QBI’s Bioinformatics Seminar Series and NGS Discussion Group

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.Introduction to BioinformaticsDownload Slides: 

 

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.Introduction to second generation sequencingDownload 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.Introduction to second generation sequencingDownload 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.Introduction to second generation sequencingDownload 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.Introduction to second generation sequencingDownload 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.Introduction to second generation sequencingDownload 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. Introduction to second generation sequencingDownload 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.Introduction to second generation sequencingDownload 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.

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