Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · see citing works

Gene Ontology: tool for the unification of biology

Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206 · see citing works

Initial sequencing and analysis of the human genome

International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216 · see citing works

Molecular Evolutionary Genetics

Nei, M. (1987) · Columbia University Press eBooks · doi:10.7312/nei-92038 · Cited by 16,583 · see citing works

Evolutionary trees from DNA sequences: A maximum likelihood approach.

Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571 · see citing works

Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology

Fitch, W. M. (1971) · Systematic Biology · doi:10.1093/sysbio/20.4.406 · Cited by 7,690 · see citing works

Initial sequencing and comparative analysis of the mouse genome

Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187 · see citing works

Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology

Fitch, W. M. (1971) · Systematic Zoology · doi:10.2307/2412116 · Cited by 5,661 · see citing works

PAML: a program package for phylogenetic analysis by maximum likelihood

Yang, Z. (1997) · Computer applications in the biosciences · doi:10.1093/bioinformatics/13.5.555 · Cited by 5,344 · see citing works

Finishing the euchromatic sequence of the human genome

International Human Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03001 · Cited by 4,971 · 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

Construction of Phylogenetic Trees

Fitch, W. M., & Margoliash, E. (1967) · Science · doi:10.1126/science.155.3760.279 · Cited by 3,611 · see citing works

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

International Chicken Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03154 · Cited by 2,750 · see citing works

Genome sequence, comparative analysis and haplotype structure of the domestic dog

members, B. S. P., Lindblad-Toh, K., Wade, C. M., Mikkelsen, T. S., Karlsson, E. K., Jaffe, D. B., Kamal, M., Clamp, M., Chang, J. L., Kulbokas, E. J., et al. (2005) · Nature · doi:10.1038/nature04338 · Cited by 2,568 · see citing works

Initial sequence of the chimpanzee genome and comparison with the human genome

The Chimpanzee Sequencing and Analysis Consortium (2005) · Nature · doi:10.1038/nature04072 · Cited by 2,459 · see citing works

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Gibbs, R. A., Weinstock, G. M., Metzker, M. L., Muzny, D. M., Sodergren, E. J., Scherer, S. E., Scott, G., Steffen, D. L., Worley, K. C., Burch, P. E., et al. (2004) · Nature · doi:10.1038/nature02426 · Cited by 2,147 · see citing works

The effect of linkage on limits to artificial selection

Hill, W. G., & Robertson, A. (1966) · Genetical Research · doi:10.1017/s0016672300010156 · Cited by 1,823 · see citing works

The origins of genome complexity

Lynch, M., & Conery, J. S. (2003) · Science · doi:10.1126/science.1089370 · Cited by 1,698 · see citing works

The effect of linkage on limits to artificial selection

Hill, W. G., & Robertson, A. (2007) · Genetics Research · doi:10.1017/s001667230800949x · Cited by 1,562 · 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

Human–Mouse Alignments with BLASTZPreprint

Schwartz, S., Kent, W. J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R. C., Haussler, D. H., & Miller, W. (2002) · Genome Research · doi:10.1101/gr.809403 · Cited by 1,231 · 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

The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics

Stein, L. D., Bao, Z., Blasiar, D., Blumenthal, T., Brent, M. R., Chen, N., Chinwalla, A., Clarke, L., Clee, C. M., Coghlan, A., et al. (2003) · PLoS Biology · doi:10.1371/journal.pbio.0000045 · Cited by 931 · 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

Determinants of Substitution Rates in Mammalian Genes: Expression Pattern Affects Selection Intensity but Not Mutation Rate

Duret, L., & Mouchiroud, D. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026239 · Cited by 505 · see citing works

An Alu Transposition Model for the Origin and Expansion of Human Segmental Duplications

Bailey, J. A., Liu, G., & Eichler, E. E. (2003) · The American Journal of Human Genetics · doi:10.1086/378594 · Cited by 434 · see citing works

Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed Pseudogenes in the Human GenomePreprint

Zhang, Z. (2003) · Genome Research · doi:10.1101/gr.1429003 · Cited by 420 · see citing works

Ensembl 2005

Hubbard, T. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki138 · Cited by 348 · see citing works

Identification and analysis of alternative splicing events conserved in human and mouse

Yeo, G. W.-M., Nostrand, E. L. V., Holste, D., Poggio, T., & Burge, C. B. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409742102 · Cited by 299 · see citing works

A Genome-Wide Survey of Human PseudogenesPreprint

Torrents, D. (2003) · Genome Research · doi:10.1101/gr.1455503 · Cited by 286 · see citing works

Transcription-associated mutational asymmetry in mammalian evolution

Program, N. C. S., Green, P., Ewing, B., Miller, W., Thomas, P. J., & Green, E. D. (2003) · Nature Genetics · doi:10.1038/ng1103 · Cited by 285 · see citing works

Transcription-mediated gene fusion in the human genomePreprint

Akiva, P., Toporik, A., Edelheit, S., Peretz, Y., Diber, A., Shemesh, R., Novik, A., & Sorek, R. (2005) · Genome Research · doi:10.1101/gr.4137606 · Cited by 285 · see citing works

Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian EvolutionPreprint

Hardison, R. C., Roskin, K., Yang, S., Diekhans, M., Kent, W. J., Weber, R., Elnitski, L., Li, J., O'Connor, M., Kolbe, D., et al. (2003) · Genome Research · doi:10.1101/gr.844103 · Cited by 280 · see citing works

Deleterious Mutations and the Evolution of Sex

Keightley, P. D., & Eyre‐Walker, A. (2000) · Science · doi:10.1126/science.290.5490.331 · Cited by 262 · see citing works

Bias of Selection on Human Copy-Number Variants

Nguyen, D.-Q., Webber, C., & Ponting, C. P. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020020 · Cited by 255 · see citing works

A 1-Mb resolution radiation hybrid map of the canine genome

Guyon, R., Lorentzen, T. D., Hitte, C., Kim, L., Cadieu, É., Parker, H. G., Quignon, P., Lowe, J. K., Renier, C. M., Gelfenbeyn, B., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0831002100 · Cited by 244 · see citing works

Ensembl 2002: accommodating comparative genomics

Clamp, M. E. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg083 · Cited by 243 · see citing works

Hotspots of mammalian chromosomal evolution

Bailey, J. A., Baertsch, R., Kent, W. J., Haussler, D. H., & Eichler, E. E. (2004) · Genome biology · doi:10.1186/gb-2004-5-4-r23 · Cited by 235 · see citing works

Comparison of the genomes of human and mouse lays the foundation of genome zoology

Emes, R. D. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg078 · Cited by 220 · see citing works

A simple algorithm to infer gene duplication and speciation events on a gene tree

Zmasek, C. M., & Eddy, S. R. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.9.821 · Cited by 206 · see citing works

Tandem chimerism as a means to increase protein complexity in the human genomePreprint

Farré, G. P., Reymond, A., Dabbouseh, N., Dermitzakis, E. T., Castelo, R., Thomson, T. M., Antonarakis, S. E., & Guigó, R. (2005) · Genome Research · doi:10.1101/gr.4145906 · Cited by 203 · see citing works

Quality assessment of the human genome sequence

Schmutz, J., Wheeler, J., Grimwood, J., Dickson, M. C., Yang, J., Caoile, C., Bajorek, E. S., Black, S., Chan, Y. M., Denys, M. E., et al. (2004) · Nature · doi:10.1038/nature02390 · Cited by 195 · 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

Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model

Lunter, G. A., Ponting, C. P., & Hein, J. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020005 · Cited by 174 · see citing works

Nature and Structure of Human Genes that Generate RetropseudogenesPreprint

Gonçalves, I., Duret, L., & Mouchiroud, D. (2000) · Genome Research · doi:10.1101/gr.10.5.672 · Cited by 174 · see citing works

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages

Bourque, G., Zdobnov, E. M., Bork, P., Pevzner, P. A., & Tesler, G. (2005) · Genome Research · doi:10.1101/gr.3002305 · Cited by 162 · see citing works

The Structure and Early Evolution of Recently Arisen Gene Duplicates in the Caenorhabditis elegans Genome

Katju, V., & Lynch, M. (2003) · Genetics · doi:10.1093/genetics/165.4.1793 · Cited by 151 · see citing works

Reciprocal Chromosome Painting Reveals Detailed Regions of Conserved Synteny between the Karyotypes of the Domestic Dog (Canis familiaris) and Human

Breen, M., Thomas, R. J., Binns, M. M., Carter, N. P., & Langford, C. F. (1999) · Genomics · doi:10.1006/geno.1999.5947 · Cited by 149 · see citing works

Alternative splicing of conserved exons is frequently species-specific in human and mouse

Pan, Q., Bakowski, M. A., Morris, Q., Zhang, W., Frey, B. J., Hughes, T. R., & Blencowe, B. J. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.12.004 · Cited by 149 · see citing works

Gene conversion drives GC content evolution in mammalian histones

Galtier, N. (2003) · Trends in Genetics · doi:10.1016/s0168-9525(02)00002-1 · Cited by 145 · see citing works

Patterns of Segmental Duplication in the Human Genome

Zhang, L. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh262 · Cited by 129 · see citing works

An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing

Margulies, E. H., Vinson, J. P., Program¶, N. C. S., Miller, W., Jaffe, D. B., Lindblad‐Toh, K., Chang, J. L., Green, E. D., Lander, E. S., Mullikin, J. C., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409882102 · Cited by 118 · see citing works

Extensive Conservation of Sex Chromosome Organization Between Cat and Human Revealed by Parallel Radiation Hybrid MappingPreprint

Murphy, W. J., Sun, S., Chen, Z.-Q., Pecon‐Slattery, J., & O’Brien, S. J. (1999) · Genome Research · doi:10.1101/gr.9.12.1223 · Cited by 115 · see citing works

Differential Expansion of Zinc-Finger Transcription Factor Loci in Homologous Human and Mouse Gene ClustersPreprint

Shannon, M., Hamilton, A. T., Gordon, L. A., Branscomb, E., & Stubbs, L. J. (2003) · Genome Research · doi:10.1101/gr.963903 · Cited by 95 · see citing works

Similar Rates but Different Modes of Sequence Evolution in Introns and at Exonic Silent Sites in Rodents: Evidence for Selectively Driven Codon Usage

Chamary, J., & Hurst, L. D. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh087 · Cited by 94 · see citing works

THE EVOLUTION OF MULTIGENE FAMILIES UNDER INTRACHROMOSOMAL GENE CONVERSION

Nagylaki, T. (1984) · Genetics · doi:10.1093/genetics/106.3.529 · Cited by 83 · see citing works

Dependence of Mutational Asymmetry on Gene-Expression Levels in the Human Genome

Majewski, J. (2003) · The American Journal of Human Genetics · doi:10.1086/378134 · Cited by 82 · see citing works

Substitution Rates in Drosophila Nuclear Genes: Implications for Translational Selection

Dunn, K. A., Bielawski, J. P., & Yang, Z. (2001) · Genetics · doi:10.1093/genetics/157.1.295 · Cited by 79 · see citing works

A weighted least-squares approach for inferring phylogenies from incomplete distance matrices

Makarenkov, V., & Lapointe, F. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth211 · Cited by 61 · see citing works

Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites

Kondrashov, F. A., Ogurtsov, A. Y., & Kondrashov, A. S. (2005) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2005.10.020 · Cited by 59 · see citing works

Erratum: Corrigendum: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

International Chicken Genome Sequencing Consortium (2005) · Nature · doi:10.1038/nature03394 · Cited by 59 · see citing works

Gene Expression, Synteny, and Local Similarity in Human Noncoding Mutation Rates

Webster, M. T. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh181 · Cited by 35 · see citing works

Conservation of Gene Order between Horse and Human X Chromosomes as Evidenced through Radiation Hybrid Mapping

Raudsepp, T., Kata, S. R., Piumi, F., Swinburne, J. E., Womack, J. E., Skow, L. C., & Chowdhary, B. P. (2002) · Genomics · doi:10.1006/geno.2002.6723 · Cited by 30 · see citing works

Local sequence dependence of rate of base replacement in mammals

Bains, W. (1992) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/0027-5107(92)90109-f · Cited by 14 · see citing works

Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22Preprint

Lipovich, L., & King, M. (2005) · Genome Research · doi:10.1101/gr.3883606 · Cited by 9 · see citing works

An insertion/deletion TEX28 polymorphism and its application to analysis of red/green visual pigment gene arrays

Ueyama, H., Torii, R., Tanabe, S., Oda, S., & Yamade, S. (2004) · Journal of Human Genetics · doi:10.1007/s10038-004-0189-5 · Cited by 7 · see citing works

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

Vilella, A. J., Severin, J., Ureta-Vidal, A., Heng, L., Durbin, R., & Birney, E. (2009) · Genome Research · doi:10.1101/gr.073585.107 · Cited by 1,238 · see citing works

Genome analysis of the platypus reveals unique signatures of evolution

paper, A. L. O. A. A. T. A. A. A. T. E. O. T. (2008) · Nature · doi:10.1038/nature06936 · Cited by 719 · see citing works

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Broad Institute Genome Sequencing Platform, Mikkelsen, T. S., Broad Institute Whole Genome Assembly Team, Wakefield, M. J., Aken, B., Amemiya, C. T., Chang, J. L., Duke, S., Garber, M., Gentles, A. J., et al. (2007) · Nature · doi:10.1038/nature05805 · Cited by 711 · see citing works

The relationship between non‐protein‐coding DNA and eukaryotic complexity

Taft, R. J., Pheasant, M., & Mattick, J. S. (2007) · BioEssays · doi:10.1002/bies.20544 · Cited by 696 · see citing works

Distinguishing protein-coding and noncoding genes in the human genome

Clamp, M., Fry, B., Kamal, M., Xie, X., Cuff, J., Lin, M. F., Kellis, M., Lindblad-Toh, K., & Lander, E. S. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709013104 · Cited by 624 · see citing works

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

Church, D. M., Goodstadt, L., Hillier, L. W., Zody, M. C., Goldstein, S., She, X., Bult, C. J., Agarwala, R., Cherry, J. L., DiCuccio, M. N., et al. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000112 · Cited by 495 · see citing works

Noncoding RNA in development

Amaral, P., & Mattick, J. S. (2008) · Mammalian Genome · doi:10.1007/s00335-008-9136-7 · Cited by 479 · see citing works

Insights into the Evolution of Longevity from the Bowhead Whale Genome

Keane, M. P., Semeiks, J. R., Webb, A. E., Li, Y., Quesada, V., Craig, T., Madsen, L. B., van Dam, S., Brawand, D., Marques, P., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2014.12.008 · Cited by 385 · see citing works

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

Shaffer, H. B., Minx, P. J., Warren, D. E., Shedlock, A. M., Thomson, R. C., Valenzuela, N., Abramyan, J., Amemiya, C. T., Badenhorst, D., Biggar, K. K., et al. (2013) · Genome biology · doi:10.1186/gb-2013-14-3-r28 · Cited by 319 · see citing works

The quest for orthologs: finding the corresponding gene across genomes

Kuzniar, A., van Ham, R. C. H. J., Pongor, S., & Leunissen, J. A. M. (2008) · Trends in Genetics · doi:10.1016/j.tig.2008.08.009 · Cited by 295 · see citing works

Noncoding RNAs and RNA Editing in Brain Development, Functional Diversification, and Neurological Disease

Mehler, M. F., & Mattick, J. S. (2007) · Physiological Reviews · doi:10.1152/physrev.00036.2006 · Cited by 293 · see citing works

Accelerated Evolution of the Prdm9 Speciation Gene across Diverse Metazoan Taxa

Oliver, P. L., Goodstadt, L., Bayes, J. J., Birtle, Z., Roach, K. C., Phadnis, N., Beatson, S. A., Lunter, G. A., Malik, H. S., & Ponting, C. P. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000753 · Cited by 283 · see citing works

The central role of RNA in human development and cognition

Mattick, J. S. (2011) · FEBS Letters · doi:10.1016/j.febslet.2011.05.001 · Cited by 274 · see citing works

Computational methods for Gene Orthology inference

Kristensen, D. M., Wolf, Y. I., Mushegian, A. R., & Koonin, E. V. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbr030 · Cited by 242 · see citing works

Raising the estimate of functional human sequences: Figure 1.Preprint

Pheasant, M., & Mattick, J. S. (2007) · Genome Research · doi:10.1101/gr.6406307 · Cited by 239 · see citing works

A new paradigm for developmental biology

Mattick, J. S. (2007) · Journal of Experimental Biology · doi:10.1242/jeb.005017 · Cited by 231 · see citing works

The HGNC Database in 2008: a resource for the human genome

Bruford, E. A., Lush, M. J., Wright, M. W., Sneddon, T. P., Povey, S., & Birney, E. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm881 · Cited by 224 · see citing works

OMA 2011: orthology inference among 1000 complete genomes

Altenhoff, A. M., Schneider, A., Gonnet, G. H., & Dessimoz, C. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1238 · Cited by 215 · see citing works

genenames.org: the HGNC resources in 2011

Seal, R. L., Gordon, S. M., Lush, M. J., Wright, M. W., & Bruford, E. A. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq892 · Cited by 206 · see citing works

Alternative Splicing and Tumor Progression

Ghigna, C., Valacca, C., & Biamonti, G. (2008) · Current Genomics · doi:10.2174/138920208786847971 · Cited by 179 · see citing works

Accelerated Rate of Gene Gain and Loss in Primates

Hahn, M. W., Demuth, J. P., & Han, S.-G. (2007) · Genetics · doi:10.1534/genetics.107.080077 · Cited by 160 · see citing works

Long Noncoding RNAs, Chromatin, and Development

Caley, D. P., Pink, R. C., Trujillano, D., & Carter, D. R. F. (2010) · The Scientific World JOURNAL · doi:10.1100/tsw.2010.7 · Cited by 148 · see citing works

Orthology prediction methods: A quality assessment using curated protein families

Trachana, K., Larsson, T. A., Powell, S., Chen, W., Doerks, T., Muller, J., & Bork, P. (2011) · BioEssays · doi:10.1002/bies.201100062 · Cited by 139 · see citing works

Automatic genome-wide reconstruction of phylogenetic gene trees

Wapinski, I., Pfeffer, A., Friedman, N., & Regev, A. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm193 · Cited by 136 · see citing works

Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomesPreprint

Heger, A., & Ponting, C. P. (2007) · Genome Research · doi:10.1101/gr.6249707 · Cited by 134 · see citing works

Alzheimer's disease: insights from Drosophila melanogaster models

Moloney, A. M., Sattelle, D. B., Lomas, D. A., & Crowther, D. C. (2009) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2009.11.004 · Cited by 133 · see citing works

Noncoding RNAs in Long-Term Memory Formation

Mercer, T. R., Dinger, M. E., Mariani, J., Kosik, K. S., Mehler, M. F., & Mattick, J. S. (2007) · The Neuroscientist · doi:10.1177/1073858408319187 · Cited by 124 · see citing works

The functional repertoires of metazoan genomes

Ponting, C. P. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2413 · Cited by 107 · see citing works

MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement

Shi, G., Zhang, L., & Jiang, T. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-10 · Cited by 105 · see citing works

Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes

Balasubramanian, S., Zheng, D., Liu, Y.-J., Fang, G., Frankish, A., Carriero, N. J., Robilotto, R., Cayting, P. D., & Gerstein, M. (2009) · Genome biology · doi:10.1186/gb-2009-10-1-r2 · Cited by 99 · see citing works

Learning to Count: Robust Estimates for Labeled Distances between Molecular Sequences

O’Brien, J., Minin, V. N., & Suchard, M. A. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp003 · Cited by 98 · see citing works

Non‐coding RNAs and their epigenetic regulatory mechanisms

Zhou, H., Hu, H., & Lai, M. (2010) · Biology of the Cell · doi:10.1042/bc20100029 · Cited by 94 · see citing works

Massive turnover of functional sequence in human and other mammalian genomesPreprint

Meader, S., Ponting, C. P., & Lunter, G. A. (2010) · Genome Research · doi:10.1101/gr.108795.110 · Cited by 90 · see citing works

Genic regions of a large salamander genome contain long introns and novel genes

Smith, J. J., Putta, S., Zhu, W., Pao, G. M., Verma, I. M., Hunter, T. R., Bryant, S. V., Gardiner, D. M., Harkins, T. T., & Voss, S. R. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-19 · Cited by 89 · see citing works

Reduced purifying selection prevails over positive selection in human copy number variant evolutionPreprint

Nguyen, D.-Q., Webber, C., Hehir‐Kwa, J. Y., Pfundt, R., Veltman, J. A., & Ponting, C. P. (2008) · Genome Research · doi:10.1101/gr.077289.108 · Cited by 83 · see citing works

Inferring Orthologs: Open Questions and Perspectives

Tekaia, F. (2016) · Genomics Insights · doi:10.4137/gei.s37925 · Cited by 82 · see citing works

Orthology relations, symbolic ultrametrics, and cographs

Hellmuth, M., Hernández-Rosales, M., Huber, K. T., Moulton, V., Stadler, P. F., & Wieseke, N. (2012) · Journal of Mathematical Biology · doi:10.1007/s00285-012-0525-x · Cited by 81 · see citing works

An analysis of the gene complement of a marsupial,<i>Monodelphis domestica</i>: Evolution of lineage-specific genes and giant chromosomes

Goodstadt, L., Heger, A., Webber, C., & Ponting, C. P. (2007) · Genome Research · doi:10.1101/gr.6093907 · Cited by 67 · see citing works

Loose ends: almost one in five human genes still have unresolved coding status

Abascal, F., Juan, D., Jungreis, I., Gómez, L. M., Rigau, M., Rodrı́guez, J. M., Vázquez, J., & Tress, M. L. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky587 · Cited by 63 · see citing works

Stressing out over long noncoding RNA

Audas, T. E., & Lee, S. (2015) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2015.06.010 · Cited by 55 · see citing works

Modeling Opportunities in Comparative Oncology for Drug Development

Gordon, I. K., & Khanna, C. (2010) · ILAR Journal · doi:10.1093/ilar.51.3.214 · Cited by 52 · see citing works

Coevolution between cannabinoid receptors and endocannabinoid ligands

McPartland, J. M., Norris, R. W., & Kilpatrick, C. W. (2007) · Gene · doi:10.1016/j.gene.2007.04.017 · Cited by 51 · see citing works

Assembling the spiralian tree of life

Giribet, G., Dunn, C. W., Edgecombe, G. D., Hejnol, A., Martindale, M. Q., & Rouse, G. W. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0006 · Cited by 50 · see citing works

Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence

Rands, C. M., Darling, A. E., Fujita, M. K., Kong, L., Webster, M. T., Clabaut, C., Emes, R. D., Heger, A., Meader, S., Hawkins, M. B., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-95 · Cited by 48 · see citing works

The opossum genome: Insights and opportunities from an alternative mammalPreprint

Samollow, P. B. (2008) · Genome Research · doi:10.1101/gr.065326.107 · Cited by 47 · see citing works

From event-labeled gene trees to species trees

Hernández-Rosales, M., Hellmuth, M., Wieseke, N., Huber, K. T., Moulton, V., & Stadler, P. F. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-s19-s6 · Cited by 46 · see citing works

Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals

Laukaitis, C. M., Heger, A., Blakley, T. D., Munclinger, P., Ponting, C. P., & Karn, R. C. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-46 · Cited by 46 · see citing works

Targeted discovery of novel human exons by comparative genomicsPreprint

Siepel, A. C., Diekhans, M., Brejová, B., Langton, L., Stevens, M. W., Comstock, C. L. G., Davis, C. P., Ewing, B., Oommen, S., Lau, C. C., et al. (2007) · Genome Research · doi:10.1101/gr.7128207 · Cited by 46 · see citing works

MicroRNAs and metazoan phylogeny: big trees from little genes

Sperling, E. A., & Peterson, K. J. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0015 · Cited by 44 · see citing works

Variable Strength of Translational Selection Among 12 Drosophila Species

Heger, A., & Ponting, C. P. (2007) · Genetics · doi:10.1534/genetics.107.070466 · Cited by 43 · see citing works

Controversies in modern evolutionary biology: the imperative for error detection and quality control

Prosdocimi, F., Linard, B., Pontarotti, P., Poch, O., & Thompson, J. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-5 · Cited by 41 · see citing works

Expressed sequence tags reveal Proctotrupomorpha (minus Chalcidoidea) as sister to Aculeata (Hymenoptera: Insecta)

Sharanowski, B. J., Robbertse, B., Walker, J., Voss, S. R., Yoder, R. J., Spatafora, J. W., & Sharkey, M. J. (2010) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2010.07.006 · Cited by 39 · see citing works

Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses

Washburn, J. D., Schnable, J. C., Conant, G. C., Brutnell, T. P., Shao, Y., Zhang, Y., Ludwig, M. L., Davidse, G., & Pires, J. C. (2017) · Scientific Reports · doi:10.1038/s41598-017-13236-z · Cited by 39 · see citing works

The mouth, the anus, and the blastopore—open questions about questionable openings

Hejnol, A., & Martindale, M. Q. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0004 · Cited by 37 · see citing works

Gene fusion as an important mechanism to generate new genes in the genus Oryza

Zhou, Y., Zhang, C., Zhang, L., Ye, Q., Liu, N., Wang, M., Long, G., Fan, W., Long, M., & Wing, R. A. (2022) · Genome biology · doi:10.1186/s13059-022-02696-w · Cited by 37 · see citing works

SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier

Hu, X., & Friedberg, I. (2019) · GigaScience · doi:10.1093/gigascience/giz118 · Cited by 32 · see citing works

Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later

Chauve, C., El-Mabrouk, N., Guéguen, L., Semeria, M., & Tannier, É. (2013) · Computational biology · doi:10.1007/978-1-4471-5298-9_4 · Cited by 31 · see citing works

A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants

Nelson, A. D. L., Forsythe, E. S., Devisetty, U. K., Clausen, D. S., Haug-Baltzell, A. K., Meldrum, A. M. R., Frank, M. R., Lyons, E. H., & Beilstein, M. A. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.030338 · Cited by 30 · see citing works

Contrast features of CpG islands in the promoter and other regions in the dog genome

Han, L., & Zhao, Z. (2009) · Genomics · doi:10.1016/j.ygeno.2009.04.007 · Cited by 29 · see citing works

Repeat performance: how do genome packaging and regulation depend on simple sequence repeats?

Kumar, R. P., Ramamoorthy, S., Singh, V. K., & Mishra, R. K. (2010) · BioEssays · doi:10.1002/bies.200900111 · Cited by 27 · see citing works

The animal in the genome: comparative genomics and evolution

Copley, R. R. (2008) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2007.2235 · Cited by 27 · see citing works

OPTIC: orthologous and paralogous transcripts in clades

Heger, A., & Ponting, C. P. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm852 · Cited by 26 · see citing works

GPCR Genes Are Preferentially Retained after Whole Genome Duplication

Semyonov, J., Park, J., Chang, C. L., & Hsu, S. Y. (2008) · PLoS ONE · doi:10.1371/journal.pone.0001903 · Cited by 25 · see citing works

Genomic, phylogenetic, and cell biological insights into metazoan origins

Nichols, S. A., Dayel, M. J., & King, N. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0003 · Cited by 24 · see citing works

Reconciliation with Non-binary Gene Trees Revisited

Zheng, Y., & Zhang, L. (2014) · Lecture notes in computer science · doi:10.1007/978-3-319-05269-4_33 · Cited by 24 · see citing works

Detection of gene orthology from gene co-expression and protein interaction networks

Towfic, F., VanderPlas, S., OIiver, C. A., Couture, O., TuggIe, C. K., GreenIee, M. H. W., & Honavar, V. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-s3-s7 · Cited by 24 · see citing works

MultiMSOAR 2.0: An Accurate Tool to Identify Ortholog Groups among Multiple Genomes

Shi, G., Peng, M.-C., & Jiang, T. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020892 · Cited by 23 · see citing works

Analysis of the canine brain transcriptome with an emphasis on the hypothalamus and cerebral cortex

Roy, M., Kim, N., Kim, K., Chung, W.-H., Achawanantakun, R., Sun, Y., & Wayne, R. K. (2013) · Mammalian Genome · doi:10.1007/s00335-013-9480-0 · Cited by 23 · see citing works

Rapid Turnover of Functional Sequence in Human and Other Genomes

Ponting, C. P., Nellåker, C., & Meader, S. (2011) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090810-183115 · Cited by 22 · see citing works

The central role of RNA in the genetic programming of complex organisms

Mattick, J. S. (2010) · Anais da Academia Brasileira de Ciências · doi:10.1590/s0001-37652010000400016 · Cited by 22 · see citing works

Application of DNA array technology to mammalian embryos

Niemann, H., Carnwath, J. W., & Kues, W. A. (2007) · Theriogenology · doi:10.1016/j.theriogenology.2007.05.041 · Cited by 22 · see citing works

Annotation of the domestic dog genome sequence: finding the missing genes

Derrien, T., Vaysse, A., André, C., & Hitte, C. (2011) · Mammalian Genome · doi:10.1007/s00335-011-9372-0 · Cited by 20 · see citing works

A genome-wide linkage scan in German shepherd dogs localizes canine platelet procoagulant deficiency (Scott syndrome) to canine chromosome 27

Brooks, M. B., Etter, K., Catalfamo, J. L., Brisbin, A. G., Bustamante, C. D., & Mezey, J. G. (2009) · Gene · doi:10.1016/j.gene.2009.09.016 · Cited by 20 · see citing works

Revisiting the missing protein-coding gene catalog of the domestic dog

Derrien, T., Thézé, J., Vaysse, A., André, C., Ostrander, E. A., Galibert, F., & Hitte, C. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-62 · Cited by 19 · see citing works

Separating derived from ancestral features of mouse and human genomes

Ponting, C. P., & Goodstadt, L. (2009) · Biochemical Society Transactions · doi:10.1042/bst0370734 · Cited by 18 · see citing works

Gene prediction: compare and CONTRAST

Flicek, P. (2007) · Genome biology · doi:10.1186/gb-2007-8-12-233 · Cited by 16 · see citing works

Heterologous expression of a Penicillium purpurogenum exo-arabinanase in Pichia pastoris and its biochemical characterization

Mardones, W., Callegari, E. A., & Eyzaguirre, J. P. (2015) · Fungal Biology · doi:10.1016/j.funbio.2015.09.009 · Cited by 15 · see citing works

A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation

Trachana, K., Forslund, S. K., Larsson, T., Powell, S. T., Doerks, T., von Mering, C., & Bork, P. (2014) · PLoS ONE · doi:10.1371/journal.pone.0111122 · Cited by 15 · see citing works

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

Lartillot, N., & Philippe, H. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0012 · Cited by 15 · see citing works

CLUSTERING OF MAIN ORTHOLOGS FOR MULTIPLE GENOMES

FU, Z., & Jiang, T. (2008) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720008003540 · Cited by 15 · see citing works

SynBlast: Assisting the analysis of conserved synteny information

Lehmann, J., Stadler, P. F., & Prohaska, S. J. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-351 · Cited by 14 · see citing works

Molecular Evolution of Translin Superfamily Proteins Within the Genomes of Eubacteria, Archaea and Eukaryotes

Gupta, G. D., Kale, A., & Kumar, V. (2012) · Journal of Molecular Evolution · doi:10.1007/s00239-012-9534-z · Cited by 14 · see citing works

Lineage-Specific Duplications of Muroidea Faim and Spag6 Genes and Atypical Accelerated Evolution of the Parental Spag6 Gene

Qiu, H., Gołas, A., Grzmil, P., & Wojnowski, L. (2013) · Journal of Molecular Evolution · doi:10.1007/s00239-013-9585-9 · Cited by 13 · see citing works

Accelerated Evolution of PAK3- and PIM1-like Kinase Gene Families in the Zebra Finch, Taeniopygia guttata

Kong, L., Lovell, P. V., Heger, A., Mello, C. V., & Ponting, C. P. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq080 · Cited by 13 · see citing works

Deciphering deuterostome phylogeny: molecular, morphological, and palaeontological perspectives

Smith, A. B., & Swalla, B. J. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0009 · Cited by 13 · see citing works

The effect of functional compensation among duplicate genes can constrain their evolutionary divergence

Bozorgmehr, J. H. (2012) · Journal of Genetics · doi:10.1007/s12041-012-0125-y · Cited by 12 · see citing works

The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records

Peterson, K. J., Cotton, J. A., Gehlîng, J. G., & Pisani, D. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0002 · Cited by 12 · see citing works

The evolution of nervous system centralization

Arendt, D., Denes, A. S., Jékely, G., & Tessmar‐Raible, K. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0007 · Cited by 12 · see citing works

Infra- and Transspecific Clues to Understanding the Dynamics of Transposable Elements

Vieira, C. P., Fablet, M., & Lerat, E. (2009) · Genome dynamics and stability · doi:10.1007/7050_2009_044 · Cited by 11 · see citing works

Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy

Brinkmeyer‐Langford, C., Balog-Alvarez, C. J., Cai, J. J., Davis, B. W., & Kornegay, J. N. (2016) · BMC Genomics · doi:10.1186/s12864-016-2948-z · Cited by 11 · see citing works

Revealing Mammalian Evolutionary Relationships by Comparative Analysis of Gene Clusters

Song, G., Riemer, C., Dickins, B., Kim, H. L., Zhang, L., Zhang, Y., Hsu, C.-H., Hardison, R. C., Program, N. C. S., Green, E. D., et al. (2012) · Genome Biology and Evolution · doi:10.1093/gbe/evs032 · Cited by 11 · see citing works

The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species

Mazza, R., Strozzi, F., Caprera, A., Ajmone‐Marsan, P., & Williams, J. L. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-604 · Cited by 11 · see citing works

Syntenator: Multiple gene order alignments with a gene-specific scoring function

Rödelsperger, C., & Dieterich, C. (2008) · Algorithms for Molecular Biology · doi:10.1186/1748-7188-3-14 · Cited by 10 · see citing works

Animal Evolution

(2009) · doi:10.1093/acprof:oso/9780199549429.001.0001 · Cited by 9 · see citing works

SuperPartitions: Detection and classification of orthologs

Tekaia, F., & Yeramian, E. (2011) · Gene · doi:10.1016/j.gene.2011.10.027 · Cited by 9 · see citing works

Correlation of microsynteny conservation and disease gene distribution in mammalian genomes

Lovell, S. C., Li, X., Weerasinghe, N. R., & Hentges, K. E. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-521 · Cited by 7 · see citing works

Invertebrate Problematica: kinds, causes, and solutions

Jenner, R. A., Timothy, D. J., & Littlewood, D. T. J. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0011 · Cited by 7 · see citing works

The earliest fossil record of the animals and its significance

Budd, G. E. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0001 · Cited by 6 · see citing works

Detection of Gene Orthology Based on Protein-Protein Interaction Networks

Towfic, F., Greenlee, M. H. W., & Honavar, V. (2009) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2009.85 · Cited by 6 · see citing works

Molecular Phylogenetics An introduction to computational methods and tools for analyzing evolutionary relationships

Dowell, K. G. (2008) · Cited by 5 · see citing works

Phylogenetic Identification and Functional Characterization of Orthologs and Paralogs across Human, Mouse, Fly, and WormPreprint

Wu, Y.-C., Bansal, M. S., Rasmussen, M. D., Herrero, J., & Kellis, M. (2014) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/005736 · Cited by 11 · see citing works

MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score

Pryszcz, L. P., Huerta‐Cepas, J., & Gabaldón, T. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq953 · Cited by 112 · see citing works

Accurate prediction of orthologs in the presence of divergence after duplication

Lafond, M., Meghdari Miardan, M., & Sankoff, D. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty242 · Cited by 27 · see citing works

Orthonome – a new pipeline for predicting high quality orthologue gene sets applicable to complete and draft genomes

Rane, R., Oakeshott, J. G., Nguyen, T. N. M., Hoffmann, A. A., & Lee, S. F. (2017) · BMC Genomics · doi:10.1186/s12864-017-4079-6 · Cited by 15 · see citing works

OrthoParaMap: Distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies

Cannon, S. B., & Young, N. D. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-35 · Cited by 68 · see citing works