The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Next-generation genome annotation: we still struggle to get it right
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Finding the genes in a genome is not a trivial task, especially in eukaryotic species in which most of the sequence is noncoding and the coding regions are separated by intronic sequences.
“Finding the genes in a genome is not a trivial task, especially in eukaryotic species in which most of the sequence is noncoding and the coding regions are separated by intronic sequences (Salzberg 2019).”
From Annotation matters: the effect of structural gene annotation on orthology inference (2025) · cites this paper as Salzberg 2019
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Cites
Pertea, M., Shumate, A., Pertea, G., Varabyou, A., Breitwieser, F. P., Chang, Y.-C., Madugundu, A. K., Pandey, A., & Salzberg, S. L. (2018) · Genome Biology · doi:10.1186/s13059-018-1590-2 · Cited by 335
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Research works printed but not linked: 9
- Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995;269(5223):496–512. · DOI
- MGC Project Team, Temple G, Gerhard DS, Rasooly R, Feingold EA, Good PJ, et al. The completion of the mammalian gene collection (MGC). Genome Res. 2009;19:2324–33. · DOI
- Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, et al. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 2008;18:188–96. · DOI
- Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 2019;47:D766–73. · DOI
- Koutsovoulos G, Kumar S, Laetsch DR, Stevens L, Daub J, Conlon C, et al. No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini. Proc Natl Acad Sci U S A. 2016;113:5053–8. · DOI · Paper page
- Salzberg SL. Horizontal gene transfer is not a hallmark of the human genome. Genome Biol. 2017;18:85. · DOI
- Lu J, Salzberg SL. Removing contaminants from databases of draft genomes. PLoS Comput Biol. 2018;14:e1006277. · DOI
- Kryukov K, Imanishi T. Human contamination in public genome assemblies. PLoS One. 2016;11:e0162424. · DOI
- Workman RE, Tang AD, Tang PS, Jain M, Tyson JR, Zuzarte PC, et al. Nanopore native RNA sequencing of a human poly(a) transcriptome. bioRxiv; 2018. p. 459529. https://doi.org/10.1101/459529 · DOI
Cited by
Sorted by citations
Machine learning: a powerful tool for gene function prediction in plants
Mahood, E. H., Kruse, L. H., & Moghe, G. D. (2020) · Applications in Plant Sciences · doi:10.1002/aps3.11376 · Cited by 153
Integrated molecular approaches for fermented food microbiome research
Walsh, A. M., Leech, J., Huttenhower, C., Delhomme-Nguyen, H., Crispie, F., Chervaux, C., & Cotter, P. D. (2023) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuad001 · Cited by 56
Annotation matters: the effect of structural gene annotation on orthology inference
Prieto-Baños, S., Nevers, Y., Altenhoff, A., Warwick Vesztrocy, A., Dessimoz, C., & Glover, N. M. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf365 · Cited by 19
Metadata
- Authors
- Salzberg, S. L.
- ORCID
- Salzberg, Steven L.
- Venue
- Genome Biology
- Published
- 2019-05-16
- Volume
- 20
- Issue
- 1
- ISSN
- 1474-760X
- PMC
- PMC6521345
- Cited by
- 327
- References
- 1
- Language
- en
- Funders
- National Institutes of Health (R35-GM130151)
- National Science Foundation (IOS-1744309)
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