Human evolution: the non-coding revolution

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

An integrated encyclopedia of DNA elements in the human genome

The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072 · see citing works

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223 · 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

Evolution at Two Levels in Humans and Chimpanzees: Their macromolecules are so alike that regulatory mutations may account for their biological differences

King, M.-C., & Wilson, A. C. (1975) · Science · doi:10.1126/science.1090005 · Cited by 2,815 · see citing works

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

Gilbert, L. A., Horlbeck, M. A., Adamson, B., Villalta, J. E., Chen, Y., Whitehead, E. H., Guimaraes, C., Panning, B., Ploegh, H. L., Bassik, M. C., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.029 · Cited by 2,728 · 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

Detection of nonneutral substitution rates on mammalian phylogenies

Pollard, K. S., Hubisz, M. J., Rosenbloom, K. R., & Siepel, A. (2010) · Genome Research · doi:10.1101/gr.097857.109 · Cited by 2,353 · see citing works

A unique chromatin signature uncovers early developmental enhancers in humans

Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233 · see citing works

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

Lupiáñez, D. G., Kraft, K., Heinrich, V., Krawitz, P., Brancati, F., Klopocki, E., Horn, D., Kayserili, H., Opitz, J. M., Laxova, R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.004 · Cited by 2,132 · see citing works

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

Carroll, S. B. (2008) · Cell · doi:10.1016/j.cell.2008.06.030 · Cited by 2,067 · see citing works

ChIP-seq accurately predicts tissue-specific activity of enhancers

Visel, A., Blow, M. J., Li, Z., Zhang, T., Akiyama, J. A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F., et al. (2009) · Nature · doi:10.1038/nature07730 · Cited by 1,639 · see citing works

Evolutionary and biomedical insights from the rhesus macaque genome.

Gibbs, R. A., Rogers, J., Katze, M. G., Bumgarner, R., Weinstock, G. M., Mardis, E. R., Remington, K. A., Strausberg, R. L., Venter, J. C., Wilson, R. K., et al. (2007) · Science · doi:10.1126/science.1139247 · Cited by 1,403 · see citing works

In vivo enhancer analysis of human conserved non-coding sequences

Pennacchio, L. A., Ahituv, N., Moses, A. M., Prabhakar, S., Nobrega, M. A., Shoukry, M., Minovitsky, S., Dubchak, I., Holt, A., Lewis, K. D., et al. (2006) · Nature · doi:10.1038/nature05295 · Cited by 1,165 · see citing works

A high-resolution map of human evolutionary constraint using 29 mammals

Broad Institute Sequencing Platform and Whole Genome Assembly Team, Lindblad-Toh, K., Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S., Kheradpour, P., et al. (2011) · Nature · doi:10.1038/nature10530 · Cited by 1,108 · see citing works

An RNA gene expressed during cortical development evolved rapidly in humans

Pollard, K. S., Salama, S. R., Lambert, N., Lambot, M.-A., Coppens, S., Pedersen, J. S., Katzman, S., King, B., Onodera, C., Siepel, A., et al. (2006) · Nature · doi:10.1038/nature05113 · Cited by 1,005 · see citing works

The remarkable, yet not extraordinary, human brain as a scaled-up primate brain and its associated cost

Herculano-Houzel, S. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1201895109 · Cited by 726 · see citing works

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

Melnikov, A., Murugan, A., Zhang, X., Tesileanu, T., Wang, L., Rogov, P., Feizi, S., Gnirke, A., Callan, C. G., Kinney, J. B., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2137 · Cited by 711 · see citing works

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

Vietri Rudan, M., Barrington, C., Henderson, S., Ernst, C., Odom, D. T., Tanay, A., & Hadjur, S. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.02.004 · Cited by 680 · see citing works

The Origin of Man: A Chromosomal Pictorial Legacy

Yunis, J. J., & Prakash, O. (1982) · Science · doi:10.1126/science.7063861 · Cited by 672 · see citing works

Human-specific gene <i>ARHGAP11B</i> promotes basal progenitor amplification and neocortex expansion

Florio, M., Albert, M., Taverna, E., Namba, T., Brandl, H., Lewitus, E., Haffner, C., Sykes, A., Wong, F. K., Peters, J., et al. (2015) · Science · doi:10.1126/science.aaa1975 · Cited by 632 · see citing works

CHD7 cooperates with PBAF to control multipotent neural crest formation

Bajpai, R., Chen, D. A., Rada-Iglesias, Á., Zhang, J., Xiong, Y., Helms, J. A., Chang, C., Zhao, Y., Swigut, T., & Wysocka, J. (2010) · Nature · doi:10.1038/nature08733 · Cited by 611 · see citing works

A humanized version of Foxp2 affects cortico-basal ganglia circuits in mice

Enard, W., Gehre, S., Hammerschmidt, K., Hölter, S. M., Blass, T., Somel, M., Brückner, M. K., Schreiweis, C., Winter, C., Sohr, R., et al. (2009) · Cell · doi:10.1016/j.cell.2009.03.041 · Cited by 605 · see citing works

Humans and great apes share a large frontal cortex

Semendeferi, K., Lu, A., Schenker-Ahmed, N. M., & Damasio, H. (2002) · Nature Neuroscience · doi:10.1038/nn814 · Cited by 540 · see citing works

Massively parallel functional dissection of mammalian enhancers in vivo

Patwardhan, R. P., Hiatt, J. B., Witten, D. M., Kim, M. J., Smith, R. P., May, D., Lee, C., Andrie, J. M., Lee, S.-I., Cooper, G. M., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2136 · Cited by 536 · see citing works

Human-specific loss of regulatory DNA and the evolution of human-specific traits

McLean, C. Y., Reno, P. L., Pollen, A. A., Bassan, A. I., Capellini, T. D., Guenther, C., Indjeian, V. B., Lim, X., Menke, D. B., Schaar, B. T., et al. (2011) · Nature · doi:10.1038/nature09774 · Cited by 535 · see citing works

Forces shaping the fastest evolving regions in the human genome

Pollard, K. S., Salama, S. R., King, B., Kern, A. D., Dreszer, T., Katzman, S., Siepel, A., Pedersen, J. S., Bejerano, G., Baertsch, R., et al. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020168 · Cited by 511 · see citing works

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

Frankel, N., Davis, G. K., Vargas, D., Wang, S., Payre, F., & Stern, D. L. (2010) · Nature · doi:10.1038/nature09158 · Cited by 510 · see citing works

On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE

Graur, D., Zheng, Y., Price, N. C., Azevedo, R. B. R., Zufall, R. A., & Elhaik, E. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt028 · Cited by 482 · see citing works

Accelerated Evolution of Conserved Noncoding Sequences in Humans

Prabhakar, S., Noonan, J. P., Pääbo, S., & Rubin, E. M. (2006) · Science · doi:10.1126/science.1130738 · Cited by 481 · see citing works

Inhibition of SRGAP2 function by its human-specific paralogs induces neoteny during spine maturation

Charrier, C., Joshi, K., Coutinho-Budd, J., Kim, J.-E., Lambert, N., de Marchena, J., Jin, W.-L., Vanderhaeghen, P., Ghosh, A., Sassa, T., et al. (2012) · Cell · doi:10.1016/j.cell.2012.03.034 · Cited by 454 · see citing works

Transcriptional Enhancers in Animal Development and Evolution

Levine, M. (2010) · Current Biology · doi:10.1016/j.cub.2010.06.070 · Cited by 449 · see citing works

Is junk DNA bunk? A critique of ENCODE

Doolittle, W. F. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1221376110 · Cited by 430 · see citing works

Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication

Dennis, M. Y., Nuttle, X., Sudmant, P. H., Antonacci, F., Graves, T. A., Nefedov, M., Rosenfeld, J. A., Sajjadian, S., Malig, M., Kotkiewicz, H., et al. (2012) · Cell · doi:10.1016/j.cell.2012.03.033 · Cited by 407 · see citing works

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

Cheng, Z., Ventura, M., She, X., Khaitovich, P., Graves, T., Osoegawa, K., Church, D., DeJong, P., Wilson, R. K., Pääbo, S., et al. (2005) · Nature · doi:10.1038/nature04000 · Cited by 398 · see citing works

Human-Specific Gain of Function in a Developmental Enhancer

Prabhakar, S., Visel, A., Akiyama, J. A., Shoukry, M. I., Lewis, K. D., Holt, A., Plajzer-Frick, I., Morrison, H., FitzPatrick, D. R., Afzal, V., et al. (2008) · Science · doi:10.1126/science.1159974 · Cited by 352 · see citing works

Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest

Prescott, S. L., Srinivasan, R., Marchetto, M. C., Grishina, I., Narvaiza, I., Selleri, L., Gage, F. H., Swigut, T., & Wysocka, J. (2015) · Cell · doi:10.1016/j.cell.2015.08.036 · Cited by 352 · see citing works

Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior

Doan, R. N., Bae, B.-I., Cubelos, B., Chang, C. Y., Hossain, A. A., Al-Saad, S., Mukaddes, N. M., Öner, Ö., Al‐Saffar, M., Balkhy, S., et al. (2016) · Cell · doi:10.1016/j.cell.2016.08.071 · Cited by 342 · see citing works

Comparing the human and chimpanzee genomes: Searching for needles in a haystackPreprint

Varki, A. P., & Altheide, T. K. (2005) · Genome Research · doi:10.1101/gr.3737405 · Cited by 339 · see citing works

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

Visel, A., Prabhakar, S., Akiyama, J. A., Shoukry, M., Lewis, K. D., Holt, A., Plajzer-Frick, I., Afzal, V., Rubin, E. M., & Pennacchio, L. A. (2008) · Nature Genetics · doi:10.1038/ng.2007.55 · Cited by 321 · see citing works

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

Li, G., Fullwood, M. J., Han, X., Mulawadi, F. H., Velkov, S., Vega, V. B., Ariyaratne, P. N., Mohamed, Y. B., Ooi, H.-S., Tennakoon, C., et al. (2010) · Genome biology · doi:10.1186/gb-2010-11-2-r22 · Cited by 316 · see citing works

Different Levels of the Homeodomain Protein Cut Regulate Distinct Dendrite Branching Patterns of Drosophila Multidendritic Neurons

Grueber, W. B., Jan, L. Y., & Jan, Y. N. (2003) · Cell · doi:10.1016/s0092-8674(03)00160-0 · Cited by 315 · see citing works

Cux1 and Cux2 Regulate Dendritic Branching, Spine Morphology, and Synapses of the Upper Layer Neurons of the Cortex

Cubelos, B., Sebastián‐Serrano, Á., Beccari, L. L., Calcagnotto, M. E., Cisneros, E., Kim, S., Dopazo, A., Álvarez‐Dolado, M., Redondo, J. M., Bovolenta, P., et al. (2010) · Neuron · doi:10.1016/j.neuron.2010.04.038 · Cited by 301 · see citing works

Evolutionary changes in promoter and enhancer activity during human corticogenesis

Reilly, S. K., Yin, J., Ayoub, A. E., Emera, D., Leng, J., Cotney, J., Sarro, R., Rakic, P., & Noonan, J. P. (2015) · Science · doi:10.1126/science.1260943 · Cited by 297 · see citing works

Human-Chimpanzee Differences in a FZD8 Enhancer Alter Cell-Cycle Dynamics in the Developing Neocortex

Boyd, J. L., Skove, S. L., Rouanet, J. P., Pilaz, L., Bepler, T., Gordân, R., Wray, G. A., & Silver, D. L. (2015) · Current Biology · doi:10.1016/j.cub.2015.01.041 · Cited by 282 · see citing works

Lineage-Specific Gene Duplication and Loss in Human and Great Ape Evolution

Fortna, A., Kim, Y., MacLaren, E. J., Marshall, K. E., Hahn, G., Meltesen, L., Brenton, M., Hink, R., Burgers, S., Hernandez‐Boussard, T., et al. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020207 · Cited by 276 · see citing works

Blood Immunity and Blood Relationship

Nuttall, G., Graham‐Smith, G. S., & Strangeways, T. S. P. (2010) · Cited by 237 · see citing works

Many human accelerated regions are developmental enhancers

Capra, J. A., Erwin, G. D., McKinsey, G., Rubenstein, J. L. R., & Pollard, K. S. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0025 · Cited by 235 · see citing works

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances

Symmons, O., Pan, L., Remeseiro, S., Aktas, T., Klein, F., Huber, W., & Spitz, F. (2016) · Developmental Cell · doi:10.1016/j.devcel.2016.10.015 · Cited by 222 · see citing works

Spatial Organization of Neurons in the Frontal Pole Sets Humans Apart from Great Apes

Semendeferi, K., Teffer, K., Buxhoeveden, D. P., Park, M. S., Bludau, S., Amunts, K., Travis, K., & Buckwalter, J. (2011) · Cerebral Cortex · doi:10.1093/cercor/bhq191 · Cited by 210 · see citing works

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

Cotney, J. L., Leng, J., Yin, J., Reilly, S. K., DeMare, L. E., Emera, D., Ayoub, A. E., RAKIC, P. T., & Noonan, J. P. (2013) · Cell · doi:10.1016/j.cell.2013.05.056 · Cited by 208 · see citing works

Evolution and diversity of copy number variation in the great ape lineagePreprint

Sudmant, P. H., Huddleston, J., Catacchio, C. R., Malig, M., Hillier, L. W., Baker, C. A., Mohajeri, K., Kondova, I. I., Bontrop, R. E., Persengiev, S. P., et al. (2013) · Genome Research · doi:10.1101/gr.158543.113 · Cited by 195 · see citing works

Fast-evolving noncoding sequences in the human genome

Bird, C., Stranger, B. E., Liu, M., Thomas, D. J., Ingle, C., Beazley, C., Miller, W., Hurles, M. E., & Dermitzakis, E. T. (2007) · Genome biology · doi:10.1186/gb-2007-8-6-r118 · Cited by 191 · see citing works

Humanized Foxp2 accelerates learning by enhancing transitions from declarative to procedural performance

Schreiweis, C., Bornschein, U., Burguière, E., Kerimoglu, C., Schreiter, S., Dannemann, M., Goyal, S., Rea, E., French, C. A., Puliyadi, R., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1414542111 · Cited by 190 · see citing works

Human adaptation and evolution by segmental duplication

Dennis, M. Y., & Eichler, E. E. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.08.001 · Cited by 189 · see citing works

Evolution of genetic and genomic features unique to the human lineage

O'Bleness, M., Searles, V. B., Varki, A., Gagneux, P., & Sikela, J. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3336 · Cited by 168 · see citing works

Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?

de Souza, F. S. J., Franchini, L. F., & Rubinstein, M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst045 · Cited by 162 · see citing works

Precise Gene Deletion and Replacement Using the CRISPR/Cas9 System in Human Cells

Zheng, Q., Cai, X., Tan, M. H., Schaffert, S. A., Arnold, C. P., Gong, X., Chen, C., & Huang, S. (2014) · BioTechniques · doi:10.2144/000114196 · Cited by 148 · see citing works

Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution

Hubisz, M. J., & Pollard, K. S. (2014) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2014.07.005 · Cited by 146 · see citing works

Synaptogenesis and development of pyramidal neuron dendritic morphology in the chimpanzee neocortex resembles humans

Bianchi, S., Stimpson, C. D., Duka, T., Larsen, M. D., Janssen, W. G. M., Collins, Z., Bauernfeind, A. L., Schapiro, S. J., Baze, W. B., McArthur, M. J., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1301224110 · Cited by 136 · see citing works

Genomic and Network Patterns of Schizophrenia Genetic Variation in Human Evolutionary Accelerated Regions

Xu, K., Schadt, E. E., Pollard, K. S., Roussos, P., & Dudley, J. T. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv031 · Cited by 133 · see citing works

Epigenomic annotation of gene regulatory alterations during evolution of the primate brain

Bank, N. B., Vermunt, M. W., Tan, S., Castelijns, B., Geeven, G., Reinink, P., de Bruijn, E., Kondova, I. I., Persengiev, S. P., Bontrop, R. E., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4229 · Cited by 123 · see citing works

Mouse and human blastocyst-derived stem cells: vive les differences

Rossant, J. (2014) · Development · doi:10.1242/dev.115451 · Cited by 120 · see citing works

Partially Redundant Enhancers Cooperatively Maintain Mammalian Pomc Expression Above a Critical Functional Threshold

Lam, D. D., de Souza, F. S. J., Nasif, S., Yamashita, M., López‐Leal, R., Otero-Corchón, V., Meece, K., Sampath, H., Mercer, A. J., Wardlaw, S. L., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1004935 · Cited by 115 · see citing works

Neuropil distribution in the cerebral cortex differs between humans and chimpanzees

Spocter, M. A., Hopkins, W. D., Barks, S. K., Bianchi, S., Hehmeyer, A. E., Anderson, S. M., Stimpson, C. D., Fobbs, A. J., Hof, P. R., & Sherwood, C. C. (2012) · Journal of Comparative Neurology · doi:10.1002/cne.23074 · Cited by 113 · see citing works

No relative expansion of the number of prefrontal neurons in primate and human evolution

Gabi, M., Neves, K., MASSERON, C. C., Ribeiro, P. F. M., Ventura‐Antunes, L., Torres, L. B., Mota, B., Kaas, J. H., & Herculano‐Houzel, S. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1610178113 · Cited by 109 · see citing works

Human brain evolution: From gene discovery to phenotype discovery

Preuss, T. M. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1201894109 · Cited by 108 · see citing works

A genome-wide screen for noncoding elements important in primate evolution

Bush, E., & Lahn, B. T. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-17 · Cited by 106 · see citing works

Comprehensive identification and analysis of human accelerated regulatory DNAPreprint

Gittelman, R. M., Hun, E., Ay, F., Madeoy, J. J., Pennacchio, L. A., Noble, W. S., Hawkins, R. D., & Akey, J. M. (2015) · Genome Research · doi:10.1101/gr.192591.115 · Cited by 106 · see citing works

The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome

Kostka, D., Hubisz, M. J., Siepel, A., & Pollard, K. S. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/msr279 · Cited by 102 · see citing works

The Developmental Brain Gene NPAS3 Contains the Largest Number of Accelerated Regulatory Sequences in the Human Genome

Kamm, G. B., Pisciottano, F., Kliger, R., & Franchini, L. F. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst023 · Cited by 102 · see citing works

Genetic basis of human brain evolution

Vallender, E. J., Mekel-Bobrov, N., & Lahn, B. T. (2008) · Trends in Neurosciences · doi:10.1016/j.tins.2008.08.010 · Cited by 102 · see citing works

The mystery of extreme non-coding conservation

Harmston, N., Barešić, A., & Lenhard, B. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0021 · Cited by 79 · see citing works

Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons

Franchini, L. F., López‐Leal, R., Nasif, S., Beati, P., Gelman, D. M., Low, M. J., de Souza, F. S. J., & Rubinstein, M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1104997108 · Cited by 78 · see citing works

Evolution of transcriptional enhancers and animal diversity

Rubinstein, M., & de Souza, F. S. J. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0017 · Cited by 78 · see citing works

Topologically associated domains: a successful scaffold for the evolution of gene regulation in animals

Acemel, R. D., Maeso, I., & Gómez-Skármeta, J. L. (2017) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.265 · Cited by 77 · see citing works

The Evolution of Human Segmental Duplications and the Core Duplicon HypothesisPreprint

Marquès‐Bonet, T., & Eichler, E. E. (2009) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2009.74.011 · Cited by 76 · see citing works

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 71 · see citing works

A fast-evolving human NPAS3 enhancer gained reporter expression in the developing forebrain of transgenic mice

Kamm, G. B., López‐Leal, R., Lorenzo, R., & Franchini, L. F. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0019 · Cited by 71 · see citing works

29 Mammalian Genomes Reveal Novel Exaptations of Mobile Elements for Likely Regulatory Functions in the Human Genome

Lowe, C. B., & Haussler, D. H. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043128 · Cited by 69 · see citing works

Evolution of Gene Regulation in Humans

Reilly, S. K., & Noonan, J. P. (2016) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090314-045935 · Cited by 67 · see citing works

Biological function in the twilight zone of sequence conservation

Ponting, C. P. (2017) · BMC Biology · doi:10.1186/s12915-017-0411-5 · Cited by 58 · see citing works

Chromatin Interaction Analysis Using Paired‐End Tag Sequencing

Fullwood, M. J., Han, Y., Wei, C., Ruan, X., & Ruan, Y. (2010) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb2115s89 · Cited by 55 · see citing works

The Molecular Basis of Human Brain Evolution

Enard, W. (2016) · Current Biology · doi:10.1016/j.cub.2016.09.030 · Cited by 55 · see citing works

Primate Brain Evolution in Phylogenetic Context

Preuss, T. M. (2007) · Evolution of Nervous Systems · doi:10.1016/b0-12-370878-8/00005-7 · Cited by 52 · see citing works

DUF1220 Dosage Is Linearly Associated with Increasing Severity of the Three Primary Symptoms of Autism

Davis, J. M., Searles, V. B., Anderson, N., Keeney, J., Dumas, L., & Sikela, J. M. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004241 · Cited by 51 · see citing works

Enhancer turnover and conserved regulatory function in vertebrate evolution

Domené, S., Bumaschny, V. F., de Souza, F. S. J., Franchini, L. F., Nasif, S., Low, M. J., & Rubinstein, M. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0027 · Cited by 45 · see citing works

Genomic divergence and brain evolution: How regulatory DNA influences development of the cerebral cortex

Silver, D. L. (2015) · BioEssays · doi:10.1002/bies.201500108 · Cited by 41 · see citing works

Functional anatomy of distant-acting mammalian enhancers

Dickel, D. E., Visel, A., & Pennacchio, L. A. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2012.0359 · Cited by 40 · see citing works

Genome-Wide Identification of Regulatory Sequences Undergoing Accelerated Evolution in the Human Genome

Dong, X., Wang, X. R., Zhang, F., & Tian, W. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw128 · Cited by 40 · see citing works

GC-Biased Evolution Near Human Accelerated Regions

Katzman, S. J., Kern, A. D., Pollard, K. S., Salama, S. R., & Haussler, D. H. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000960 · Cited by 39 · see citing works

Loss-of-Function Mutation in a Repressor Module of Human-Specifically Activated Enhancer HACNS1

Sumiyama, K., & Saitou, N. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr231 · Cited by 33 · see citing works

Deep conservation of cis -regulatory elements in metazoans

Maeso, I., Irimia, M., Tena, J. J., Casares, F., & Gómez-Skármeta, J. L. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0020 · Cited by 32 · see citing works

Identification of the ER-resident E3 ubiquitin ligase RNF145 as a novel LXR-regulated gene

Cook, E. C. L., Nelson, J. K., Sorrentino, V., et al. (2017) · PLoS ONE · doi:10.1371/journal.pone.0172721 · Cited by 32 · see citing works

Genomic approaches to studying human-specific developmental traits

Franchini, L. F., & Pollard, K. S. (2015) · Development · doi:10.1242/dev.120048 · Cited by 29 · see citing works

Targeted Capture and High-Throughput Sequencing Using Molecular Inversion Probes (MIPs)

Cantsilieris, S., Stessman, H. A. F., Shendure, J., et al. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6442-0_6 · Cited by 25 · see citing works

Can a few non‐coding mutations make a human brain?

Franchini, L. F., & Pollard, K. S. (2015) · BioEssays · doi:10.1002/bies.201500049 · Cited by 22 · see citing works

Noncoding Sequences Near Duplicated Genes Evolve Rapidly

Kostka, D., Hahn, M. W., & Pollard, K. S. (2010) · Genome Biology and Evolution · doi:10.1093/gbe/evq037 · Cited by 20 · see citing works

Cis-regulatory landscapes in development and evolution

Maeso, I., Acemel, R. D., & Gómez-Skármeta, J. L. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.10.004 · Cited by 16 · see citing works

Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution

Sakabe, N. J., & Nóbrega, M. A. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0022 · Cited by 13 · see citing works

Human Evolution: Enhancing the Brain

Enard, W. (2015) · Current Biology · doi:10.1016/j.cub.2015.03.031 · Cited by 4 · see citing works

Rewiring of human neurodevelopmental gene regulatory programs by human accelerated regions

Girskis, K. M., Stergachis, A. B., DeGennaro, E. M., Doan, R. N., Qian, X., Johnson, M. B., Wang, P. P., Sejourne, G. M., Nagy, M. A., Pollina, E. A., et al. (2021) · Neuron · doi:10.1016/j.neuron.2021.08.005 · Cited by 193 · see citing works

Three-dimensional genome rewiring in loci with human accelerated regions

Keough, K. C., Whalen, S., Inoue, F., Przytycki, P. F., Fair, T., Deng, C., Steyert, M., Ryu, H., Lindblad-Toh, K., Karlsson, E., et al. (2023) · Science · doi:10.1126/science.abm1696 · Cited by 113 · see citing works

The human-specific paralogs SRGAP2B and SRGAP2C differentially modulate SRGAP2A-dependent synaptic development

Schmidt, E. R. E., Kupferman, J. V., Stackmann, M., & Polleux, F. (2019) · Scientific Reports · doi:10.1038/s41598-019-54887-4 · Cited by 55 · see citing works

Denisovan introgression has shaped the immune system of present-day Papuans

Vespasiani, D. M., Jacobs, G. S., Cook, L. E., Brucato, N., Leavesley, M., Kinipi, C., Ricaut, F.-X., Cox, M. P., & Gallego Romero, I. (2022) · PLOS Genetics · doi:10.1371/journal.pgen.1010470 · Cited by 46 · see citing works

Consequences of trisomy 21 for brain development in Down syndrome

Russo, M. L., Sousa, A. M. M., & Bhattacharyya, A. (2024) · Nature Reviews Neuroscience · doi:10.1038/s41583-024-00866-2 · Cited by 28 · see citing works

The Human Accelerated Region HAR202 Controls <i>NPAS3</i> Expression in the Developing Forebrain Displaying Differential Enhancer Activity Between Modern and Archaic Human Sequences

Caporale, A. L., Cinalli, A. R., Rubinstein, M., & Franchini, L. F. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae186 · Cited by 7 · see citing works

Human-Mouse Comparative Genomics: Successes and Failures to Reveal Functional Regions of the Human GenomePreprint

Pennacchio, L. A., Baroukh, N., & Rubin, E. M. (2003) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2003.68.303 · Cited by 10 · see citing works

The Human genome

Strachan, T. (2003) · Medical Entomology and Zoology · Cited by 7 · see citing works

Beyond the Paleolithic prescription: incorporating diversity and flexibility in the study of human diet evolution

Turner, B. L., & Thompson, A. L. (2013) · Nutrition Reviews · doi:10.1111/nure.12039 · Cited by 71 · see citing works

Human genome analysis and medicine in the 21st century (abstract only)

Nakamura, Y. (2000) · doi:10.1145/332306.332557

Complete Human Genome Sequencing for Large-Scale Human Disease Studies

Drmanac, R. (2010) · PubMed Central