R sig jobs - Oct 2014 - JOB - PhD position: applying HPC in cancer research

Dear all, we have an exciting PhD position applying HPC to the analysis of large
scale cancer datasets.

The post will suit an applicant from a strong computational background who
wishes to apply their knowledge to help develop a better understanding of the
processes that control how tumours develop.

Details below:-

High Performance Computing applied to cancer research: Computational analysis of
Noncoding RNA regulators of gene expression in individual tumour cells

RNABiology/Computational Biology
The goal of this project is to use computational tools to ask how patterns in
gene expression are disrupted in cancer. The project will suit a graduate
student from a computational background with exceptional programming ability and
strength in mathematics and statistics.

The main focus of our group is directed at understanding the role played by
noncoding RNAs (ncRNAs) in modulating the behaviour of cancer cells. These are
RNA molecules that are transcribed, but never translated into protein sequences.
Advances in sequencing technology have revealed large numbers of novel ncRNA
loci in the genome, to the point where they are now known to outnumber
protein-coding genes. Whilst most are uncharacterised, recent work has shown an
increasing number to be functional ? and to act in a variety of regulatory roles
within the cell. The successful applicant will join a highly interdisciplinary
team comprising numerical- and biological-scientists who together exploit the
power of new technologies such as single-cell RNA sequencing and protein mass
spectrometry to investigate the fundamentals of gene expression in cancer. This
project will involve applying machine learning and pattern recognition
techniques to high volumes of RNA-sequencing data representing a combination of
single cells, clinical samples, and experimental data generated using cell
lines.

The scale of the data mean that novel algorithms will be required in order to
achieve the volume of computation required, and this will involve programming on
the latest architectures. The successful applicant will make extensive use of
our on-site High Performance Computing (HPC) facility, purpose built for the
analysis of cancer genomics data. Experience coding in C, C++ or Java are
critical, and familiarity with aspects of graph theory, machine learning, and
parallel programming will be advantageous. While an understanding of basic
genomics and cancer biology would be useful, it is not a prerequisite; the
project is open to an enthusiastic individual from a numerical discipline who
wishes to use their skills to help develop a better understanding of the
processes that control gene expression, and how they are perturbed in tumours.

Please visit our website to find out more:
http://cruk.manchester.ac.uk/Education/PhD-Studentships/2015-Projects/Crispin-Miller

best wishes,
Crispin

________________________________

This email is confidential and intended solely for the u...{{dropped:12}}

>
> Please visit our website to find out more:
http://cruk.manchester.ac.uk/Education/PhD-Studentships/2015-Projects/Crispin-Miller
>
Server not found.

Apologies - the web address below should be:
http://www.cruk.manchester.ac.uk/Education/PhD-Studentships/2015-Projects/Crispin-Miller
Crispin


On 1 Oct 2014, at 11:37, Crispin Miller <Crispin.Miller at
cruk.manchester.ac.uk> wrote:
> Dear all, we have an exciting PhD position applying HPC to the analysis of
large scale cancer datasets.
>
> The post will suit an applicant from a strong computational background who
wishes to apply their knowledge to help develop a better understanding of the
processes that control how tumours develop.
>
> Details below:-
>
> High Performance Computing applied to cancer research: Computational
analysis of Noncoding RNA regulators of gene expression in individual tumour
cells
>
> RNABiology/Computational Biology
> The goal of this project is to use computational tools to ask how patterns
in gene expression are disrupted in cancer. The project will suit a graduate
student from a computational background with exceptional programming ability and
strength in mathematics and statistics.
>
> The main focus of our group is directed at understanding the role played by
noncoding RNAs (ncRNAs) in modulating the behaviour of cancer cells. These are
RNA molecules that are transcribed, but never translated into protein sequences.
Advances in sequencing technology have revealed large numbers of novel ncRNA
loci in the genome, to the point where they are now known to outnumber
protein-coding genes. Whilst most are uncharacterised, recent work has shown an
increasing number to be functional ? and to act in a variety of regulatory roles
within the cell. The successful applicant will join a highly interdisciplinary
team comprising numerical- and biological-scientists who together exploit the
power of new technologies such as single-cell RNA sequencing and protein mass
spectrometry to investigate the fundamentals of gene expression in cancer. This
project will involve applying machine learning and pattern recognition
techniques to high volumes of RNA-sequencing data representing a combination of
single cells, clinical samples, and experimental data generated using cell
lines.
>
> The scale of the data mean that novel algorithms will be required in order
to achieve the volume of computation required, and this will involve programming
on the latest architectures. The successful applicant will make extensive use of
our on-site High Performance Computing (HPC) facility, purpose built for the
analysis of cancer genomics data. Experience coding in C, C++ or Java are
critical, and familiarity with aspects of graph theory, machine learning, and
parallel programming will be advantageous. While an understanding of basic
genomics and cancer biology would be useful, it is not a prerequisite; the
project is open to an enthusiastic individual from a numerical discipline who
wishes to use their skills to help develop a better understanding of the
processes that control gene expression, and how they are perturbed in tumours.
>
> Please visit our website to find out more:
http://cruk.manchester.ac.uk/Education/PhD-Studentships/2015-Projects/Crispin-Miller
>
> best wishes,
> Crispin
>
> ________________________________
>
> This email is confidential and intended solely for the...{{dropped:22}}