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Method: Large-scale identification of chemically induced mutations in Drosophila melanogaster
- Nele A. Haelterman,
- Lichun Jiang,
- Yumei Li,
- Vafa Bayat,
- Hector Sandoval,
- Berrak Ugur,
- Kai Li Tan,
- Ke Zhang,
- Danqing Bei,
- Bo Xiong,
- Wu-Lin Charng,
- Theodore Busby,
- Adeel Jawaid,
- Gabriela David,
- Manish Jaiswal,
- Koen J.T. Venken,
- Shinya Yamamoto,
- Rui Chen,
- and Hugo J. Bellen
Genome Res. October 2014 24: 1707-1718; Published in Advance September 25, 2014, doi:10.1101/gr.174615.114
...Large-scale identification of chemically induced mutations in Drosophila melanogaster Nele A. Haelterman 1 , Lichun Jiang 2 , 3 , Yumei Li 2 , 3 , Vafa Bayat 1 , 4 , Hector Sandoval 2 , Berrak Ugur 1...
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Methods: High-throughput functional screen of mouse gastrula cDNA libraries reveals new components of endoderm and mesoderm specification
- Eric Chiao,
- Jeff Leonard,
- Kari Dickinson,
- and Julie C. Baker
Genome Res. January 2005 15: 44-53; doi:10.1101/gr.2993405
..., these approaches are resource intensive, time consuming, and primarily uncover loss-of-function mutations. Important genes in functionally redundant pathways are difficult to identify, as are groups of molecules acting in concert. Recently, a large-scale in situ hybridization analysis of cDNA library clones...
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Methods: Efficient Target-Selected Mutagenesis in Zebrafish
- Erno Wienholds,
- Freek van Eeden,
- Marit Kosters,
- Josine Mudde,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. December 2003 13: 2700-2707; Published in Advance January 1, 2003, doi:10.1101/gr.1725103
...zebrafish embryos. Mol. Mar. Biol. Biotechnol. 4 : 193 -199. ↵ Till, B.J., Reynolds, S.H., Greene, E.A., Codomo, C.A., Enns, L.C., Johnson, J.E., Burtner, C., Odden, A.R., Young, K., Taylor, N.E., et al. 2003 . Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res. 13...
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Resource: Genome-scale targeted mutagenesis in Brassica napus using a pooled CRISPR library
- Jianjie He,
- Kai Zhang,
- Shuxiang Yan,
- Mi Tang,
- Weixian Zhou,
- Yongtai Yin,
- Kang Chen,
- Chunyu Zhang,
- and Maoteng Li
Genome Res. May 2023 33: 798-809; Published in Advance June 8, 2023, doi:10.1101/gr.277650.123
...@mail.hzau.edu.cn, limaoteng426@hust.edu.cnAbstractThe recently constructed mutant libraries of diploid crops by the CRISPR-Cas9 system have provided abundant resources for functional genomics and crop breeding. However, because of the complexity, it is a big challenge to accomplish large-scale targeted mutagenesis...
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Resource: An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis
- Guanjue Xiang,
- Cheryl A. Keller,
- Elisabeth Heuston,
- Belinda M. Giardine,
- Lin An,
- Alexander Q. Wixom,
- Amber Miller,
- April Cockburn,
- Michael E.G. Sauria,
- Kathryn Weaver,
- Jens Lichtenberg,
- Berthold Göttgens,
- Qunhua Li,
- David Bodine,
- Shaun Mahony,
- James Taylor,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- Yong Cheng,
- Feng Yue,
- Jim Hughes,
- Douglas R. Higgs,
- Yu Zhang,
- and Ross C. Hardison
Genome Res. March 2020 30: 472-484; Published in Advance March 4, 2020, doi:10.1101/gr.255760.119
...is to integrate the deep and diverse data sets (Ernst and Kellis 2010, 2012; Hoffman et al. 2012, 2013; Zhou and Troyanskaya 2015; Greenside et al. 2018; Lee et al. 2018; Ludwig et al. 2019). An effective integration will produce simplified representations of the data that facilitate discoveries and lead...
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Research: Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery
- Xiuli Bi,
- Ying-Juan Cheng,
- Bo Hu,
- Xiaoli Ma,
- Rui Wu,
- Jia-Wei Wang,
- and Chang Liu
Genome Res. July 2017 27: 1162-1173; Published in Advance April 6, 2017, doi:10.1101/gr.215186.116
...-C experiments (Feng et al. 2014b; Grob et al. 2014;Wang et al. 2015). The Hi-Cmethod combines chromatin conformation capture (3C) and high-throughput sequencing to generate a comprehensive view of how chromatin is folded (Lieberman-Aiden et al. 2009). Due to the nature of this method, the Hi-C data only...
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Resource: The million mutation project: A new approach to genetics in Caenorhabditis elegans
- Owen Thompson,
- Mark Edgley,
- Pnina Strasbourger,
- Stephane Flibotte,
- Brent Ewing,
- Ryan Adair,
- Vinci Au,
- Iasha Chaudhry,
- Lisa Fernando,
- Harald Hutter,
- Armelle Kieffer,
- Joanne Lau,
- Norris Lee,
- Angela Miller,
- Greta Raymant,
- Bin Shen,
- Jay Shendure,
- Jon Taylor,
- Emily H. Turner,
- LaDeana W. Hillier,
- Donald G. Moerman,
- and Robert H. Waterston
Genome Res. October 2013 23: 1749-1762; Published in Advance June 25, 2013, doi:10.1101/gr.157651.113
...The million mutation project: A new approach to genetics in Caenorhabditis elegans Owen Thompson 1 , Mark Edgley 2 , Pnina Strasbourger 1 , Stephane Flibotte 2 , Brent Ewing 1 , Ryan Adair 2 , Vinci Au 2 , Iasha...
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Methods: Efficient target-selected mutagenesis in Caenorhabditis elegans: Toward a knockout for every gene
- Edwin Cuppen,
- Eelke Gort,
- Esther Hazendonk,
- Josine Mudde,
- José van de Belt,
- Isaäc J. Nijman,
- Victor Guryev,
- and Ronald H.A. Plasterk
Genome Res. May 2007 17: 649-658; Published in Advance April 6, 2007, doi:10.1101/gr.6080607
...data in C. elegans , for which it was found that 13 out of 238 EMS-induced single base pair mutations (5.5%) are not G/C to A/T ( Anderson 1995 ), but much higher than the 1% found in Arabidopsis in a large-scale EMS-driven TILLING screen ( Greene et al. 2003 ) and lower than the 16% observed...
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Perspective: Functional transcriptomics in the post-ENCODE era
- Jonathan M. Mudge,
- Adam Frankish,
- and Jennifer Harrow
Genome Res. December 2013 23: 1961-1973; Published in Advance October 30, 2013, doi:10.1101/gr.161315.113
...functionality can be captured in gene annotation. The capture and annotation of transcript models Clearly, transcript capture precedes transcript annotation. Previously, transcripts were captured as cDNAs, mRNAs, and ESTs, whereas today RNA-seq methodologies predominate given their high-throughput nature...
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LETTER: Genetic Variation in Coding Regions Between and Within Commonly Used Inbred Rat Strains
- Bart M.G. Smits,
- Bert F.M. van Zutphen,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. July 2004 14: 1285-1290; doi:10.1101/gr.2155004
.... Phylogenetics of rat inbred strains. Mamm. Genome 14 : 61 –64. ↵ Till, B.J., Reynolds, S.H., Greene, E.A., Codomo, C.A., Enns, L.C., Johnson, J.E., Burtner, C., Odden, A.R., Young, K., Taylor, N.E., et al. 2003 . Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res. 13 : 524...

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