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Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
- Jung-Wan Mok,
- Shelley B. Gibson,
- Haley A. Dostalik,
- and Shinya Yamamoto
Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
...et al. 2021). Among the variety of methodological approaches, Drosophila RNAi Screening Center Integrative Ortholog Prediction Tool (DIOPT) is widely used to identify ortholog candidates across multiple species, including flies and humans (see Supplemental Text 1; Hu et al. 2011). It is notable...
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Method: Genome-wide CRISPR screening reveals genes essential for cell viability and resistance to abiotic and biotic stresses in Bombyx mori
- Jiasong Chang,
- Ruolin Wang,
- Kai Yu,
- Tong Zhang,
- Xiaoxu Chen,
- Yue Liu,
- Run Shi,
- Xiaogang Wang,
- Qingyou Xia,
- and Sanyuan Ma
Genome Res. May 2020 30: 757-767; Published in Advance May 18, 2020, doi:10.1101/gr.249045.119
..., Heidelberg Fly Array Consortium, Paro R, Perrimon N. 2004. Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 303: 832–835. doi:10.1126/science.1091266 ↵Carette JE, Guimaraes CP, Varadarajan M, Park AS, Wuethrich I, Godarova A, Kotecki M, Cochran BH, Spooner E, Ploegh HL, et al...
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RESOURCE: Temporal and spatial transcriptional profiles of aging in Drosophila melanogaster
- Ming Zhan,
- Haruyoshi Yamaza,
- Yu Sun,
- Jason Sinclair,
- Huai Li,
- and Sige Zou
Genome Res. August 2007 17: 1236-1243; Published in Advance July 10, 2007, doi:10.1101/gr.6216607
.... Previous genomic studies on invertebrate aging mostly utilized the whole body or body parts and limited age-points, and failed to address tissue-specific aging. Here we measured genome-wide expression profiles of aging in Drosophila melanogaster for seven tissues representing nervous, muscular, digestive...
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Research: Cnidarian microRNAs frequently regulate targets by cleavage
- Yehu Moran,
- David Fredman,
- Daniela Praher,
- Xin Z. Li,
- Liang Meng Wee,
- Fabian Rentzsch,
- Phillip D. Zamore,
- Ulrich Technau,
- and Hervé Seitz
Genome Res. April 2014 24: 651-663; Published in Advance March 18, 2014, doi:10.1101/gr.162503.113
...cleavage. (A) Distribution of miRNA:mRNA alignment mismatch scores in Nematostella vectensis, Homo sapiens, Drosophila melanogaster, and Arabidopsis thaliana, shown as the difference in abundance between miRNAs and matching shuffledmiRNAs, counting the fraction of sequences in each set having a best match...
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Research: Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency
- Chan-Shuo Wu,
- Chun-Ying Yu,
- Ching-Yu Chuang,
- Michael Hsiao,
- Cheng-Fu Kao,
- Hung-Chih Kuo,
- and Trees-Juen Chuang
Genome Res. January 2014 24: 25-36; Published in Advance October 16, 2013, doi:10.1101/gr.159483.113
...hybrid mRNAs (i.e., Drosophila melanogaster females vs. Drosophila sechellia males) demonstrated that experimental artifacts are the predominant source of apparent trans-spliced RNA products observed in mRNA (McManus et al. 2010). It would, however, be impossible to apply such a system to humans...
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PERSPECTIVE: Genomics in C. elegans: So many genes, such a little worm
- LaDeana W. Hillier,
- Alan Coulson,
- John I. Murray,
- Zhirong Bao,
- John E. Sulston,
- and Robert H. Waterston
Genome Res. December 2005 15: 1651-1660; doi:10.1101/gr.3729105
...expressing the dsRNA ( Timmons and Fire 1998 ). Inhibition is rarely complete, and neuronally expressed genes are particularly resistant to RNAi effects. Nonetheless, the ease of use of feeding libraries and other modes of delivery has facilitated systematic -wide RNAi screens by several groups ( Fraser et...
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PERSPECTIVE: The Arabidopsis genome: A foundation for plant research
- Michael Bevan and
- Sean Walsh
Genome Res. December 2005 15: 1632-1642; doi:10.1101/gr.3723405
...was the first plant, and the third multicellular organism after Caenorhabditis elegans ( The C. elegans Sequencing Consortium 1998 ) and Drosophila melanogaster ( Adams et al. 2000 ), to be completely sequenced ( The Arabidopsis Genome Initiative 2000 ). At the time, it was claimed that the Arabidopsis sequence...
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RESOURCE: Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications
- Pierre Hilson,
- Joke Allemeersch,
- Thomas Altmann,
- Sébastien Aubourg,
- Alexandra Avon,
- Jim Beynon,
- Rishikesh P. Bhalerao,
- Frédérique Bitton,
- Michel Caboche,
- Bernard Cannoot,
- Vasil Chardakov,
- Cécile Cognet-Holliger,
- Vincent Colot,
- Mark Crowe,
- Caroline Darimont,
- Steffen Durinck,
- Holger Eickhoff,
- Andéol Falcon de Longevialle,
- Edward E. Farmer,
- Murray Grant,
- Martin T.R. Kuiper,
- Hans Lehrach,
- Céline Léon,
- Antonio Leyva,
- Joakim Lundeberg,
- Claire Lurin,
- Yves Moreau,
- Wilfried Nietfeld,
- Javier Paz-Ares,
- Philippe Reymond,
- Pierre Rouzé,
- Goran Sandberg,
- Maria Dolores Segura,
- Carine Serizet,
- Alexandra Tabrett,
- Ludivine Taconnat,
- Vincent Thareau,
- Paul Van Hummelen,
- Steven Vercruysse,
- Marnik Vuylsteke,
- Magdalena Weingartner,
- Peter J. Weisbeek,
- Valtteri Wirta,
- Floyd R.A. Wittink,
- Marc Zabeau,
- and Ian Small
Genome Res. October 15, 2004 14: 2176-2189; doi:10.1101/gr.2544504
...for large-scale functional surveys. Two key methods have greatly enhanced our ability to assign functions to genes in systematic analyses: microarray transcript profiling ( Holloway et al. 2002 ) and silencing via RNA interference or RNAi ( Hannon 2002 ; Waterhouse and Helliwell 2003 ). Full transcriptome...

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