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Secondment to Second Genome

By Nina Konstantinidou, Postdoctoral Scientist APC

I am a bioinformatics post-doctoral scientist at the APC Microbiome Ireland, but am seconded to a California based company, Second Genome, to carry out multi-omics bioinformatics analysis for a study on Inflammatory Bowel Disease research (IBD). This secondment operates under an established research collaboration programme between Marcus Claesson, a Principal Investigator at the APC and Todd DeSantis, a Co-Founder and Vice President of Informatics at Second Genome.

Second Genome is focused on therapeutics research in a range of diseases by combining Next Generation Sequencing (NGS) with their custom PhyloChipTM hybridization assays to measure disease specific changes in bacterial populations within the human.  From this discovery process the company identifies entirely novel therapeutic leads employing in vitro and in vivo and models in the path to the clinic. The company possesses a sophisticated system for metadata enrichment analyses using its central KnowledgeBase of expertly curated studies. The multi-omics data from multiple studies are curated using controlled vocabulary that allows identification of the shared attributes among different biospecimens amenable for machine learning.

Before joining Marcus’s team and Second Genome, I managed a European microbiome analyses platform development project MetaPlat ( as a bioinformatician straight after completing my Ph.D. in Molecular Cell Biology and Medical Microbiology at UCC.  I now work with SG’s KnowledgeBase and the multi-omics discovery team to elucidate microbial abundance, activity and the gene expression in the IBD patients.  This includes optimizing bioinformatics pipelines for diverse data processing, visualization and result interpretation.