Year |
Citation |
Score |
2023 |
Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, ... ... Jungreis I, et al. SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell. PMID 37738970 DOI: 10.1016/j.cell.2023.08.026 |
0.517 |
|
2022 |
Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, Arnan C, Barnes I, Banerjee A, Bennett R, Berry A, Bignell A, Boix C, et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Research. PMID 36420896 DOI: 10.1093/nar/gkac1071 |
0.626 |
|
2022 |
Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Albà MM, Aspden JL, Baranov PV, Bazzini AA, et al. Standardized annotation of translated open reading frames. Nature Biotechnology. PMID 35831657 DOI: 10.1038/s41587-022-01369-0 |
0.482 |
|
2022 |
Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, et al. Publisher Correction: Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature. PMID 35332335 DOI: 10.1038/s41586-022-04653-w |
0.408 |
|
2021 |
Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, et al. Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature. PMID 34942634 DOI: 10.1038/s41586-021-04352-y |
0.493 |
|
2021 |
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, ... ... Jungreis I, et al. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nature Biotechnology. PMID 34663921 DOI: 10.1038/s41587-021-01021-3 |
0.475 |
|
2021 |
Sun C, Huang J, Wang Y, Zhao X, Su L, Thomas GWC, Zhao M, Zhang X, Jungreis I, Kellis M, Vicario S, Sharakhov IV, Bondarenko SM, Hasselmann M, Kim CN, et al. Erratum to: Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. Molecular Biology and Evolution. PMID 34015138 DOI: 10.1093/molbev/msab100 |
0.516 |
|
2021 |
Jungreis I, Sealfon R, Kellis M. SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Nature Communications. 12: 2642. PMID 33976134 DOI: 10.1038/s41467-021-22905-7 |
0.62 |
|
2021 |
Jungreis I, Nelson CW, Ardern Z, Finkel Y, Krogan NJ, Sato K, Ziebuhr J, Stern-Ginossar N, Pavesi A, Firth AE, Gorbalenya AE, Kellis M. Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution. Virology. 558: 145-151. PMID 33774510 DOI: 10.1016/j.virol.2021.02.013 |
0.6 |
|
2020 |
Iserman C, Roden CA, Boerneke MA, Sealfon RSG, McLaughlin GA, Jungreis I, Fritch EJ, Hou YJ, Ekena J, Weidmann CA, Theesfeld CL, Kellis M, Troyanskaya OG, Baric RS, Sheahan TP, et al. Genomic RNA Elements Drive Phase Separation of the SARS-CoV-2 Nucleocapsid. Molecular Cell. PMID 33290746 DOI: 10.1016/j.molcel.2020.11.041 |
0.538 |
|
2020 |
Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, et al. GENCODE 2021. Nucleic Acids Research. PMID 33270111 DOI: 10.1093/nar/gkaa1087 |
0.624 |
|
2020 |
Kousi M, Söylemez O, Ozanturk A, Mourtzi N, Akle S, Jungreis I, Muller J, Cassa CA, Brand H, Mokry JA, Wolf MY, Sadeghpour A, McFadden K, Lewis RA, Talkowski ME, et al. Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy. Nature Genetics. PMID 33046855 DOI: 10.1038/s41588-020-0707-1 |
0.5 |
|
2020 |
Jungreis I, Sealfon R, Kellis M. SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Research Square. PMID 33024961 DOI: 10.21203/rs.3.rs-80345/v1 |
0.644 |
|
2020 |
Sun C, Huang J, Wang Y, Zhao X, Su L, Thomas GWC, Zhao M, Zhang X, Jungreis I, Kellis M, Vicario S, Sharakhov IV, Bondarenko SM, Hasselmann M, Kim CN, et al. Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. Molecular Biology and Evolution. PMID 32946576 DOI: 10.1093/Molbev/Msaa240 |
0.617 |
|
2020 |
Eisenberg AR, Higdon AL, Hollerer I, Fields AP, Jungreis I, Diamond PD, Kellis M, Jovanovic M, Brar GA. Translation Initiation Site Profiling Reveals Widespread Synthesis of Non-AUG-Initiated Protein Isoforms in Yeast. Cell Systems. PMID 32710835 DOI: 10.1016/J.Cels.2020.06.011 |
0.663 |
|
2020 |
Jungreis I, Sealfon R, Kellis M. Sarbecovirus comparative genomics elucidates gene content of SARS-CoV-2 and functional impact of COVID-19 pandemic mutations. Biorxiv : the Preprint Server For Biology. PMID 32577641 DOI: 10.1101/2020.06.02.130955 |
0.636 |
|
2020 |
Khan YA, Jungreis I, Wright JC, Mudge JM, Choudhary JS, Firth AE, Kellis M. Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon. Bmc Genetics. 21: 25. PMID 32138667 DOI: 10.1186/S12863-020-0828-7 |
0.553 |
|
2020 |
Martinez-Gomez L, Abascal F, Jungreis I, Pozo F, Kellis M, Mudge JM, Tress ML. Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation. Nar Genomics and Bioinformatics. 2: lqz023. PMID 31886458 DOI: 10.1093/nargab/lqz023 |
0.604 |
|
2019 |
Mudge JM, Jungreis I, Hunt T, Gonzalez JM, Wright JC, Kay M, Davidson C, Fitzgerald S, Seal R, Tweedie S, He L, Waterhouse RM, Li Y, Bruford E, Choudhary JS, et al. Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci. Genome Research. PMID 31537640 DOI: 10.1101/Gr.246462.118 |
0.695 |
|
2019 |
Novoa EM, Jungreis I, Jaillon O, Kellis M. Elucidation of Codon Usage Signatures across the Domains of Life. Molecular Biology and Evolution. PMID 31220870 DOI: 10.1093/Molbev/Msz124 |
0.592 |
|
2019 |
McCorkindale AL, Wahle P, Werner S, Jungreis I, Menzel P, Shukla CJ, Abreu RLP, Irizarry RA, Meyer IM, Kellis M, Zinzen RP. A gene expression atlas of embryonic neurogenesis in reveals complex spatiotemporal regulation of lncRNAs. Development (Cambridge, England). 146. PMID 30923056 DOI: 10.1242/Dev.175265 |
0.579 |
|
2018 |
Abascal F, Juan D, Jungreis I, Kellis M, Martinez L, Rigau M, Rodriguez JM, Vazquez J, Tress ML. Loose ends: almost one in five human genes still have unresolved coding status. Nucleic Acids Research. PMID 30395326 DOI: 10.1093/Nar/Gky1146 |
0.606 |
|
2018 |
Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Research. PMID 30357393 DOI: 10.1093/Nar/Gky955 |
0.648 |
|
2018 |
Abascal F, Juan D, Jungreis I, Martinez L, Rigau M, Rodriguez JM, Vazquez J, Tress ML. Loose ends: almost one in five human genes still have unresolved coding status. Nucleic Acids Research. PMID 29982784 DOI: 10.1093/Nar/Gky587 |
0.517 |
|
2018 |
Loughran G, Jungreis I, Tzani I, Power M, Dmitriev RI, Ivanov IP, Kellis M, Atkins JF. Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response. The Journal of Biological Chemistry. PMID 29386352 DOI: 10.1074/Jbc.M117.818526 |
0.596 |
|
2016 |
Jungreis I, Chan CS, Waterhouse RM, Fields G, Lin MF, Kellis M. Evolutionary dynamics of abundant stop codon readthrough. Molecular Biology and Evolution. PMID 27604222 DOI: 10.1093/Molbev/Msw189 |
0.66 |
|
2016 |
Ma J, Diedrich JK, Jungreis I, Donaldson C, Vaughan J, Kellis M, Yates JR, Saghatelian A. Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides. Analytical Chemistry. PMID 27010111 DOI: 10.1021/Acs.Analchem.6B00191 |
0.614 |
|
2015 |
Park DJ, Dudas G, Wohl S, Goba A, Whitmer SL, Andersen KG, Sealfon RS, Ladner JT, Kugelman JR, Matranga CB, Winnicki SM, Qu J, Gire SK, Gladden-Young A, Jalloh S, ... ... Jungreis I, et al. Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone. Cell. 161: 1516-26. PMID 26091036 DOI: 10.1016/J.Cell.2015.06.007 |
0.399 |
|
2015 |
Sealfon RS, Lin MF, Jungreis I, Wolf MY, Kellis M, Sabeti PC. FRESCo: finding regions of excess synonymous constraint in diverse viruses. Genome Biology. 16: 38. PMID 25853568 DOI: 10.1186/S13059-015-0603-7 |
0.616 |
|
2015 |
Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, ... ... Jungreis I, et al. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science (New York, N.Y.). 347: 1258522. PMID 25554792 DOI: 10.1126/Science.1258522 |
0.657 |
|
2014 |
Loughran G, Chou MY, Ivanov IP, Jungreis I, Kellis M, Kiran AM, Baranov PV, Atkins JF. Evidence of efficient stop codon readthrough in four mammalian genes. Nucleic Acids Research. 42: 8928-38. PMID 25013167 DOI: 10.1093/Nar/Gku608 |
0.655 |
|
2014 |
Ma J, Ward CC, Jungreis I, Slavoff SA, Schwaid AG, Neveu J, Budnik BA, Kellis M, Saghatelian A. Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue. Journal of Proteome Research. 13: 1757-65. PMID 24490786 DOI: 10.1021/Pr401280W |
0.613 |
|
2013 |
Chan CS, Jungreis I, Kellis M. Heterologous stop codon readthrough of metazoan readthrough candidates in yeast. Plos One. 8: e59450. PMID 23544069 DOI: 10.1371/Journal.Pone.0059450 |
0.644 |
|
2011 |
Jungreis I, Lin MF, Spokony R, Chan CS, Negre N, Victorsen A, White KP, Kellis M. Evidence of abundant stop codon readthrough in Drosophila and other metazoa. Genome Research. 21: 2096-113. PMID 21994247 DOI: 10.1101/Gr.119974.110 |
0.698 |
|
2011 |
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, ... ... Jungreis I, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/Nature10530 |
0.653 |
|
2011 |
Lin MF, Jungreis I, Kellis M. PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics (Oxford, England). 27: i275-82. PMID 21685081 DOI: 10.1038/Npre.2010.4784.1 |
0.653 |
|
2010 |
Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, ... ... Jungreis I, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/Science.1198374 |
0.635 |
|
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