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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. April 2026 36: 695-712; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...and to associated organs including the liver and pancreas. We used functional genomic approaches to identify highly conserved endodermal cis-regulatory modules (CRMs) functioning across the 400 million years of evolution separating zebrafish and humans. Our analyses suggest that there are few endoderm-specific CRMs...
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Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...Corresponding authors: twang@wustl.edu, gzhao@wustl.eduAbstractFollowing amputation, zebrafish regenerate their injured caudal fin through lineage-restricted reprogramming. Although previous studies have charted various genetic and epigenetic dimensions of this process, the intricate gene regulatory programs...
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Research: Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing
- Wouter Steyaert,
- Lydia Sagath,
- German Demidov,
- Vicente A. Yépez,
- Anna Esteve-Codina,
- Julien Gagneur,
- Kornelia Ellwanger,
- Ronny Derks,
- Marjan Weiss,
- Amber den Ouden,
- Simone van den Heuvel,
- Hilde Swinkels,
- Nick Zomer,
- Marloes Steehouwer,
- Luke O'Gorman,
- Galuh Astuti,
- Kornelia Neveling,
- Rebecca Schüle,
- Jishu Xu,
- Matthis Synofzik,
- Danique Beijer,
- Holger Hengel,
- Ludger Schöls,
- Kristl G. Claeys,
- Jonathan Baets,
- Liedewei Van de Vondel,
- Alessandra Ferlini,
- Rita Selvatici,
- Heba Morsy,
- Marwa Saeed Abd Elmaksoud,
- Volker Straub,
- Juliane Müller,
- Veronica Pini,
- Luke Perry,
- Anna Sarkozy,
- Irina Zaharieva,
- Francesco Muntoni,
- Enrico Bugiardini,
- Kiran Polavarapu,
- Rita Horvath,
- Evan Reid,
- Hanns Lochmüller,
- Marco Spinazzi,
- Marco Savarese,
- Solve-RD DITF-ITHACA, Solve-RD DITF-Euro-NMD, Solve-RD DITF-RND, Solve-RD DITF-EpiCARE,
- Leslie Matalonga,
- Steven Laurie,
- Han G. Brunner,
- Holm Graessner,
- Sergi Beltran,
- Stephan Ossowski,
- Lisenka E.L.M. Vissers,
- Christian Gilissen,
- Alexander Hoischen,
- and on behalf of the Solve-RD consortium
Genome Res. April 2025 35: 755-768; Published in Advance March 26, 2025, doi:10.1101/gr.279414.124
...Unraveling undiagnosed rare disease cases by HiFi long-read sequencing Wouter Steyaert1,36, Lydia Sagath1,36, German Demidov2, Vicente A. Yépez3, Anna Esteve-Codina4,5, Julien Gagneur3,6,7, Kornelia Ellwanger2,8, Ronny Derks1, Marjan Weiss1, Amber den Ouden1, Simone van den Heuvel1, Hilde Swinkels1...
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Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
- Tanner D. Jensen,
- Bohan Ni,
- Chloe M. Reuter,
- John E. Gorzynski,
- Sarah Fazal,
- Devon Bonner,
- Rachel A. Ungar,
- Pagé C. Goddard,
- Archana Raja,
- Euan A. Ashley,
- Jonathan A. Bernstein,
- Stephan Zuchner,
- Undiagnosed Diseases Network,
- Michael D. Greicius,
- Stephen B. Montgomery,
- Michael C. Schatz,
- Matthew T. Wheeler,
- and Alexis Battle
Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
...Tanner D. Jensen1,14, Bohan Ni2,14, Chloe M. Reuter3,4, John E. Gorzynski1,3,4, Sarah Fazal5, Devon Bonner3,6, Rachel A. Ungar1, Pagé C. Goddard1, Archana Raja3,4, Euan A. Ashley3,4, Jonathan A. Bernstein3,7, Stephan Zuchner5, Undiagnosed Diseases Network, Michael D. Greicius8, Stephen B...
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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
....vaquerizas@lms.mrc.ac.ukAbstractThere is considerable interest in understanding the effect of transposable elements (TEs) on embryonic development. Studies in humans and mice are limited by the difficulty of working with mammalian embryos and by the relative scarcity of active TEs in these organisms. The zebrafish is an outstanding model...
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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
...; Modzelewski et al. 2021).Zebrafish is an important model organism for various research areas including development (Kimmel et al. 1995; Lee et al. 2015), human disease (Lieschke and Currie 2007; Kaufman et al. 2016), and regeneration (Gemberling et al. 2013; Lee et al. 2020). Zebrafish TEs have unique...
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Resource: Systematic genome editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9
- Yonghua Sun,
- Bo Zhang,
- Lingfei Luo,
- De-Li Shi,
- Han Wang,
- Zongbin Cui,
- Honghui Huang,
- Ying Cao,
- Xiaodong Shu,
- Wenqing Zhang,
- Jianfeng Zhou,
- Yun Li,
- Jiulin Du,
- Qingshun Zhao,
- Jun Chen,
- Hanbing Zhong,
- Tao P. Zhong,
- Li Li,
- Jing-Wei Xiong,
- Jinrong Peng,
- Wuhan Xiao,
- Jian Zhang,
- Jihua Yao,
- Zhan Yin,
- Xianming Mo,
- Gang Peng,
- Jun Zhu,
- Yan Chen,
- Yong Zhou,
- Dong Liu,
- Weijun Pan,
- Yiyue Zhang,
- Hua Ruan,
- Feng Liu,
- Zuoyan Zhu,
- Anming Meng,
- and The ZAKOC Consortium
Genome Res. January 2020 30: 118-126; Published in Advance December 12, 2019, doi:10.1101/gr.248559.119
..., we discovered that mutants of nearly one in four genes are related to human diseases.Although there exist some differences, the overall tendencies of the sequence or mutagenesis features of the CRISPR/Cas9 target sites are largely comparable with previous publications based on zebrafish large...
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Research: Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
- Charles E. Vejnar,
- Mario Abdel Messih,
- Carter M. Takacs,
- Valeria Yartseva,
- Panos Oikonomou,
- Romain Christiano,
- Marlon Stoeckius,
- Stephanie Lau,
- Miler T. Lee,
- Jean-Denis Beaudoin,
- Damir Musaev,
- Hiba Darwich-Codore,
- Tobias C. Walther,
- Saeed Tavazoie,
- Daniel Cifuentes,
- and Antonio J. Giraldez
Genome Res. July 2019 29: 1100-1114; Published in Advance June 21, 2019, doi:10.1101/gr.245159.118
..., USA; 4Department of Systems Biology, Columbia University, New York, New York 10032, USA; 5Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA; 6New York Genome Center, New York, New York 10013, USA; 7Department of Biological Sciences...
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Method: De novo mutation rates at the single-mutation resolution in a human HBB gene region associated with adaptation and genetic disease
- Daniel Melamed,
- Yuval Nov,
- Assaf Malik,
- Michael B. Yakass,
- Evgeni Bolotin,
- Revital Shemer,
- Edem K. Hiadzi,
- Karl L. Skorecki,
- and Adi Livnat
Genome Res. March 2022 32: 488-498; Published in Advance January 14, 2022, doi:10.1101/gr.276103.121
...(Inoue et al. 2001; Crow et al. 2009; Dumas et al. 2012; Losos 2017; Kratochwil et al. 2019; Kratochwil and Meyer 2019; Lind 2019; Xie et al. 2019), to its contribution to recurrent genetic disease and cancer (Lupski 1998; McClellan and King 2010; Veltman and Brunner 2012; Shendure and Akey 2015).The...
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Method: High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9
- Gaurav K. Varshney,
- Wuhong Pei,
- Matthew C. LaFave,
- Jennifer Idol,
- Lisha Xu,
- Viviana Gallardo,
- Blake Carrington,
- Kevin Bishop,
- MaryPat Jones,
- Mingyu Li,
- Ursula Harper,
- Sunny C. Huang,
- Anupam Prakash,
- Wenbiao Chen,
- Raman Sood,
- Johan Ledin,
- and Shawn M. Burgess
Genome Res. July 2015 25: 1030-1042; Published in Advance June 5, 2015, doi:10.1101/gr.186379.114
.... Phenotypic correlation between human disease loci and zebrafish mutations To get an initial estimate of how often zebrafish can be used to rapidly confirm candidate genes for human diseases, we chose eight genes (Table 3) from a highly curated list of genes that when mutated are known to cause nonsyndromic...
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