| 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 | 1009 | 2017 |
| 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 | 527 | 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 | 470 | 2018 |
| Computational pan-genomics: status, promises and challenges Briefings in bioinformatics 19 (1), 118-135, 2018 | 327 | 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 | 312 | 2023 |
| Genome graphs and the evolution of genome inference B Paten, AM Novak, JM Eizenga, E Garrison Genome research 27 (5), 665-676, 2017 | 310 | 2017 |
| 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 | 280 | 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 | 243 | 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 | 181 | 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 | 177 | 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 | 176* | 2021 |
| Haplotype-aware graph indexes J Sirén, E Garrison, AM Novak, B Paten, R Durbin Bioinformatics 36 (2), 400-407, 2020 | 86 | 2020 |
| TumorMap: exploring the molecular similarities of cancer samples in an interactive portal Y Newton, AM Novak, T Swatloski, DC McColl, S Chopra, K Graim, ... Cancer research 77 (21), e111-e114, 2017 | 77 | 2017 |
| 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 | 69 | 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 |
| A graph extension of the positional Burrows–Wheeler transform and its applications AM Novak, E Garrison, B Paten Algorithms for Molecular Biology 12, 1-12, 2017 | 62 | 2017 |
| Genome graphs AM Novak, G Hickey, E Garrison, S Blum, A Connelly, A Dilthey, ... BioRxiv, 101378, 2017 | 55 | 2017 |
| Mapping to a reference genome structure B Paten, A Novak, D Haussler arXiv preprint arXiv:1404.5010, 2014 | 49 | 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 | 40 | 2019 |
| The NIH BD2K center for big data in translational genomics B Paten, M Diekhans, BJ Druker, S Friend, J Guinney, N Gassner, ... Journal of the American Medical Informatics Association 22 (6), 1143-1147, 2015 | 37 | 2015 |
Benedict PatenAssociate Professor; Associate Director, UC Santa Cruz Genomics Institute, University of CaliforniaVerified email at ucsc.edu
