Bioinformatics and comparative genomics (Xiangchao Gan)
Dr Gan has now became a Professor at the State Key Laboratory for Crop Genetics and Germplasm Enhancement, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, where he has moved.
Nanjing Agricultural University
NO.1 Weigang, Nanjing
P. R. China
De novo genome assembly is still challenging. We developed and are maintaining the software IMR/DENOM which can incorporate reads-mapping based methods and de novo assembly. We are applying these methods to assembly and characterization of the genomes of Arabidospis thaliana, Cardamine hirsuta and Mus musculus. We are also developing new algorithms for de novo genome assembly.
Many structural variants are associated with trait diversity, but their genome-wide study is still limited due to computational challenges in their reliable identification. We are developing tools to investigate structural variation and novel genes. We are also interested in exploring the impact of structural variation on genetic architecture of trait diversity.
NGS data management and analysis support
The group provides NGS data management and analysis support for other groups in the department of Comparative Development and Genetics. We have created pipelines to support various projects involving high throughput sequencing including DNAseq, RNAseq, microRNAseq and CHiPseq. These pipelines are implemented via an integrated web portal and linked to a manually curated database.