all involved labs in its network.


Duration of fellowship: from April 2013 to March 2016




MLPM2012 Publications: 


- Zhong Y, Karaletsos T, Drewe P, Sreedharan V, Kuo D, Singh K, Wendel HG and Rätsch G. RiboDiff: Detecting Changes of mRNA Translation Efficiency from Ribosome FootprintsBioinformatics 2016.

- The Cancer Genome Atlas Research Network. The Molecular Taxonomy of Primary Prostate Cancer. Cell 2015; 163(4): 1011-25 

- Su X, Yu Y, Zhong Y, Giannopoulou EG, Hu X, Liu H, Cross JR, Rätsch G, Rice CM, Ivashkiv LB. Interferon-γ regulates cellular metabolism and mRNA translation to potentiate macrophage activation. Nature Immunology 2015; 16: 838–849 

- Zhong Y, Drewe P, Rätsch G, et alProtein translational control and its contribution to oncogenesis revealed by computational methods. BMC Bioinformatics 2015; 16(Suppl 2):A6.

- Wolfe AL, Singh K, Zhong Y, et al RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. Nature 2014; 513: 65-70
- Behr J, Kahles K, Zhong Y, et alMITIE: Simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple SamplesBioinformatics 2013; 29(20): 2529-2538


- Yi Zhong, Theofanis Karaletsos, Philipp Drewe, Vipin Sreedharan, Kamini Singh, Hans-Guido Wendel, Gunnar Rätsch. Probabilistic model for detecting mRNA translation efficiency changes from ribosome profiling. Genome Informatics 2015, October 30 (poster)

- Zhong Y, Wolfe AL, Singh K, et al.  RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. ISCB-SCS 2014 (poster).


Further selected Publications:

- Zhong Y, Chang X, Cao XJ et al. Comparative Proteogenomic Analysis of the Leptospira interrogans Virulence Attenuated Strain IPAV against the Pathogenic Strain 56601. Cell Res 2011; 21: 1210-29.

- Zhao W, Zhong Y, Yuan H et al. Complete genome sequence of the rifamycin SV-producing Amycolatopsis mediterranei U32 revealed its genetic characteristics in phylogeny and metabolism. Cell Res 2010; 20: 1096-108.