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.
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.
McGregor SM, Alikhan MB, John RA, Kotler H, Bridge JA, Mujacic I, Kadri S, Segal J, Krausz T. Melanotic PEComa of the Sinonasal Mucosa With NONO-TFE3 Fusion: An Elusive Mimic of Sinonasal Melanoma. Am J Surg Pathol. 2016 Dec 22. doi: 10.1097/PAS.0000000000000778. [Epub ahead of print]
Choy B, Hyjek E, Montag AG, Pytel P, Haydon R, Luu HH, Zhen CJ, Long BC, Kadri S, Segal JP, Furtado LV, Cipriani NA. High prevalence of MiTF staining in undifferentiated pleomorphic sarcoma: caution in use of melanocytic markers in sarcoma. Histopathology. 2016 Dec 7. doi: 10.1111/his.13139. [Epub ahead of print]
Yap KL, Furtado LV, Kiyotani K, Curran E, Stock W, McNeer JL, Kadri S, Segal JP, Nakamura Y, Le Beau MM, Gurbuxani S, Raca G. Diagnostic evaluation of RNA sequencing for the detection of genetic abnormalities associated with Ph-like acute lymphoblastic leukemia (ALL). Leuk Lymphoma. 2017 Apr;58(4):950-958. doi: 10.1080/10428194.2016.1219902. Epub 2016 Nov 17
Kadri S., Long BC, Mujacic I, Zhen CJ, Wurst MN, Sharma S, McDonald N., Niu N, Benhamed S, Tuteja J, Seiwert T, White KP, McNerney ME, Fitzpatrick C, Wang YL, Furtado LV, Segal JP . UCM-OncoPlus: Clinical Validation of a Comprehensive Genomic Oncology Panel Via Cross-Platform Comparison with Established Next Generation Sequencing Assays J Mol Diagn. 2017 Jan;19(1):43-56. doi: 10.1016/j.jmoldx.2016.07.012. Epub 2016 Nov 9.
Sharma S, Galanina N, Guo A, Lee J, Kadri S, Van Slambrouck C, Long B, Wang W, Ming M, Furtado LV, Segal JP, Stock W, Venkataraman G, Tang WJ, Lu P, Wang YL. Identification of a structurally novel BTK mutation that drives ibrutinib resistance in CLL. Oncotarget. 2016 Sep 10. doi: 10.18632/oncotarget.11932. [Epub ahead of print] PubMed PMID: 27626698
Lan TT, Keller-Ramey J, Fitzpatrick C, Kadri S, Taxy JB, Segal JP, Furtado LV, Antic T. Unclassified renal cell carcinoma with tubulopapillary architecture, clear cell phenotype, and chromosome 8 monosomy: a new kid on the block. Virchows Arch. 2016 Jul;469(1):81-91. doi: 10.1007/s00428-016-1952-7. Epub 2016 May 12. PubMed PMID: 27173781.
Chen J, Shishkin AA, Zhu X,Kadri S., Maza I, Guttman M, Hanna JH, Regev A, Garber M. Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs. Genome Biol. 2016 Feb 2;17(1):19. doi: 10.1186/s13059-016-0880-9.
Furtado L.V., Kadri S., Wurst M.N., Long B.C., Segal J.P., Pytel P. Polyglucosan bodies in intramuscular nerve branches are a poor predictor of GBE1 mutation and adult polyglucosan body disease. Muscle Nerve. 2016 Mar;53(3):473-5. doi: 10.1002/mus.25017.
Kadri S., Zhen CJ., Wurst M.N., Long B.C., Jiang Z., Wang Y.L., Furtado L.V., Segal J.P. Amplicon Indel Hunter: A Novel Bioinformatics Tool to Detect Large Somatic Insertion/Deletion Mutations in Amplicon-Based NGS Data. J Mol Diagn. 2015 Nov;17(6):635-43. doi: 10.1016/j.jmoldx.2015.06.005. Epub 2015 Aug 28.
Bornstein C., Barnett-Itzhaki Z., David E., Winter D., Kadri S., Garber M., Amit I. A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States. Mol Cell. 2014 Dec 18;56(6):749-62.
Suvà M., Rheinbay E., Gillespie S., Patel A., Wakimoto H., Rabkin S., Chi A.,Cahill D., Nahed B., Curry W., Martuza R., Rivera M., Riggi N., Rosetti N., Kasif S., Beik S., Kadri S., Tirosh I., Wortman Ivo, Shalek A., Rozenblatt-Rosen O., Regev A., Loius D., Bernstein B. 2014 Reconstructing and reprogramming the tumor propagating potential of glioblastoma stem-like cells. Cell. 2014 Apr 24;157(3):580-94
Engreitz J., Pandya-Jones A., McDonel P., Shishkin A., Sirokman K., Surka C., Kadri S., Xing J., Goren A., Lander E., Plath K., and Guttman M. 2013 The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome. Science Vol. 341 no. 6147 doi: 10.1126/science.1237973
Kadri S., Hinman V., and Benos P. 2011 RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star. PLoS ONE 6(12): e29217. doi:10.1371/journal.pone.0029217
Kadri S., Hinman V., and Benos P. 2009 HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models. BMC Bioinformatics 10, no. 1: S35. doi:10.1186/1471-2105-10-S1-S35
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.
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