| An integrated encyclopedia of DNA elements in the human genome ENCODE Project Consortium Nature 489 (7414), 57, 2012 | 18934 | 2012 |
| GENCODE reference annotation for the human and mouse genomes A Frankish, M Diekhans, AM Ferreira, R Johnson, I Jungreis, J Loveland, ... Nucleic acids research 47 (D1), D766-D773, 2019 | 3385 | 2019 |
| GENCODE 2021 A Frankish, M Diekhans, I Jungreis, J Lagarde, JE Loveland, JM Mudge, ... Nucleic acids research 49 (D1), D916-D923, 2021 | 1371 | 2021 |
| A high-resolution map of human evolutionary constraint using 29 mammals K Lindblad-Toh, M Garber, O Zuk, MF Lin, BJ Parker, S Washietl, ... Nature 478 (7370), 476-482, 2011 | 1338 | 2011 |
| Identification of functional elements and regulatory circuits by Drosophila modENCODE S Roy, J Ernst, PV Kharchenko, P Kheradpour, N Negre, ML Eaton, ... Science 330 (6012), 1787, 2010 | 1158 | 2010 |
| PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions MF Lin, I Jungreis, M Kellis Bioinformatics 27 (13), i275-i282, 2011 | 1079 | 2011 |
| Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes DE Neafsey, RM Waterhouse, MR Abai, SS Aganezov, MA Alekseyev, ... Science 347 (6217), 1258522, 2015 | 671 | 2015 |
| GENCODE: reference annotation for the human and mouse genomes in 2023 A Frankish, S Carbonell-Sala, M Diekhans, I Jungreis, JE Loveland, ... Nucleic acids research 51 (D1), D942-D949, 2023 | 462 | 2023 |
| Evolution of enhanced innate immune evasion by SARS-CoV-2 LG Thorne, M Bouhaddou, AK Reuschl, L Zuliani-Alvarez, B Polacco, ... Nature 602 (7897), 487-495, 2022 | 416 | 2022 |
| Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone DJ Park, G Dudas, S Wohl, A Goba, SLM Whitmer, KG Andersen, ... Cell 161 (7), 1516-1526, 2015 | 367 | 2015 |
| Genomic RNA elements drive phase separation of the SARS-CoV-2 nucleocapsid C Iserman, CA Roden, MA Boerneke, RSG Sealfon, GA McLaughlin, ... Molecular cell 80 (6), 1078-1091. e6, 2020 | 351 | 2020 |
| Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer T Ouspenskaia, T Law, KR Clauser, S Klaeger, S Sarkizova, F Aguet, B Li, ... Nature biotechnology 40 (2), 209-217, 2022 | 300 | 2022 |
| Evidence of efficient stop codon readthrough in four mammalian genes G Loughran, MY Chou, IP Ivanov, I Jungreis, M Kellis, AM Kiran, ... Nucleic acids research 42 (14), 8928-8938, 2014 | 292 | 2014 |
| Evidence of abundant stop codon readthrough in Drosophila and other metazoa I Jungreis, MF Lin, R Spokony, CS Chan, N Negre, A Victorsen, KP White, ... Genome research 21 (12), 2096-2113, 2011 | 270 | 2011 |
| Standardized annotation of translated open reading frames JM Mudge, J Ruiz-Orera, JR Prensner, MA Brunet, F Calvet, I Jungreis, ... Nature biotechnology 40 (7), 994-999, 2022 | 242 | 2022 |
| SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes I Jungreis, R Sealfon, M Kellis Nature communications 12 (1), 2642, 2021 | 223 | 2021 |
| Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue J Ma, CC Ward, I Jungreis, SA Slavoff, AG Schwaid, J Neveu, BA Budnik, ... Journal of proteome research 13 (3), 1757-1765, 2014 | 222 | 2014 |
| GENCODE 2025: reference gene annotation for human and mouse JM Mudge, S Carbonell-Sala, M Diekhans, JG Martinez, T Hunt, I Jungreis, ... Nucleic acids research 53 (D1), D966-D975, 2025 | 215 | 2025 |
| Improved identification and analysis of small open reading frame encoded polypeptides J Ma, JK Diedrich, I Jungreis, C Donaldson, J Vaughan, M Kellis, ... Analytical chemistry 88 (7), 3967-3975, 2016 | 170 | 2016 |
| Calcifediol treatment and hospital mortality due to COVID-19: a cohort study JF Alcala-Diaz, L Limia-Perez, R Gomez-Huelgas, MD Martin-Escalante, ... Nutrients 13 (6), 1760, 2021 | 119 | 2021 |
