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Research: Transposon accumulation at xenobiotic gene family loci in aphids
- Tobias Baril,
- Adam Pym,
- Chris Bass,
- and Alex Hayward
Genome Res. October 2023 33: 1718-1733; Published in Advance October 18, 2023, doi:10.1101/gr.277820.123
...directly upstream of or downstream from the gene body.The amount of TE sequence and the frequency of TE insertions in genic versus intergenic regions in aphid s are not significantly correlated with compactness, described as the ratio of genic (intron and exon) to intergenic (gene flanks and intergenic...
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Methods: Conrad: Gene prediction using conditional random fields
- David DeCaprio,
- Jade P. Vinson,
- Matthew D. Pearson,
- Philip Montgomery,
- Matthew Doherty,
- and James E. Galagan
Genome Res. September 2007 17: 1389-1398; Published in Advance August 9, 2007, doi:10.1101/gr.6558107
..., DeCaprio Jade Jade P, Vinson Montgomery, Philip Pearson, M.D 10.1101/gr.6558107 genome;gr.6558107 1088-9051 Conrad: Gene prediction using conditional random fields Conrad: Gene prediction using conditional random fields David DeCaprio 1 , 3 , Jade P. Vinson 1 , 2 , Matthew D. Pearson 1 , Philip...
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Methods: Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
- Vardges Ter-Hovhannisyan,
- Alexandre Lomsadze,
- Yury O. Chernoff,
- and Mark Borodovsky
Genome Res. December 2008 18: 1979-1990; Published in Advance August 29, 2008, doi:10.1101/gr.081612.108
...Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training Vardges Ter-Hovhannisyan 1 , 4 , Alexandre Lomsadze 2 , 4 , Yury O. Chernoff 1 , and Mark Borodovsky 2 , 3 , 5 1 School of Biology...
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PERSPECTIVE: Genome annotation past, present, and future: How to define an ORF at each locus
- Michael R. Brent
Genome Res. December 2005 15: 1777-1786; doi:10.1101/gr.3866105
...of our ORF annotation. To provide historical context for the argument outlined above, I will first review the state of the major gene prediction methods roughly 10 years ago, when Genome Research began publishing. The second section below provides a brief summary of the progress that has been made...
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LETTER: Genomic analysis of the immune gene repertoire of amphioxus reveals extraordinary innate complexity and diversity
- Shengfeng Huang,
- Shaochun Yuan,
- Lei Guo,
- Yanhong Yu,
- Jun Li,
- Tao Wu,
- Tong Liu,
- Manyi Yang,
- Kui Wu,
- Huiling Liu,
- Jin Ge,
- Yingcai Yu,
- Huiqing Huang,
- Meiling Dong,
- Cuiling Yu,
- Shangwu Chen,
- and Anlong Xu
Genome Res. July 2008 18: 1112-1126; Published in Advance June 18, 2008, doi:10.1101/gr.069674.107
...Genomic analysis of the immune gene repertoire of amphioxus reveals extraordinary innate complexity and diversity Shengfeng Huang , Shaochun Yuan , Lei Guo , Yanhong Yu , Jun Li , Tao Wu , Tong Liu , Manyi Yang...
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LETTER: Segmental Duplications: Organization and Impact Within the Current Human Genome Project Assembly
- Jeffrey A. Bailey,
- Amy M. Yavor,
- Hillary F. Massa,
- Barbara J. Trask,
- and Evan E. Eichler
Genome Res. June 1, 2001 11: 1005-1017; Published in Advance May 8, 2001, doi:10.1101/gr.187101
...from 1–200 kb (IHGSC 2001). They often contain sequence features such as high-copy repeats and gene sequences with intron–exon structure. Thus, being composed of apparently normal genomic DNA, segmental duplications cannot be detected a priori; rather, most segmental duplications have to date been...
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RESEARCH: Computational and Biological Analysis of 680 kb of DNA Sequence from the Human 5q31 Cytokine Gene Cluster Region
- Kelly A. Frazer,
- Yukihiko Ueda,
- Yiwen Zhu,
- Vincent R. Gifford,
- Maria R. Garofalo,
- Narla Mohandas,
- Christopher H. Martin,
- Michael J. Palazzolo,
- Jan-Fang Cheng,
- and Edward M. Rubin
Genome Res. May 1, 1997 7: 495-512; doi:10.1101/gr.7.5.495
...the GRAIL predictions of five genes, IRF1, IL-4, IL-5, IL-13, and GM-CSF, in which the genomic structure, including the intron/exon boundaries, has been reported previously in detail. Of the 25 coding exons comprising these five genes, GRAIL Ia identified 18 (72%) with a false-positive rate of 10% (percent...
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Method: Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe
- Arnaud Belcour,
- Jeanne Got,
- Méziane Aite,
- Ludovic Delage,
- Jonas Collén,
- Clémence Frioux,
- Catherine Leblanc,
- Simon M. Dittami,
- Samuel Blanquart,
- Gabriel V. Markov,
- and Anne Siegel
Genome Res. June 2023 33: 972-987; Published in Advance July 19, 2023, doi:10.1101/gr.277056.122
...propagation. OrthoFinder predicts orthologs by aligning protein sequences of all s. The robustness of orthology relationships is evaluated (see Methods), and gene–protein–reaction (GPR) of robust orthologs are propagated. (C) Structural verification. The absence of a GPR in s is verified through pairwise...
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Research: Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii
- Eugenio López-Cortegano,
- Rory J. Craig,
- Jobran Chebib,
- Eniolaye J. Balogun,
- and Peter D. Keightley
Genome Res. January 2023 33: 45-60; Published in Advance December 12, 2022, doi:10.1101/gr.276957.122
..., and untranslated regions (UTRs). Because >70% of genes are separated by <1 kb in the compact C. reinhardtii , we divided intergenic regions into “proximal” (within 500 bp of a gene) and “distal” sequences (>500 bp from a gene), the latter category largely capturing long, highly repetitive intergenic regions...
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RESOURCE: Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions
- Chaochun Wei,
- Philippe Lamesch,
- Manimozhiyan Arumugam,
- Jennifer Rosenberg,
- Ping Hu,
- Marc Vidal,
- and Michael R. Brent
Genome Res. April 2005 15: 577-582; doi:10.1101/gr.3329005
...: Enhancing the utility of C. elegans as a model organism . National Human Genome Research Institute. ↵ Tenney, A., Brown, R.H., Vaske, C., Lodge, J.K., Doering, T.L., and Brent, M.R. 2004 . Gene prediction and verification in a compact with numerous small introns. Genome Res. 14 : 2330 -2335. ↵ Walhout, A...

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