A genome-wide comparison of recent chimpanzee and human segmental duplications

Finishing the euchromatic sequence of the human genome

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Detection of large-scale variation in the human genome

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Large-scale copy number polymorphism in the human genome

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

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Recent Segmental Duplications in the Human Genome

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The Influence of CCL3L1 Gene-Containing Segmental Duplications on HIV-1/AIDS Susceptibility

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Fine-scale structural variation of the human genome

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Segmental Duplications and Copy-Number Variation in the Human Genome

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Genome architecture, rearrangements and genomic disorders

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A common inversion under selection in Europeans

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Recurrent inversion toggling and great ape genome evolution

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The Evolution of Human Segmental Duplications and the Core Duplicon HypothesisPreprint

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Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzeePreprint

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Complex patterns of copy number variation at sites of segmental duplications: an important category of structural variation in the human genome

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Comparative Genomic Analysis of Human and Chimpanzee Indicates a Key Role for Indels in Primate Evolution

Wetterbom, A., Sevov, M., Cavelier, L. B., & Bergström, T. F. (2006) · Journal of Molecular Evolution · doi:10.1007/s00239-006-0045-7 · Cited by 72

Molecular mechanisms of chromosomal rearrangement during primate evolution

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The Jewels of Our Genome: The Search for the Genomic Changes Underlying the Evolutionarily Unique Capacities of the Human Brain

Sikela, J. M. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020080 · Cited by 72

The Evolutionary Position of Subfunctionalization, Downgraded

Freeling, M. (2008) · KARGER eBooks · doi:10.1159/000126004 · Cited by 69

Lineage-specific transcription factors and the evolution of gene regulatory networks

Nowick, K., & Stubbs, L. J. (2010) · Briefings in Functional Genomics · doi:10.1093/bfgp/elp056 · Cited by 70

Impact of low copy repeats on the generation of balanced and unbalanced chromosomal aberrations in mental retardation

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Copy number variation in the cattle genome

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Ultrafast DNA sequencing on a microchip by a hybrid separation mechanism that gives 600 bases in 6.5 minutes

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Chromosome‐level analysis of the Crassostrea hongkongensis genome reveals extensive duplication of immune‐related genes in bivalves

Peng, J., Li, Q., Xu, L., Wei, P., He, P., Zhang, X., Zhang, L., Guan, J., Zhang, X., Lin, Y., et al. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13157 · Cited by 62

Sequencing Primate Genomes: What Have We Learned?

Marquès‐Bonet, T., Ryder, O. A., & Eichler, E. E. (2009) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.9.081307.164420 · Cited by 65

Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes

Lunter, G. A. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm185 · Cited by 64

A prominent role for segmental duplications in modeling Eukaryotic genomes

Koszul, R., & Fischer, G. (2008) · Comptes Rendus Biologies · doi:10.1016/j.crvi.2008.07.005 · Cited by 67

Challenges and potential in tissue engineering

Slavkin, H. C., & Bartold, P. M. (2006) · Periodontology 2000 · doi:10.1111/j.1600-0757.2006.00172.x · Cited by 60

The chimpanzee and us

Li, W., & Saunders, M. A. (2005) · Nature · doi:10.1038/437050a · Cited by 59

Dark Matter of Primate Genomes: Satellite DNA Repeats and Their Evolutionary Dynamics

Ahmad, S. F., Singchat, W., Jehangir, M., Suntronpong, A., Panthum, T., Malaivijitnond, S., & Srikulnath, K. (2020) · Cells · doi:10.3390/cells9122714 · Cited by 62

Footprints of X-to-Y Gene Conversion in Recent Human Evolution

Trombetta, B., Cruciani, F., Underhill, P. A., Sellitto, D., & Scozzari, R. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp231 · Cited by 56

Patchwork people

Check, E. (2005) · Nature · doi:10.1038/4371084a · Cited by 53

Structural divergence between the human and chimpanzee genomes

Kehrer‐Sawatzki, H., & Cooper, D. N. (2006) · Human Genetics · doi:10.1007/s00439-006-0270-6 · Cited by 54

A recurrent inversion on the eutherian X chromosome

Cáceres, M., Sullivan, R. T., & Thomas, J. W. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706604104 · Cited by 52

Enhanced fixation and preservation of a newly arisen duplicate gene by masking deleterious loss-of-function mutations

Tanaka, K. M., Takahasi, K. R., & Takano‐Shimizu, T. (2009) · Genetics Research · doi:10.1017/s0016672309000196 · Cited by 51

Ubiquitous internal gene duplication and intron creation in eukaryotes

Gao, X., & Lynch, M. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0911093106 · Cited by 49

Different Facets of Copy Number Changes: Permanent, Transient, and Adaptive

Mishra, S., & Whetstine, J. R. (2016) · Molecular and Cellular Biology · doi:10.1128/mcb.00652-15 · Cited by 53

JY-1 , an oocyte-specific gene, regulates granulosa cell function and early embryonic development in cattle

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Direct estimation of de novo mutation rates in a chimpanzee parent-offspring trio by ultra-deep whole genome sequencing

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The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are importantPreprint

Kvikstad, E. M., & Makova, K. D. (2010) · Genome Research · doi:10.1101/gr.099044.109 · Cited by 50

REVIEW: Non‐human primate models of inheritance vulnerability to alcohol use disorders

Barr, C. S., & Goldman, D. A. (2006) · Addiction Biology · doi:10.1111/j.1369-1600.2005.00034.x · Cited by 49

DupMasker: A tool for annotating primate segmental duplicationsPreprint

Jiang, Z., Hubley, R. M., Smit, A. F. A., & Eichler, E. E. (2008) · Genome Research · doi:10.1101/gr.078477.108 · Cited by 48

Diagnosing duplications – can it be done?

Durand, D., & Hoberman, R. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.01.002 · Cited by 48

Analysis of high-identity segmental duplications in the grapevine genome

Giannuzzi, G., D’Addabbo, P., Gasparro, M., Martinelli, M., Carelli, F. N., Antonacci, D., & Ventura, M. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-436 · Cited by 46

Ecological context of savanna chimpanzee (Pan troglodytes verus) termite fishing at Fongoli, Senegal

Bogart, S. L., & Pruetz, J. D. (2008) · American Journal of Primatology · doi:10.1002/ajp.20530 · Cited by 44

Using brain organoids to study human neurodevelopment, evolution and disease

Kyrousi, C., & Cappello, S. (2019) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.347 · Cited by 41

The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2

Ventura, M., Catacchio, C. R., Sajjadian, S., Vives, L., Sudmant, P. H., Marques-Bonet, T., Graves, T. A., Wilson, R. K., & Eichler, E. E. (2012) · Genome Research · doi:10.1101/gr.136556.111 · Cited by 42

Hairless mutation: a driving force of humanization from a human–ape common ancestor by enforcing upright walking while holding a baby with both hands

Sutou, S. (2012) · Genes to Cells · doi:10.1111/j.1365-2443.2012.01592.x · Cited by 41

Bovine NK-lysin : Copy number variation and functional diversification

Chen, J., Huddleston, J., Buckley, R. M., Malig, M., Lawhon, S. D., Skow, L. C., Lee, M. O., Eichler, E. E., Andersson, L., & Womack, J. E. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1519374113 · Cited by 41

Is Schizophrenia the Price of Human Central Nervous System Complexity?

Dean, B. (2009) · Australian and New Zealand journal of psychiatry (Print) · doi:10.1080/00048670802534416 · Cited by 63

Different Selective Pressures Shape the Molecular Evolution of Color Vision in Chimpanzee and Human Populations

Verrelli, B. C., Lewis, C. M., Stone, A. C., & Perry, G. H. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn220 · Cited by 40

Evaluation of Bayesian Models of Substitution Rate Evolution—Parental Guidance versus Mutual Independence

Linder, M., Britton, T., & Sennblad, B. (2011) · Systematic Biology · doi:10.1093/sysbio/syr009 · Cited by 39

Homeotic Evolution in the Mammalia: Diversification of Therian Axial Seriation and the Morphogenetic Basis of Human Origins

Filler, A. G. (2007) · PLoS ONE · doi:10.1371/journal.pone.0001019 · Cited by 38

Orphans and new gene origination, a structural and evolutionary perspective

Light, S., Basile, W., & Elofsson, A. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.05.006 · Cited by 37

Hyper-expansion of large DNA segments in the genome of kuruma shrimp, Marsupenaeus japonicus

Koyama, T., Asakawa, S., Katagiri, T., Shimizu, A., Fagutao, F. F., Mavichak, R., Santos, M. D., Fuji, K., Sakamoto, T., Kitakado, T., et al. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-141 · Cited by 36

Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sitesPreprint

Girirajan, S., Chen, L., Graves, T., Marques-Bonet, T., Ventura, M., Fronick, C., Fulton, L., Rocchi, M., Fulton, R. S., Wilson, R. K., et al. (2008) · Genome Research · doi:10.1101/gr.086041.108 · Cited by 36

CNVannotator: A Comprehensive Annotation Server for Copy Number Variation in the Human Genome

Zhao, M., & Zhao, Z. (2013) · PLoS ONE · doi:10.1371/journal.pone.0080170 · Cited by 35

Teaching Diversity

McChesney, K. Y. (2015) · SAGE Open · doi:10.1177/2158244015611712 · Cited by 38

Systems biology approach to integrative comparative genomics

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Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing

Wetterbom, A., Ameur, A., Feuk, L., Gyllensten, U. B., & Cavelier, L. B. (2010) · Genome biology · doi:10.1186/gb-2010-11-7-r78 · Cited by 34

Contrasting Histories of G6PD Molecular Evolution and Malarial Resistance in Humans and Chimpanzees

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Identification of large-scale human-specific copy number differences by inter-species array comparative genomic hybridization

Goidts, V., Armengol, L., Schempp, W., Conroy, J. M., Nowak, N. J., Müller, S., Cooper, D. N., Estivill, X., Enard, W., Szamalek, J. M., et al. (2006) · Human Genetics · doi:10.1007/s00439-005-0130-9 · Cited by 34

The evolutionary significance of copy number variation in the human genome

Perry, G. H. (2008) · Cytogenetic and Genome Research · doi:10.1159/000184719 · Cited by 35

What is the future of electrophoresis in large‐scale genomic sequencing?

Fredlake, C. P., Hert, D. G., Mardis, E. R., & Barron, A. E. (2006) · Electrophoresis · doi:10.1002/elps.200600408 · Cited by 33

Tandem repeats modify the structure of human genes hosted in segmental duplications

Grassi, A., & Ciccarelli, F. D. (2009) · Genome biology · doi:10.1186/gb-2009-10-12-r137 · Cited by 32

Analysis of Nuclear Receptor Pseudogenes in Vertebrates: How the Silent Tell Their Stories

Zhang, Z. D., Cayting, P. D., Weinstock, G. M., & Gerstein, M. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm251 · Cited by 32

Genome Assembly, Rearrangement, and Repeats

Tang, H. (2007) · Chemical Reviews · doi:10.1021/cr0683008 · Cited by 33

On parameters of the human genome

Li, W. (2011) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2011.07.021 · Cited by 29

Human-Specific Changes of Genome Structure Detected by Genomic Triangulation

Harris, R. A., Rogers, J., & Milosavljevic, A. (2007) · Science · doi:10.1126/science.1139477 · Cited by 31

Exceptionally high cumulative percentage of NUMTs originating from linear mitochondrial DNA molecules in the Hydra magnipapillata genome

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Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regionsPreprint

Kirsch, S., Münch, C., Jiang, Z., Cheng, Z., Chen, L., Batz, C., Eichler, E. E., & Schempp, W. (2008) · Genome Research · doi:10.1101/gr.076711.108 · Cited by 30

Differential Evolution of MAGE Genes Based on Expression Pattern and Selection Pressure

Zhao, Q., Caballero, O. L., Simpson, A. J. G., & Strausberg, R. L. (2012) · PLoS ONE · doi:10.1371/journal.pone.0048240 · Cited by 29

Modelling the evolution of transcription factor binding preferences in complex eukaryotes

Rosanova, A., Colliva, A., Osella, M., & Caselle, M. (2017) · Scientific Reports · doi:10.1038/s41598-017-07761-0 · Cited by 29

Genomics of the evolutionary process

Clark, A. G. (2006) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2006.04.004 · Cited by 29

Lower Linkage Disequilibrium at CNVs is due to Both Recurrent Mutation and Transposing Duplications

Schrider, D. R., & Hahn, M. W. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp210 · Cited by 31

Expression Differentiation Is Constrained to Low-Expression Proteins over Ecological Timescales

Margres, M. J., Wray, K. P., Seavy, M. A., McGivern, J. J., Herrera, N. D., & Rokyta, D. R. (2015) · Genetics · doi:10.1534/genetics.115.180547 · Cited by 29

An Autosomal Analysis Gives No Genetic Evidence for Complex Speciation of Humans and Chimpanzees

Yamamichi, M., Gojobori, J., & Innan, H. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr172 · Cited by 29

Segmental Duplications Contribute to Gene Expression Differences Between Humans and Chimpanzees

Blekhman, R., Oshlack, A., & Gilad, Y. (2009) · Genetics · doi:10.1534/genetics.108.099960 · Cited by 27

Evolution of Tubulin Gene Arrays in Trypanosomatid parasites: genomic restructuring in Leishmania

Jackson, A. P., Vaughan, S., & Gull, K. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-261 · Cited by 27

Biting into the Genome to Phenome Map: Developmental Genetic Modularity of Cichlid Fish Dentitions

Hulsey, C. D., Fraser, G. J., & Meyer, A. (2016) · Integrative and Comparative Biology · doi:10.1093/icb/icw059 · Cited by 24

Genes with human-specific features are primarily involved with brain, immune and metabolic evolution

Bitar, M., Kuiper, S., O’Brien, E. A., & Barry, G. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-2886-2 · Cited by 27

Signals of Historical Interlocus Gene Conversion in Human Segmental Duplications

Dumont, B. L., & Eichler, E. E. (2013) · PLoS ONE · doi:10.1371/journal.pone.0075949 · Cited by 26

On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees

Marquès‐Bonet, T., Sànchez-Ruiz, J., Armengol, L., Khaja, R., Bertranpetit, J., López-Bigas, N., Rocchi, M., Gazave, É., & Navarro, A. (2007) · Genome biology · doi:10.1186/gb-2007-8-10-r230 · Cited by 26

High divergence in primate-specific duplicated regions: Human and chimpanzee Chorionic Gonadotropin Betagenes

Hallast, P., Saarela, J., Palotie, A. V., & Laan, M. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-195 · Cited by 26

Redundancy, Plasticity, and Detachment: The Implications of Comparative Genomics for Evolutionary Thinking

Moss, L. (2006) · Philosophy of Science · doi:10.1086/518778 · Cited by 24

Exploring the potential relevance of human-specific genes to complex disease

Cooper, D. N., & Kehrer‐Sawatzki, H. (2011) · Human Genomics · doi:10.1186/1479-7364-5-2-99 · Cited by 25

Genomic Comparisons of Humans and Chimpanzees

Varki, A. P., & Nelson, D. L. (2007) · Annual Review of Anthropology · doi:10.1146/annurev.anthro.36.081406.094339 · Cited by 25

Almost all human genes resulted from ancient duplication

Britten, R. J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0608796103 · Cited by 24

Functional requirements driving the gene duplication in 12 Drosophila species

Zhong, Y., Jia, Y., Gao, Y., Tian, D., Yang, S., & Zhang, X. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-555 · Cited by 23

Sequencing of rhesus macaque Y chromosome clarifies origins and evolution of the DAZ (Deleted in AZoospermia) genes

Hughes, J. F., Skaletsky, H., & Page, D. C. (2012) · BioEssays · doi:10.1002/bies.201200066 · Cited by 23

Nonadaptive processes in primate and human evolution

Harris, E. E. (2010) · American Journal of Physical Anthropology · doi:10.1002/ajpa.21439 · Cited by 23

Segmental duplications in the silkworm genome

Zhao, Q., Zhu, Z., Kasahara, M., Morishita, S., & Zhang, Z. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-521 · Cited by 23

Lessons from Chimpanzee-based Research on Human Disease: The Implications of Genetic Differences

Bailey, J. (2011) · Alternatives to Laboratory Animals · doi:10.1177/026119291103900608 · Cited by 22

Charles Robert Darwin (to the 200th Birthday and the 150th Anniversary of the publication of the book «On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life»

Vagin, Y. V. (2009) · Biopolymers and Cell · doi:10.7124/bc.0007ed · Cited by 23

A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0)

Kuderna, L. F. K., Tomlinson, C., Hillier, L., Tran, A., Fiddes, I. T., Armstrong, J. C., Laayouni, H., Gordon, D., Huddleston, J., García-Pérez, R., et al. (2017) · GigaScience · doi:10.1093/gigascience/gix098 · Cited by 23

Rapid, Paralog-Sensitive CNV Analysis of 2457 Human Genomes Using QuicK-mer2

Shen, F., & Kidd, J. M. (2020) · Genes · doi:10.3390/genes11020141 · Cited by 24

The Ontogeny of the Endocrine Pancreas in the Fetal/Newborn Baboon

Quinn, A. R., Blanco, C., Perego, C., Finzi, G., Rosa, S. L., Capella, C., Guardado-Mendoza, R., Casiraghi, F., Gastaldelli, A., Johnson, M. C., et al. (2012) · Journal of Endocrinology · doi:10.1530/joe-12-0070 · Cited by 23

Copy number variants in a highly inbred I berian porcine strain

Fernández, A. I., Barragán, C., Fernández, A., Rodríguez, M. C., & Villanueva, B. (2014) · Animal Genetics · doi:10.1111/age.12137 · Cited by 22

Fourfold paralogy regions on human HOX-bearing chromosomes: Role of ancient segmental duplications in the evolution of vertebrate genome

Asrar, Z., Haq, F. U., & Abbasi, A. A. (2012) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2012.10.024 · Cited by 23

Monkey-based Research on Human Disease: The Implications of Genetic Differences

Bailey, J. (2014) · Alternatives to Laboratory Animals · doi:10.1177/026119291404200504 · Cited by 22

Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locusPreprint

Horvath, J. E., Sheedy, C. B., Merrett, S. L., Diallo, A. B., Swofford, D. L., Program, N. C. S., Green, E. D., & Willard, H. F. (2011) · Genome Research · doi:10.1101/gr.111849.110 · Cited by 21

Revised time estimation of the ancestral human chromosome 2 fusion

Poszewiecka, B., Gogolewski, K., Stankiewicz, P., & Gambin, A. (2022) · BMC Genomics · doi:10.1186/s12864-022-08828-7 · Cited by 20

Genetic and Biological Effects of ICAM-1 E469K Polymorphism in Diabetic Kidney Disease

Zhang, X., Seman, N. A., Falhammar, H., Brismar, K., & Gu, H. F. (2020) · Journal of Diabetes Research · doi:10.1155/2020/8305460 · Cited by 21

Copy Number Variation at the APOL1 Locus

Ruchi, R., Genovese, G., Lee, J., Charoonratana, V. T., Bernhardy, A. J., Alper, S. L., Kopp, J. B., Thadhani, R., Friedman, D. J., & Pollak, M. R. (2015) · PLoS ONE · doi:10.1371/journal.pone.0125410 · Cited by 21

Insights on the functional interactions between miRNAs and copy number variations in the aging brain

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Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals

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