Searching journal content for articles similar to Skinner et al. 19 (9): 1630.

Displaying results 1-9 of 9

For checked items

view abstracts
download to citation manager

Select this article
Resource: The PanOryza pangene catalog of Asian cultivated rice
- Bruno Contreras-Moreira,
- Eshan Sharma,
- Shradha Saraf,
- Guy Naamati,
- Parul Gupta,
- Justin Elser,
- Dmytro Chebotarov,
- Kapeel Chougule,
- Zhenyuan Lu,
- Sharon Wei,
- Andrew Olson,
- Ian Tsang,
- Disha Lodha,
- Yong Zhou,
- Zhichao Yu,
- Wen Zhao,
- Jianwei Zhang,
- Sandeep Amberkar,
- Kawinnat Sue-Ob,
- Zhi Sun,
- Maria Martin,
- Kenneth L. McNally,
- Doreen Ware,
- Eric W. Deutsch,
- Dario Copetti,
- Rod A. Wing,
- Pankaj Jaiswal,
- Sarah Dyer,
- and Andrew R. Jones
Genome Res. January 2026 36: 226-238; Published in Advance December 12, 2025, doi:10.1101/gr.280790.125
...variation is suggested within exon 2 in the N22, IR64, and Azucena varieties. Another example is shown in Supplemental Figure S9 that shows the Gramene search result and PanOryza browser (JBrowse) for Os4530.POR.1.pan0035634. The members of this pangene coding for NB-ARC domain-containing proteins...
OPEN ACCESS ARTICLE
Select this article
Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...the N2-derived strain VC2010. Moreover, genetically divergent versions of N2 have arisen over decades of research and hindered reproducibility of C. elegans genetics and genomics. Here we provide a 106.4 Mb gap-free, telomere-to-telomere assembly of C. elegans, generated from CGC1, an isogenic...
OPEN ACCESS ARTICLE
Select this article
Method: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2
- Alexander Zee,
- Dori Z.Q. Deng,
- Matthew Adams,
- Kayla D. Schimke,
- Russell Corbett-Detig,
- Shelbi L. Russell,
- Xuan Zhang,
- Robert J. Schmitz,
- and Christopher Vollmers
Genome Res. November/December 2022 32: 2092-2106; Published in Advance November 9, 2022, doi:10.1101/gr.277031.122
.... (C) Comparisons of R2C2 and Illumina MiSeq read-based gene expression and splice junction usage quantification by STAR and kallisto are shown as scatter plots with marginal distributions (log2 normalized) shown as histograms. (D) Genome browser-style visualization of read alignments to the Actb locus...
Select this article
Resource: dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development
- Xin Huang,
- Xiaohan Tang,
- Xuemei Bai,
- Honglei Li,
- Huan Tao,
- Junting Wang,
- Yaru Li,
- Yu Sun,
- Yang Zheng,
- Xiang Xu,
- Longteng Wang,
- Yang Ding,
- Meisong Lu,
- Pingkun Zhou,
- Xiaochen Bo,
- Hao Li,
- and Hebing Chen
Genome Res. August 2022 32: 1612-1625; Published in Advance August 17, 2022, doi:10.1101/gr.276744.122
...downstream analysis. The expression data and genomic annotations are stored in bedGraph-format files for quick access by JBrowse (version 1.16.6) (https://jbrowse.org/blog/) (Supplemental Fig. S7; Buels et al. 2016).Our study was based on the mm9 reference. To harmonize the reference , the data sets aligned...
OPEN ACCESS ARTICLE
Select this article
Resource: Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV)
- Sanjida H. Rangwala,
- Anatoliy Kuznetsov,
- Victor Ananiev,
- Andrea Asztalos,
- Evgeny Borodin,
- Vladislav Evgeniev,
- Victor Joukov,
- Vadim Lotov,
- Ravinder Pannu,
- Dmitry Rudnev,
- Andrew Shkeda,
- Eric M. Weitz,
- and Valerie A. Schneider
Genome Res. January 2021 31: 159-169; Published in Advance November 25, 2020, doi:10.1101/gr.266932.120
..., Sirotkin K. 2001. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29: 308–311. doi:10.1093/nar/29.1.308 ↵Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. 2009. JBrowse: a next-generation browser. Genome Res 19: 1630–1638. doi:10.1101/gr.094607.109 ↵Tryka KA, Hao L, Sturcke A, Jin Y...
Select this article
Resource: Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis
- Yingshu Li,
- Yongjie Liu,
- Hang Yang,
- Ting Zhang,
- Kiyoshi Naruse,
- and Qiang Tu
Genome Res. June 2020 30: 924-937; Published in Advance June 26, 2020, doi:10.1101/gr.258871.119
...portalTo facilitate the use of these data sets, we built a medaka omics data portal containing three web tools (http://tulab.genetics.ac.cn/medaka_omics/). The first one is the browser implemented using JBrowse (Supplemental Fig. S22A; Buels et al. 2016). With this tool, users could compare gene models...
OPEN ACCESS ARTICLE
Select this article
Resource: Recompleting the Caenorhabditis elegans genome
- Jun Yoshimura,
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Idan Gabdank,
- Lamia Wahba,
- Cheryl L. Smith,
- Mark L. Edgley,
- Ann E. Rougvie,
- Andrew Z. Fire,
- Shinichi Morishita,
- and Erich M. Schwarz
Genome Res. June 2019 29: 1009-1022; Published in Advance May 23, 2019, doi:10.1101/gr.244830.118
...as Supplemental Data File S1). For large-scale structural comparisons of the N2 reference assembly versus our final VC2010 assembly, we used the version of N2 from WormBase release WS220 (Lee et al. 2018). This has the advantage of being a highly used version that is available in the UCSC Genome Browser (where...
OPEN ACCESS ARTICLE
Select this article
Research: A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements
- Stefan Oberlin,
- Alexis Sarazin,
- Clément Chevalier,
- Olivier Voinnet,
- and Arturo Marí-Ordóñez
Genome Res. September 2017 27: 1549-1562; Published in Advance August 7, 2017, doi:10.1101/gr.220723.117
...and transcriptionally active transposons in A. thaliana is illustrated by our comprehensive analysis of the cotranscriptional and translational features of Ty1/Copia elements, a family of young and active retroelements in plant s, and how such features impact their biology. Genome-wide transcript profiling revealed...
Select this article
Perspective: What does our genome encode?
- John A. Stamatoyannopoulos
Genome Res. September 2012 22: 1602-1611; doi:10.1101/gr.146506.112
...by the scale-up to a production phase that saw the expansion of ENCODE annotation efforts to the entire genomic sequence. In a happy and fateful coincidence, the ENCODE scale-up commenced contemporaneously with the introduction of massively parallel ‘‘next-generation’’ sequencing technologies—a development...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Skinner et al. 19 (9): 1630.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: