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Liftoff: accurate mapping of gene annotations A Shumate, SL Salzberg Bioinformatics 37 (12), 1639-1643, 2021 | 341 | 2021 |
CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise M Pertea, A Shumate, G Pertea, A Varabyou, FP Breitwieser, YC Chang, ... Genome biology 19, 1-14, 2018 | 295 | 2018 |
A complete reference genome improves analysis of human genetic variation S Aganezov, SM Yan, DC Soto, M Kirsche, S Zarate, P Avdeyev, ... Science 376 (6588), eabl3533, 2022 | 200 | 2022 |
Epigenetic patterns in a complete human genome A Gershman, MEG Sauria, X Guitart, MR Vollger, PW Hook, SJ Hoyt, ... Science 376 (6588), eabj5089, 2022 | 166 | 2022 |
Curated variation benchmarks for challenging medically relevant autosomal genes J Wagner, ND Olson, L Harris, J McDaniel, H Cheng, A Fungtammasan, ... Nature biotechnology 40 (5), 672-680, 2022 | 121 | 2022 |
The complete sequence of a human Y chromosome A Rhie, S Nurk, M Cechova, SJ Hoyt, DJ Taylor, N Altemose, PW Hook, ... Nature 621 (7978), 344-354, 2023 | 110 | 2023 |
Improved transcriptome assembly using a hybrid of long and short reads with StringTie A Shumate, B Wong, G Pertea, M Pertea PLoS computational biology 18 (6), e1009730, 2022 | 109 | 2022 |
Semi-automated assembly of high-quality diploid human reference genomes ED Jarvis, G Formenti, A Rhie, A Guarracino, C Yang, J Wood, A Tracey, ... Nature 611 (7936), 519-531, 2022 | 104 | 2022 |
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies AM Mc Cartney, K Shafin, M Alonge, AV Bzikadze, G Formenti, ... Nature methods 19 (6), 687-695, 2022 | 60 | 2022 |
Assembly and annotation of an Ashkenazi human reference genome A Shumate, AV Zimin, RM Sherman, D Puiu, JM Wagner, ND Olson, ... Genome biology 21, 1-18, 2020 | 52 | 2020 |
Chromosome-scale assembly of the bread wheat genome reveals thousands of additional gene copies M Alonge, A Shumate, D Puiu, AV Zimin, SL Salzberg Genetics 216 (2), 599-608, 2020 | 45 | 2020 |
CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure A Varabyou, MJ Sommer, B Erdogdu, I Shinder, I Minkin, KH Chao, S Park, ... Genome biology 24 (1), 249, 2023 | 11 | 2023 |
A reference-quality, fully annotated genome from a Puerto Rican individual AV Zimin, A Shumate, I Shinder, J Heinz, D Puiu, M Pertea, SL Salzberg Genetics 220 (2), iyab227, 2022 | 9 | 2022 |
LiftoffTools: a toolkit for comparing gene annotations mapped between genome assemblies A Shumate, S Salzberg F1000Research 11, 1230, 2022 | 4 | 2022 |
A complete human reference genome improves variant calling for population and clinical genomics S Aganezov, SM Yan, DC Soto, M Kirsche, S Zarate, P Avdeyev, ... bioRxiv (to appear), 2021 | 4 | 2021 |
The genome of the American groundhog, Marmota monax D Puiu, A Zimin, A Shumate, Y Ge, J Qiu, M Bhaskaran, SL Salzberg F1000Research 9, 2020 | 3 | 2020 |
The Development and Application of Computational Methods for Genome Annotation A Shumate Johns Hopkins University, 2022 | 1 | 2022 |
A complete reference genome improves long-read analysis of human genetic variation S Aganezov, SM Yan, DC Soto, M Kirsche, S Zarate, P Avdeyev, ... COMPUTATIONAL METHODS FOR STRUCTURAL VARIATION ANALYSIS IN POPULATIONS, 72, 2022 | | 2022 |
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