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Alaina Shumate, Ph.D.
Alaina Shumate, Ph.D.
Assistant Principal Investigator of Bioinformatics at NBACC
No verified email
Title
Cited by
Cited by
Year
The complete sequence of a human genome
S Nurk, S Koren, A Rhie, M Rautiainen, AV Bzikadze, A Mikheenko, ...
Science 376 (6588), 44-53, 2022
17662022
Liftoff: accurate mapping of gene annotations
A Shumate, SL Salzberg
Bioinformatics 37 (12), 1639-1643, 2021
3412021
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
2952018
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
2002022
Epigenetic patterns in a complete human genome
A Gershman, MEG Sauria, X Guitart, MR Vollger, PW Hook, SJ Hoyt, ...
Science 376 (6588), eabj5089, 2022
1662022
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
1212022
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
1102023
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
1092022
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
1042022
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
602022
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
522020
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
452020
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
112023
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
92022
LiftoffTools: a toolkit for comparing gene annotations mapped between genome assemblies
A Shumate, S Salzberg
F1000Research 11, 1230, 2022
42022
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
42021
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
32020
The Development and Application of Computational Methods for Genome Annotation
A Shumate
Johns Hopkins University, 2022
12022
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
GIAB Benchmarking of HG002 Assemblies from HPRC Year 1 Bakeoff
W Harvey, M Haukness, A Hastie, P Ebert, J Wood, M Kirsche, ...
National Institute of Standards and Technology (NIST), 2022
2022
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