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

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

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

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

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

Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner

Blanchette, M., Kent, W. J., Riemer, C., Elnitski, L., Smit, A. F. A., Roskin, K. M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E. D., et al. (2004) · Genome Research · doi:10.1101/gr.1933104 · Cited by 1,452 · see citing works

Resolution of the Early Placental Mammal Radiation Using Bayesian Phylogenetics

Murphy, W. J., Eizirik, E., O’Brien, S. J., Madsen, O., Scally, M., Douady, C. J., Teeling, E. C., Ryder, O. A., Stanhope, M. J., JONG, W. W. D., et al. (2001) · Science · doi:10.1126/science.1067179 · Cited by 1,292 · 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

Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes

Kent, W. J., Baertsch, R., Hinrichs, A., Miller, W., & Haussler, D. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1932072100 · Cited by 850 · see citing works

Placental mammal diversification and the Cretaceous–Tertiary boundary

Springer, M. S., Murphy, W. J., Eduardo Eizirik, C., & O’Brien, S. J. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0334222100 · Cited by 837 · see citing works

Plant mitochondrial DNA evolved rapidly in structure, but slowly in sequence

Palmer, J. D., & Herbon, L. A. (1988) · Journal of Molecular Evolution · doi:10.1007/bf02143500 · Cited by 760 · see citing works

Comparative Genome and Proteome Analysis of <i>Anopheles gambiae</i> and <i>Drosophila melanogaster</i>

Zdobnov, E. M., von Mering, C., Letunic, I., Torrents, D., Suyama, M., Copley, R. R., Christophides, G. K., Thomasova, D., Holt, R. A., Subramanian, G. M., et al. (2002) · Science · doi:10.1126/science.1077061 · Cited by 553 · see citing works

The Promise of Comparative Genomics in Mammals

O’Brien, S. J., Menotti-Raymond, M. A., Murphy, W. J., Nash, W. G., Wienberg, J., Stanyon, R., Copeland, N. G., Jenkins, N. A., Womack, J. E., & Graves, J. A. M. (1999) · Science · doi:10.1126/science.286.5439.458 · Cited by 442 · see citing works

Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome.

Sankoff, D., Leduc, G., Antoine, N., Paquin, B., Lang, B. F., & Cedergren, R. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.14.6575 · Cited by 424 · see citing works

Genome-scale evolution: reconstructing gene orders in the ancestral species.

Bourque, G., & Pevzner, P. A. (2002) · PubMed · Cited by 421 · see citing works

The Promise of Comparative Genomics in Mammals

박홍석 (2001) · 한국실험동물학회 학술발표대회 논문집 · Cited by 389 · see citing works

Genome rearrangements in mammalian evolution: lessons from human and mouse genomes

Pevzner, P., & Tesler, G. (2003) · Genome Research · doi:10.1101/gr.757503 · Cited by 369 · see citing works

GRIMM: genome rearrangements web server

Tesler, G. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.3.492 · Cited by 331 · see citing works

Transforming men into mice (polynomial algorithm for genomic distance problem)

Hannenhalli, S. S., & Pevzner, P. A. (2002) · Annual Symposium on Foundations of Computer Science · doi:10.1109/sfcs.1995.492588 · Cited by 328 · see citing works

Precision of molecular time estimates

Hedges, S. B., & Kumar, S. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.03.004 · Cited by 289 · see citing works

Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat GenomesPreprint

Bourque, G., Pevzner, P. A., & Tesler, G. (2004) · Genome Research · doi:10.1101/gr.1975204 · Cited by 240 · see citing works

Gene Order Breakpoint Evidence in Animal Mitochondrial Phylogeny

Blanchette, M., Kunisawa, T., & Sankoff, D. (1999) · Journal of Molecular Evolution · doi:10.1007/pl00006542 · Cited by 193 · see citing works

Precision of molecular time estimates

BLAIRHEDGES, S. (2004) · Trends in Genetics · doi:10.1016/s0168-9525(04)00072-1 · Cited by 186 · see citing works

Molecular timescales and the fossil record: a paleontological perspective

Reisz, R. R., & Müller, J. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.03.007 · Cited by 170 · see citing works

Efficient algorithms for multichromosomal genome rearrangements

Tesler, G. (2002) · Journal of Computer and System Sciences · doi:10.1016/s0022-0000(02)00011-9 · Cited by 165 · see citing works

A Radiation Hybrid Map of the Cat Genome: Implications for Comparative MappingPreprint

Murphy, W. J., Sun, S., Chen, Z.-Q., Yuhki, N., Hirschmann, D., Menotti-Raymond, M. A., & O’Brien, S. J. (2000) · Genome Research · doi:10.1101/gr.10.5.691 · Cited by 135 · see citing works

Sorting by Reversals: Genome Rearrangements in Plant Organelles and Evolutionary History of X Chromosome

Bafna, V., & Pevzner, P. (1995) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040208 · Cited by 122 · see citing works

Reciprocal chromosome painting shows that squirrels, unlike murid rodents, have a highly conserved genome organization

Stanyon, R., Stone, G. A., Garcia-Caldés, M., & Froenicke, L. (2003) · Genomics · doi:10.1016/s0888-7543(03)00109-5 · Cited by 66 · see citing works

Bayesian Phylogenetic Inference from Animal Mitochondrial Genome Arrangements

Larget, B. R., Simon, D. L., & Kadane, J. B. (2002) · Journal of the Royal Statistical Society Series B (Statistical Methodology) · doi:10.1111/1467-9868.00356 · Cited by 64 · see citing works

A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data.

Cosner, M. E., Jansen, R. K., Moret, B. M. E., Raubeson, L. A., Wang, L. S., Warnow, T. J., & Wyman, S. K. (2000) · PubMed · Cited by 52 · see citing works

Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps

Murphy, W. J., Bourque, G., Tesler, G., Pevzner, P. A., & O’Brien, S. J. (2003) · Human Genomics · doi:10.1186/1479-7364-1-1-30 · Cited by 32 · see citing works

Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization

Putnam, N. H., Srivastava, M., Hellsten, U., Dirks, B., Chapman, J., Salamov, A., Terry, A., Shapiro, H., Lindquist, E., Kapitonov, V. V., et al. (2007) · Science · doi:10.1126/science.1139158 · Cited by 1,555 · 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

Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution

DUJON, B. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.05.007 · Cited by 224 · see citing works

Principles of Genome Evolution in the Drosophila melanogaster Species Group

Ranz, J. M., Maurin, D., Chan, Y. S., von Grotthuss, M., Hillier, L. W., Roote, J., Ashburner, M., & Bergman, C. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050152 · Cited by 197 · see citing works

Chicken genome: Current status and future opportunitiesPreprint

Burt, D. W. (2005) · Genome Research · doi:10.1101/gr.4141805 · Cited by 173 · see citing works

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage

Zody, M. C., Garber, M. G., Adams, D. J., Sharpe, T., Harrow, J., Lupski, J. R., Nicholson, C., Searle, S., Wilming, L. G., Young, S., et al. (2006) · Nature · doi:10.1038/nature04689 · Cited by 162 · see citing works

Fast-X on the Z: Rapid evolution of sex-linked genes in birdsPreprint

Mank, J. E., Axelsson, E., & Ellegren, H. (2007) · Genome Research · doi:10.1101/gr.6031907 · Cited by 157 · see citing works

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

Goodstadt, L., & Ponting, C. P. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020133 · Cited by 154 · see citing works

The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications

Smith, J. J., & Keinath, M. C. (2015) · Genome Research · doi:10.1101/gr.184135.114 · Cited by 152 · see citing works

Extensive conservation of ancient microsynteny across metazoans due to <i>cis</i> -regulatory constraints

Irimia, M., Tena, J. J., Alexis, M. S., Fernandez-Miñan, A., Maeso, I., Bogdanović, O., de la Calle-Mustienes, E., Roy, S. W., Gómez-Skarmeta, J. L., & Fraser, H. B. (2012) · Genome Research · doi:10.1101/gr.139725.112 · Cited by 146 · see citing works

Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence

Shopland, L. S., Lynch, C. R., Peterson, K. A., Thornton, K. R., Kepper, N., Hase, J. V., Stein, S., Vincent, S., Molloy, K. R., Kreth, G., et al. (2006) · The Journal of Cell Biology · doi:10.1083/jcb.200603083 · Cited by 149 · see citing works

The genome diversity and karyotype evolution of mammals

Graphodatsky, A. S., Trifonov, V. A., & Stanyon, R. (2011) · Molecular Cytogenetics · doi:10.1186/1755-8166-4-22 · Cited by 145 · see citing works

A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes

Chauve, C., & Tannier, É. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000234 · Cited by 141 · see citing works

Breakpoint graphs and ancestral genome reconstructionsPreprint

Alekseyev, M. A., & Pevzner, P. A. (2009) · Genome Research · doi:10.1101/gr.082784.108 · Cited by 142 · see citing works

Evolutionary movement of centromeres in horse, donkey, and zebra

Carbone, L., Nergadze, S. G., Magnani, E., Misceo, D., Cardone, M. F., Roberto, R., Bertoni, L., Attolini, C., Piras, M. F., de Jong, P., et al. (2006) · Genomics · doi:10.1016/j.ygeno.2005.11.012 · Cited by 138 · see citing works

Molecular evolutionary genomics of birds

Ellegren, H. (2007) · Cytogenetic and Genome Research · doi:10.1159/000103172 · Cited by 134 · see citing works

Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing

Wheat, C. W. (2008) · Genetica · doi:10.1007/s10709-008-9326-y · Cited by 134 · see citing works

Reference-assisted chromosome assembly

Kim, J., Larkin, D. M., Cai, Q., Asan, Zhang, Y., Ge, R.-L., Auvil, L., Capitanu, B., Zhang, G., Lewin, H. A., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1220349110 · Cited by 128 · see citing works

The Fragile Breakage versus Random Breakage Models of Chromosome Evolution

Peng, Q., Pevzner, P. A., & Tesler, G. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020014 · Cited by 114 · see citing works

Strong Regional Biases in Nucleotide Substitution in the Chicken Genome

Webster, M. T., Axelsson, E., & Ellegren, H. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msk008 · Cited by 106 · see citing works

A consensus linkage map of the grass carp (Ctenopharyngodon idella) based on microsatellites and SNPs

Xia, J. H., Liu, F., Zhu, Z. Y., Fu, J., Feng, J., Li, J., & Yue, G. H. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-135 · Cited by 105 · see citing works

Rearrangement Rate following the Whole-Genome Duplication in Teleosts

Sémon, M., & Wolfe, K. H. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msm003 · Cited by 103 · see citing works

Genetic Mapping in a Natural Population of Collared Flycatchers (Ficedula albicollis): Conserved Synteny but Gene Order Rearrangements on the Avian Z Chromosome

Backström, N., Durling, M. B., Gustafsson, L., Qvarnström, A., Cheng, H. H., & Ellegren, H. (2006) · Genetics · doi:10.1534/genetics.106.058917 · Cited by 104 · see citing works

Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages

Fischer, G., Rocha, E. P. C., Brunet, F., Vergassola, M., & Dujon, B. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020032 · Cited by 101 · see citing works

Using comparative genomics to reorder the human genome sequence into a virtual sheep genome

Dalrymple, B. P., Kirkness, E. F., Nefedov, M. D., McWilliam, S. M., Ratnakumar, A., Barris, W., Zhao, S., Shetty, J., Maddox, J. F., O'Grady, M., et al. (2007) · Genome biology · doi:10.1186/gb-2007-8-7-r152 · Cited by 101 · see citing works

Emergence of the Chicken as a Model Organism: Implications for Agriculture and Biology

Burt, D. W. (2007) · Poultry Science · doi:10.1093/ps/86.7.1460 · Cited by 102 · see citing works

Reconstruction of a 450-My-old ancestral vertebrate protokaryotype

KOHN, M., HOGEL, J., VOGEL, W., MINICH, P., KEHRERSAWATZKI, H., GRAVES, J., & HAMEISTER, H. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.02.008 · Cited by 99 · see citing works

The infinite sites model of genome evolution

Ma, J., Ratan, A., Raney, B. J., Suh, B. B., Miller, W., & Haussler, D. H. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0805217105 · Cited by 98 · see citing works

Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genusPreprint

Vakirlis, N., Sarilar, V., Drillon, G., Fleiss, A., Agier, N., Meyniel, J.-P., Blanpain, L. T., Carbone, A., Devillers, H., Dubois, K., et al. (2016) · Genome Research · doi:10.1101/gr.204420.116 · Cited by 94 · see citing works

Evidence of a Large-Scale Functional Organization of Mammalian Chromosomes

Petkov, P. M., Graber, J. H., Churchill, G. A., DiPetrillo, K., King, B. L., & Paigen, K. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010033 · Cited by 90 · see citing works

A Gene-Based Genetic Linkage Map of the Collared Flycatcher (Ficedula albicollis) Reveals Extensive Synteny and Gene-Order Conservation During 100 Million Years of Avian Evolution

Backström, N., Karaiskou, N., Leder, E. H., Gustafsson, L., Primmer, C. R., Qvarnström, A., & Ellegren, H. (2008) · Genetics · doi:10.1534/genetics.108.088195 · Cited by 92 · see citing works

The ZW Micro-Sex Chromosomes of the Chinese Soft-Shelled Turtle (Pelodiscus sinensis, Trionychidae, Testudines) Have the Same Origin as Chicken Chromosome 15

Kawagoshi, T., Uno, Y., Matsubara, K., Matsuda, Y., & Nishida, C. (2009) · Cytogenetic and Genome Research · doi:10.1159/000227837 · Cited by 90 · see citing works

Evolution of the ancestral mammalian karyotype and syntenic regions

Damas, J., Corbo, M., Kim, J., Turner-Maier, J., Farré, M., Larkin, D. M., Ryder, O. A., Steiner, C., Houck, M. L., Hall, S., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2209139119 · Cited by 91 · see citing works

Ancient Vertebrate Conserved Noncoding Elements Have Been Evolving Rapidly in Teleost Fishes

Lee, A., Kerk, S. Y., Tan, Y., Brenner, S., & Venkatesh, B. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq304 · Cited by 85 · see citing works

Recovering genome rearrangements in the mammalian phylogenyPreprint

Zhao, H., & Bourque, G. (2009) · Genome Research · doi:10.1101/gr.086009.108 · Cited by 83 · see citing works

Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?Preprint

Froenicke, L., Garcia-Caldés, M., Graphodatsky, A. S., Müller, S., Lyons, L. A., Robinson, T. J., Volleth, M., Yang, F., & Wienberg, J. (2006) · Genome Research · doi:10.1101/gr.3955206 · Cited by 81 · see citing works

Analysis of the DNA sequence and duplication history of human chromosome 15

Zody, M. C., Garber, M. G., Sharpe, T., Young, S., Rowen, L., O'Neill, K., Whittaker, C. A., Kamal, M., Chang, J. L., Cuomo, C. A., et al. (2006) · Nature · doi:10.1038/nature04601 · Cited by 78 · see citing works

Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

Longo, M. S., Carone, D. M., Program, N. C. S., Green, E. D., O’Neill, M. J., & O'Neill, R. J. W. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-334 · Cited by 73 · see citing works

Comparative genomics of the syndecans defines an ancestral genomic context associated with matrilins in vertebrates

Chakravarti, R., & Adams, J. C. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-83 · Cited by 74 · see citing works

Vertebrate Chromosome Evolution

Damas, J., Corbo, M., & Lewin, H. A. (2020) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-020518-114924 · Cited by 72 · see citing works

Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution

Kemkemer, C., Kohn, M., Cooper, D. N., Froenicke, L., Högel, J., Hameister, H., & Kehrer‐Sawatzki, H. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-84 · Cited by 68 · see citing works

The DNA sequence, annotation and analysis of human chromosome 3

Muzny, D. M., Scherer, S. E., Kaul, R., Wang, J., Yu, J. M., Sudbrak, R., Buhay, C., Chen, R., Cree, A., Ding, Y., et al. (2006) · Nature · doi:10.1038/nature04728 · Cited by 68 · see citing works

Molecular cytogenetic and genomic insights into chromosomal evolution

Ruiz‐Herrera, A., Farré, M., & Robinson, T. J. (2011) · Heredity · doi:10.1038/hdy.2011.102 · Cited by 68 · see citing works

Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

Lemaitre, C., Zaghloul, L., Sagot, M., Gautier, C., Arnéodo, A., Tannier, É., & Audit, B. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-335 · Cited by 66 · see citing works

The determinants of gene order conservation in yeasts

Poyatos, J. F., & Hurst, L. D. (2007) · Genome biology · doi:10.1186/gb-2007-8-11-r233 · Cited by 66 · see citing works

Neuropeptide Y‐family receptors Y 6 and Y 7 in chicken

Bromée, T., Sjödin, P., Fredriksson, R., Boswell, T. C., Larsson, T., Salaneck, E., Zoorob, R., Mohell, N., & Larhammar, D. (2006) · FEBS Journal · doi:10.1111/j.1742-4658.2006.05221.x · Cited by 62 · see citing works

Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes

Damas, J., Kim, J., Farré, M., Griffin, D. K., & Larkin, D. M. (2018) · Genome biology · doi:10.1186/s13059-018-1544-8 · Cited by 58 · see citing works

Perfect Sorting by Reversals Is Not Always Difficult

Bérard, S., Bergeron, A., Chauve, C., & Paul, C. (2007) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2007.1011 · Cited by 59 · see citing works

Stability of Large Segmental Duplications in the Yeast Genome

Koszul, R., Dujon, B., & Fischer, G. (2006) · Genetics · doi:10.1534/genetics.105.048058 · Cited by 57 · see citing works

Progress from Chicken Genetics to the Chicken Genome

Siegel, P. B., Dodgson, J. B., & Andersson, L. (2006) · Poultry Science · doi:10.1093/ps/85.12.2050 · Cited by 55 · see citing works

The finished DNA sequence of human chromosome 12

Scherer, S. E., Muzny, D. M., Buhay, C., Chen, R., Cree, A., Ding, Y., Dugan-Rocha, S., Gill, R., Gunaratne, P. H., Harris, R. A., et al. (2006) · Nature · doi:10.1038/nature04569 · Cited by 50 · see citing works

Membrane-associated collagens with interrupted triple-helices (MACITs): evolution from a bilaterian common ancestor and functional conservation in C. elegans

Tu, H., Huhtala, P., Lee, H., Adams, J. C., & Pihlajaniemi, T. A. (2015) · BMC Evolutionary Biology · doi:10.1186/s12862-015-0554-3 · Cited by 48 · see citing works

A Novel Activating Chicken IgY FcR Is Related to Leukocyte Receptor Complex (LRC) Genes but Is Located on a Chromosomal Region Distinct from the LRC and FcR Gene Clusters

Viertlboeck, B. C., Schmitt, R., Hanczaruk, M. A., Crooijmans, R. P. M. A., Groenen, M. A. M., & Göbel, T. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.182.3.1533 · Cited by 44 · see citing works

Paleogenomics in vertebrates, or the recovery of lost genomes from the mist of time

Muffato, M., & Crollius, H. R. (2008) · BioEssays · doi:10.1002/bies.20707 · Cited by 44 · see citing works

Microinversions in mammalian evolution

Chaisson, M., Raphael, B. J., & Pevzner, P. A. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603984103 · Cited by 44 · see citing works

Precise detection of rearrangement breakpoints in mammalian chromosomes

Lemaitre, C., Tannier, É., Gautier, C., & Sagot, M. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-286 · Cited by 42 · see citing works

Twisted Signatures of GC-Biased Gene Conversion Embedded in an Evolutionary Stable Karyotype

Mugal, C. F., Arndt, P. F., & Ellegren, H. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst067 · Cited by 42 · see citing works

Whole Genome Sequencing, de Novo Assembly and Phenotypic Profiling for the New Budding Yeast Species Saccharomyces jurei

Naseeb, S., Alsammar, H., Burgis, T., Donaldson, I. J., Knyazev, N., Knight, C., & Delneri, D. (2018) · G3 Genes Genomes Genetics · doi:10.1534/g3.118.200476 · Cited by 42 · see citing works

The Incompatible Desiderata of Gene Cluster Properties

Hoberman, R., & Durand, D. (2005) · Lecture notes in computer science · doi:10.1007/11554714_7 · Cited by 41 · see citing works

The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction: Figure 1.Preprint

Bourque, G., Tesler, G., & Pevzner, P. A. (2006) · Genome Research · doi:10.1101/gr.4631806 · Cited by 41 · see citing works

Poultry Genome Sequences: Progress and Outstanding Challenges

Dodgson, J. B., Delany, M. E., & Cheng, H. H. (2011) · Cytogenetic and Genome Research · doi:10.1159/000324413 · Cited by 38 · see citing works

Comparing Genomes with Duplications: A Computational Complexity Point of View

Blin, G., Chauve, C., Guillaume Fertin, A., Rizzi, R., & Vialette, S. (2007) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2007.1069 · Cited by 37 · see citing works

Accurate identification of orthologous segments among multiple genomes

Hachiya, T., Osana, Y., Popendorf, K., & Sakakibara, Y. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp070 · Cited by 37 · see citing works

Tracing the evolution of amniote chromosomes

Deakin, J. E., & Ezaz, T. (2014) · Chromosoma · doi:10.1007/s00412-014-0456-y · Cited by 35 · see citing works

TheC. savignyigenetic map and its integration with the reference sequence facilitates insights into chordate genome evolutionPreprint

Hill, M. M., Broman, K. W., Stupka, E., Smith, W. C., Jiang, D., & Sidow, A. (2008) · Genome Research · doi:10.1101/gr.078576.108 · Cited by 36 · see citing works

Genome streamlining via complete loss of introns has occurred multiple times in lichenized fungal mitochondria

Pogoda, C. S., Keepers, K. G., Nadiadi, A. Y., Bailey, D. W., Lendemer, J. C., Tripp, E. A., & Kane, N. C. (2019) · Ecology and Evolution · doi:10.1002/ece3.5056 · Cited by 35 · see citing works

Phylogenomic analysis of vertebrate thrombospondins reveals fish-specific paralogues, ancestral gene relationships and a tetrapod innovation

McKenzie, P., Chadalavada, S. C., Bohrer, J. C., & Adams, J. C. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-33 · Cited by 35 · see citing works

Dissecting the mammalian genome – new insights into chromosomal evolution

Robinson, T. J., Ruiz‐Herrera, A., & Froenicke, L. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.04.002 · Cited by 34 · see citing works

Gene order data from a model amphibian (Ambystoma): new perspectives on vertebrate genome structure and evolution

Smith, J. J., & Voss, S. R. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-219 · Cited by 34 · see citing works

The Statistical Analysis of Spatially Clustered Genes under the Maximum Gap Criterion

Hoberman, R., Sankoff, D., & Durand, D. (2005) · Journal of Computational Biology · doi:10.1089/cmb.2005.12.1083 · Cited by 34 · see citing works

Whole genome detection of sequence and structural polymorphism in six diverse horses

Al‐Abri, M., Holl, H. M., Kalla, S. E., Sutter, N. B., & Brooks, S. A. (2020) · PLoS ONE · doi:10.1371/journal.pone.0230899 · Cited by 33 · see citing works

Fusion and Fission of Genes Define a Metric between Fungal Genomes

Durrens, P., Nikolski, M., & Sherman, D. J. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000200 · Cited by 31 · see citing works

Comparative study on synteny between yeasts and vertebrates

Drillon, G., & Fischer, G. (2011) · Comptes Rendus Biologies · doi:10.1016/j.crvi.2011.05.011 · Cited by 31 · see citing works

Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis)

Miller, J. M., Moore, S. S., Stothard, P., Liao, X., & Coltman, D. W. (2015) · BMC Genomics · doi:10.1186/s12864-015-1618-x · Cited by 31 · see citing works

Conserved distances between vertebrate highly conserved elements

Sun, H., Skogerbø, G., & Chen, R. (2006) · Human Molecular Genetics · doi:10.1093/hmg/ddl232 · Cited by 30 · see citing works

Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes

Lv, J., Havlak, P., & Putnam, N. H. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-s9-s11 · Cited by 29 · see citing works

Bird and Mammal Sex-Chromosome Orthologs Map to the Same Autosomal Region in a Salamander (Ambystoma)

Smith, J. J., & Voss, S. R. (2007) · Genetics · doi:10.1534/genetics.107.072033 · Cited by 29 · see citing works

Ancestral Vertebrate Complexity of the Opioid System

Larhammar, D., Bergqvist, C., & Sundström, G. (2015) · Vitamins and hormones · doi:10.1016/bs.vh.2014.11.001 · Cited by 28 · see citing works

Impact of genomics on animal agriculture and opportunities for animal health

Rothschild, M. F., & Plastow, G. S. (2007) · Trends in biotechnology · doi:10.1016/j.tibtech.2007.10.001 · Cited by 28 · see citing works

Heterogeneous Tempo and Mode of Conserved Noncoding Sequence Evolution among Four Mammalian Orders

Babarinde, I. A., & Saitou, N. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt177 · Cited by 30 · see citing works

Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution

Kiazim, L. G., O’Connor, R. E., Larkin, D. M., Romanov, M. N., Narushin, V. G., Brazhnik, E. A., & Griffin, D. K. (2021) · Cells · doi:10.3390/cells10020362 · Cited by 26 · see citing works

A Comparative Synteny Map of Burkholderia Species Links Large-Scale Genome Rearrangements to Fine-Scale Nucleotide Variation in Prokaryotes

Lin, C. H., Bourque, G., & Tan, P. B. O. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm282 · Cited by 26 · see citing works

Murine segmental duplications are hot spots for chromosome and gene evolution

Armengol, L., Marquès‐Bonet, T., Cheung, J., Khaja, R., González, J. R., Scherer, S. W., Navarro, A., & Estivill, X. (2005) · Genomics · doi:10.1016/j.ygeno.2005.08.008 · Cited by 26 · see citing works

Ancestral animal genomes reconstruction

Rascol, V. L., Pontarotti, P., & Levasseur, A. (2007) · Current Opinion in Immunology · doi:10.1016/j.coi.2007.06.009 · Cited by 25 · see citing works

The Chicken Genome

Burt, D. W. (2006) · KARGER eBooks · doi:10.1159/000095100 · Cited by 24 · see citing works

Whole genome duplications, multi-break rearrangements, and genome halving problem

Alekseyev, M. A., & Pevzner, P. A. (2007) · Symposium on Discrete Algorithms · doi:10.5555/1283383.1283455 · Cited by 23 · see citing works

Divergent patterns of breakpoint reuse in Muroid rodents

Mlynarski, E. E., Obergfell, C. J., O’Neill, M. J., & O'Neill, R. J. W. (2009) · Mammalian Genome · doi:10.1007/s00335-009-9242-1 · Cited by 23 · see citing works

Genes Order and Phylogenetic Reconstruction: Application to γ-Proteobacteria

Blin, G., Chauve, C., & Guillaume Fertin, A. (2005) · Lecture notes in computer science · doi:10.1007/11554714_2 · Cited by 22 · see citing works

Stability of Rearrangement Measures in the Comparison of Genome Sequences

Mazowita, M., Haque, L., & Sankoff, D. (2006) · Journal of Computational Biology · doi:10.1089/cmb.2006.13.554 · Cited by 21 · see citing works

Reversals of Fortune

Sankoff, D., Zheng, C., & Lenert, A. (2005) · Lecture notes in computer science · doi:10.1007/11554714_12 · Cited by 21 · see citing works

Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology

Levasseur, A., Pontarotti, P., Poch, O., & Thompson, J. (2008) · Evolutionary Bioinformatics · doi:10.4137/ebo.s597 · Cited by 20 · see citing works

Whole Genome Duplications and Contracted Breakpoint Graphs

Alekseyev, M. A., & Pevzner, P. A. (2007) · SIAM Journal on Computing · doi:10.1137/05064727x · Cited by 20 · see citing works

Avian genomics in the 21st century

Burt, D. W., & White, S. J. (2007) · Cytogenetic and Genome Research · doi:10.1159/000103159 · Cited by 18 · see citing works

Comparative chromosomics

Graphodatsky, A. S. (2007) · Molecular Biology · doi:10.1134/s002689330703003x · Cited by 17 · see citing works

Evolutionary plasticity and cancer breakpoints in human chromosome 3

Ruiz‐Herrera, A., & Robinson, T. J. (2008) · BioEssays · doi:10.1002/bies.20829 · Cited by 16 · see citing works

Addressing chromosome evolution in the whole-genome sequence era

Faraut, T. (2008) · Chromosome Research · doi:10.1007/s10577-007-1208-0 · Cited by 16 · see citing works

Linkage mapping and physical localization of the major histocompatibility complex region of the marsupial Monodelphis domestica

Gouin, N., Deakin, J. E., Miska, K. B., Miller, R. D., Kammerer, C. M., Graves, J. A. M., VandeBerg, J. L., & Samollow, P. B. (2006) · Cytogenetic and Genome Research · doi:10.1159/000089882 · Cited by 16 · see citing works

DA and Xiao—two giant and composite LTR–retrotransposon-like elements identified in the human genome

Ji, X., & Zhao, S. (2008) · Genomics · doi:10.1016/j.ygeno.2007.10.014 · Cited by 16 · see citing works

Patterns and mechanisms of genome organization in the mouse

Graber, J. H., Churchill, G. A., DiPetrillo, K., King, B. L., Petkov, P. M., & Paigen, K. (2006) · Journal of Experimental Zoology Part A Comparative Experimental Biology · doi:10.1002/jez.a.322 · Cited by 16 · see citing works

Deep ancestry of mammalian X chromosome revealed by comparison with the basal tetrapod Xenopus tropicalis

Mácha, J., Teichmanová, R., Sater, A. K., Wells, D. E., Tlapáková, T., Zimmerman, L. B., & Krylov, V. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-315 · Cited by 15 · see citing works

References

Bourque, G., Zdobnov, E. M., Peer Bork, B., Pevzner, P. A., Tesler, G., Alerting, E., Zdobnov, E. M., Pevzner, P. A., & Tesler, G. (2005)

Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat GenomesPreprint

Bourque, G., Pevzner, P. A., & Tesler, G. (2004) · Genome Research · doi:10.1101/gr.1975204 · Cited by 240 · see citing works

Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?Preprint

Froenicke, L., Garcia-Caldés, M., Graphodatsky, A. S., Müller, S., Lyons, L. A., Robinson, T. J., Volleth, M., Yang, F., & Wienberg, J. (2006) · Genome Research · doi:10.1101/gr.3955206 · Cited by 81 · see citing works

Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes? - eScholarship

Froenicke, L., Garcia-Caldés, M., Graphodatsky, A. S., Müller, S., Lyons, L. A., Robinson, T. J., Volleth, M., Yang, F., & Wienberg, J. (2006)

The dynamics of chromosome evolution in birds and mammals

Burt, D. W., Bruley, C., Dunn, I., Jones, C. T., Ramage, A. D., Law, A. S., Morrice, D., Paton, I. R., Smith, J., Windsor, D., et al. (1999) · Nature · doi:10.1038/46555 · Cited by 288 · see citing works