PhD studentship in Machine Learning for Synthetic Biology

Two new PhD studentship in the group of Dr Jaume Bacardit at the School of Computing, Newcastle University, UK.

(https://portabolomics.ico2s.org/dr-jaume-bacardit/)

The PhD studentships are part of the Portabolomics project. The vision of Portabolomics (https://portabolomics.ico2s.org/) is to bring forth a breakthrough in Synthetic Biology that will enable the development of portable biocircuits across chassis (i.e. from one bacteria species to another). This vision is akin to the Java virtual machine having enabled the reuse and portability of software across different operating systems and hardware platforms.

In this doctoral project you will focus on the challenge of devising innovative strategies to transform the vast volumes of data generated in the wet lab experiments of Portabolomics into actionable knowledge that can feed into the computational work on network analysis and verification in the project. The data generated by the project is vast and diverse: imaging data, omics data, complex and heterogeneous annotation from public and private sources. Using a combination of biological data integration, state-of-the-art machine learning, knowledge extraction and information visualisation techniques we seek to build methods to identify biomarkers and infer biological networks.

The specific topic of each studentship will be decided based on the skill set of the successful applicants, although we envision that they will require a combination of the following:
– Strong machine learning background and proficiency in the state of the art data science languages (e.g. R, python)
– Deep Learning
– Knowledge discovery
– Biological data integration
– Information visualisation
– High Performance Computing (e.g. classic HPC clusters, GPUs, Intel PHI, Big Data frameworks, Cloud resources).

For more information, please visit

http://www.ncl.ac.uk/postgraduate/funding/sources/allstudents/comp002.html

 EPSRC 5-year program grant: Synthetic Portabolomics

“Leading the way at the crossroads of the Digital and the Bio-Economies”