Sabah Kadri, PhD
Computational Biologist . Improvisor . Dancer

RESEARCH


I am the Director of Bioinformatics at the Genomic and Molecular Pathology division at the University of Chicago. As a scientist, I am intrigued by the applications of Next generation sequencing (NGS) in clinical diagnostics and the world of RNA biology. I am currently involved in development of novel tools and pipelines for clinical testing of cancer using NGS. You can check out more information about my team here. 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.


Softwares





Amplicon Indel Hunter (Click for download page): Large indel detection in amplicon-based NGS data.




HHMMiR (Click for download page): MicroRNA Hairpin detection.



ESAT (Click for download page): End RNA sequencing Analysis toolkit.


Publications



Clinical Diagnostics


Large Indel detection in amplicon-based NGS assays without using a reference genome. The software can be found here.

Development and maintenance of computational pipelines to detect somatic mutations and structural variants (CNVs and gene fusions) in various amplicon based, hybrid capture NGS and molecular barcoding assays.

Single cell RNASeq

Clinical Assay developement

Studying clonal evolution in longitudinal Richter’s Syndrome patients.

Dual Targeting in Ibrutinib-Resistant CLL and subsequent work on clinical trial data.


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