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Research: Cell type–specific analysis by single-cell profiling identifies a stable mammalian tRNA–mRNA interface and increased translation efficiency in neurons
- William Gao,
- Carlos J. Gallardo-Dodd,
- and Claudia Kutter
Genome Res. January 2022 32: 97-110; Published in Advance December 2, 2021, doi:10.1101/gr.275944.121
...and Lee 2020). Moreover, because tRNA genes are very short and occupy a small percentage of mammalian s, the number of cuts to tRNA genes per cell could be low at normal sequencing depths (Supplemental Fig. S1B). To determine how many cuts to tRNA genes (gene body plus 100 bp upstream and downstream...
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Method: Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation
- Joshua Traynelis,
- Michael Silk,
- Quanli Wang,
- Samuel F. Berkovic,
- Liping Liu,
- David B. Ascher,
- David J. Balding,
- and Slavé Petrovski
Genome Res. October 2017 27: 1715-1729; Published in Advance September 1, 2017, doi:10.1101/gr.226589.117
...and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia; 6Centre for Systems Genomics, School of BioSciences and School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3010, Australia Gene panel and exome sequencing have revealed a high rate...
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Research: Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma
- Swati Venkat,
- Arwen A. Tisdale,
- Johann R. Schwarz,
- Abdulrahman A. Alahmari,
- H. Carlo Maurer,
- Kenneth P. Olive,
- Kevin H. Eng,
- and Michael E. Feigin
Genome Res. March 2020 30: 347-360; Published in Advance February 6, 2020, doi:10.1101/gr.257550.119
..., TP53, SMAD4, CDKN2A) and dysregulated pathways (axon guidance, cell adhesion, small GTPase signaling, protein metabolism) driving disease initiation and progression (Jones et al. 2008; Waddell et al. 2015; The Cancer Genome Atlas Research Network 2017). Gene expression profiles from hundreds...
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LETTER: The prion protein gene in humans revisited: Lessons from a worldwide resequencing study
- Marta Soldevila,
- Aida M. Andrés,
- Anna Ramírez-Soriano,
- Tomàs Marquès-Bonet,
- Francesc Calafell,
- Arcadi Navarro,
- and Jaume Bertranpetit
Genome Res. February 2006 16: 231-239; Published in Advance December 20, 2005, doi:10.1101/gr.4345506
....F., Wang, K., Seto, J., Chen, L., Acharya, C., Ankener, M., Baskin, D., Cooper, C., et al. 1998 . Complete genomic sequence and analysis of the prion protein gene region from three mammalian species. Genome Res. 8 : 1022 -1037. ↵ Livingston, R.J., von Niederhausern, A., Jegga, A.G., Crawford, D.C., Carlson...
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LETTER: Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse
- Ann-Marie Mallon,
- Laurens Wilming,
- Joseph Weekes,
- James G.R. Gilbert,
- Jennifer Ashurst,
- Sandrine Peyrefitte,
- Lucy Matthews,
- Matthew Cadman,
- Richard McKeone,
- Chris A. Sellick,
- Ruth Arkell,
- Marc R.M. Botcherby,
- Mark A. Strivens,
- R. Duncan Campbell,
- Simon Gregory,
- Paul Denny,
- John M. Hancock,
- Jane Rogers,
- and Steve D.M. Brown
Genome Res. October 2004 14: 1888-1901; Published in Advance September 13, 2004, doi:10.1101/gr.2478604
...Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13) Svea 36H Mouse Ann-Marie Mallon 1 , 4 , Laurens Wilming 2 , 4 , Joseph Weekes 1 , James G.R. Gilbert 2 , Jennifer Ashurst 2...
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LETTER: A Comparative Gene Map of the Horse (Equus caballus)
- Alexandre R. Caetano,
- Yow-Ling Shiue,
- Leslie A. Lyons,
- Steven J. O'Brien,
- Thomas F. Laughlin,
- Ann T. Bowling,
- and James D. Murray
Genome Res. December 1, 1999 9: 1239-1249; doi:10.1101/gr.9.12.1239
...Abstract A comparative gene map of the horse genome composed of 127 loci was assembled based on the new assignment of 68 equine type I loci and on data published previously. PCR primers based on consensus gene sequences conserved across mammalian species were used to amplify markers for assigning 68...
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ARTICLE: The Genexpress Index: a resource for gene discovery and the genic map of the human genome.
- R Houlgatte,
- R Mariage-Samson,
- S Duprat,
- A Tessier,
- S Bentolila,
- B Lamy,
- and C Auffray
Genome Res. October 1995 5: 272-304; doi:10.1101/gr.5.3.272
...patterns in mouse brain. Eur. J. Neurosci. 2 : 704 – 711 . Kato, K. 1992 . Finding new genes in the nervous system by cDNA analysis. Trends Neurosci. 15 : 319 – 323 . Kerr, S.M., Vambrie, S. McKay, S.J. and Cooke. H.J. 1994 . Analysis of cDNA sequences from mouse testis. Mammalian Genome 5 : 557 – 565...
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ARTICLE: Developmental Roles of Pufferfish Hox Clusters and Genome Evolution in Ray-Fin Fish
- Angel Amores,
- Tohru Suzuki,
- Yi-Lin Yan,
- Jordan Pomeroy,
- Amy Singer,
- Chris Amemiya,
- and John H. Postlethwait
Genome Res. January 2004 14: 1-10; doi:10.1101/gr.1717804
...that gene duplication may facilitate the evolution of new functions and the reciprocal retention of ancestral functions ( Ohno 1970 ; Hughes and Hughes 1993 ; Force et al. 1999 ). Our results showed that pufferfish have two orthologs of mammalian HOXD4 , but zebrafish has just one ( Fig. 3 ). In fugu, Hoxd4...
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REPORT: Conservation of Microstructure between a Sequenced Region of the Genome of Rice and Multiple Segments of the Genome of Arabidopsis thaliana
- Klaus Mayer,
- George Murphy,
- Renato Tarchini,
- Rolf Wambutt,
- Guido Volckaert,
- Thomas Pohl,
- Andreas Düsterhöft,
- Willem Stiekema,
- Karl-Dieter Entian,
- Nancy Terryn,
- Kai Lemcke,
- Dirk Haase,
- Caroline R. Hall,
- Anne-Marie van Dodeweerd,
- Scott V. Tingey,
- Hans-Werner Mewes,
- Michael W. Bevan,
- and Ian Bancroft
Genome Res. July 1, 2001 11: 1167-1174; Published in Advance June 12, 2001, doi:10.1101/gr.161701
...involve mobile genetic elements, as has been found to contribute to “exon shuffling” in mammalian systems ( Boeke and Pickeral 1999 ). It is also likely that unequal crossing over contributes to both tandem duplications of genes, and deletion of single or small groups of genes ( Bancroft 2001 ). Many...
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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
...that are not conserved in Drosophila (Fig. 2). For example, orthologous genes that correspond to SNCA (Parkinson's disease), PRNP (prion diseases), and MECP2 (Rett syndrome) are not found in the Drosophila . However, ectopic overexpression of these human proteins can cause scorable phenotypes in flies (Feany and Bender...

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