This seminar series is intended to give a broad overview of bioinformatics, its techniques and challenges, and to highlight how bioinformatics is contributing to the research workflow in neuroscience.
The discussion group focuses in-depth on a variety of topics related to QC and downstream analysis of “called” second generation sequencing data. The idea is to collaboratively develop expertise for handling and analyzing these data, as well as for accessing and exploiting the many publically available genome datasets and databases.
Furthermore, after each seminar there will be a “bioinf-walk-in-clinic” where we can discuss your concrete bioinformatics questions and solve some tasks on the fly.
Please contact Denis Bauer (d.bauer-at-uq.edu.au) or Jake Gratten (j.gratten1-at-uq.edu.au) if you wish to contribute to the series or lead a discussion group.
When: Thursdays, 10:30 am (NEW time)
Where: Level 7, seminar room
| Date | Room | Topic |
| 16 June | Level 7 | Introduction to Bioinformatics Speaker: Denis Bauer Abstract: An introduction to bioinformatics practices and aims will be given and contrasted against approaches from other fields. Most importantly, it will be discussed how bioinformatics fits into the discovery cycle for hypothesis driven neuroscience research.  Download Slides:
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| 23 June | Level 7 | Introduction to second generation sequencing data analysis Speaker: Denis Bauer Abstract: An introduction to second generation sequencing will be given with focus on the basic production informatics: The approach of raw data conversion and quality control will be discussed.  Download Slides: |
| 30 June | Level 5 | Variant calling for disease association (Part 1: Mapping) Speaker: Denis Bauer Abstract: This session will focus on the first steps involved in identifying SNPs from whole genome, exome capture or targeted resequencing data: The different read mapping approaches to a DNA reference sequence will be introduced and quality metrics discussed.  Download Slides: |
| 7 July | No seminar today because of IMB’s Winter School in Mathematical and Computational Biology. | |
| 14 July | Level 7 | Variant calling for disease association (Part2: Variant calling) Speaker: Denis Bauer Abstract: This session will focus on the steps involved in identifying genomic variants after an initial mapping was achieved: improvement the mapping, SNP and indel calling and variant filtering/recalibration will be introduced.  Download Slides: |
| 21 July | No Seminar today because of QBI’s Science of Learning Symposium. | |
| 28 July | No Seminar today because of QBI’s Christmas in July | |
| 04 August | Level 7 | Functionally annotate variants Speaker: Denis Bauer Abstract: This seminar aims at answering the question of what to make of the identified variants, specifically how to evaluate the quality, prioritize and functionally annotate the variants.  Download Slides: |
| 11 August | Level 7 | Transcript detection in RNAseq Speaker: Denis Bauer Abstract: The focus in this session will be put on the differences between standard DNA mapping and RNAseq-specific transcript mapping: identifying splice variants and isoforms. The issue of transcript quantification and genomic variants that can be identified from RNAseq data will be discussed.  Download Slides: |
| 25 August | Level 7 | Differential gene expression Speaker: Denis Bauer Abstract: This session will follow up from transcript quantification of RNAseq data and discusses statistical means of identifying differentially regulated transcripts, and isoforms and contrasts these against microarray analysis approaches.  Download Slides: |
| 1 Sept | Level 7 | NGS Discussion group: RNA editing Speaker: Jake Gratten Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, Cheung VG. Widespread RNA and DNA sequence differences in the human transcriptome. Science. 2011 Jul 1;333(6038):53-8. Epub 2011 May 19. PubMed PMID: 21596952. |
| 8 Sept | Level 7 | QBI’s Centre for Brain genomics – the informatics side Speaker: Denis Bauer Abstract: An overview of QBI’s production informatics framework with an emphasis on what service will be provided and how the resulting data is made available: from interactive quality control to integration with external data on the genome browser.  Download Slides: |
| 15 Sept | Level 7 | Postponed |
| 22 Sept | Level 7 | Identification of genes for myoclonic astatic epilepsy using next generation sequencing Speaker: Marie Mangelsdorf Abstract: TBA |
| 29 Sept | Level 7 | Postponed due to COMBIO conference |
| 6 Oct | Level 7 | NGS Discussion group: Methylation Analysis Speaker: Kevin Dudley and Danay Baker-Andresen |
| 24 November | Level 7 | Using integrated genomics to investigate transcription factor function: speaking for personal experience Speaker: Jens Bunt |
The seminar series is an open forum and contributions (talks/journal presentations/discussions) are more than welcome.
