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Research Associate - Computational Biologist (Fixed Term)
We seek a highly motivated computational researcher for a key role within Professor Balasubramanian's pioneering research programme at the Cancer Research UK Cambridge Institute (CI). The CI focuses on multi-disciplinary approaches to link laboratory findings to the clinic with over 300 researchers supported by state-of-the-art facilities and outstanding core resources including a high-performance computing cluster (HPC) and high-throughput DNA sequencing platforms. The Balasubramanian laboratory has significant infrastructure for interdisciplinary science spanning chemical biology and genomics and owns its own NGS platforms (MiSeq, NextSeq), facilitating the acceleration of technology development. The group also fosters significant collaborations with clinicians, other academics and selected industrial partners.
Our research focuses on the chemical biology of the genome and epigenome (http://www.ch.cam.ac.uk/group/shankar/publications).
The post-holder will work as a bioinformatics analyst contributing to several projects such as:
* Elucidating the fundamental role of non-canonical nucleic acid structures, such as G-quadruplexes, in the genome and transcriptome (Chambers et al., Nature Biotechnology 2015, DOI: 10.1038/nbt.3295; Kwok et al., Nature Methods 2016, DOI: 10.1038/nmeth.3965; Hänsel-Hertsch et al., Nature Genetics 2016, DOI: 10.1038/ng.3662).
* Identification and mapping of modified bases, such as cytosine and thymidine modifications, and understanding their function in the genome and epigenome (Booth et al., Science 2012, DOI: 10.1126/science.1220671; Booth et al., Nature Chemistry 2014, DOI:10.1038/nchem.1893; Bachman et al. Nature Chemical Biology 2015, DOI: 10.1038/nchembio.1848; Mayer et al., Angew. Chem. Int. Ed. 2016, DOI: 10.1002/anie.201605531).
Key functions of the role include:
* Using existing pipelines or implementing new ones to play a leading role in experimental design, optimal sample size estimation, data QC, visualization and interpretation of genome-wide datasets.
* Performing ad hoc analyses with customised algorithms on experimental data obtained from novel ChIP-Seq, RNA-Seq, and genome sequencing methodologies. This encompasses, for example, expected outcome simulation, signal normalization, data mining, enrichment detection and prediction of secondary structures.
Our lab invents and applies new computational methods for the analysis of sequence, structure and chemical modification of DNA and RNA. This position provides opportunities to collaborate with experimental scientists across the chemistry-biology interface from experimental design to the analysis of novel types of data.
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/chemistry. Previous experience in analysing genomic datasets, especially NGS data, is highly desirable.
Skills required include:
* Excellent programming/scripting skills in languages such as R or Matlab, Python or Perl, C/C++, Ruby or Java.
* A good working knowledge of Linux/Unix, with experience in data processing in a HPC cluster environment.
* Algorithm development, data mining and statistical analysis of large datasets.
* Experience in statistical modelling and mathematical tools (e.g. Bayesian statistics, Markov models, simulation models).
* Knowledge of biological data banks (e.g., NCBI, EMBL-EBI, Ensembl, KEGG, ENCODE).
* Ability to share own code (e.g. GitHub).
The position requires strong communication and teamwork skills and involves regular interactions with our research scientists and computational researchers. The successful candidate will be highly organized, with good time management and the ability to support multiple concurrent projects. Experience in project management would also be welcomed.
The post is available immediately. See www.cruk.cam.ac.uk/research-groups/balasubramanian-group and www.ch.cam.ac.uk/group/shankar for further information.
For queries regarding applying online for this post, please contact Jo Lockhart, PA to Professor Shankar Balasubramanian, email: [email protected].
For an informal discussion on the technical aspects of the role please contact Dario Beraldi and Giovanni Marsico ([email protected]; [email protected]).
Fixed-term: The funds for this post are available for 2 years in the first instance.
The closing date for applications is Sunday 20 November 2016.
To apply and for further information see also here.
We seek a highly motivated computational researcher for a key role within Professor Balasubramanian's pioneering research programme at the Cancer Research UK Cambridge Institute (CI). The CI focuses on multi-disciplinary approaches to link laboratory findings to the clinic with over 300 researchers supported by state-of-the-art facilities and outstanding core resources including a high-performance computing cluster (HPC) and high-throughput DNA sequencing platforms. The Balasubramanian laboratory has significant infrastructure for interdisciplinary science spanning chemical biology and genomics and owns its own NGS platforms (MiSeq, NextSeq), facilitating the acceleration of technology development. The group also fosters significant collaborations with clinicians, other academics and selected industrial partners.
Our research focuses on the chemical biology of the genome and epigenome (http://www.ch.cam.ac.uk/group/shankar/publications).
The post-holder will work as a bioinformatics analyst contributing to several projects such as:
* Elucidating the fundamental role of non-canonical nucleic acid structures, such as G-quadruplexes, in the genome and transcriptome (Chambers et al., Nature Biotechnology 2015, DOI: 10.1038/nbt.3295; Kwok et al., Nature Methods 2016, DOI: 10.1038/nmeth.3965; Hänsel-Hertsch et al., Nature Genetics 2016, DOI: 10.1038/ng.3662).
* Identification and mapping of modified bases, such as cytosine and thymidine modifications, and understanding their function in the genome and epigenome (Booth et al., Science 2012, DOI: 10.1126/science.1220671; Booth et al., Nature Chemistry 2014, DOI:10.1038/nchem.1893; Bachman et al. Nature Chemical Biology 2015, DOI: 10.1038/nchembio.1848; Mayer et al., Angew. Chem. Int. Ed. 2016, DOI: 10.1002/anie.201605531).
Key functions of the role include:
* Using existing pipelines or implementing new ones to play a leading role in experimental design, optimal sample size estimation, data QC, visualization and interpretation of genome-wide datasets.
* Performing ad hoc analyses with customised algorithms on experimental data obtained from novel ChIP-Seq, RNA-Seq, and genome sequencing methodologies. This encompasses, for example, expected outcome simulation, signal normalization, data mining, enrichment detection and prediction of secondary structures.
Our lab invents and applies new computational methods for the analysis of sequence, structure and chemical modification of DNA and RNA. This position provides opportunities to collaborate with experimental scientists across the chemistry-biology interface from experimental design to the analysis of novel types of data.
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/chemistry. Previous experience in analysing genomic datasets, especially NGS data, is highly desirable.
Skills required include:
* Excellent programming/scripting skills in languages such as R or Matlab, Python or Perl, C/C++, Ruby or Java.
* A good working knowledge of Linux/Unix, with experience in data processing in a HPC cluster environment.
* Algorithm development, data mining and statistical analysis of large datasets.
* Experience in statistical modelling and mathematical tools (e.g. Bayesian statistics, Markov models, simulation models).
* Knowledge of biological data banks (e.g., NCBI, EMBL-EBI, Ensembl, KEGG, ENCODE).
* Ability to share own code (e.g. GitHub).
The position requires strong communication and teamwork skills and involves regular interactions with our research scientists and computational researchers. The successful candidate will be highly organized, with good time management and the ability to support multiple concurrent projects. Experience in project management would also be welcomed.
The post is available immediately. See www.cruk.cam.ac.uk/research-groups/balasubramanian-group and www.ch.cam.ac.uk/group/shankar for further information.
For queries regarding applying online for this post, please contact Jo Lockhart, PA to Professor Shankar Balasubramanian, email: [email protected].
For an informal discussion on the technical aspects of the role please contact Dario Beraldi and Giovanni Marsico ([email protected]; [email protected]).
Fixed-term: The funds for this post are available for 2 years in the first instance.
The closing date for applications is Sunday 20 November 2016.
To apply and for further information see also here.