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Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer.
Ouspenskaia T, Law T, Clauser KR, Klaeger S, Sarkizova S, Aguet F, Li B, Christian E, Knisbacher BA, Le PM, Hartigan CR, Keshishian H, Apffel A, Oliveira G, Zhang W, Chen S, Chow YT, Ji Z, Jungreis I, Shukla SA, Justesen S, Bachireddy P, Kellis M, Getz G, Hacohen N, Keskin DB, Carr SA, Wu CJ, Regev A. Ouspenskaia T, et al. Among authors: jungreis i. Nat Biotechnol. 2022 Feb;40(2):209-217. doi: 10.1038/s41587-021-01021-3. Epub 2021 Oct 18. Nat Biotechnol. 2022. PMID: 34663921 Free PMC article.
A high-resolution map of human evolutionary constraint using 29 mammals.
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC; Broad Institute Sequencing Platform and Whole Genome Assembly Team; Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team; Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK; Genome Institute at Washington University; Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M. Lindblad-Toh K, et al. Among authors: jungreis i. Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530. Nature. 2011. PMID: 21993624 Free PMC article.
Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue.
Ma J, Ward CC, Jungreis I, Slavoff SA, Schwaid AG, Neveu J, Budnik BA, Kellis M, Saghatelian A. Ma J, et al. Among authors: jungreis i. J Proteome Res. 2014 Mar 7;13(3):1757-65. doi: 10.1021/pr401280w. Epub 2014 Feb 14. J Proteome Res. 2014. PMID: 24490786 Free PMC article.
Evidence of efficient stop codon readthrough in four mammalian genes.
Loughran G, Chou MY, Ivanov IP, Jungreis I, Kellis M, Kiran AM, Baranov PV, Atkins JF. Loughran G, et al. Among authors: jungreis i. Nucleic Acids Res. 2014 Aug;42(14):8928-38. doi: 10.1093/nar/gku608. Epub 2014 Jul 10. Nucleic Acids Res. 2014. PMID: 25013167 Free PMC article.
Evolutionary Dynamics of Abundant Stop Codon Readthrough.
Jungreis I, Chan CS, Waterhouse RM, Fields G, Lin MF, Kellis M. Jungreis I, et al. Mol Biol Evol. 2016 Dec;33(12):3108-3132. doi: 10.1093/molbev/msw189. Epub 2016 Sep 7. Mol Biol Evol. 2016. PMID: 27604222 Free PMC article.
45 results