Irwin Jungreis, Ph.D. — Research Scientist

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Research Interests

I am fascinated by evolution. I use computation to investigate biological questions, with a focus on using evolutionary signatures to distinguish protein-coding regions of genomes. This has led to the discovery of previously unknown genes and conserved stop codon readthrough extensions. Of late, I have been investigating the genome of the SARS-CoV-2 virus. I am a member of the Kellis lab at MIT.

First and co-first author papers

• Jungreis I, Sealfon R, Kellis M (2021). SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Nature Communications 12(1), 2642. doi:10.1038/s41467-021-22905-7.
• Jungreis I^*, Nelson CW^*, Ardern Z, Finkel Y, Krogan NJ, et al. (2021). Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution. Virology 558, 145-151. doi:10.1016/j.virol.2021.02.013.
• Jungreis I, Kellis M (2020). Mathematical analysis of Córdoba calcifediol trial suggests strong role for Vitamin D in reducing ICU admissions of hospitalized COVID-19 patients. medRxiv, 1-14. doi:10.1101/2020.11.08.20222638.
• Khan YA^*, Jungreis I^*, Wright JC, Mudge JM, Choudhary JS, et al. (2020). Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon. BMC Genet 21(1), 25. doi:10.1186/s12863-020-0828-7.

• Mudge JM^*, Jungreis I^*, Hunt T, Gonzalez JM, Wright JC, et al. (2019). Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci. Genome Res 29, 2073-2087. doi:10.1101/gr.246462.118.
• Jungreis I^*, Tress ML^*, Mudge J^*, Sisu C, Hunt T, et al. (2018). Nearly all new protein-coding predictions in the CHESS database are not protein-coding. bioRxiv. doi:10.1101/360602.
• Jungreis I^*, Chan CS^*, Waterhouse RM, Fields G, Lin MF, et al. (2016). Evolutionary Dynamics of Abundant Stop Codon Readthrough. Mol Biol Evol 33(12), 3108-3132. doi:10.1093/molbev/msw189.
• Jungreis I, Lin MF, Spokony R, Chan CS, Negre N, et al. (2011). Evidence of abundant stop codon readthrough in Drosophila and other metazoa. Genome Res 21(12), 2096-2113. doi:10.1101/gr.119974.110.

*Authors contributed equally.

Some projects I have contributed to

• Lin MF, Jungreis I, Kellis M (2011). PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics 27(13), i275-82. doi:10.1093/bioinformatics/btr209.
• Thorne LG, Bouhaddou M, Reuschl A, Zuliani-Alvarez L, Polacco B, et al. (2021). Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature. doi:10.1038/s41586-021-04352-y.
• Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, et al. (2021). GENCODE 2021. Nucleic Acids Res 49(D1), D916-D923. doi:10.1093/nar/gkaa1087.
• Alcalá Díaz JF, Limia-Perez L, Gomez-Huelgas R, Martin-Escalante MD, Cortes-Rodriguez B, et al. (2021). Calcifediol Treatment and Hospital Mortality Due to COVID‐19: A Cohort Study. Nutrients, 1-13. doi:10.3390/nu13061760.
• Sun C, Huang J, Wang Y, Zhao X, Su L, et al. (2020). Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. Mol Biol Evol. doi:10.1093/molbev/msaa240.
• Loughran G, Chou M, Ivanov IP, Jungreis I, Kellis M, et al. (2014). Evidence of efficient stop codon readthrough in four mammalian genes. Nucleic Acids Res 42(14), 8928-8938. doi:10.1093/nar/gku608.
• Eisenberg AR, Higdon AL, Hollerer I, Fields AP, Jungreis I, et al. (2020). Translation Initiation Site Profiling Reveals Widespread Synthesis of Non-AUG-Initiated Protein Isoforms in Yeast. Cell Systems 11(2), 145-160.e5. doi:10.1016/j.cels.2020.06.011.
• Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, et al. (2015). Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes. Science 347(6217), 1258522. doi:10.1126/science.1258522.
• Sealfon RS, Lin MF, Jungreis I, Wolf MY, Kellis M, et al. (2015). FRESCo: finding regions of excess synonymous constraint in diverse viruses. Genome Biol 16(1), 38. doi:10.1186/s13059-015-0603-7.
• Park DJ, Dudas G, Wohl S, Goba A, Whitmer SLM, et al. (2015). Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone. Cell 161(7), 1516-1526. doi:10.1016/j.cell.2015.06.007.
• Kousi M, Söylemez O, Ozanturk A, Mourtzi N, Akle S, et al. (2020). Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy. Nat Genet 52(11), 1145-1150. doi:10.1038/s41588-020-0707-1.
• Ouspenskaia T, Law T, Clauser KR, Klaeger S, Sarkizova S, et al. (2021). Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nat Biotechnol. doi:10.1038/s41587-021-01021-3.

A blast from the past

• Jungreis I (1985). The uniformization of the complement of the Mandelbrot set. Duke Mathematical Journal 52(4), 935-938. doi:10.1215/S0012-7094-85-05250-0.
• Jungreis I (1991). Some results on the Sarkovskii partial ordering of permutations. Transactions of the American Mathematical Society 325(1), 319-344. doi:10.1090/S0002-9947-1991-0998354-X.

Software

• CodAlignView, the Codon Alignment Viewer, is a tool for visually exploring genomic alignments of related species, with substitutions and indels color-coded to make it easy to distinguish protein-coding regions. CodAlignView User's Guide
• I support and enhance PhyloCSF, a tool that uses comparative genomics to distinguish protein-coding regions of genomes.

History

I did my graduate work at Harvard (Ph.D. in math), and undergraduate at Cornell.

In a previous career, I cofounded Revit Technology Corporation, maker of the leading software for architects and the construction industry.