Nima Rafati

Nima Rafati NBIS expert

NGS, Genomics, Genome/Transcriptome assembly, Genome annotation, Transcriptomics, Small and large variant analyses, Comparative genomics, GWAS, scRNASeq, Methylation
phone +46 (0)18 471 4249

I have always been fascinated by finding patterns in DNA sequence and music and tried to follow my passion by doing a B.Sc and M.Sc in animal breeding and genetics at Tehran University, Iran. Then, I received a scholarship from Erasmus Mundus to do another M.Sc (Wageningen university and Uppsala University) where I focused on bioinformatics and did my thesis at Leif Andersson’s group (Uppsala University) developing “Exome assembly” pipeline for Atlantic herring. I continued this project during my PhD where I was involved in other projects studying genetic variation in domestic and natural population of rabbit, horse, and chicken by using now generation sequencing data (NGS). After that I joined Åsa Johansson’s group (UU) and did GWAS for human complex traits analysing more than 1000 WGS. During my PostDoc I worked on a pipeline to perform region-based association analyses as well as CNV discovery and their association with disease-related biomarkers.

During my PhD and partly PostDoc, I explored “dark matter” of genome, regions that are underrepresented or missing from the genome/transcriptome assembly. For instance, a large deletion associated with skeletal disorder in Shetland ponies removing two important genes involved in skeletal development. This study resulted in a genetic test which breeders can use to manage the breeding programs. Also, few examples in evolutionary biology: discovery of sex chromosome in atlantic herring, discovery of leptin gene in chicken. and ….

At NBIS, I have been working on genome annotation, WGS analyses, bulk RNASeq, scRNASeq, methylation of cancer and clinical samples.