| 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 | 2580 | 2019 |
| The UCSC genome browser database: 2015 update KR Rosenbloom, J Armstrong, GP Barber, J Casper, H Clawson, ... Nucleic acids research 43 (D1), D670-D681, 2015 | 1078 | 2015 |
| Toil enables reproducible, open source, big biomedical data analyses J Vivian, AA Rao, FA Nothaft, C Ketchum, J Armstrong, A Novak, J Pfeil, ... Nature biotechnology 35 (4), 314-316, 2017 | 990 | 2017 |
| GENCODE 2021 A Frankish, M Diekhans, I Jungreis, J Lagarde, JE Loveland, JM Mudge, ... Nucleic acids research 49 (D1), D916-D923, 2021 | 722 | 2021 |
| Telomere-to-telomere assembly of a complete human X chromosome KH Miga, S Koren, A Rhie, MR Vollger, A Gershman, A Bzikadze, ... Nature 585 (7823), 79-84, 2020 | 683 | 2020 |
| The UCSC genome browser database: 2018 update J Casper, AS Zweig, C Villarreal, C Tyner, ML Speir, KR Rosenbloom, ... Nucleic acids research 46 (D1), D762-D769, 2018 | 500 | 2018 |
| Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes K Shafin, T Pesout, R Lorig-Roach, M Haukness, HE Olsen, C Bosworth, ... Nature biotechnology 38 (9), 1044-1053, 2020 | 385 | 2020 |
| Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs RE Green, EL Braun, J Armstrong, D Earl, N Nguyen, G Hickey, ... Science 346 (6215), 1254449, 2014 | 366 | 2014 |
| High-resolution comparative analysis of great ape genomes ZN Kronenberg, IT Fiddes, D Gordon, S Murali, S Cantsilieris, ... Science 360 (6393), eaar6343, 2018 | 365 | 2018 |
| Long-read sequence assembly of the gorilla genome D Gordon, J Huddleston, MJP Chaisson, CM Hill, ZN Kronenberg, ... Science 352 (6281), aae0344, 2016 | 346 | 2016 |
| Dense sampling of bird diversity increases power of comparative genomics S Feng, J Stiller, Y Deng, J Armstrong, QI Fang, AH Reeve, D Xie, G Chen, ... Nature 587 (7833), 252-257, 2020 | 304 | 2020 |
| Progressive Cactus is a multiple-genome aligner for the thousand-genome era J Armstrong, G Hickey, M Diekhans, IT Fiddes, AM Novak, A Deran, ... Nature 587 (7833), 246-251, 2020 | 279 | 2020 |
| Whole-genome sequencing reveals host factors underlying critical COVID-19 A Kousathanas, E Pairo-Castineira, K Rawlik, A Stuckey, CA Odhams, ... Nature 607 (7917), 97-103, 2022 | 223 | 2022 |
| A comparative genomics multitool for scientific discovery and conservation Nature 587 (7833), 240-245, 2020 | 221 | 2020 |
| Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci J Lilue, AG Doran, IT Fiddes, M Abrudan, J Armstrong, R Bennett, ... Nature genetics 50 (11), 1574-1583, 2018 | 189 | 2018 |
| Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility WC Warren, RA Harris, M Haukness, IT Fiddes, SC Murali, J Fernandes, ... Science 370 (6523), eabc6617, 2020 | 109 | 2020 |
| Chromosome assembly of large and complex genomes using multiple references M Kolmogorov, J Armstrong, BJ Raney, I Streeter, M Dunn, F Yang, ... Genome research 28 (11), 1720-1732, 2018 | 105 | 2018 |
| Whole-genome alignment and comparative annotation J Armstrong, IT Fiddes, M Diekhans, B Paten Annual review of animal biosciences 7, 41-64, 2019 | 99 | 2019 |
| Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation IT Fiddes, J Armstrong, M Diekhans, S Nachtweide, ZN Kronenberg, ... Genome research 28 (7), 1029-1038, 2018 | 97 | 2018 |
| Evolutionary constraint and innovation across hundreds of placental mammals MJ Christmas, IM Kaplow, DP Genereux, MX Dong, GM Hughes, X Li, ... Science 380 (6643), eabn3943, 2023 | 72 | 2023 |
