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Jordan M Eizenga
Jordan M Eizenga
Postdoctoral Researcher, Genomics Institute, University of California Santa Cruz
Dirección de correo verificada de ucsc.edu
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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
4762018
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
4112017
Genome graphs and the evolution of genome inference
B Paten, AM Novak, JM Eizenga, E Garrison
Genome research 27 (5), 665-676, 2017
2952017
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
1592020
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
1532023
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
1502020
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
1182021
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
1162021
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
642018
Genome graphs
AM Novak, G Hickey, E Garrison, S Blum, A Connelly, A Dilthey, ...
BioRxiv, 101378, 2017
542017
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
442017
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, 2021.03. 04.433952, 2021
302021
Efficient dynamic variation graphs
JM Eizenga, AM Novak, E Kobayashi, F Villani, C Cisar, S Heumos, ...
Bioinformatics 36 (21), 5139-5144, 2020
302020
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
292017
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
262019
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, 2020
242020
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, 1-11, 2023
222023
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
222023
Optimal gap-affine alignment in O(s) space
S Marco-Sola, JM Eizenga, A Guarracino, B Paten, E Garrison, M Moreto
Bioinformatics 39 (2), btad074, 2023
172023
Gaps and complex structurally variant loci in phased genome assemblies
D Porubsky, MR Vollger, WT Harvey, AN Rozanski, P Ebert, G Hickey, ...
Genome Research 33 (4), 496-510, 2023
142023
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