Orthologs, Paralogs, and Evolutionary Genomics

Evolution by Gene Duplication

Ohno, S. (1970) · doi:10.1007/978-3-642-86659-3 · Cited by 7,833 · see citing works

The Neutral Theory of Molecular Evolution

Kimura, M. (1979) · Scientific American · doi:10.1038/scientificamerican1179-98 · Cited by 7,698 · see citing works

The Neutral Theory of Molecular Evolution

Kimura, M. (1983) · Cambridge University Press eBooks · doi:10.1017/cbo9780511623486 · Cited by 6,300 · see citing works

Whole-Genome Random Sequencing and Assembly of Haemophilus influenzae Rd

Fleischmann, R. D., Adams, M. D., White, O. R., Clayton, R. A., Kirkness, E. F., Kerlavage, A. R., Bult, C. J., Tomb, J.-F., Dougherty, B. A., Merrick, J. M., et al. (1995) · Science · doi:10.1126/science.7542800 · Cited by 5,641 · see citing works

The Evolutionary Fate and Consequences of Duplicate Genes

Lynch, M., & Conery, J. S. (2000) · Science · doi:10.1126/science.290.5494.1151 · Cited by 4,988 · see citing works

The COG database: an updated version includes eukaryotes

Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S., Nikolskaya, A. N., et al. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-41 · Cited by 4,410 · see citing works

A genomic perspective on protein families.

Tatusov, R., Koonin, E., & Lipman, D. (1997) · Science · doi:10.1126/science.278.5338.631 · Cited by 3,777 · see citing works

Preservation of Duplicate Genes by Complementary, Degenerative Mutations

Force, A., Lynch, M., Pickett, F. B., Amores, A., Yan, Y.-L., & Postlethwait, J. (1999) · Genetics · doi:10.1093/genetics/151.4.1531 · Cited by 3,529 · see citing works

Evolutionary divergence and convergence in proteins.

ZUCKERKANDL, E., & PAULING, L. (1965) · Evolving Genes and Proteins · doi:10.1016/b978-1-4832-2734-4.50017-6 · Cited by 3,020 · see citing works

The Minimal Gene Complement of <i>Mycoplasma genitalium</i>

Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., Clayton, R. A., Fleischmann, R. D., Bult, C. J., Kerlavage, A. R., Sutton, G., Kelley, J. M., et al. (1995) · Science · doi:10.1126/science.270.5235.397 · Cited by 2,545 · see citing works

Phylogenetic Classification and the Universal Tree

Doolittle, W. F. (1999) · Science · doi:10.1126/science.284.5423.2124 · Cited by 1,888 · see citing works

The COG database: new developments in phylogenetic classification of proteins from complete genomes

Tatusov, R. L. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.22 · Cited by 1,873 · see citing works

The Probability of Duplicate Gene Preservation by Subfunctionalization

Lynch, M. F., & Force, A. G. (2000) · Genetics · doi:10.1093/genetics/154.1.459 · Cited by 1,557 · see citing works

Distinguishing Homologous from Analogous Proteins

Fitch, W. M. (1970) · Systematic Zoology · doi:10.2307/2412448 · Cited by 1,503 · see citing works

The Complete DNA Sequence of Varicella-Zoster Virus

Davison, A. J., & Scott, J. E. (1986) · Journal of General Virology · doi:10.1099/0022-1317-67-9-1759 · Cited by 1,423 · see citing works

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons

Remm, M., Storm, C. E. V., & Sonnhammer, E. L. L. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.5197 · Cited by 1,175 · see citing works

Horizontal gene transfer in prokaryotes: Quantification and classification

Koonin, E. V., Makarova, K. S., & Aravind, L. (2001) · Annual Review of Microbiology · doi:10.1146/annurev.micro.55.1.709 · Cited by 1,126 · see citing works

Conservation of gene order: a fingerprint of proteins that physically interact.

Dandekar, T., Snel, B., Huynen, M., & Bork, P. (1998) · TIBS -Trends in Biochemical Sciences. Regular ed · doi:10.1016/s0968-0004(98)01274-2 · Cited by 1,108 · see citing works

A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes

Koonin, E. V., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Krylov, D. M., Makarova, K. S., Mazumder, R., Mekhedov, S., Nikolskaya, A. N., Rao, B. S., et al. (2004) · Genome biology · doi:10.1186/gb-2004-5-2-r7 · Cited by 1,092 · see citing works

Prokaryotic origin of the actin cytoskeleton

van den Ent, F., Amos, L. A., & Löwe, J. (2001) · Nature · doi:10.1038/35092500 · Cited by 821 · see citing works

Dosage sensitivity and the evolution of gene families in yeast

Papp, B., Pál, C., & Hurst, L. D. (2003) · Nature · doi:10.1038/nature01771 · Cited by 807 · see citing works

Selection in the evolution of gene duplications

Kondrashov, F. A., Rogozin, I. B., Wolf, Y. I., & Koonin, E. V. (2002) · Genome biology · doi:10.1186/gb-2002-3-2-research0008 · Cited by 774 · see citing works

Inparanoid: a comprehensive database of eukaryotic orthologs

O'Brien, K. P. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki107 · Cited by 731 · see citing works

Mitochondrial Genome Evolution and the Origin of Eukaryotes

Lang, B. F., Gray, M. W., & Burger, G. (1999) · Annual Review of Genetics · doi:10.1146/annurev.genet.33.1.351 · Cited by 724 · see citing works

Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution

He, X., & Zhang, J. (2005) · Genetics · doi:10.1534/genetics.104.037051 · Cited by 694 · see citing works

Comparative genomics, minimal gene-sets and the last universal common ancestor

Koonin, E. V. (2003) · Nature Reviews Microbiology · doi:10.1038/nrmicro751 · Cited by 661 · see citing works

Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary AnalysisPreprint

Eisen, J. A. (1998) · Genome Research · doi:10.1101/gr.8.3.163 · Cited by 628 · see citing works

The modern molecular clock

Bromham, L., & Penny, D. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1020 · Cited by 615 · see citing works

Tubulin and FtsZ form a distinct family of GTPases

Nogales, E., Downing, K. H., Amos, L., & L�we, J. (1998) · Nature Structural Biology · doi:10.1038/nsb0698-451 · Cited by 614 · see citing works

You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes

Doolittle, W. F. (1998) · Trends in Genetics · doi:10.1016/s0168-9525(98)01494-2 · Cited by 600 · see citing works

Homology

Fitch, W. M. (2000) · Trends in Genetics · doi:10.1016/s0168-9525(00)02005-9 · Cited by 592 · see citing works

The structure of the protein universe and genome evolution

Koonin, E. V., Wolf, Y. I., & Karev, G. P. (2002) · Nature · doi:10.1038/nature01256 · Cited by 553 · see citing works

On the archetype and homologies of the vertebrate skeleton

Owen, R. P. (1848) · John Van Voorst eBooks · doi:10.5962/bhl.title.118611 · Cited by 542 · see citing works

The origin and early evolution of mitochondria.

Gray, M. W., Burger, G., & Lang, B. F. (2001) · Genome biology · doi:10.1186/gb-2001-2-6-reviews1018 · Cited by 460 · see citing works

Homology in classical and molecular biology.

Patterson, C. (1988) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040523 · Cited by 438 · see citing works

From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem

Page, R., & Charleston, M. (1997) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1996.0390 · Cited by 428 · see citing works

COMMON THEMES IN ASSEMBLY AND FUNCTION OF EUKARYOTIC TRANSCRIPTION COMPLEXES

Zawel, L. S., & Reinberg, D. (1995) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.64.070195.002533 · Cited by 428 · see citing works

'Conserved hypothetical' proteins: prioritization of targets for experimental study

Galperin, M. Y. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh885 · Cited by 419 · see citing works

Orthology, paralogy and proposed classification for paralog subtypes

Sonnhammer, E. L. L., & Koonin, E. V. (2002) · Trends in Genetics · doi:10.1016/s0168-9525(02)02793-2 · Cited by 380 · see citing works

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

Mirkin, B. G., Fenner, T. I., Galperin, M. Y., & Koonin, E. V. (2003) · BMC Evolutionary Biology · doi:10.1186/1471-2148-3-2 · Cited by 368 · see citing works

Genome trees and the tree of life

Wolf, Y. I., Rogozin, I. B., Grishin, N. V., & Koonin, E. V. (2002) · Trends in Genetics · doi:10.1016/s0168-9525(02)02744-0 · Cited by 362 · see citing works

Genome Alignment, Evolution of Prokaryotic Genome Organization, and Prediction of Gene Function Using Genomic ContextPreprint

Wolf, Y. I., Rogozin, I. B., Kondrashov, A. S., & Koonin, E. V. (2001) · Genome Research · doi:10.1101/gr.gr-1619r · Cited by 357 · see citing works

Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene ContentPreprint

Snel, ‎., Bork, P., & Huynen, M. A. (2001) · Genome Research · doi:10.1101/gr.176501 · Cited by 351 · see citing works

The Possible Modification of the Response of the Wild Type to Recurrent Mutations

Fisher, R. A. (1928) · The American Naturalist · doi:10.1086/280193 · Cited by 338 · see citing works

Replisome-Mediated DNA Replication

Benkovic, S. J., Valentine, A. M., & Salinas, F. G. (2001) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.70.1.181 · Cited by 329 · see citing works

The altered evolutionary trajectories of gene duplicates

Lynch, M., & Katju, V. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.09.001 · Cited by 305 · see citing works

Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli

Tatusov, R. L., Mushegian, A. R., Peer Bork, B., Brown, N. P., Hayes, W. S., Borodovsky, M. Y., Rudd, K. E., & Koonin, E. V. (1996) · Current Biology · doi:10.1016/s0960-9822(02)00478-5 · Cited by 301 · see citing works

Prokaryotic Homologs of the Eukaryotic DNA-End-Binding Protein Ku, Novel Domains in the Ku Protein and Prediction of a Prokaryotic Double-Strand Break Repair SystemPreprint

Aravind, L., & Koonin, E. V. (2001) · Genome Research · doi:10.1101/gr.181001 · Cited by 291 · see citing works

Sequence ― Evolution ― Function: Computational Approaches in Comparative Genomics

Koonin, E. V., & Galperin, M. Y. (2010) · Cited by 283 · see citing works

The Impact of Comparative Genomics on Our Understanding of Evolution

Koonin, E. V., Aravind, L., & Kondrashov, A. S. (2000) · Cell · doi:10.1016/s0092-8674(00)80867-3 · Cited by 282 · see citing works

Uprooting the Tree of Life

Doolittle, W. F. (2000) · Scientific American · doi:10.1038/scientificamerican0200-90 · Cited by 281 · see citing works

Comparative Genomics of the Archaea (Euryarchaeota): Evolution of Conserved Protein Families, the Stable Core, and the Variable ShellPreprint

Makarova, K. S., Aravind, L., Galperin, M. Y., Grishin, N. V., Tatusov, R. L., Wolf, Y. I., & Koonin, E. V. (1999) · Genome Research · doi:10.1101/gr.9.7.608 · Cited by 274 · see citing works

Non-orthologous gene displacement

Koonin, E. V., Mushegian, A. R., & Peer Bork, B. (1996) · Trends in Genetics · doi:10.1016/s0168-9525(96)80003-5 · Cited by 251 · see citing works

Non-orthologous gene displacement

Koonin, E. V. (1996) · Trends in Genetics · doi:10.1016/0168-9525(96)20010-1 · Cited by 250 · see citing works

Lateral genomics

Doolittle, W. F. (1999) · Trends in Cell Biology · doi:10.1016/s0962-8924(99)01664-5 · Cited by 241 · see citing works

“Homology” in proteins and nucleic acids: A terminology muddle and a way out of it

Reeck, G. R., de Haën, C., Teller, D. C., et al. (1987) · Cell · doi:10.1016/0092-8674(87)90322-9 · Cited by 231 · see citing works

Mycobacterial Ku and Ligase Proteins Constitute a Two-Component NHEJ Repair Machine

Della, M., Palmbos, P. L., Tseng, H.-M., Tonkin, L. M., Daley, J. M., Topper, L. M., Pitcher, R. S., Tomkinson, A. E., Wilson, T. E., & Doherty, A. J. (2004) · Science · doi:10.1126/science.1099824 · Cited by 220 · see citing works

The molecular clock may be an episodic clock.

Gillespie, J. H. (1984) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.81.24.8009 · Cited by 218 · see citing works

The frequency distribution of gene family sizes in complete genomes

Huynen, M. A., & van Nimwegen, E. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025959 · Cited by 213 · see citing works

HOVERGEN: a database of homologous vertebrate genes

Duret, L., Mouchiroud, D., & Gouy, M. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.12.2360 · Cited by 212 · see citing works

Relative rates of gene fusion and fission in multi-domain proteins

Kummerfeld, S., & Teichmann, S. A. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.11.007 · Cited by 208 · see citing works

The Balance of Driving Forces During Genome Evolution in ProkaryotesPreprint

Kunin, V., & Ouzounis, C. A. (2003) · Genome Research · doi:10.1101/gr.1092603 · Cited by 203 · see citing works

The Dual Origin of the Yeast Mitochondrial Proteome

Karlberg, O., Canbäck, B., Kurland, C. G., & Andersson, S. G. E. (2000) · Yeast · doi:10.1002/1097-0061(20000930)17:3 · Cited by 190 · see citing works

Duplicated genes evolve slower than singletons despite the initial rate increase

Jordan, I. K., Wolf, Y. I., & Koonin, E. V. (2004) · BMC Evolutionary Biology · doi:10.1186/1471-2148-4-22 · Cited by 189 · see citing works

RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs

Zmasek, C. M., & Eddy, S. R. (2002) · BMC Bioinformatics · doi:10.1186/1471-2105-3-14 · Cited by 188 · see citing works

Lateral gene transfer: when will adolescence end?

Lawrence, J. G., & Hendrickson, H. L. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03778.x · Cited by 185 · see citing works

Automated ortholog inference from phylogenetic trees and calculation of orthology reliability

Storm, C. E. V., & Sonnhammer, E. L. L. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.1.92 · Cited by 183 · see citing works

Genome evolution

Snel, ‎., Bork, P., & Huynen, M. A. (2000) · Trends in Genetics · doi:10.1016/s0168-9525(99)01924-1 · Cited by 183 · see citing works

Genes for the cytoskeletal protein tubulin in the bacterial genus Prosthecobacter

Jenkins, C., Samudrala, R., Anderson, I., Hedlund, B. P., Petroni, G., Michailova, N., Pinel, N., Overbeek, R., Rosati, G., & Staley, J. T. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.012516899 · Cited by 179 · see citing works

Bayesian gene/species tree reconciliation and orthology analysis using MCMC

Arvestad, L., Berglund, A.-C., Lagergren, J., & Sennblad, B. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg1000 · Cited by 178 · see citing works

Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases

Dufayard, J.-F., Duret, L., Penel, S., Gouy, M., Rechenmann, F., & Perrière, G. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti325 · Cited by 175 · see citing works

Preferential Duplication of Conserved Proteins in Eukaryotic Genomes

Davis, J. C., & Petrov, D. A. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020055 · Cited by 174 · see citing works

Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ

Omelchenko, M. V., Makarova, K. S., Wolf, Y. I., et al. (2003) · Genome biology · doi:10.1186/gb-2003-4-9-r55 · Cited by 166 · see citing works

Evolution of antibiotic resistance genes: the DNA sequence of a kanamycin resistance gene from Staphylococcus aureus.

Gray, G. S., & Fitch, W. M. (1984) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040298 · Cited by 165 · see citing works

Lineage-Specific Gene Expansions in Bacterial and Archaeal GenomesPreprint

Jordan, I. K., Makarova, K. S., Spouge, J. L., Wolf, Y. I., & Koonin, E. V. (2001) · Genome Research · doi:10.1101/gr.166001 · Cited by 163 · see citing works

Lineage-Specific Gene Expansions in Bacterial and Archaeal GenomesPreprint

Jordan, I. K. (2001) · Genome Research · doi:10.1101/gr.gr-1660r · Cited by 158 · see citing works

Orthologs and paralogs - we need to get it right.

Jensen, R. A. (2001) · Genome biology · doi:10.1186/gb-2001-2-8-interactions1002 · Cited by 143 · see citing works

An exosome‐like complex in Sulfolobus solfataricus

Evguenieva‐Hackenberg, E., Walter, P., Hochleitner, E. O., et al. (2003) · EMBO Reports · doi:10.1038/sj.embor.embor929 · Cited by 142 · see citing works

On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies

Zhang, L. (1997) · Journal of Computational Biology · doi:10.1089/cmb.1997.4.177 · Cited by 132 · see citing works

Molecules of the Bacterial Cytoskeleton

Löwe, J., van den Ent, F., & Amos, L. (2004) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.33.110502.132647 · Cited by 131 · see citing works

Genome Data Shake Tree of Life

Pennisi, E. (1998) · Science · doi:10.1126/science.280.5364.672 · Cited by 125 · see citing works

Evolution of gene fusions: horizontal transfer versus independent events

Yanai, I., Wolf, Y. I., & Koonin, E. V. (2002) · Genome biology · doi:10.1186/gb-2002-3-5-research0024 · Cited by 116 · see citing works

Genome Sequence Comparison and Scenarios for Gene Rearrangements: A Test Case

Hannenhalli, S., Chappey, C., Koonin, E. V., et al. (1995) · Genomics · doi:10.1006/geno.1995.9873 · Cited by 114 · see citing works

Genome-Wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution

Novichkov, P. S., Omelchenko, M. V., Gelfand, M. S., Mironov, A. A., Wolf, Y. I., & Koonin, E. V. (2004) · Journal of Bacteriology · doi:10.1128/jb.186.19.6575-6585.2004 · Cited by 105 · see citing works

Understanding the Overdispersed Molecular Clock

Cutler, D. J. (2000) · Genetics · doi:10.1093/genetics/154.3.1403 · Cited by 103 · see citing works

Solution structure of ThiS and implications for the evolutionary roots of ubiquitin.

Nicholson, L. K., Wang, C., Xi, J., & Begley, T. P. (2001) · Nature Structural Biology · doi:10.1038/83041 · Cited by 100 · see citing works

A Biologically Consistent Model for Comparing Molecular Phylogenies

Mirkin, B., Muchnik, I. B., & Smith, T. F. (1995) · Journal of Computational Biology · doi:10.1089/cmb.1995.2.493 · Cited by 98 · see citing works

Gene Dosage Balance in Cellular Pathways

Veitia, R. A. (2004) · Genetics · doi:10.1534/genetics.104.029785 · Cited by 98 · see citing works

HOBACGEN: Database System for Comparative Genomics in BacteriaPreprint

Perrière, G., Duret, L., & Gouy, M. (2000) · Genome Research · doi:10.1101/gr.10.3.379 · Cited by 84 · see citing works

Gene dosage balance: deletions, duplications and dominance

Veitia, R. A. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.11.002 · Cited by 82 · see citing works

Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomes

Ochman, H. (2002) · Trends in Genetics · doi:10.1016/s0168-9525(02)02668-9 · Cited by 78 · see citing works

Structural/functional homology between the bacterial and eukaryotic cytoskeletons

Amos, L., van den Ent, F., & Löwe, J. (2003) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2003.11.005 · Cited by 75 · see citing works

Uses for evolutionary trees

Fitch, W. M. (1995) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.1995.0095 · Cited by 70 · see citing works

Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes

Doerks, T., von Mering, C., & Peer Bork, B. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh973 · Cited by 68 · see citing works

An apology for orthologs - or brave new memes.

Koonin, E. V. (2001) · Genome biology · doi:10.1186/gb-2001-2-4-comment1005 · Cited by 60 · see citing works

‘Spalog’ and ‘sequelog’: neutral terms for spatial and sequence similarity

Varshavsky, A. J. (2004) · Current Biology · doi:10.1016/j.cub.2004.02.014 · Cited by 59 · see citing works

RICHARD OWEN AND THE CONCEPT OF HOMOLOGY

Panchen, A. L. (1994) · Elsevier eBooks · doi:10.1016/b978-0-08-057430-1.50007-x · Cited by 59 · see citing works

Comprehensive Analysis of Orthologous Protein Domains Using the HOPS DatabasePreprint

Storm, C. E. V., & Sonnhammer, E. L. L. (2003) · Genome Research · doi:10.1101/gr1305203 · Cited by 52 · see citing works

Which is the most conserved group of proteins? Homology-orthology, paralogy, xenology, and the fusion of independent lineages

Gogarten, J. P. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00173425 · Cited by 51 · see citing works

Duplication-Based Measures of Difference Between Gene and Species Trees

Eulenstein, O., Mirkin, B., & Vingron, M. (1998) · Journal of Computational Biology · doi:10.1089/cmb.1998.5.135 · Cited by 43 · see citing works

Genes and homology

Webber, C., & Ponting, C. P. (2004) · Current Biology · doi:10.1016/j.cub.2004.04.016 · Cited by 30 · see citing works

Estimation of the Number of Authentic Orphan Genes in Bacterial Genomes

Satoshi, F. (2004) · DNA Research · doi:10.1093/dnares/11.4.219 · Cited by 24 · see citing works

Orthology: another terminology muddle

Ouzounis, C. A. (1999) · Trends in Genetics · doi:10.1016/s0168-9525(99)01845-4 · Cited by 18 · see citing works

Estimation of the Number of Authentic Orphan Genes in Bacterial Genomes

Fukuchi, S. (2004) · DNA Research · doi:10.1093/dnares/11.4.311 · Cited by 15 · see citing works

Sequences Reveal Borrowed Genes

Pennisi, E. (2001) · Science · doi:10.1126/science.294.5547.1634b · Cited by 12 · see citing works

Homologuephobia.

Petsko, G. A. (2001) · Genome biology · doi:10.1186/gb-2001-2-2-comment1002 · Cited by 5 · see citing works

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., von Mering, C., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1094 · Cited by 4,398 · see citing works

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

King, N., Westbrook, M. J., Young, S. L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., et al. (2008) · Nature · doi:10.1038/nature06617 · Cited by 1,139 · see citing works

TreeFam: a curated database of phylogenetic trees of animal gene families

Li, H. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj118 · Cited by 523 · see citing works

TreeFam: 2008 update

Ruan, J., Li, H., Chen, Z., Coghlan, A., Coin, L. J. M., Guo, Y., Heriche, J.-K., Hu, Y., Kristiansen, K., Li, R., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm1005 · Cited by 332 · see citing works

A Post-Synaptic Scaffold at the Origin of the Animal Kingdom

Sakarya, O., Armstrong, K. A., Adamska, M., Adamski, M., Wang, I.-F., Tidor, B., Degnan, B. M., Oakley, T. H., & Kosik, K. S. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000506 · Cited by 291 · see citing works

AF2Complex predicts direct physical interactions in multimeric proteins with deep learning

Gao, M., Nakajima An, D., Parks, J. M., & Skolnick, J. (2022) · Nature Communications · doi:10.1038/s41467-022-29394-2 · Cited by 252 · see citing works

A Systems Biology Approach for the Investigation of the Heparin/Heparan Sulfate Interactome

Ori, A., Wilkinson, M. C., & Fernig, D. G. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.228114 · Cited by 251 · see citing works

Null mutations in human and mouse orthologs frequently result in different phenotypes

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Evolution of diverse cell division and vesicle formation systems in Archaea

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