[BBC] Fwd: Open position for Postdoc bioinformatics – High-performance genomic data fusion

[mimi deprez]

Dear team:


On behalf of prof. Moreau , we are looking for a enthousiastic  and motivated postdoctoral researcher for the prestigious ExaScience  Life  Pharma IWT O&O project 
(www.exascience.com) in collaboration with Janssen Pharmaceuticals, Intel, IMEC and Flemish universities. 

Please find the detailed  description of the position below .

Sincerely,

Mimi 

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Postdoc bioinformatics – High-performance genomic data fusion

For the Bioinformatics research group of Yves Moreau at ESAT – STADIUS Centre for Dynamical Systems, Signal Processing and Data Analytics (KU Leuven), we are looking for a

postdoctoral researcher to scale up machine learning algorithms for data fusion of genomic data

Computational biology is entering the big data era. Genomic data and relatives are indeed archetypes of the big data paradigm: Volume, Velocity and Variety. Researchers need to analyse and integrate sequences and their variants, expression data, protein-protein interactions, functional annotations, biomedical literature, and so on – all at the same time. This integrated mining is essential for correct interpretation of the mass of Next Gen Sequencing data currently produced, with its importance diffusing from biomedical research into drug discovery pipelines and clinical trials. Mining multiple heterogeneous sources of genomic data in an integrated fashion, is still an open problem. It therefore is a key research question for the ExaScience Lab, a world-class collaboration with Intel (intel.eu), Janssen Pharmaceuticals (janssenpharmaceuticalsinc.com), and Imec (imec.be) on the next generation of high-performance computing for biomedical challenges.

Genomic data fusion (Moreau and Tranchevent, 2012; Aerts et al., 2006) offers a range of approaches to tackle the challenge described above. Among such methods, the University of Leuven has been a pioneer in the use of kernel methods to integrate heterogeneous omics data (De Bie et al., 2007; Yu et al., 2009). The key advantage of kernel methods for mining heterogeneous data is that when multiple data sets are available, they all lead to kernel similarity matrices independently of the original type of data. Those kernels can then be efficiently integrated using Multiple Kernel Learning (De Bie et al., 2007; Yu et al., 2009). The goal of the project is to develop simple, efficient, and scalable kernel methods for genomic data fusion using low-rank approximation, random projections, or ensemble methods and implement them in a large-scale parallel execution environment.

We offer a competitive package and a fun, dynamic environment as part of the ExaScience Lab, a world-class collaboration with Intel (intel.eu), Janssen Pharmaceuticals (janssenpharmaceuticalsinc.com), and Imec (imec.be). The University of Leuven is one of Europe’s leading research universities, with English as the working language for research. Leuven lies just east of Brussels, at the heart of Europe.

The STADIUS Center for Dynamical Systems, Signal Processing, and Data Analytics at KU Leuven is an academic research center, with a research focus on mathematical engineering, where mathematical tools from numerical linear and multi-linear algebra, statistics and optimization are used for applications of dynamical systems and control, signal processing, data modeling and analytics. STADIUS offers recognized expertise in diverse application fields such as industrial automation, audio and speech communication, digital communications, biomedical signal and data processing, and bio-informatics

Profile

The ideal candidate holds a PhD degree in computer science or computational biology. Exceptional PhD candidates can also be considered. Experience with efficient algorithms for machine learning and scale-up of such algorithms to large genomic data sets via high-performance, cloud, or grid computing are core assets. Programming and data analysis experience is essential. Willingness to interact with genomics experts is mandatory. Good communication skills are important for this role. The candidate will collaborate closely with researchers across the consortium and contribute to the reporting of the project. Qualified candidates will be offered the opportunity to work semi-independently under the supervision of a senior investigator, mentor PhD students, and contribute to the acquisition of new funding. A two-year commitment is expected from the candidate. Preferred start date as soon as possible.

Relevant publications

Moreau Y, Tranchevent LC. Computational tools for prioritizing candidate genes: boosting disease gene discovery. Nat Rev Genet. 2012 Jul 3;13(8):523-36.

Yu S, Falck T, Daemen A, Tranchevent LC, Suykens JA, De Moor B, Moreau Y. L2-norm multiple kernel learning and its application to biomedical data fusion. BMC Bioinformatics. 2010 Jun 8;11:309.

De Bie T, Tranchevent LC, van Oeffelen LM, Moreau Y. Kernel-based data fusion for gene prioritization. Bioinformatics. 2007 Jul 1;23(13):i125-32.

Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F, Tranchevent LC, De Moor B, Marynen P, Hassan B, Carmeliet P, Moreau Y. Gene prioritization through genomic data fusion. Nat Biotechnol. 2006 May;24(5):537-44.

How to apply

Please send in PDF before 15 December 2013:

1.  CV including education, research experience, and bibliography

2.  Three references (with phone and email)

3.  A statement of purpose describing why you are qualified for the position and what your contribution could be

to Ms. Mimi Deprez (mimi.deprez at esat.kuleuven.be), cc Prof. Yves Moreau (yves.moreau at esat.kuleuven.be) and Ms. Ida Tassens (ida.tassens at esat.kuleuven.be).

Pre-application inquiries can be sent to Yves.Moreau at esat.kuleuven.be.

URL: http://www.kuleuven.be/bioinformatics/