| 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 | 328 | 2018 |
| Mapping DNA methylation with high-throughput nanopore sequencing AC Rand, M Jain, JM Eizenga, A Musselman-Brown, HE Olsen, M Akeson, ... Nature methods 14 (4), 411-413, 2017 | 308 | 2017 |
| Genome graphs and the evolution of genome inference B Paten, AM Novak, JM Eizenga, E Garrison Genome research 27 (5), 665-676, 2017 | 232 | 2017 |
| 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), 1-17, 2020 | 97 | 2020 |
| Pangenome graphs JM Eizenga, AM Novak, JA Sibbesen, S Heumos, A Ghaffaari, G Hickey, ... Annual review of genomics and human genetics 21, 139, 2020 | 56 | 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 | 54 | 2018 |
| Genome graphs AM Novak, G Hickey, E Garrison, S Blum, A Connelly, A Dilthey, ... BioRxiv, 101378, 2017 | 54 | 2017 |
| 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 | 33 | 2017 |
| A phylogenetic approach for haplotype analysis of sequence data from complex mitochondrial mixtures SH Vohr, R Gordon, JM Eizenga, HA Erlich, CD Calloway, RE Green Forensic Science International: Genetics 30, 93-105, 2017 | 32 | 2017 |
| Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads K Shafin, T Pesout, PC Chang, M Nattestad, A Kolesnikov, S Goel, G Baid, ... Nature methods 18 (11), 1322-1332, 2021 | 28 | 2021 |
| Aerosol microbiome over the Mediterranean Sea diversity and abundance E Mescioglu, E Rahav, N Belkin, P Xian, JM Eizenga, A Vichik, B Herut, ... Atmosphere 10 (8), 440, 2019 | 22 | 2019 |
| Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks K Shafin, T Pesout, PC Chang, M Nattestad, A Kolesnikov, S Goel, G Baid, ... BioRxiv, 2021 | 20 | 2021 |
| Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkit J Sirén, J Monlong, X Chang, AM Novak, JM Eizenga, C Markello, ... Biorxiv, 2020.12. 04.412486, 2021 | 20 | 2021 |
| 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 | 19 | 2021 |
| Efficient dynamic variation graphs JM Eizenga, AM Novak, E Kobayashi, F Villani, C Cisar, S Heumos, ... Bioinformatics 36 (21), 5139-5144, 2021 | 14 | 2021 |
| Modelling haplotypes with respect to reference cohort variation graphs Y Rosen, J Eizenga, B Paten Bioinformatics 33 (14), i118-i123, 2017 | 11 | 2017 |
| A strategy for building and using a human reference pangenome B Llamas, G Narzisi, V Schneider, PA Audano, E Biederstedt, L Blauvelt, ... F1000Research 8, 2019 | 10 | 2019 |
| Cytosine variant calling with high-throughput nanopore sequencing AC Rand, M Jain, J Eizenga, A Musselman-Brown, HE Olsen, M Akeson, ... bioRxiv, 047134, 2016 | 10 | 2016 |
| Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii DT Schultz, JM Eizenga, RB Corbett-Detig, WR Francis, LM Christianson, ... PeerJ 8, e8356, 2020 | 9 | 2020 |
| Genome graphs. bioRxiv AM Novak, G Hickey, E Garrison, S Blum, A Connelly, A Dilthey, ... Publisher: Cold Spring Harbor Laboratory Section: New Results). https://www …, 2017 | 9 | 2017 |
Benedict PatenAssociate Professor; Associate Director, UC Santa Cruz Genomics Institute, University of CaliforniaVerified email at ucsc.edu
