Searching journal content for articles similar to Nudelman et al. 28 (9): 1415.

Displaying results 1-10 of 21

For checked items

view abstracts
download to citation manager

Select this article
Resource: Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish
- Alice S. Naftaly,
- Shana Pau,
- and Michael A. White
Genome Res. August 2021 31: 1486-1497; Published in Advance June 15, 2021, doi:10.1101/gr.274282.120
...al. 2019). Long-read RNA sequencing has refined existing gene annotations as well as characterized pervasive alternative splicing among organs (Abdel-Ghany et al. 2016; Wang et al. 2016a; Kuo et al. 2017; Li et al. 2018; Zhang et al. 2019).Although transcriptome complexity has been increasingly...
Select this article
Method: Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing
- Charles Cole,
- Ashley Byrne,
- Matthew Adams,
- Roger Volden,
- and Christopher Vollmers
Genome Res. April 2020 30: 589-601; Published in Advance April 20, 2020, doi:10.1101/gr.257188.119
...between them. Although this suggests that R2C2 captures the transcriptome in a quantitative manner, it is not the focus of this analysis as the strength of long-read sequencing like R2C2 is not gene-level but instead isoform-level transcriptome analysis.Isoform identification and evaluationTo identify...
Select this article
Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...overall contiguity metrics to other long-read assembled teleost s with a scaffold number and N50 length of 68–102 and 30–32 Mb, respectively (Table 1). All 24 chromosomes were assembled with a 0.4%–0.8% range of unassigned sequences. We found few ordering discrepancies and show significant chromosome...
Select this article
Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...–TE transcripts is technically challenging, but long-read transcriptome sequencing will ease many of these difficulties and is therefore a promising avenue for future studies.Using bulk and single-cell RNA-seq to untangle temporal and lineage-specific patterns of TE expression, we observe broadly distinct...
OPEN ACCESS ARTICLE
Select this article
Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...analysis of zebrafish TEs in the context of gene regulation is lacking. Here, we systematically investigate the epigenomic and transcriptomic landscape of TEs across 11 adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory...
OPEN ACCESS ARTICLE
Select this article
Method: High-confidence coding and noncoding transcriptome maps
- Bo-Hyun You,
- Sang-Ho Yoon,
- and Jin-Wu Nam
Genome Res. June 2017 27: 1050-1062; Published in Advance April 10, 2017, doi:10.1101/gr.214288.116
...Table S4). To examine their quality, all annotations were compared to those of RefSeq, GENCODE (manual), GENCODE (automatic), Pacific Biosciences (PacBio) long read assembly, and MiTranscriptome in terms of the number of full-length independent transcripts. Although BIGTranscriptome reconstructed fewer...
OPEN ACCESS ARTICLE
Select this article
Resource: GENCODE: The reference human genome annotation for The ENCODE Project
- Jennifer Harrow,
- Adam Frankish,
- Jose M. Gonzalez,
- Electra Tapanari,
- Mark Diekhans,
- Felix Kokocinski,
- Bronwen L. Aken,
- Daniel Barrell,
- Amonida Zadissa,
- Stephen Searle,
- If Barnes,
- Alexandra Bignell,
- Veronika Boychenko,
- Toby Hunt,
- Mike Kay,
- Gaurab Mukherjee,
- Jeena Rajan,
- Gloria Despacio-Reyes,
- Gary Saunders,
- Charles Steward,
- Rachel Harte,
- Michael Lin,
- Cédric Howald,
- Andrea Tanzer,
- Thomas Derrien,
- Jacqueline Chrast,
- Nathalie Walters,
- Suganthi Balasubramanian,
- Baikang Pei,
- Michael Tress,
- Jose Manuel Rodriguez,
- Iakes Ezkurdia,
- Jeltje van Baren,
- Michael Brent,
- David Haussler,
- Manolis Kellis,
- Alfonso Valencia,
- Alexandre Reymond,
- Mark Gerstein,
- Roderic Guigó,
- and Tim J. Hubbard
Genome Res. September 2012 22: 1760-1774; doi:10.1101/gr.135350.111
...(Metzker 2010) have had automatic gene annotation applied to them, whereas high-quality finished s such as the human (InternationalHumanGenomeSequencingConsortium2004), mouse (Church et al. 2009), and zebrafish (Becker and Rinkwitz 2011) have manual annotation projects associated with them. Publicly...
OPEN ACCESS ARTICLE
Select this article
Research: Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing
- Fernando H. Biase,
- Xiaoyi Cao,
- and Sheng Zhong
Genome Res. November 2014 24: 1787-1796; Published in Advance August 5, 2014, doi:10.1101/gr.177725.114
...cells composed of nine 1-cell (zygote), 10midstage 2-cell, and five 4-cell embryos (Fig. 1A). The generation of data from every sister blastomere turned out indispensable for testing the hypotheses above.We deeply sequenced each library to produce on average 37.9 million 100-base long reads (Fig. 1B...
Select this article
Resource: High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration
- Zihe Li,
- Ziyu Xu,
- Lei Zhu,
- Tao Qin,
- Jinrui Ma,
- Zhanying Feng,
- Huishan Yue,
- Qing Guan,
- Botong Zhou,
- Ge Han,
- Guokun Zhang,
- Chunyi Li,
- Shuaijun Jia,
- Qiang Qiu,
- Dingjun Hao,
- Yong Wang,
- and Wen Wang
Genome Res. January 2025 35: 188-201; Published in Advance November 14, 2024, doi:10.1101/gr.279448.124
...in previous annotations owing to the splitting strategy. Finally, by integrating short-read and long-read transcriptomic data, we annotated 5′ UTR for 14,979 genes and 3′ UTR for 15,760 genes.By utilizing our assembly and annotation to reanalyze previous single-cell data, we found a substantial increase...
OPEN ACCESS ARTICLE
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
...-quality sequence and a variety of genetic tools are available for this model organism. However, existing annotation is still rudimentary, as it was mainly based on computational prediction and short-read RNA-seq data. Here we report a dynamic transcriptome landscape of medaka embryogenesis profiled by long-read...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Nudelman et al. 28 (9): 1415.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: