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Bioinformatics Analyst: The Genomics and Epigenetics of Nucleic Acid Structures in Cancer
Department of Chemistry
Salary £27,578-£35,938 pa
Reference MA16512
Category: Research
Published 7 May 2012
Closing date 29 June 2012
We are seeking a highly motivated bioinformatics analyst to play a key role in supporting the pioneering research programme of Professor Balasubramanian's group at Cancer Research UK's Cambridge Research Institute (CRI). The Institute emphasises multi-disciplinary approaches to link laboratory findings to the clinic and has state-of-the-art research facilities for over 300 scientists supported by outstanding core resources including a high-performance computing cluster (HPC) and high-throughput DNA sequencing platforms.
Professor Balasubramanian's research is focused on the chemical biology of the genome, and the post-holder will be involved in data analysis for several projects in this domain. Two areas of key interest to us are: the fundamental roles that non-canonical nucleic acid structures, such as G-quadruplexes, play within the genome and transcriptome; and identification, mapping and function of novel bases in nucleic acids. We are developing genome-wide methods to address biological problems in these areas as exemplified by our latest work on the induction of DNA damage by a G-quadruplex-binding small molecule (see Nature Chemical Biology, 8 301-10, 2012), and through our recent invention of a method to sequence 5-hydroxymethylcytosine in the genome with single base resolution (see Science published online 26 April 2012, DOI:10.1126/science.1220671). The post-holder will be based at the CRI and join our increasing informatics effort for these projects, providing bioinformatics support and analytical capability across Professor Balasubramanian's wider group at the CRI and the University's Department of Chemistry.
Characteristics of the role will include:
a) Collaboration with Professor Balasubramanian's research scientists and the CRI Bioinformatics Core. Using existing pipelines or implementing new ones, the post-holder will play a leading role in experimental design, optimal sample size estimation, data QC, and visualisation of genome-wide datasets.
b) Our experimental approaches employ novel ChIP-Seq, RNA-Seq, and genome sequencing methodologies, and therefore require ad hoc analyses together with customised algorithms. This will include, for example, expected outcome simulation, algorithm design for read density normalization and enrichment detection, clustering and prediction of secondary DNA/RNA sequence. The novel experimental approaches taken by the group require new bioinformatics techniques and it is expected that the role will provide opportunities for computational method development.
Applicants should have a PhD in a computational discipline such as computer science, quantitative biology or similar and have significant experience in bioinformatics or computational biology. We are especially interested in candidates with experience in statistical modelling and use of mathematical tools (e.g. Bayesian statistics, Markov models, simulation models) to interrogate and model genomic datasets.
Skills required include:
(i) Good programming/scripting skills in languages such as R or Matlab, Python or Perl, C/C++, ruby or Java.
(ii) A good working knowledge of Linux/Unix, with experience in data processing in a HPC cluster environment.
(iii) Familiarity with SQL and relational databases (e.g. PostgreSQL, MySQL).
(iv) Algorithm development and statistical analysis of large datasets.
The role requires excellent communication skills and involves regular interactions with our research scientists and other bioinformaticians. The successful candidate will also need to be highly organised with good time management skills to support multiple concurrent projects, with an ability to work well within a team. Experience in project management would be welcomed, providing opportunities for career progression within the role.
The post is available immediately. Applications should include a CV, publications list, contact details for three professional referees, and a completed form CHRIS/6 Parts I and III (downloadable from http://www.admin.cam.ac.uk/offices/hr/forms/chris6) and should be sent to Professor Shankar Balasubramanian, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW (email: [email protected]). Informal enquiries can be made to either Professor Balasubramanian or Dr David Tannahill at CRI ([email protected]).
* The funds for this post are available for two years in the first instance.
Quote Reference: MA16512,Closing Date: 29 June 2012
Department of Chemistry
Salary £27,578-£35,938 pa
Reference MA16512
Category: Research
Published 7 May 2012
Closing date 29 June 2012
We are seeking a highly motivated bioinformatics analyst to play a key role in supporting the pioneering research programme of Professor Balasubramanian's group at Cancer Research UK's Cambridge Research Institute (CRI). The Institute emphasises multi-disciplinary approaches to link laboratory findings to the clinic and has state-of-the-art research facilities for over 300 scientists supported by outstanding core resources including a high-performance computing cluster (HPC) and high-throughput DNA sequencing platforms.
Professor Balasubramanian's research is focused on the chemical biology of the genome, and the post-holder will be involved in data analysis for several projects in this domain. Two areas of key interest to us are: the fundamental roles that non-canonical nucleic acid structures, such as G-quadruplexes, play within the genome and transcriptome; and identification, mapping and function of novel bases in nucleic acids. We are developing genome-wide methods to address biological problems in these areas as exemplified by our latest work on the induction of DNA damage by a G-quadruplex-binding small molecule (see Nature Chemical Biology, 8 301-10, 2012), and through our recent invention of a method to sequence 5-hydroxymethylcytosine in the genome with single base resolution (see Science published online 26 April 2012, DOI:10.1126/science.1220671). The post-holder will be based at the CRI and join our increasing informatics effort for these projects, providing bioinformatics support and analytical capability across Professor Balasubramanian's wider group at the CRI and the University's Department of Chemistry.
Characteristics of the role will include:
a) Collaboration with Professor Balasubramanian's research scientists and the CRI Bioinformatics Core. Using existing pipelines or implementing new ones, the post-holder will play a leading role in experimental design, optimal sample size estimation, data QC, and visualisation of genome-wide datasets.
b) Our experimental approaches employ novel ChIP-Seq, RNA-Seq, and genome sequencing methodologies, and therefore require ad hoc analyses together with customised algorithms. This will include, for example, expected outcome simulation, algorithm design for read density normalization and enrichment detection, clustering and prediction of secondary DNA/RNA sequence. The novel experimental approaches taken by the group require new bioinformatics techniques and it is expected that the role will provide opportunities for computational method development.
Applicants should have a PhD in a computational discipline such as computer science, quantitative biology or similar and have significant experience in bioinformatics or computational biology. We are especially interested in candidates with experience in statistical modelling and use of mathematical tools (e.g. Bayesian statistics, Markov models, simulation models) to interrogate and model genomic datasets.
Skills required include:
(i) Good programming/scripting skills in languages such as R or Matlab, Python or Perl, C/C++, ruby or Java.
(ii) A good working knowledge of Linux/Unix, with experience in data processing in a HPC cluster environment.
(iii) Familiarity with SQL and relational databases (e.g. PostgreSQL, MySQL).
(iv) Algorithm development and statistical analysis of large datasets.
The role requires excellent communication skills and involves regular interactions with our research scientists and other bioinformaticians. The successful candidate will also need to be highly organised with good time management skills to support multiple concurrent projects, with an ability to work well within a team. Experience in project management would be welcomed, providing opportunities for career progression within the role.
The post is available immediately. Applications should include a CV, publications list, contact details for three professional referees, and a completed form CHRIS/6 Parts I and III (downloadable from http://www.admin.cam.ac.uk/offices/hr/forms/chris6) and should be sent to Professor Shankar Balasubramanian, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW (email: [email protected]). Informal enquiries can be made to either Professor Balasubramanian or Dr David Tannahill at CRI ([email protected]).
* The funds for this post are available for two years in the first instance.
Quote Reference: MA16512,Closing Date: 29 June 2012