| 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 | 1039 | 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 | 406 | 2018 |
| 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 | 334 | 2015 |
| 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 | 330 | 2014 |
| 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 | 147 | 2020 |
| 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 | 129 | 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 | 121 | 2013 |
| 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 | 116 | 2014 |
| Pangenome graphs JM Eizenga, AM Novak, JA Sibbesen, S Heumos, A Ghaffaari, G Hickey, ... Annual review of genomics and human genetics 21, 139-162, 2020 | 107 | 2020 |
| SPR Distance Computation for Unrooted Trees G Hickey, F Dehne, A Rau-Chaplin, C Blouin Evolutionary Bioinformatics 4, EBO. S419, 2008 | 97 | 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 | 87 | 2015 |
| 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 | 63 | 2021 |
| Building a pan-genome reference for a population N Nguyen, G Hickey, DR Zerbino, B Raney, D Earl, J Armstrong, WJ Kent, ... Journal of Computational Biology 22 (5), 387-401, 2015 | 62 | 2015 |
| 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 | 61 | 2018 |
| Genome graphs AM Novak, G Hickey, E Garrison, S Blum, A Connelly, A Dilthey, ... BioRxiv, 101378, 2017 | 55 | 2017 |
| Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling ES Rice, S Kohno, JS John, S Pham, J Howard, LF Lareau, BL O'Connell, ... Genome research 27 (5), 686-696, 2017 | 39 | 2017 |
| Comparative Assembly Hubs: Web Accessible Browsers for Comparative Genomics N Nguyen, G Hickey, BJ Raney, J Armstrong, H Clawson, A Zweig, J Kent, ... Bioinformatics 30 (23), 3293-301, 2014 | 31 | 2014 |
| Sequence variation aware genome references and read mapping with the variation graph toolkit E Garrison, J Sirén, AM Novak, G Hickey, JM Eizenga, ET Dawson, ... BioRxiv, 234856, 2017 | 30 | 2017 |
| A draft human pangenome reference WW Liao, M Asri, J Ebler, D Doerr, M Haukness, G Hickey, S Lu, JK Lucas, ... bioRxiv, 2022.07. 09.499321, 2022 | 29 | 2022 |
| Sequence tube maps: making graph genomes intuitive to commuters W Beyer, AM Novak, G Hickey, J Chan, V Tan, B Paten, DR Zerbino Bioinformatics 35 (24), 5318, 2019 | 26 | 2019 |
