| 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 | 1100 | 2015 |
| Variation graph toolkit improves read mapping by representing genetic variation in the reference E Garrison, J Sirén, AM Novak, G Hickey, JM Eizenga, ET Dawson, ... Nature biotechnology 36 (9), 875-879, 2018 | 642 | 2018 |
| A draft human pangenome reference WW Liao, M Asri, J Ebler, D Doerr, M Haukness, G Hickey, S Lu, JK Lucas, ... Nature 617 (7960), 312-324, 2023 | 602 | 2023 |
| 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 | 418 | 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 | 384 | 2014 |
| The Genome 10K Project: A Way Forward KP Koepfli, B Paten, the Genome 10K Community of Scientists, ... Annual Review of Animal Biosciences 3, 57-111, 2015 | 374 | 2015 |
| Pangenome graphs JM Eizenga, AM Novak, JA Sibbesen, S Heumos, A Ghaffaari, G Hickey, ... Annual review of genomics and human genetics 21 (1), 139-162, 2020 | 247 | 2020 |
| Pangenomics enables genotyping of known structural variants in 5202 diverse genomes J Sirén, J Monlong, X Chang, AM Novak, JM Eizenga, C Markello, ... Science 374 (6574), abg8871, 2021 | 233 | 2021 |
| Genotyping structural variants in pangenome graphs using the vg toolkit G Hickey, D Heller, J Monlong, JA Sibbesen, J Sirén, J Eizenga, ... Genome biology 21, 1-17, 2020 | 231 | 2020 |
| HAL: a hierarchical format for storing and analyzing multiple genome alignments G Hickey, B Paten, D Earl, D Zerbino, D Haussler Bioinformatics 29 (10), 1341-1342, 2013 | 205 | 2013 |
| 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 | 154 | 2023 |
| Pangenome graph construction from genome alignments with Minigraph-Cactus G Hickey, J Monlong, J Ebler, AM Novak, JM Eizenga, Y Gao, T Marschall, ... Nature biotechnology 42 (4), 663-673, 2024 | 141 | 2024 |
| Alignathon: a competitive assessment of whole-genome alignment methods D Earl, N Nguyen, G Hickey, RS Harris, S Fitzgerald, K Beal, I Seledtsov, ... Genome research 24 (12), 2077-2089, 2014 | 131 | 2014 |
| SPR Distance Computation for Unrooted Trees G Hickey, F Dehne, A Rau-Chaplin, C Blouin Evolutionary Bioinformatics 4, EBO. S419, 2008 | 112 | 2008 |
| A call for benchmarking transposable element annotation methods DR Hoen, G Hickey, G Bourque, J Casacuberta, R Cordaux, C Feschotte, ... Mobile DNA 6, 1-9, 2015 | 101 | 2015 |
| The UCSC genome browser database: 2024 update BJ Raney, GP Barber, A Benet-Pagès, J Casper, H Clawson, MS Cline, ... Nucleic Acids Research 52 (D1), D1082-D1088, 2024 | 99 | 2024 |
| Integrating gene annotation with orthology inference at scale BM Kirilenko, C Munegowda, E Osipova, D Jebb, V Sharma, M Blumer, ... Science 380 (6643), eabn3107, 2023 | 87 | 2023 |
| A genomic timescale for placental mammal evolution NM Foley, VC Mason, AJ Harris, KR Bredemeyer, J Damas, HA Lewin, ... Science 380 (6643), eabl8189, 2023 | 82 | 2023 |
| Superbubbles, ultrabubbles, and cacti B Paten, JM Eizenga, YM Rosen, AM Novak, E Garrison, G Hickey Journal of Computational Biology 25 (7), 649-663, 2018 | 80 | 2018 |
| Leveraging base-pair mammalian constraint to understand genetic variation and human disease PF Sullivan, JRS Meadows, S Gazal, BDN Phan, X Li, DP Genereux, ... Science 380 (6643), eabn2937, 2023 | 73 | 2023 |
