Joshua C Stein
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Explore the profile of Joshua C Stein including associated specialties, affiliations and a list of published articles.
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22
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Recent Articles
1.
Vaughn J, Korani W, Stein J, Edwards J, Peterson D, Simpson S, et al.
PLoS Genet
. 2021 Mar;
17(3):e1009389.
PMID: 33735256
The genetic basis of general plant vigor is of major interest to food producers, yet the trait is recalcitrant to genetic mapping because of the number of loci involved, their...
2.
Ou S, Liu J, Chougule K, Fungtammasan A, Seetharam A, Stein J, et al.
Nat Commun
. 2020 May;
11(1):2288.
PMID: 32385271
Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for...
3.
Stein J, Yu Y, Copetti D, Zwickl D, Zhang L, Zhang C, et al.
Nat Genet
. 2018 Oct;
50(11):1618.
PMID: 30291357
This article was not made open access when initially published online, which was corrected before print publication. In addition, ORCID links were missing for 12 authors and have been added...
4.
Chougule K, Wang L, Stein J, Wang X, Devisetty U, Klein R, et al.
Curr Protoc Bioinformatics
. 2018 Sep;
63(1):e53.
PMID: 30168903
RNA-seq is a vital method for understanding gene structure and expression patterns. Typical RNA-seq analysis protocols use sequencing reads of length 50 to 150 nucleotides for alignment to the reference...
5.
Springer N, Anderson S, Andorf C, Ahern K, Bai F, Barad O, et al.
Nat Genet
. 2018 Aug;
50(9):1282-1288.
PMID: 30061736
The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a...
6.
Sun S, Zhou Y, Chen J, Shi J, Zhao H, Zhao H, et al.
Nat Genet
. 2018 Aug;
50(9):1289-1295.
PMID: 30061735
Maize is an important crop with a high level of genome diversity and heterosis. The genome sequence of a typical female line, B73, was previously released. Here, we report a...
7.
Stein J, Yu Y, Copetti D, Zwickl D, Zhang L, Zhang C, et al.
Nat Genet
. 2018 Jan;
50(2):285-296.
PMID: 29358651
The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning...
8.
Tello-Ruiz M, Naithani S, Stein J, Gupta P, Campbell M, Olson A, et al.
Nucleic Acids Res
. 2017 Nov;
46(D1):D1181-D1189.
PMID: 29165610
Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most...
9.
Jiao Y, Peluso P, Shi J, Liang T, Stitzer M, Wang B, et al.
Nature
. 2017 Jun;
546(7659):524-527.
PMID: 28605751
Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research...
10.
Wang B, Tseng E, Regulski M, Clark T, Hon T, Jiao Y, et al.
Nat Commun
. 2016 Jun;
7:11708.
PMID: 27339440
Zea mays is an important genetic model for elucidating transcriptional networks. Uncertainties about the complete structure of mRNA transcripts limit the progress of research in this system. Here, using single-molecule...