Searching journal content for articles similar to Broughton et al. 11 (11): 1958.

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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cisregulatory modules acting during vertebrate organogenesis Daniela M. Riley,1,7 Randa Elsayed,1,7 Mark D. Walsh,2,7 Simaran Johal,2 Ying Lin,3,4 Harry Walton,1 Till Bretschneider,5 Sascha Ott,1...
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Resource: A single-cell transcriptome atlas of the maturing zebrafish telencephalon
- Shristi Pandey,
- Anna J. Moyer,
- and Summer B. Thyme
Genome Res. April 2023 33: 658-671; Published in Advance April 18, 2023, doi:10.1101/gr.277278.122
...Bioinformatics, Genentech, South San Francisco, CA 94080, USA Corresponding authors: p.shristi@gmail.com, sthyme@gmail.comAbstractThe zebrafish telencephalon is composed of highly specialized subregions that regulate complex behaviors such as learning, memory, and social interactions. The transcriptional...
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Research: The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores
- Yulong Liu,
- Gang Zhai,
- Jingzhi Su,
- Yulong Gong,
- Bingyuan Yang,
- Qisheng Lu,
- Longwei Xi,
- Yutong Zheng,
- Jingyue Cao,
- Haokun Liu,
- Junyan Jin,
- Zhimin Zhang,
- Yunxia Yang,
- Xiaoming Zhu,
- Zhongwei Wang,
- Gaorui Gong,
- Jie Mei,
- Zhan Yin,
- Rodolphe E. Gozlan,
- Shouqi Xie,
- and Dong Han
Genome Res. July 2024 34: 981-996; Published in Advance August 9, 2024, doi:10.1101/gr.278476.123
...catfish (Pelteobagrus fulvidraco), channel catfish (Ictalurus punctatus), zebrafish (Danio rerio), grass carp (Ctenopharyngodon idellus), and blunt snout bream (Megalobrama amblycephala). (F) Phylogenetic tree and time tree showing the expansion and contraction of gene families in 13 species ranging from...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
..., possibly driven by distinct and underappreciated factors.The comparative atlas enhances teleost gene and annotationsFinally, we investigated how the comparative atlas may improve crucial resources for fish evolutionary, ecological, and functional genomics. The Zebrafish Information Network (ZFIN) provides...
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LETTER: Genetic variation in the zebrafish
- Victor Guryev,
- Marco J. Koudijs,
- Eugene Berezikov,
- Stephen L. Johnson,
- Ronald H.A. Plasterk,
- Fredericus J.M. van Eeden,
- and Edwin Cuppen
Genome Res. April 2006 16: 491-497; Published in Advance March 13, 2006, doi:10.1101/gr.4791006
...of Molecular and Cell Biology, Singapore). We used Ensembl trace archive (http://trace. ensembl.org) as a source of genomic traces. EST and mRNA sequences were masked for zebrafish-specific repeats, low-complexity regions, and zebrafish mitochondrial DNA by using RepeatMasker. Local SSAHA searches were...
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Research: Differential retention and divergent resolution of duplicate genes following whole-genome duplication
- Casey L. McGrath,
- Jean-Francois Gout,
- Parul Johri,
- Thomas G. Doak,
- and Michael Lynch
Genome Res. October 2014 24: 1665-1675; Published in Advance August 1, 2014, doi:10.1101/gr.173740.114
...), Danio rerio (Postlethwait et al. 2000), and Arabidopsis thaliana (Simillion et al. 2002). There is increasing support for the hypothesis that two WGDs preceded the radiation of the vertebrate lineage (Panopoulou and Poustka 2005; Hughes and Liberles 2008; Putnam et al. 2008; Decatur et al. 2013...
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ARTICLE: Zebrafish Comparative Genomics and the Origins of Vertebrate Chromosomes
- John H. Postlethwait,
- Ian G. Woods,
- Phuong Ngo-Hazelett,
- Yi-Lin Yan,
- Peter D. Kelly,
- Felicia Chu,
- Hui Huang,
- Alicia Hill-Force,
- and William S. Talbot
Genome Res. December 1, 2000 10: 1890-1902; doi:10.1101/gr.164800
...). It will be revealing to examine these gene maps in light of a fully sequenced human . METHODS Sequences of Danio rerio genes and ESTs (M. Clark and S. Johnson, Washington University Zebrafish Genome Resources Project; http://zfish.wustl.edu ) were obtained from NCBI, and primers were designed as described by Kelly et...
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Letter: Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates
- Karin S. Kassahn,
- Vinh T. Dang,
- Simon J. Wilkins,
- Andrew C. Perkins,
- and Mark A. Ragan
Genome Res. August 2009 19: 1404-1418; Published in Advance May 13, 2009, doi:10.1101/gr.086827.108
...WGD in the pufferfishes Tetraodon nigroviridis and Takifugu rubripes may be as low as 1%–5% (Aparicio et al. 2002; Jaillon et al. 2004), although there has been debate regarding these estimates (Brunet et al. 2006). Analysis of individual gene families in the zebrafish Danio rerio suggested that up...
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RESOURCE: 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
- Webb Miller,
- Kate Rosenbloom,
- Ross C. Hardison,
- Minmei Hou,
- James Taylor,
- Brian Raney,
- Richard Burhans,
- David C. King,
- Robert Baertsch,
- Daniel Blankenberg,
- Sergei L. Kosakovsky Pond,
- Anton Nekrutenko,
- Belinda Giardine,
- Robert S. Harris,
- Svitlana Tyekucheva,
- Mark Diekhans,
- Thomas H. Pringle,
- William J. Murphy,
- Arthur Lesk,
- George M. Weinstock,
- Kerstin Lindblad-Toh,
- Richard A. Gibbs,
- Eric S. Lander,
- Adam Siepel,
- David Haussler,
- and W. James Kent
Genome Res. December 2007 17: 1797-1808; Published in Advance November 5, 2007, doi:10.1101/gr.6761107
...Mods) ( Blanchette et al. 2006 ) and a strong signal for alignment patterns that discriminate between regulatory regions and neutral DNA (high RP; see Methods) ( Taylor et al. 2006 ). We also included a collection of 3900 putative transcriptional regulatory regions (pTRRs) discovered by chromatin immunoprecipitation...
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RESOURCE: Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation
- Melody S. Clark,
- Yvonne J.K. Edwards,
- Dan Peterson,
- Sandra W. Clifton,
- Amanda J. Thompson,
- Masahide Sasaki,
- Yutaka Suzuki,
- Kiyoshi Kikuchi,
- Shugo Watabe,
- Koichi Kawakami,
- Sumio Sugano,
- Greg Elgar,
- and Stephen L. Johnson
Genome Res. December 2003 13: 2747-2753; Published in Advance January 1, 2003, doi:10.1101/gr.1691503
...), and zebrafish ( http://www.ensembl.org/Danio_rerio ) which are completed or well underway. Others are expected to follow and include Xenopus , sea urchin, and chicken. The Fugu draft sequence indicates a total size of 365 Mb ( Aparicio et al. 2002 ). This draft sequence represents 95% coverage...

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