Isidore Rigoutsos, PhD
Richard W. Hevner Professor in Computational Medicine, Department of Pathology & Genomic Medicine
Director, Center for Computational Medicine
Contact
1020 Locust Street
Jefferson Alumni Hall
Philadelphia, PA 19107
215-503-6152
215-955-5058 fax
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Isidore Rigoutsos, PhD
Richard W. Hevner Professor in Computational Medicine, Department of Pathology & Genomic Medicine
Director, Center for Computational Medicine
Research & Clinical Interests
Pattern discovery; motif discovery; regulatory motifs; microRNAs; miRNAs; piRNAs; microRNA and piRNA targeting; non-coding RNAs; RNAi; RNA interference; retrotransposons; cell process regulation; genomics; computational genetics; computational medicine; diagnostics; therapeutics; high-throughput sequencing analysis; microbial genomics; metagenomics; high performance computing.
Publications
- MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs)
- The Typical tRNA Co-Expresses Multiple 5′ tRNA Halves Whose Sequences and Abundances Depend on Isodecoder and Isoacceptor and Change with Tissue Type, Cell Type, and Disease
- Characterization of all small RNAs in and comparisons across cultured megakaryocytes and platelets of healthy individuals and COVID-19 patients
- Roles of mitochondrial genetics in cancer metastasis
- Reproducibility efforts as a teaching tool: A pilot study
Most Recent Peer-Reviewed Publications
- Short RNA regulators: the past, the present, the future, and implications for precision medicine and health disparities
- TRNA fragments show intertwining with mRNAs of specific repeat content and have links to disparities
- Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation
- Profiles of miRNA Isoforms and tRNA Fragments in Prostate Cancer
- Race disparities in the contribution of miRNA isoforms and tRNA-derived fragments to Triple-negative breast cancer
- Accurate profiling and quantification of tRNA fragments from RNA-Seq Data: A Vade Mecum for MINTmap
- MINTbase v2.0: A comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all the Cancer Genome Atlas projects
- Increasing cell density globally enhances the biogenesis of Piwi-interacting RNAs in Bombyx mori germ cells
- The biogenesis pathway of tRNA-derived piRNAs in Bombyx germ cells
- Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma
- An miRNA expression signature for the human colonic stem cell niche distinguishes malignant from normal epithelia
- Threshold-seq: A tool for determining the threshold in short RNA-seq datasets
- N-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration
- YAMAT-seq: An efficient method for high-throughput sequencing of mature transfer RNAs
- Assessment of isomiR discrimination using commercial qPCR methods
- MINTmap: Fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data
- Knowledge about the presence or absence of miRNA isoforms (isomiRs) can successfully discriminate amongst 32 TCGA cancer types
- Post-transcriptional regulation of BRCA2 through interactions with miR-19a and miR-19b
- MINTbase: A framework for the interactive exploration of mitochondrial and nuclear tRNA fragments
- Integrative Multi-omic Analysis of Human Platelet eQTLs Reveals Alternative Start Site in Mitofusin 2