Large-Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes

PHYLIP-Phylogeny inference package (Version 3.2)

Felsenstein, J. (1989) · Cladistics · Cited by 17,848 · 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

A molecular evolutionary framework for the phylum Nematoda

Blaxter, M., Ley, P. D., Garey, J. R., Liu, L. X., Scheldeman, P., Vierstraete, A. R., Vanfleteren, J. R., Mackey, L. Y., Dorris, M., Frisse, L. M., et al. (1998) · Nature · doi:10.1038/32160 · Cited by 1,975 · see citing works

Evidence for a clade of nematodes, arthropods and other moulting animals

Aguinaldo, A. M. A., Turbeville, J. M., Linford, L. S., Rivera, M. C., Garey, J. R., Raff, R. A., & Lake, J. A. (1997) · Nature · doi:10.1038/387489a0 · Cited by 1,609 · 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

Optimal alignments in linear space

Myers, E. W., & Miller, W. (1988) · Computer applications in the biosciences · doi:10.1093/bioinformatics/4.1.11 · Cited by 1,241 · see citing works

MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers

Kumar, S., Tamura, K., & Nei, M. (1994) · Computer applications in the biosciences · doi:10.1093/bioinformatics/10.2.189 · Cited by 1,166 · see citing works

Animal evolution: interrelationships of the living phyla

(2012) · Choice Reviews Online · doi:10.5860/choice.50-1469 · Cited by 1,041 · see citing works

A workbench for multiple alignment construction and analysis

Schuler, G. D., Altschul, S. F., & Lipman, D. J. (1991) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340090304 · Cited by 985 · see citing works

HOMEODOMAIN PROTEINS

Gehring, W. J., Affolter, M., & Bürglin, T. R. (1994) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.63.070194.002415 · Cited by 861 · see citing works

Issues in searching molecular sequence databases

Altschul, S. F., Boguski, M. S., Gish, W. R., & Wootton, J. C. (1994) · Nature Genetics · doi:10.1038/ng0294-119 · Cited by 773 · see citing works

[33] Analysis of compositionally biased regions in sequence databases

Wootton, J. C., & Federhen, S. (1996) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(96)66035-2 · Cited by 745 · see citing works

[27] Local alignment statistics

Altschul, S. F., & Gish, W. R. (1996) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(96)66029-7 · Cited by 720 · see citing works

Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock

Doolittle, R. F., Feng, D.-F., Tsang, S., Cho, G., & Little, E. (1996) · Science · doi:10.1126/science.271.5248.470 · Cited by 581 · see citing works

[30] Prediction and analysis of coiled-coil structures

Lupas, A. N. (1996) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(96)66032-7 · Cited by 575 · see citing works

The multiplicity of domains in proteins.

Doolittle, R. (1995) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.64.070195.001443 · Cited by 540 · see citing works

Application and Accuracy of Molecular Phylogenies

Hillis, D. M., Huelsenbeck, J. P., & Cunningham, C. (1994) · Science · doi:10.1126/science.8171318 · Cited by 494 · see citing works

The Role of the Genome Project in Determining Gene Function: Insights from Model Organisms

Miklos, G. L. G., & Rubin, G. M. (1996) · Cell · doi:10.1016/s0092-8674(00)80126-9 · Cited by 445 · see citing works

Determining divergence times with a protein clock: Update and reevaluation

Feng, D.-F., Cho, G. S., & Doolittle, R. F. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.24.13028 · Cited by 416 · see citing works

Gene Families: The Taxonomy of Protein Paralogs and Chimeras

Henikoff, S., Greene, E. A., Pietrokovski, S., Peer Bork, B., Attwood, T. K., & Hood, L. (1997) · Science · doi:10.1126/science.278.5338.609 · Cited by 389 · see citing works

Molecular evidence that echiurans and pogonophorans are derived annelids

McHugh, D. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.15.8006 · Cited by 369 · see citing works

Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea

Koonin, E. V., Mushegian, A. R., Galperin, M. Y., & Walker, D. R. (1997) · Molecular Microbiology · doi:10.1046/j.1365-2958.1997.4821861.x · Cited by 310 · 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

Positionally cloned human disease genes: Patterns of evolutionary conservation and functional motifs

Mushegian, A. R., Bassett, D. E., Boguski, M. S., Peer Bork, B., & Koonin, E. V. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.11.5831 · Cited by 239 · see citing works

Identification and mapping of human cDNAs homologous to Drosophila mutant genes through EST database searching

Banfi, S., Borsani, G., Rossi, E., Bernard, L., Guffanti, A., Rubboli, F., Marchitiello, A., Giglio, S., Coluccia, E., Zollo, M., et al. (1996) · Nature Genetics · doi:10.1038/ng0696-167 · Cited by 189 · see citing works

18S rRNA data indicate that Aschelminthes are polyphyletic in origin and consist of at least three distinct clades.

Winnepenninckx, B., Backeljau, T., Mackey, L. Y., Brooks, J. M., Wächter, R. D., Kumar, S., & Garey, J. R. (1995) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040287 · Cited by 187 · see citing works

SEALS: a system for easy analysis of lots of sequences.

Walker, D. R., & Koonin, E. V. (1997) · PubMed · Cited by 143 · see citing works

Molecular Analysis Supports a Tardigrade-Arthropod Association

Garey, J. R., Krotec, M., Nelson, D. R., & Brooks, J. (1996) · Invertebrate Biology · doi:10.2307/3226943 · Cited by 116 · see citing works

A molecular evolutionary framework for eukaryotic model organisms

Sidow, A., & Thomas, W. K. (1994) · Current Biology · doi:10.1016/s0960-9822(00)00131-7 · Cited by 108 · see citing works

Escaping from the Felsenstein Zone by Detecting Long Branches in Phylogenetic Data

Lyons‐Weiler, J., & Hoelzer, G. A. (1997) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1997.0450 · Cited by 91 · see citing works

Genome cross-referencing and XREFdb: Implications for the identification and analysis of genes mutated in human disease

Bassett, D. E., Boguski, M. S., Spencer, F. A., Reeves, R. H., Kim, S.-H., Weaver, T., & Hieter, P. (1997) · Nature Genetics · doi:10.1038/ng0497-339 · Cited by 90 · see citing works

[18] Protein sequence comparison at genome scale

Koonin, E. V., Tatusov, R. L., & Rudd, K. E. (1996) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(96)66020-0 · Cited by 80 · see citing works

The Coming of Age of Molecular Systematics

Maley, L. E., & Marshall, C. R. (1998) · Science · doi:10.1126/science.279.5350.505 · Cited by 64 · see citing works

Turn to the worm!

Ahringer, J. (1997) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(97)80157-8 · Cited by 42 · see citing works

Around the genomes: the Drosophila genome project.Preprint

Rubin, G. M. (1996) · Genome Research · doi:10.1101/gr.6.2.71 · Cited by 39 · see citing works

Biomaterials and Granulomas

Griffiths, M. M., Langone, J. J., & Lightfoote, M. M. (1996) · Methods · doi:10.1006/meth.1996.0034 · Cited by 27 · see citing works

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 · 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

Evolution of protein kinase signaling from yeast to man

Manning, G., Plowman, G. D., Hunter, T. R., & Sudarsanam, S. (2002) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(02)02179-5 · Cited by 986 · see citing works

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

Wang, Y., Coleman‐Derr, D., Chen, G., & Gu, Y. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv487 · Cited by 888 · see citing works

The origin and evolution of model organisms

Hedges, S. B. (2002) · Nature Reviews Genetics · doi:10.1038/nrg929 · Cited by 806 · see citing works

Multigene Analyses of Bilaterian Animals Corroborate the Monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia

Philippe, H., Lartillot, N., & Brinkmann, H. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi111 · Cited by 551 · see citing works

The 630-kb lung cancer homozygous deletion region on human chromosome 3p21.3: identification and evaluation of the resident candidate tumor suppressor genes. The International Lung Cancer Chromosome 3p21.3 Tumor Suppressor Gene Consortium.

Lerman, M. I., & Minna, J. D. (2000) · PubMed · Cited by 537 · see citing works

OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes

Sun, J., Lü, F., Luo, Y., Bie, L., Xu, L., & Wang, Y. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad313 · Cited by 536 · see citing works

Estimating metazoan divergence times with a molecular clock

Peterson, K. J., Lyons, J. B., Nowak, K. S., Takacs, C. M., Wargo, M. J., & McPeek, M. A. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401670101 · Cited by 461 · see citing works

The Basic Helix-Loop-Helix Protein Family: Comparative Genomics and Phylogenetic AnalysisPreprint

Ledent, V., & Vervoort, M. (2001) · Genome Research · doi:10.1101/gr.177001 · Cited by 455 · see citing works

Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments

Philippe, H., Snell, E. A., Bapteste, E. P., Lopez, P., Holland, P. W. H., & Casañe, D. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh182 · Cited by 398 · see citing works

Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss

Kiontke, K. C., Gavin, N. P., Raynes, Y., Roehrig, C., Piano, F., & Fitch, D. H. A. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0403094101 · Cited by 367 · see citing works

EST Analysis of the Cnidarian Acropora millepora Reveals Extensive Gene Loss and Rapid Sequence Divergence in the Model Invertebrates

Kortschak, R. D., Samuel, G., Saint, R., & Miller, D. J. (2003) · Current Biology · doi:10.1016/j.cub.2003.11.030 · Cited by 353 · see citing works

The draft genome of the parasitic nematode Trichinella spiralis

Mitreva, M., Jasmer, D. P., Zarlenga, D. S., Wang, Z., Abubucker, S., Martin, J. C., Taylor, C. M., Yin, Y., Fulton, L. A., Minx, P., et al. (2011) · Nature Genetics · doi:10.1038/ng.769 · Cited by 326 · see citing works

Eukaryotic Signalling Domain Homologues in Archaea and Bacteria. Ancient Ancestry and Horizontal Gene Transfer

Ponting, C. P., Aravind, L., Schultz, J., Peer Bork, B., & Koonin, E. V. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2827 · Cited by 321 · see citing works

The Taxonomy of Developmental Control in <i>Caenorhabditis elegans</i>

Ruvkun, G., & Hobert, O. (1998) · Science · doi:10.1126/science.282.5396.2033 · Cited by 305 · see citing works

Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch

Mallatt, J. M., & Giribet, G. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.04.021 · Cited by 301 · see citing works

Caenorhabditis elegans Is a Nematode

Blaxter, M. (1998) · Science · doi:10.1126/science.282.5396.2041 · Cited by 283 · see citing works

Divergence Times in Caenorhabditis and Drosophila Inferred from Direct Estimates of the Neutral Mutation Rate

Cutter, A. D. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn024 · Cited by 268 · see citing works

Automatic clustering of orthologs and inparalogs shared by multiple proteomes

Alexeyenko, A., Tamaš, I., Liu, G., & Sonnhammer, E. L. L. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl213 · Cited by 248 · see citing works

Coelomata and Not Ecdysozoa: Evidence From Genome-Wide Phylogenetic AnalysisPreprint

Wolf, Y. I., Rogozin, I. B., & Koonin, E. V. (2004) · Genome Research · doi:10.1101/gr.1347404 · Cited by 247 · see citing works

Urochordates Are Monophyletic Within the Deuterostomes

Swalla, B. J., Cameron, C. B., Lavine, L. C., & Garey, J. R. (2000) · Systematic Biology · doi:10.1080/10635150050207384 · Cited by 245 · see citing works

Gene Family Evolution and Homology: Genomics Meets Phylogenetics

Thornton, J. W., & DeSalle, R. (2000) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.1.1.41 · Cited by 225 · see citing works

The evolutionary position of nematodes

Blair, J. E., Ikeo, K., Gojobori, T., & Hedges, S. B. (2002) · BMC Evolutionary Biology · doi:10.1186/1471-2148-2-7 · Cited by 218 · see citing works

Fourfold Faster Rate of Genome Rearrangement in Nematodes Than in DrosophilaPreprint

Coghlan, A., & Wolfe, K. H. (2002) · Genome Research · doi:10.1101/gr.172702 · Cited by 212 · see citing works

Phylogenetic analysis of the human basic helix-loop-helix proteins

Ledent, V., Paquet, O., & Vervoort, M. (2002) · Genome biology · doi:10.1186/gb-2002-3-6-research0030 · Cited by 208 · see citing works

Dating the Time of Origin of Major Clades: Molecular Clocks and the Fossil Record

Smith, A. B., & Peterson, K. J. (2002) · Annual Review of Earth and Planetary Sciences · doi:10.1146/annurev.earth.30.091201.140057 · Cited by 193 · see citing works

Cupriavidus metallidurans: evolution of a metal-resistant bacterium

von Rozycki, T., & Nies, D. H. (2008) · Antonie van Leeuwenhoek · doi:10.1007/s10482-008-9284-5 · Cited by 192 · 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

High-Throughput Isolation of Caenorhabditis elegans Deletion MutantsPreprint

Liu, L. X., Spoerke, J. M., Mulligan, E. L., Chen, J., Reardon, B., Westlund, B., Sun, L., Abel, K., Armstrong, B. A., Hardiman, G., et al. (1999) · Genome Research · doi:10.1101/gr.9.9.859 · Cited by 175 · see citing works

The Opisthokonta and the Ecdysozoa May Not Be Clades: Stronger Support for the Grouping of Plant and Animal than for Animal and Fungi and Stronger Support for the Coelomata than Ecdysozoa

Philip, G. K., Creevey, C. J., & McInerney, J. O. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi102 · Cited by 170 · see citing works

Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa

Sperling, E. A., Peterson, K. J., & Pisani, D. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp148 · Cited by 172 · see citing works

Prediction of the odorant binding site of olfactory receptor proteins by human–mouse comparisons

Man, O., Gilad, Y., & Lancet, D. (2003) · Protein Science · doi:10.1110/ps.03296404 · Cited by 155 · see citing works

Nuclear receptors in nematodes: themes and variations

Sluder, A. E. (2001) · Trends in Genetics · doi:10.1016/s0168-9525(01)02242-9 · Cited by 157 · see citing works

What Was the Set of Ubiquitin and Ubiquitin-Like Conjugating Enzymes in the Eukaryote Common Ancestor?

Michelle, C., Vourc’h, P., Mignon, L., & Andres, C. R. (2009) · Journal of Molecular Evolution · doi:10.1007/s00239-009-9225-6 · Cited by 153 · see citing works

The Evolution of SMC Proteins: Phylogenetic Analysis and Structural Implications

Cobbe, N., & Heck, M. M. S. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh023 · Cited by 146 · see citing works

The tardigrade Hypsibius dujardini, a new model for studying the evolution of development

Gabriel, W. N., McNuff, R., Patel, S. K., Gregory, T. R., Jeck, W. R., Jones, C. D., & Goldstein, B. (2007) · Developmental Biology · doi:10.1016/j.ydbio.2007.09.055 · Cited by 147 · see citing works

Poriferan mtDNA and Animal Phylogeny Based on Mitochondrial Gene Arrangements

Lavrov, D. V., & Lang, B. F. (2005) · Systematic Biology · doi:10.1080/10635150500221044 · Cited by 147 · see citing works

S-adenosyl-L-homocysteine hydrolase and methylation disorders: Yeast as a model system

Tehlivets, O., Malanović, N., Visram, M., Pavkov‐Keller, T., & Keller, W. (2012) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2012.09.007 · Cited by 145 · see citing works

Explosive Lineage-Specific Expansion of the Orphan Nuclear Receptor HNF4 in Nematodes

Robinson‐Rechavi, M., Maina, C. V., Gissendanner, C. R., Laudet, V., & Sluder, A. E. (2005) · Journal of Molecular Evolution · doi:10.1007/s00239-004-0175-8 · Cited by 141 · see citing works

Nematoda: Genes, Genomes and the Evolution of Parasitism

Blaxter, M. (2003) · Advances in Parasitology/Advances in parasitology · doi:10.1016/s0065-308x(03)54003-9 · Cited by 127 · see citing works

Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

Riesgo, A., Andrade, S. C. S., Sharma, P. P., Novo, M., Pérez-Porro, A. R., Vahtera, V., González, V. L., Kawauchi, G. Y., & Giribet, G. (2012) · Frontiers in Zoology · doi:10.1186/1742-9994-9-33 · Cited by 126 · see citing works

Phylogenomics of Life-Or-Death Switches in Multicellular Animals: Bcl-2, BH3-Only, and BNip Families of Apoptotic Regulators

Aouacheria, A., Brunet, F., & Gouy, M. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi234 · Cited by 125 · see citing works

Evolution of secretin family GPCR members in the metazoa

Cardoso, J. C. R., Pinto, V., Vieira, F. A., Clark, M. S., & Power, D. M. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-108 · Cited by 123 · see citing works

Molecules, development and fossils in the study of metazoan evolution; Articulata versus Ecdysozoa revisited

Giribet, G. (2003) · Zoology · doi:10.1078/0944-2006-00131 · Cited by 119 · see citing works

Dating the early evolution of plants: detection and molecular clock analyses of orthologs

Zimmer, A. D., Lang, D., Richardt, S., Frank, W., Reski, R., & Rensing, S. A. (2007) · Molecular Genetics and Genomics · doi:10.1007/s00438-007-0257-6 · Cited by 115 · see citing works

Insights into Early Extracellular Matrix Evolution: Spongin Short Chain Collagen-Related Proteins Are Homologous to Basement Membrane Type IV Collagens and Form a Novel Family Widely Distributed in Invertebrates

Aouacheria, A., Geourjon, C., Aghajari, N., Navratil, V., Deléage, G., Lethias, C., & Exposito, J. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl100 · Cited by 110 · see citing works

Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the idiosyncrasies of <i>Caenorhabditis elegans</i>

Copley, R. R., Aloy, P., Russell, R. B., & Telford, M. J. (2004) · Evolution &amp; Development · doi:10.1111/j.1525-142x.2004.04021.x · Cited by 108 · see citing works

Diversity, taxonomy and evolution of medium‐chain dehydrogenase/reductase superfamily

Riveros‐Rosas, H., Julián‐Sánchez, A., Villalobos‐Molina, R., Pardo, J. P., & Piña, E. (2003) · European Journal of Biochemistry · doi:10.1046/j.1432-1033.2003.03704.x · Cited by 103 · see citing works

Functional and Pathological Roles of AHCY

Vizán, P., Croce, L. D., & Aranda, S. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.654344 · Cited by 99 · see citing works

Mitogenomics and phylogenomics reveal priapulid worms as extant models of the ancestral Ecdysozoan

Webster, B. L., Copley, R. R., Jenner, R. A., Mackenzie‐Dodds, J. A., Bourlat, S. J., Rota‐Stabelli, O., Littlewood, D. T. J., & Telford, M. J. (2006) · Evolution & Development · doi:10.1111/j.1525-142x.2006.00123.x · Cited by 98 · see citing works

Bilaterian Phylogeny: A Broad Sampling of 13 Nuclear Genes Provides a New Lophotrochozoa Phylogeny and Supports a Paraphyletic Basal Acoelomorpha

Paps, J., Baguñà, J., & Riutort, M. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp150 · Cited by 95 · see citing works

Genome-scale evidence of the nematode-arthropod clade

Dopazo, H., & Dopazo, J. (2005) · Genome biology · doi:10.1186/gb-2005-6-5-r41 · Cited by 93 · see citing works

Epigenetics and Cancer

Verma, M., Maruvada, P., & Srivastava, S. (2004) · Critical Reviews in Clinical Laboratory Sciences · doi:10.1080/10408360490516922 · Cited by 85 · see citing works

Loss of ancestral genes in the genomic evolution of Ciona intestinalis

Hughes, A. L., & Friedman, R. (2005) · Evolution & Development · doi:10.1111/j.1525-142x.2005.05022.x · Cited by 84 · see citing works

The Essential Role of “Minor” Phyla in Molecular Studies of Animal Evolution

Garey, J. R., & Schmidt‐Rhaesa, A. (1998) · American Zoologist · doi:10.1093/icb/38.6.907 · Cited by 77 · see citing works

First Sequenced Mitochondrial Genome from the Phylum Acanthocephala(Leptorhynchoides thecatus) and Its Phylogenetic Position Within Metazoa

Steinauer, M. L., Nickol, B. B., Broughton, R. E., & Ortı́, G. (2005) · Journal of Molecular Evolution · doi:10.1007/s00239-004-0159-8 · Cited by 76 · see citing works

Ancient Origin of the Parkinson Disease Gene LRRK2

Marı́n, I. (2008) · Journal of Molecular Evolution · doi:10.1007/s00239-008-9122-4 · Cited by 76 · see citing works

Nematode genome evolution

Coghlan, A. (2005) · WormBook · doi:10.1895/wormbook.1.15.1 · Cited by 74 · see citing works

S-Adenosyl-L-homocysteine Hydrolase, Key Enzyme of Methylation Metabolism, Regulates Phosphatidylcholine Synthesis and Triacylglycerol Homeostasis in Yeast

Malanović, N., Streith, I. E., Wolinski, H., Rechberger, G. N., Kohlwein, S. D., & Tehlivets, O. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m800830200 · Cited by 74 · see citing works

Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series

Rogozin, I. B., Thomson, K., Csürös, M., Carmel, L., & Koonin, E. V. (2008) · Biology Direct · doi:10.1186/1745-6150-3-7 · Cited by 73 · see citing works

Ecdysozoa: The Relationship between Cycloneuralia and Panarthropoda

Garey, J. R. (2001) · Zoologischer Anzeiger · doi:10.1078/0044-5231-00039 · Cited by 72 · see citing works

Support for the Coelomata Clade of Animals from a Rigorous Analysis of the Pattern of Intron Conservation

Zheng, J., Rogozin, I. B., Koonin, E. V., & Przytycka, T. M. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm207 · Cited by 70 · see citing works

Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation

Wang, Z., Abubucker, S., Martin, J. C., Wilson, R. K., Hawdon, J. M., & Mitreva, M. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-307 · Cited by 69 · see citing works

Large-Scale Comparison of Fungal Sequence Information: Mechanisms of Innovation in Neurospora crassa and Gene Loss in Saccharomyces cerevisiaePreprint

Braun, E. L., Halpern, A. L., Nelson, M. A., & Natvig, D. O. (2000) · Genome Research · doi:10.1101/gr.10.4.416 · Cited by 69 · see citing works

Ecdysozoan Clade Rejected by Genome-Wide Analysis of Rare Amino Acid Replacements

Rogozin, I. B., Wolf, Y. I., Carmel, L., & Koonin, E. V. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm029 · Cited by 68 · see citing works

SimiTri—visualizing similarity relationships for groups of sequences

Parkinson, J., & Blaxter, M. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btf870 · Cited by 66 · see citing works

Multi-Omics Driven Assembly and Annotation of the Sandalwood (Santalum album) Genome

Mahesh, H. B., Subba, P., Advani, J., Shirke, M. D., Loganathan, R. M., Chandana, S., Shilpa, S., Chatterjee, O., Pinto, S. M., Prasad, T. S. K., et al. (2018) · PLANT PHYSIOLOGY · doi:10.1104/pp.17.01764 · Cited by 66 · see citing works

Bilaterian Phylogeny Based on Analyses of a Region of the Sodium–Potassium ATPase β-Subunit Gene

Anderson, F. E., Córdoba, A. J., & Thollesson, M. (2004) · Journal of Molecular Evolution · doi:10.1007/s00239-003-2548-9 · Cited by 65 · see citing works

Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens

Rensing, S. A., Fritzowsky, D., Lang, D., & Ralf Reski, A. (2005) · BMC Genomics · doi:10.1186/1471-2164-6-43 · Cited by 64 · see citing works

OrthoDisease: A database of human disease orthologs

O'Brien, K. P., Westerlund, I., & Sonnhammer, E. L. L. (2004) · Human Mutation · doi:10.1002/humu.20068 · Cited by 64 · see citing works

Protein families in multicellular organisms

Copley, R. R., Schultz, J., Ponting, C. P., & Peer Bork, B. (1999) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(99)80055-4 · Cited by 63 · see citing works

The multimeric β‐thymosin found in nematodes and arthropods is not a synapomorphy of the Ecdysozoa

Telford, M. J. (2004) · Evolution & Development · doi:10.1111/j.1525-142x.2004.04013.x · Cited by 59 · see citing works

A retrograde signal is involved in activity-dependent remodeling at a <i>C. elegans</i> neuromuscular junction

Zhao, H., & Nonet, M. L. (2000) · Development · doi:10.1242/dev.127.6.1253 · Cited by 57 · see citing works

Medical significance ofCaenorhabditis elegans

Aboobaker, A. A., & Blaxter, M. (2000) · Annals of Medicine · doi:10.3109/07853890008995906 · Cited by 56 · see citing works

The Caenorhabditis elegans voltage-gated calcium channel subunits UNC-2 and UNC-36 and the calcium-dependent kinase UNC-43/CaMKII regulate neuromuscular junction morphology

Caylor, R. C., Jin, Y., & Ackley, B. D. (2013) · Neural Development · doi:10.1186/1749-8104-8-10 · Cited by 53 · see citing works

A Novel Hybrid Yeast-Human Network Analysis Reveals an Essential Role for FNBP1L in Antibacterial Autophagy

Huett, A. S., Ng, A., Cao, Z., Kuballa, P., Komatsu, M., Daly, M. J., Podolsky, D. K., & Xavier, R. J. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0803050 · Cited by 52 · see citing works

Molecular characterization and phylogenetic evaluation of the hsp90 gene from selected nematodes.

Skantar, A. M., & Carta, L. K. (2004) · PubMed Central · Cited by 52 · 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

The Caenorhabditis elegans fate-determining gene mab-9 encodes a T-box protein required to pattern the posterior hindgutPreprint

Woollard, A. C. S., & Hodgkin, J. (2000) · Genes & Development · doi:10.1101/gad.14.5.596 · Cited by 51 · see citing works

Methionine Adenosyltransferase as a Useful Molecular Systematics Tool Revealed by Phylogenetic and Structural Analyses

Sanchez‐Perez, G. F., Bautista, J. M., & Pajares, M. A. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.11.022 · Cited by 50 · see citing works

Marine ecological genomics: when genomics meets marine ecology

Dupont, S., Wilson, K., Obst, M., Sköld, H. N., Nakano, H., & Thorndyke, M. C. (2007) · Marine Ecology Progress Series · doi:10.3354/meps332257 · Cited by 46 · see citing works

The Family of Caenorhabditis elegans Tyrosine Kinase Receptors: Similarities and Differences with Mammalian ReceptorsPreprint

Popovici, C., Roubin, R., Coulier, F., Pontarotti, P., & Birnbaum, D. (1999) · Genome Research · doi:10.1101/gr.9.11.1026 · Cited by 46 · see citing works

Sequence Survey of the Genome of the Opportunistic Microsporidian Pathogen, Vittaforma corneae

Mittleider, D., Green, L. C., Mann, V. H., Michael, S. F., Didier, E. S., & Brindley, P. J. (2002) · Journal of Eukaryotic Microbiology · doi:10.1111/j.1550-7408.2002.tb00218.x · Cited by 45 · see citing works

Analysis of Rare Amino Acid Replacements Supports the Coelomata Clade

Rogozin, I. B., Wolf, Y. I., Carmel, L., & Koonin, E. V. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm218 · Cited by 45 · see citing works

Comparative analysis of in vivo interactions between Rev1 protein and other Y-family DNA polymerases in animals and yeasts

Kosarek, J. N., Woodruff, R. V., Rivera-Begeman, A., Guo, C., D’Souza, S., Koonin, E. V., Walker, G. C., & Friedberg, E. C. (2008) · DNA repair · doi:10.1016/j.dnarep.2007.11.016 · Cited by 44 · see citing works

Hazardous effect of tannery solid waste leachates on development and reproduction in Drosophila melanogaster: 70kDa heat shock protein as a marker of cellular damage

Siddique, H. R., Mitra, K., Bajpai, V. K., Ram, K. R., Saxena, D. K., & Chowdhuri, D. K. (2009) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2009.06.010 · Cited by 41 · see citing works

Comparative Analysis of the Flavobacterium columnare Genomovar I and II Genomes

Kumru, S., Tekedar, H. C., Gülsoy, N., Waldbieser, G. C., Lawrence, M. L., & Karsi, A. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01375 · Cited by 41 · see citing works

Homocysteine regulates fatty acid and lipid metabolism in yeast

Visram, M., Radulovic, M., Steiner, S., Malanović, N., Eichmann, T. O., Wolinski, H., Rechberger, G. N., & Tehlivets, O. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.m117.809236 · Cited by 39 · see citing works

Classification of Transmembrane Protein Families in the Caenorhabditis elegans Genome and Identification of Human OrthologsPreprint

Remm, M. (2000) · Genome Research · doi:10.1101/gr.gr-1491r · Cited by 39 · see citing works

Model species in evo‐devo: a philosophical perspective

Bolker, J. A. (2014) · Evolution & Development · doi:10.1111/ede.12056 · Cited by 34 · see citing works

Therapeutic target discovery using Caenorhabditis elegans

Link, E. M., Hardiman, G., Sluder, A. E., Johnson, C. D., & Liu, L. X. (2000) · Pharmacogenomics · doi:10.1517/14622416.1.2.203 · Cited by 35 · see citing works

Molecular Cloning of a Zinc Finger Autoantigen Transiently Associated with Interphase Nucleolus and Mitotic Centromeres and Midbodies

Bolı́var, J., Dı́az, I., Iglesias, C., & Valdivia, M. M. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.51.36456 · Cited by 33 · see citing works

Interspecies conservation of gene order and intron-exon structure in a genomic locus of high gene density and complexity in Plasmodium

van Lin, L. H. M. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.10.2059 · Cited by 33 · see citing works

Allelic variation within the S-adenosyl-L-homocysteine hydrolase gene family is associated with wood properties in Chinese white poplar (Populus tomentosa)

Du, Q., Wang, L., Zhou, D., Yang, H., Gong, C., Pan, W., & Zhang, D. (2014) · BMC Genetics · doi:10.1186/1471-2156-15-s1-s4 · Cited by 32 · see citing works

Paralogy and Orthology of Tyrosine Kinases that Can Extend the Life Span of Caenorhabditis elegans

Rikke, B. A., Murakami, S., & Johnson, T. E. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026346 · Cited by 31 · see citing works

Characterization of the Deleted in Autism 1 Protein Family: Implications for Studying Cognitive Disorders

Aziz, A., Harrop, S. P., & Bishop, N. E. (2011) · PLoS ONE · doi:10.1371/journal.pone.0014547 · Cited by 30 · see citing works

The essential Drosophila melanogaster gene wds (will die slowly) codes for a WD-repeat protein with seven repeats

Hollmann, M., Simmerl, E., Schäfer, U., & Schäfer, M. (2002) · Molecular Genetics and Genomics · doi:10.1007/s00438-002-0768-0 · Cited by 30 · see citing works

Rare Genomic Characters Do Not Support Coelomata: RGC_CAMs

Roy, S. W., & Irimia, M. (2008) · Journal of Molecular Evolution · doi:10.1007/s00239-008-9077-5 · Cited by 30 · see citing works

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics

Schreiber, F., Pick, K., Erpenbeck, D., Wörheide, G., & Morgenstern, B. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-219 · Cited by 29 · see citing works

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 · see citing works

Orthology and Functional Conservation in Eukaryotes

Dolinski, K. J., & Botstein, D. (2007) · Annual Review of Genetics · doi:10.1146/annurev.genet.40.110405.090439 · Cited by 118 · see citing works

et al., Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes

Schrimpf, S., Weiß, M., Jovanovic, M., Lercher, M. J., Hunziker, P., Aebersold, R. H., & Hengartner, M. O. (2015)

Investigating 42 candidate orthologous protein groups by molecular evolutionary analysis on genome scale

Xie, T., & Ding, D.-F. (2000) · Gene · doi:10.1016/s0378-1119(00)00506-0 · Cited by 17 · see citing works

Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes

Schrimpf, S. P., Weiss, M., Reiter, L., Ahrens, C. H., Jovanovic, M., Malmström, J., Brunner, E., Mohanty, S., Lercher, M. J., Hunziker, P. E., et al. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000048 · Cited by 229 · see citing works