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Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
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Citations
Cites
Comparative Genomics of the Eukaryotes
Rubin, G. M., Yandell, M. D., Wortman, J. R., Gabor, G. L., Miklos, Nelson, C. R., Hariharan, I. K., Fortini, M. E., Li, P. W., Apweiler, R., et al. (2000) · Science · doi:10.1126/science.287.5461.2204 · Cited by 1,698 · cited 3×
“The A-B sequence pairs are eliminated if either sequence A or sequence B scores higher to outgroup sequence than they score to each other (3, 4 ).”
BackgroundMethodInfluentialMushegian, A. R., Garey, J. R., Martin, J., & Liu, L. X. (1998) · Genome Research · doi:10.1101/gr.8.6.590 · Cited by 164 · cited 1×
“Additional orthologs (in-paralogs) are clustered together with each remaining pair of potential orthologs as shown in 5}Figure 2 (5,6).”
Background
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OrthoFinder: phylogenetic orthology inference for comparative genomics
Emms, D. M., & Kelly, S. (2019) · Genome Biology · doi:10.1186/s13059-019-1832-y · Cited by 7,676
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, L., Stoeckert, C. J., & Roos, D. S. (2003) · Genome Research · doi:10.1101/gr.1224503 · Cited by 5,707
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Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J.-M., Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A., et al. (2002) · Science · doi:10.1126/science.1072104 · Cited by 1,591
Orthologs, Paralogs, and Evolutionary Genomics
Koonin, E. V. (2005) · Annual Review of Genetics · doi:10.1146/annurev.genet.39.073003.114725 · Cited by 1,323
A Recently Evolved Transcriptional Network Controls Biofilm Development in Candida albicans
Nobile, C. J., Fox, E. P., Nett, J. E., Sorrells, T. R., Mitrovich, Q. M., Hernday, A. D., Tuch, B. B., Andes, D. R., & Johnson, A. D. (2012) · Cell · doi:10.1016/j.cell.2011.10.048 · Cited by 711
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Ovchinnikov, S., Kamisetty, H., & Baker, D. (2014) · eLife · doi:10.7554/elife.02030 · Cited by 629
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Wapinski, I., Pfeffer, A., Friedman, N., & Regev, A. (2007) · Nature · doi:10.1038/nature06107 · Cited by 614
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Homann, O. R., Dea, J., Noble, S. M., & Johnson, A. D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000783 · Cited by 444
“algorithms, SYNERGY [59] and INPARANOID [60] supple-”
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Philippe, H., Delsuc, F., Brinkmann, H., & Lartillot, N. (2005) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev.ecolsys.35.112202.130205 · Cited by 306
Inglis, D. O., Binkley, J., Skrzypek, M. S., Arnaud, M. B., Cerqueira, G. C., Shah, P., Wymore, F., Wortman, J. R., & Sherlock, G. (2013) · BMC Microbiology · doi:10.1186/1471-2180-13-91 · Cited by 293
Lee, I., Lehner, B., Crombie, C., Wong, W., Fraser, A. G., & Marcotte, E. M. (2008) · Nature Genetics · doi:10.1038/ng.2007.70 · Cited by 281
HaMStR: Profile hidden markov model based search for orthologs in ESTs
Ebersberger, I., Strauss, S., & von Haeseler, A. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-157 · Cited by 288
The binary protein-protein interaction landscape of Escherichia coli
Rajagopala, S. V., Sikorski, P., Kumar, A., Mosca, R., Vlasblom, J., Arnold, R., Franca-Koh, J., Pakala, S. B., Phanse, S., Ceol, A., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2831 · Cited by 233
Phylogenetic diversity of stress signalling pathways in fungi
Nikolaou, E., Agrafioti, I., Stumpf, M., Quinn, J., Stansfield, I., & Brown, A. J. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-44 · Cited by 206
Conservation of core gene expression in vertebrate tissues
Chan, E. T., Quon, G. T., Chua, G., Babak, T., Trochesset, M., Zirngibl, R. A., Aubin, J., Ratcliffe, M. J., Wilde, A., Brudno, M., et al. (2009) · Journal of Biology · doi:10.1186/jbiol130 · Cited by 190
Bhardwaj, N., & Lu, H. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti398 · Cited by 186
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Laurent, J. M., Vogel, C., Kwon, T., Craig, S. A., Boutz, D. R., Huse, H. K., Nozue, K., Walia, H., Whiteley, M., Ronald, P. C., et al. (2010) · PROTEOMICS · doi:10.1002/pmic.201000327 · Cited by 156
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Goodstadt, L., & Ponting, C. P. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020133 · Cited by 154
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Altenhoff, A. M., Glover, N. M., & Dessimoz, C. (2019) · Methods in Molecular Biology · doi:10.1007/978-1-4939-9074-0_5 · Cited by 148
Aite, M., Chevallier, M., Frioux, C., Trottier, C., Got, J., Cortés, M. P., Mendoza, S. N., Carrier, G., Dameron, O., Guillaudeux, N., et al. (2018) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006146 · Cited by 137
“5.11) [18], Inparanoid (v4.”
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Cosentino, S., & Iwasaki, W. (2019) · Bioinformatics · doi:10.1093/bioinformatics/bty631 · Cited by 134
Bian, C., Hu, Y., Ravi, V., Kuznetsova, I. S., Shen, X., Mu, X., Sun, Y., You, X., Li, J., Li, X., et al. (2016) · Scientific Reports · doi:10.1038/srep24501 · Cited by 107
Train, C.-M., Glover, N. M., Gonnet, G. H., Altenhoff, A. M., & Dessimoz, C. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx229 · Cited by 96
A map of human protein interactions derived from co‐expression of human mRNAs and their orthologs
Ramani, A. K., Li, Z., Hart, G. T., Carlson, M. W., Boutz, D. R., & Marcotte, E. M. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.19 · Cited by 78
Lipinski, K. A., Puchta, O., Surendranath, V., Kudla, M., & Golik, P. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr120 · Cited by 62
Ancient genomic architecture for mammalian olfactory receptor clusters
Aloni, R., Olender, T., & Lancet, D. (2006) · Genome Biology · doi:10.1186/gb-2006-7-10-r88 · Cited by 56
Conserved Translatome Remodeling in Nematode Species Executing a Shared Developmental Transition
Stadler, M., & Fire, A. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003739 · Cited by 53
Unique, Diverged, and Conserved Mitochondrial Functions Influencing Candida albicans Respiration
Sun, N., Parrish, R. S., Calderone, R. A., & Fonzi, W. A. (2019) · mBio · doi:10.1128/mbio.00300-19 · Cited by 51
Arnoux, J. (2026) · Thèse de doctorat, Université Paris-Saclay / PPanGGOLiN · doi:10.70675/eee354d9zf63dz48ebz9444zd1809f8fb74d
Metadata
- Authors
- Remm, M., Storm, C. E. V., & Sonnhammer, E. L. L.
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2001-12
- Volume
- 314
- Issue
- 5
- Pages
- 1041-1052
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W2167188257
- Cited by
- 1,174
- References
- 2
- FWCI
- 7.27
- Type
- journal article
- Language
- en
- Open access
- closed
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.