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Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation
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“All 509 placental mammal alignment chains with human (hg38) and with mouse (mm10) as the reference were computed with the same parameters that are sufficiently sensitive to align orthologous exons between placental mammals (48).”
From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [48]
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Citations
Cites
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
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“Genome alignments provide a powerful basis to obtain such comparative gene annotations, since coding exons are typically well conserved between species (17,18) and the aligning genomic context is helpful to distinguish orthologous genes from paralogs and pseudogenes that are located in a different genomic context.”
BackgroundA high-resolution map of human evolutionary constraint using 29 mammals
Broad Institute Sequencing Platform and Whole Genome Assembly Team, Lindblad-Toh, K., Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S., Kheradpour, P., et al. (2011) · Nature · doi:10.1038/nature10530 · Cited by 1,108
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Flagged first, then by citations
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Cited by
Sorted by citations
A genomics approach reveals insights into the importance of gene losses for mammalian adaptations
Sharma, V., Hecker, N., Roscito, J. G., Foerster, L., Langer, B. E., & Hiller, M. (2018) · Nature Communications · doi:10.1038/s41467-018-03667-1 · Cited by 237
Self-citationIntegrating gene annotation with orthology inference at scale
Kirilenko, B. M., Munegowda, C., Osipova, E., Jebb, D., Sharma, V., Blumer, M., Morales, A. E., Ahmed, A.-W., Kontopoulos, D.-G., Hilgers, L., et al. (2023) · Science · doi:10.1126/science.abn3107 · Cited by 209
Self-citationVision-related convergent gene losses reveal SERPINE3’s unknown role in the eye
Indrischek, H., Hammer, J., Machate, A., Hecker, N., Kirilenko, B., Roscito, J., Hans, S., Norden, C., Brand, M., & Hiller, M. (2022) · eLife · doi:10.7554/elife.77999 · Cited by 21
Self-citationMalovichko, Y. V., Bein, B., Gonzales-Irribarren, A., Leushkin, E., Hilgers, L., Stephen, A., Yi, X., Albertini, M., Stadager, T., Zumpt, M., et al. (2026) · doi:10.64898/2026.06.30.735536 · Cited by 5
Self-citation
Metadata
- Authors
- Sharma, V., & Hiller, M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-06-21
- Volume
- 45
- Issue
- 14
- Pages
- 8369-8377
- ISSN
- 0305-1048
- 1362-4962
- PMC
- PMC5737078
- Cited by
- 72
- References
- 3
- Language
- en
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