| 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 | 540 | 2018 |
| Human-specific NOTCH2NL genes affect notch signaling and cortical neurogenesis IT Fiddes, GA Lodewijk, M Mooring, CM Bosworth, AD Ewing, ... Cell 173 (6), 1356-1369. e22, 2018 | 477 | 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 | 355 | 2023 |
| Computational pan-genomics: status, promises and challenges Briefings in bioinformatics 19 (1), 118-135, 2018 | 331 | 2018 |
| 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 | 299 | 2020 |
| The Human Pangenome Project: a global resource to map genomic diversity T Wang, L Antonacci-Fulton, K Howe, HA Lawson, JK Lucas, AM Phillippy, ... Nature 604 (7906), 437-446, 2022 | 260 | 2022 |
| 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 | 193 | 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 | 180 | 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 | 166 | 2021 |
| StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees Á Novák, I Miklós, R Lyngsø, J Hein Bioinformatics 24 (20), 2403-2404, 2008 | 117 | 2008 |
| Haplotype-aware graph indexes J Sirén, E Garrison, AM Novak, B Paten, R Durbin Bioinformatics 36 (2), 400-407, 2020 | 86 | 2020 |
| 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 | 70 | 2018 |
| A graph-based approach to diploid genome assembly S Garg, M Rautiainen, AM Novak, E Garrison, R Durbin, T Marschall Bioinformatics 34 (13), i105-i114, 2018 | 68 | 2018 |
| 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 | 64 | 2024 |
| Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure JL Herman, CJ Challis, A Novák, J Hein, SC Schmidler Molecular biology and evolution 31 (9), 2251-2266, 2014 | 50 | 2014 |
| 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 | 41 | 2019 |
| BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC R Satija, A Novak, I Miklós, R Lyngsø, J Hein BMC Evolutionary Biology 9, 1-14, 2009 | 32 | 2009 |
| Efficient dynamic variation graphs JM Eizenga, AM Novak, E Kobayashi, F Villani, C Cisar, S Heumos, ... Bioinformatics 36 (21), 5139-5144, 2020 | 31 | 2020 |
| 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 |
| Haplotype-aware pantranscriptome analyses using spliced pangenome graphs JA Sibbesen, JM Eizenga, AM Novak, J Sirén, X Chang, E Garrison, ... Nature Methods 20 (2), 239-247, 2023 | 29 | 2023 |
