During his PhD studies, Vikas Gupta utilised next-generation sequencing (NGS) to analyse the genomes of lotus, blueberries and spiders. The need for analysing the large and increasing amount of sequencing data has boosted demand for efficient, user-friendly and broadly applicable computational tools. Vikas Gupta developed two tools – shortran and GABox – for small RNA data analysis and genome annotation, respectively.

Vikas Gupta generated genomics and transcriptomics resources to facilitate research into three species on a genomic scale. In lotus plants, he found that a specific miRNA was involved in the plant-microbe symbiosis, where he used a parallel approach of small RNA sequencing and degradome sequencing. In blueberry plants, he found that anthocyanin-encoding genes were enriched in ripe fruit, and he identified several other genes in developmentally regulated alternative splicing. In spiders, he used proteomics-supported genome annotation to study silk and venom genes.

These findings contribute to the understanding of lotus, blueberries and spiders at the molecular level, and resources and tools presented in the study should be valuable to scientific research communities pursuing related work.

The PhD degree was completed at the Bioinformatics Research Centre (BiRC) and the Department of Molecular Biology and Genetics, Science and Technology, Aarhus University.

Time: Friday 24 October 2014 at 13.15
Place: Lecture Theatre, building 1110, room 223, Bioinformatics Research Centre (BiRC), Aarhus University, C. F. Møllers Allé 8, 8000 Aarhus C
Title of dissertation: Applied bioinformatics: Genome annotation and transcriptome analysis
Contact information: Vikas Gupta, vgupta@birc.au.dk, +45 5039 3834
Members of the assessment committee:
Associate Professor James Taylor, Department of Biology, Johns Hopkins University, USA
Senior Scientist Igor Kardailsky, CLC bio, a QIAGEN Company, Denmark
Associate Professor Ira Assent (chair), Department of Computer Science, Aarhus University
Main supervisor:
Associate Professor Christian Nørgaard Storm Pedersen, Bioinformatics Research Centre (BiRC), Aarhus University
Co-supervisor:
Assistant Professor Stig Uggerhøj Andersen, Department of Molecular Biology and Genetics, Aarhus University
Language: The dissertation will be defended in English

The defence is public.
The dissertation is available for reading at the Graduate School of Science and Technology/GSST, Ny Munkegade 120, building 1521, room 112, 8000 Aarhus C.