Sabah Kadri, PhD
Scientist | Artist | Podcaster

RESEARCH


I am the Director of Bioinformatics at Lurie Children's Hospital of Chicago and Assistant Professor of Pathology at Northwestern University. As a scientist, I am intrigued by the applications of Next generation sequencing (NGS) in clinical diagnostics and the world of RNA biology. I lead a team of bioinformaticians and scientists to design, develop and implement cloud-based computational infrastructure and containerized bioinformatics software for clinical diagnostic services for germline and somatic next generation sequencing (NGS) testing. I continue to work on informatics solutions and research questions for translational ‘omics’ and biomedical research to promote precision medicine goals. At the Broad Institute, I worked with large non-coding RNAs and developed a software to mine end RNA-sequencing data. During my PhD, I studied the evolution of miRNA regulation involved in developmental gene regulatory networks in echinoderms, especially, sea urchin and sea stars.

My PhD thesis: miRNA regulation in development

My Google Scholar profile can be found HERE.

Check out this article about my work on GenomeWeb.


Software





insiM: In silico Mutations simulator.




Amplicon Indel Hunter: Large indel detection in amplicon-based NGS data.




HHMMiR: MicroRNA Hairpin detection.


Selected Publications



PhD research


I have developed a probabilistic model for microRNA precursor prediction, called HHMMiR based on hierarchical hidden Markov models (HHMMs), without requirement of conservation of sequence between closely related species. It can be downloaded here .

We studied small RNA libraries in sea uchin and sea star embryonic samples to study microRNA populations.

Whole mount in situ hybridization to study spatial and temporal microRNAs expression patterns, and knocked down critical genes involved in the microRNAs biogenesis pathway to knock down microRNA function in early sea urchin embryos and studied effects on embryonic development.

My PhD thesis: miRNA regulation in development