Bioinformatics

Our specialist research associates have experience in many different areas of Bioinformatics. In particular we have extensive experience in Neuroscience which presents some unique challenges to investigators Our expertise in experimental design, analysis and use of on line databases and resources, such as the Allen Brain Atlas, can serve to bring an innovative new dimension to your research project.

We support both basic science and clinical research by providing expertise from specialist researchers with experience in both neuroscience and a wide range of bioinformatics analysis methods. We do not process biological samples but will assist in experimental design and identifying appropriate protocols and service providers for sample processing.

Who we are

Bioinformatics Core associate investigators, along with relevant expertise:

 

Vicky Perreau PhD

Analytical:  Transcriptomics, Microarray analysis, RNAseq, CHIP-seq

Selected Informatics Tools:  Allan Brain Atlas, UCSC Genome Browser, Gene Expression Omnibus, Intact (EBI), Neuroscience Information Framework, Gemma

Other:  Experimental design, RNA preparation, Student supervision, Human ethics, Pathway analysis, Gene ontology

Andrew Fox PhD

Analytical: Next generation sequencing (NGS) analysis, DNA variant calling and discovery, Genome-wide Association Studies (GWAS), Pathway and network analysis, DNA methylation analysis, Survival analysis, Machine Learning

Selected Informatics Tools: Plink, Genome Analysis Toolkit (GATK), BWA, Samtools, IGV, String DB, DAVID Bioinformatics Resource, Weka

Other:  Experimental design, Power analysis

Our services

Services

Bioinformatics related experiment design advice on:

  • Specific protocols that may be employed to answer biological questions
  • Sample preparation and quality control
  • Sample numbers required for statistical analysis
  • Depth and type of sequencing required for specific questions
  • Facilitating communication with external services for sample processing
  • Targeted searching of online databases and applications to research biological questions
  • Assistance with grant writing and budget justification
  • Advice on data management
  • Bioinformatics data analysis
  • Training and development
  • Workshops

FAQ

Do you process samples?

No, we do not maintain any hardware or lab space for sample processing. However we will assist you in identifying an appropriate external service facility to process your samples and can advise on sample preparation.

Do you charge for a meeting about a possible project and to discuss design issues?

No, an initial meeting to identify if we may be able to help you or assist in basic experimental design for bioinformatics projects will not cost you anything. Please feel free to contact us. We will ask that you complete a brief questionnaire prior to the first meeting to ensure that we have all relevant information about your project prior to the meeting.

Can you help me with an experimental design that I want to put in a grant?

Yes, we are keen to assist researchers in grant preparation and can help draft appropriate text for experimental design, data management pipelines, technology justification and budget justification.

Can I list the Bioinformatics Core in my grant as doing my data analysis?

Yes, we are happy to be included on grants with prior arrangement. Please contact us when you are thinking about your design and in the early stages of grant writing, as we need sufficient time to determine the requirements for your project.

I have an old microarray/RNAseq dataset that I want to reanalyze can you help me?

Yes, depending on the quality of the data and associated metadata, we may be able to assist with reanalysis of the data, pathway analysis of gene lists and accessing on line informatics resources to generate hypothesis for the results.

I want to use on line resources such as the Allen Brain atlas, can you show me how it works?

Yes, we provide training in many online bioinformatics resources including the Allen Brain atlas, Gene Expression Omnibus and genome browsers.

Does the core provide co-supervision of students?

Co-supervision of students by a nominated academic researcher associated with the Bioinformatics core is encouraged. Student supervision is negotiated with specific researchers and conducted outside core funded activities thus would not incur a charge. Student supervision must also comply with the University guidelines.

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