The cis-regulatory effects of modern human-specific variants
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Abstract
The Neanderthal and Denisovan genomes enabled the discovery of sequences that differ between modern and archaic humans, the majority of which are noncoding. However, our understanding of the regulatory consequences of these differences remains limited, in part due to the decay of regulatory marks in ancient samples. Here, we used a massively parallel reporter assay in embryonic stem cells, neural progenitor cells, and bone osteoblasts to investigate the regulatory effects of the 14,042 single-nucleotide modern human-specific variants. Overall, 1791 (13%) of sequences containing these variants showed active regulatory activity, and 407 (23%) of these drove differential expression between human groups. Differentially active sequences were associated with divergent transcription factor binding motifs, and with genes enriched for vocal tract and brain anatomy and function. This work provides insight into the regulatory function of variants that emerged along the modern human lineage and the recent evolution of human gene expression.
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Recent work has shown that variants which arose in the human lineage following its split from the Neanderthal-Denisovan common ancestor, and which have reached (near) fixation in modern humans since then, can exhibit significant differences in regulatory activity relative to the ancestral state.
“Recent work by [72] has shown that variants which arose in the human lineage following its split from the Neanderthal-Denisovan common ancestor, and which have reached (near) fixation in modern humans since then can exhibit significant differences in regulatory activity relative to the ancestral state.”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [72]
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Cites
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works
A global reference for human genetic variation
The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247 · 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
dbSNP: the NCBI database of genetic variation
Sherry, S. T. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.308 · Cited by 7,502 · see citing works
Integrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368 · see citing works
Functions of DNA methylation: islands, start sites, gene bodies and beyond
Jones, P. A. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3230 · Cited by 6,061 · see citing works
The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
The GTEx Consortium, Ardlie, K. G., Deluca, D. S., Segrè, A. V., Sullivan, T. J., Young, T. R., Gelfand, E. T., Trowbridge, C. A., Maller, J. B., Tukiainen, T., et al. (2015) · Science · doi:10.1126/science.1262110 · Cited by 5,062 · see citing works
Human DNA methylomes at base resolution show widespread epigenomic differences
Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q.-M., et al. (2009) · Nature · doi:10.1038/nature08514 · Cited by 4,673 · see citing works
GENCODE: The reference human genome annotation for The ENCODE Project
Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., et al. (2012) · Genome Research · doi:10.1101/gr.135350.111 · Cited by 4,585 · see citing works
FIMO: scanning for occurrences of a given motif
Grant, C. E., Bailey, T. L., & Noble, W. S. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr064 · Cited by 4,247 · see citing works
Buniello, A., MacArthur, J. A. L., Cerezo, M., Harris, L. W., Hayhurst, J., Malangone, C., McMahon, A., Morales, J., Mountjoy, E., Sollis, E., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1120 · Cited by 4,000 · see citing works
Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling
Chambers, S. M., Fasano, C. A., Papapetrou, E. P., Tomishima, M., Sadelain, M., & Studer, L. (2009) · Nature Biotechnology · doi:10.1038/nbt.1529 · Cited by 3,620 · see citing works
GENCODE reference annotation for the human and mouse genomes
Frankish, A., Diekhans, M., Ferreira, A.-M., Johnson, R., Jungreis, I., Loveland, J. E., Mudge, J. M., Sisu, C., Wright, J. C., Armstrong, J. C., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky955 · Cited by 2,929 · see citing works
King, M.-C., & Wilson, A. C. (1975) · Science · doi:10.1126/science.1090005 · Cited by 2,815 · see citing works
ChromHMM: automating chromatin-state discovery and characterization
Ernst, J., & Kellis, M. (2012) · Nature Methods · doi:10.1038/nmeth.1906 · Cited by 2,489 · see citing works
The complete genome sequence of a Neanderthal from the Altai Mountains
Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P. H., de Filippo, C., et al. (2014) · Nature · doi:10.1038/nature12886 · Cited by 2,254 · see citing works
A high-coverage genome sequence from an archaic denisovan individual
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science · doi:10.1126/science.1224344 · Cited by 1,967 · see citing works
DNA-binding factors shape the mouse methylome at distal regulatory regions
Stadler, M. B., Murr, R., Burger, L., Ivanek, R., Lienert, F., Schöler, A., Nimwegen, E. V., Wirbelauer, C., Oakeley, E. J., Gaidatzis, D., et al. (2011) · Nature · doi:10.1038/nature10716 · Cited by 1,383 · see citing works
GeneHancer: genome-wide integration of enhancers and target genes in GeneCards
Fishilevich, S., Nudel, R., Rappaport, N., Hadar, R., Plaschkes, I., Stein, T. I., Rosen, N., Kohn, A., Twik, M., Safran, M., et al. (2017) · Database · doi:10.1093/database/bax028 · Cited by 1,219 · see citing works
Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations
Fulco, C. P., Nasser, J., Jones, T. R., Munson, G., Bergman, D. T., Subramanian, V., Grossman, S. R., Anyoha, R., Doughty, B. R., Patwardhan, T. A., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0538-0 · Cited by 1,111 · see citing works
VISTA Enhancer Browser—a database of tissue-specific human enhancers
Visel, A., Minovitsky, S., Dubchak, I., & Pennacchio, L. A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl822 · Cited by 1,080 · see citing works
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
Köhler, S., Doelken, S., Mungall, C. J., Bauer, S., Firth, H., Bailleul-Forestier, I., Black, G., Brown, D. L., Brudno, M., Campbell, J., et al. (2013) · Nucleic Acids Res. · doi:10.1093/nar/gkt1026 · Cited by 840 · see citing works
Enhancer Evolution across 20 Mammalian Species
Villar, D., Berthelot, C., Aldridge, S., Rayner, T. F., Lukk, M., Pignatelli, M., Park, T. J., Deaville, R., Erichsen, J. T., Jasinska, A. J., et al. (2015) · Cell · doi:10.1016/j.cell.2015.01.006 · Cited by 825 · see citing works
Repetitive and Non-Repetitive DNA Sequences and a Speculation on the Origins of Evolutionary Novelty
Britten, R. J., & Davidson, E. H. (1971) · The Quarterly Review of Biology · doi:10.1086/406830 · Cited by 789 · see citing works
An Introduction to Human Evolutionary Anatomy
(2002) · Elsevier eBooks · doi:10.1016/c2009-0-02515-x · Cited by 733 · see citing works
A high-coverage Neandertal genome from Vindija Cave in Croatia
Prüfer, K., de Filippo, C., Grote, S., Mafessoni, F., Korlević, P., Hajdinjak, M., Vernot, B., Skov, L., Hsieh, P., Peyrégne, S., et al. (2017) · Science · doi:10.1126/science.aao1887 · Cited by 719 · see citing works
A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens
Gasperini, M., Hill, A. J., McFaline-Figueroa, J. L., Martin, B., Kim, S., Zhang, M. D., Jackson, D., Leith, A., Schreiber, J., Noble, W. S., et al. (2019) · Cell · doi:10.1016/j.cell.2018.11.029 · Cited by 613 · see citing works
Self-citationSATB2 Is a Multifunctional Determinant of Craniofacial Patterning and Osteoblast Differentiation
Dobreva, G. D., Chahrour, M. H., Dautzenberg, M., Chirivella, L., Kanzler, B., Fariñas, I., Karsenty, G., & Grosschedl, R. (2006) · Cell · doi:10.1016/j.cell.2006.05.012 · Cited by 522 · see citing works
Consensus Paper: Language and the Cerebellum: an Ongoing Enigma
Mariën, P., Ackermann, H., Adamaszek, M., Barwood, C. H. S., Beaton, A. A., Desmond, J. E., Witte, E. D., Fawcett, A. J., Hertrich, I., Küper, M., et al. (2013) · The Cerebellum · doi:10.1007/s12311-013-0540-5 · Cited by 505 · see citing works
Gene Co-Option in Physiological and Morphological Evolution
True, J., & Carroll, S. B. (2002) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev.cellbio.18.020402.140619 · Cited by 502 · see citing works
Tewhey, R., Kotliar, D., Park, D. S., Liu, B., Winnicki, S., Reilly, S. K., Andersen, K. G., Mikkelsen, T. S., Lander, E. S., Schaffner, S. F., et al. (2016) · Cell · doi:10.1016/j.cell.2016.04.027 · Cited by 480 · see citing works
Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease
Loots, G. G., Kneissel, M., Keller, H., Baptist, M., Chang, J., Collette, N. M., Ovcharenko, D., Plajzer-Frick, I., & Rubin, E. M. (2005) · Genome Research · doi:10.1101/gr.3437105 · Cited by 442 · see citing works
Towards a comprehensive catalogue of validated and target-linked human enhancers
Gasperini, M., Tome, J. M., & Shendure, J. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-019-0209-0 · Cited by 396 · see citing works
Efficient Test and Visualization of Multi-Set Intersections
Wang, M., Zhao, Y., & Zhang, B. (2015) · Scientific Reports · doi:10.1038/srep16923 · Cited by 395 · see citing works
The evolution of modern human brain shape
Neubauer, S., Hublin, J.-J., & Gunz, P. (2018) · Science Advances · doi:10.1126/sciadv.aao5961 · Cited by 389 · see citing works
A compendium of promoter-centered long-range chromatin interactions in the human genome
Jung, I., Schmitt, A., Diao, Y., Lee, A. J., Liu, T., Yang, D., Tan, C., Eom, J., Chan, M., Chee, S., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0494-8 · Cited by 362 · 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
LIEBERMAN, P. H. (2007) · Current Anthropology · doi:10.1086/509092 · Cited by 347 · see citing works
Inoue, F., Kircher, M., Martin, B., Cooper, G. M., Witten, D. M., McManus, M. T., Ahituv, N., & Shendure, J. (2017) · Genome Research · doi:10.1101/gr.212092.116 · Cited by 331 · see citing works
Self-citationA high-coverage Neandertal genome from Chagyrskaya Cave
Mafessoni, F., Grote, S., de Filippo, C., Slon, V., Kolobova, K. A., Viola, B., Markin, S. V., Chintalapati, M., Peyrégne, S., Skov, L., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2004944117 · Cited by 309 · see citing works
Chimpanzee genomic diversity reveals ancient admixture with bonobos
de Manuel, M., Kuhlwilm, M., Frandsen, P., Sousa, V. C., Desai, T., Prado-Martinez, J., Hernández-Rodríguez, J., Dupanloup, I., Lao, Ó., Hallast, P., et al. (2016) · Science · doi:10.1126/science.aag2602 · Cited by 297 · see citing works
Decoding enhancers using massively parallel reporter assays
Inoue, F., & Ahituv, N. (2015) · Genomics · doi:10.1016/j.ygeno.2015.06.005 · Cited by 272 · see citing works
Self-citationModeling 3D Facial Shape from DNA
Claes, P. D., Liberton, D. K., Daniels, K., Rosana, K. M., Quillen, E. E., Pearson, L. N., McEvoy, B., Bauchet, M., Zaidi, A. A., Yao, W., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004224 · Cited by 247 · see citing works
Gene expression drives local adaptation in humans
Fraser, H. B. (2013) · Genome Research · doi:10.1101/gr.152710.112 · Cited by 247 · see citing works
Self-citationMoriarity, B. S., Otto, G. M., Rahrmann, E. P., Rathe, S. K., Wolf, N. K., Weg, M. T., Manlove, L. A., LaRue, R. S., Temiz, N. A., Molyneux, S. D., et al. (2015) · Nature Genetics · doi:10.1038/ng.3293 · Cited by 238 · 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
Kircher, M., Xiong, C., Martin, B., Schubach, M., Inoue, F., Bell, R. J. A., Costello, J. F., Shendure, J., & Ahituv, N. (2019) · Nature Communications · doi:10.1038/s41467-019-11526-w · Cited by 234 · see citing works
Self-citationA systematic evaluation of the design and context dependencies of massively parallel reporter assays
Klein, J. C., Agarwal, V., Inoue, F., Keith, A., Martin, B., Kircher, M., Ahituv, N., & Shendure, J. (2020) · Nature Methods · doi:10.1038/s41592-020-0965-y · Cited by 226 · see citing works
High-throughput functional testing of ENCODE segmentation predictions
Kwasnieski, J. C., Fiore, C., Chaudhari, H. G., & Cohen, B. A. (2014) · Genome Research · doi:10.1101/gr.173518.114 · Cited by 224 · see citing works
Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan
Gokhman, D., Lavi, E., Prüfer, K., Fraga, M. F., Riancho, J. A., Kelso, J. F., Pääbo, S., Meshorer, E., & Carmel, L. (2014) · Science · doi:10.1126/science.1250368 · Cited by 219 · see citing works
Self-citationThe Bivalent Genome: Characterization, Structure, and Regulation
Blanco, E., González-Ramírez, M., Alcaine-Colet, A., Aranda, S., & Croce, L. D. (2019) · Trends in Genetics · doi:10.1016/j.tig.2019.11.004 · Cited by 215 · see citing works
Limits of long-term selection against Neandertal introgression
Petr, M., Pääbo, S., Kelso, J., & Vernot, B. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1814338116 · Cited by 211 · see citing works
Dynamics of DNA Methylation in Recent Human and Great Ape Evolution
Hernando-Herraez, I., Prado-Martinez, J., Garg, P., Fernández-Callejo, M., Heyn, H., Hvilsom, C., Navarro, A., Esteller, M., Sharp, A. J., & Marquès‐Bonet, T. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003763 · Cited by 200 · see citing works
Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression
McCoy, R. C., Wakefield, J., & Akey, J. M. (2017) · Cell · doi:10.1016/j.cell.2017.01.038 · Cited by 200 · see citing works
Kawane, T., Qin, X., Jiang, Q., Miyazaki, T., Komori, H., Yoshida, C. A., Kawata-Matsuura, V. K. S., Sakane, C., Matsuo, Y., Nagai, K., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-31853-0 · Cited by 189 · see citing works
Genome-wide nucleosome map and cytosine methylation levels of an ancient human genomePreprint
Pedersen, J. S., Valen, E., Velazquez, A. M. V., Parker, B. J., Rasmussen, M., Lindgreen, S., Lilje, B., Tobin, D. J., Kelly, T. K., Vang, S., et al. (2013) · Genome Research · doi:10.1101/gr.163592.113 · Cited by 171 · see citing works
Lu, L., Liu, X., Huang, W., Giusti‐Rodríguez, P., Cui, J., Zhang, S., Xu, W., Wen, Z., Ma, S., Rosen, J. D., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.06.007 · Cited by 170 · see citing works
Genome-wide signals of positive selection in human evolutionPreprint
Enard, D., Messer, P. W., & Petrov, D. A. (2014) · Genome Research · doi:10.1101/gr.164822.113 · Cited by 167 · see citing works
Self-citationReconstructing the Neanderthal brain using computational anatomy
Kochiyama, T., Ogihara, N., Tanabe, H. C., Kondo, O., Amano, H., Hasegawa, K., Suzuki, H., Ponce de León, M. S., Zollikofer, C. P. E., Bastir, M., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-24331-0 · Cited by 156 · see citing works
ZNF341 controls STAT3 expression and thereby immunocompetence
Frey-Jakobs, S., Hartberger, J. M., Fliegauf, M., Bossen, C., Wehmeyer, M. L., Neubauer, J. C., Bulashevska, A., Proietti, M., Fröbel, P., Nöltner, C., et al. (2018) · Science Immunology · doi:10.1126/sciimmunol.aat4941 · Cited by 148 · see citing works
Gokhman, D., Nissim-Rafinia, M., Agranat-Tamir, L., Housman, G., García-Pérez, R., Lizano, E., Cheronet, O., Mallick, S., Nieves-Colón, M. A., Li, H., et al. (2017) · doi:10.1101/106955 · Cited by 144 · see citing works
Self-citationlentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements
Gordon, M. G., Inoue, F., Martin, B., Schubach, M., Agarwal, V., Whalen, S., Feng, S., Zhao, J., Ashuach, T., Ziffra, R. S., et al. (2020) · Nature Protocols · doi:10.1038/s41596-020-0333-5 · Cited by 144 · see citing works
Self-citationGene Regulatory Elements, Major Drivers of Human Disease
Chatterjee, S., & Ahituv, N. (2017) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-091416-035537 · Cited by 136 · see citing works
Self-citationHojo, H., Ohba, S., He, X., Lai, L. P., & McMahon, A. P. (2016) · Developmental Cell · doi:10.1016/j.devcel.2016.04.002 · Cited by 134 · see citing works
Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity
Gunz, P., Tilot, A. K., Wittfeld, K., Teumer, A., Shapland, C. Y., van Erp, T. G. M., Dannemann, M., Vernot, B., Neubauer, S., Guadalupe, T., et al. (2019) · Current Biology · doi:10.1016/j.cub.2018.10.065 · Cited by 117 · cited 4× · see citing works
“Next, we filtered out pairs of 676 reads that (1) did not map to the same oligo, (2) did not have at least one of the reads in the pair 677”
BackgroundMethodInfluentialSATB2‐associated syndrome: Mechanisms, phenotype, and practical recommendations
Zárate, Y. A., & Fish, J. L. (2016) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.38022 · Cited by 112 · see citing works
Massively parallel discovery of human-specific substitutions that alter enhancer activity
Uebbing, S., Gockley, J., Reilly, S. K., Kocher, A. A., Geller, E. T., Gandotra, N., Scharfe, C., Cotney, J. L., & Noonan, J. P. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2007049118 · Cited by 111 · see citing works
Machine learning dissection of human accelerated regions in primate neurodevelopment
Whalen, S., Inoue, F., Ryu, H., Fair, T., Markenscoff-Papadimitriou, E., Keough, K. C., Kircher, M., Martin, B., Alvarado, B., Elor, O., et al. (2023) · Neuron · doi:10.1016/j.neuron.2022.12.026 · Cited by 109 · see citing works
Self-citationInoue, F., Kreimer, A., Ashuach, T., Ahituv, N., & Yosef, N. (2019) · Cell stem cell · doi:10.1016/j.stem.2019.09.010 · Cited by 107 · see citing works
Self-citationMPRAnalyze: statistical framework for massively parallel reporter assays
Ashuach, T., Fischer, D. S., Kreimer, A., Ahituv, N., Theis, F. J., & Yosef, N. (2019) · Genome biology · doi:10.1186/s13059-019-1787-z · Cited by 104 · see citing works
Self-citationGenomic Targets of the KRAB and SCAN Domain-containing Zinc Finger Protein 263*
Frietze, S., Lan, X., Jin, V. X., & Farnham, P. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.063032 · Cited by 103 · see citing works
Two Sides of the Same Coin: The Roles of KLF6 in Physiology and Pathophysiology
Syafruddin, S. E., Mohtar, M. A., Nazarie, W. F. W. M., & Low, T. Y. (2020) · Biomolecules · doi:10.3390/biom10101378 · Cited by 96 · see citing works
De novo DNA demethylation and noncoding transcription define active intergenic regulatory elementsPreprint
Schlesinger, F. J., Smith, A. D., Gingeras, T., Hannon, G. J., & Hodges, E. C. (2013) · Genome Research · doi:10.1101/gr.157271.113 · Cited by 92 · see citing works
Reconstructing Denisovan Anatomy Using DNA Methylation Maps
Gokhman, D., Mishol, N., de Manuel, M., Juan, D., Shuqrun, J., Meshorer, E., Marquès‐Bonet, T., Rak, Y., & Carmel, L. (2019) · Cell · doi:10.1016/j.cell.2019.08.035 · Cited by 90 · see citing works
Self-citationSomething old, something borrowed: admixture and adaptation in human evolution
Dannemann, M., & Racimo, F. (2018) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2018.05.009 · Cited by 87 · see citing works
Human–chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution
Gokhman, D., Agoglia, R. M., Kinnebrew, M., Gordon, W. E., Sun, D., Bajpai, V. K., Naqvi, S., Chen, C., Chan, A. W. S., Chen, C., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00804-3 · Cited by 87 · see citing works
Self-citationRegulation of the Development and Function of B Cells by ZBTB Transcription Factors
Zhu, C., Chen, G., Zhao, Y., Gao, X., & Wang, J. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.00580 · Cited by 84 · see citing works
Epigenetics: It's Getting Old. Past Meets Future in Paleoepigenetics
Gokhman, D., Meshorer, E., & Carmel, L. (2016) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2016.01.010 · Cited by 66 · see citing works
Self-citationFukami, M., Kato, F., Tajima, T., Yokoya, S., & Ogata, T. (2005) · The American Journal of Human Genetics · doi:10.1086/499254 · Cited by 64 · see citing works
Functional characterization of enhancer evolution in the primate lineage
Klein, J. C., Keith, A., Agarwal, V., Durham, T., & Shendure, J. (2018) · Genome Biology · doi:10.1186/s13059-018-1473-6 · Cited by 63 · see citing works
Silvert, M., Quintana-Murci, L., & Rotival, M. (2019) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2019.04.016 · Cited by 58 · see citing works
Gene ORGANizer: linking genes to the organs they affect
Gokhman, D., Kelman, G., Amartely, A., Gershon, G., Tsur, S., & Carmel, L. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx302 · Cited by 57 · see citing works
Self-citationNF-Y and SP transcription factors — New insights in a long-standing liaison
Suske, G. (2016) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2016.08.011 · Cited by 52 · see citing works
Selection against archaic hominin genetic variation in regulatory regions
Telis, N., Aguilar, R., & Harris, K. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-01284-0 · Cited by 51 · see citing works
Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences
Colbran, L. L., Gamazon, E. R., Zhou, D., Evans, P., Cox, N. J., & Capra, J. A. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-019-0996-x · Cited by 50 · see citing works
ZNF281 inhibits neuronal differentiation and is a prognostic marker for neuroblastoma
Pieraccioli, M., Nicolai, S., Pitolli, C., Agostini, M., Antonov, A., Malewicz, M., Knight, R. A., Raschellà, G., & Melino, G. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1801435115 · Cited by 49 · see citing works
Song, J., Ugai, H., Nakata-Tsutsui, H., Kishikawa, S., Suzuki, É., Murata, T., & Yokoyama, K. K. (2003) · International Journal of Molecular Medicine · doi:10.3892/ijmm.11.5.547 · Cited by 48 · 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
Li, Y., You, Q.-L., Zhang, S.-R., Huang, W., Zou, W.-J., Jie, W., Li, S.-J., Liu, J.-H., Lv, C.-Y., Cong, J., et al. (2017) · Molecular Neurobiology · doi:10.1007/s12035-017-0531-5 · Cited by 42 · see citing works
Cis and trans effects differentially contribute to the evolution of promoters and enhancers
Mattioli, K., Oliveros, W., Gerhardinger, C., Andergassen, D., Maass, P., Rinn, J., & Melé, M. (2020) · Genome Biology · doi:10.1186/s13059-020-02110-3 · Cited by 41 · see citing works
Loss of Satb2 in the Cortex and Hippocampus Leads to Abnormal Behaviors in Mice
Zhang, Q., Huang, Y., Zhang, L., Ding, Y., & Song, N. (2019) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2019.00033 · Cited by 40 · see citing works
Emerging roles of Egr2 and Egr3 in the control of systemic autoimmunity
Morita, K., Okamura, T., Sumitomo, S., Iwasaki, Y., Fujio, K., & Yamamoto, K. (2016) · Lara D. Veeken · doi:10.1093/rheumatology/kew342 · Cited by 39 · see citing works
A molecular model for neurodevelopmental disorders
Gigek, C. O., Chen, E., Ota, V., Maussion, G., Peng, H., Vaillancourt, K., Diallo, A., López, J. P., Crapper, L., Vasuta, C., et al. (2015) · Translational Psychiatry · doi:10.1038/tp.2015.56 · Cited by 38 · see citing works
GATA4 Directly Regulates Runx2 Expression and Osteoblast Differentiation
Khalid, A. B., Slayden, A. V., Kumpati, J., Perry, C. D., Osuna, M. Á. L., Arroyo, S. R., Miranda‐Carboni, G. A., & Krum, S. A. (2017) · JBMR Plus · doi:10.1002/jbm4.10027 · Cited by 28 · see citing works
Role of HOXA9 and VEZF1 in Endothelial Biology
Bruderer, M., Alini, M., & Stoddart, M. J. (2013) · Journal of Vascular Research · doi:10.1159/000353287 · Cited by 27 · see citing works
Liu, S., Zhu, J., Xu, H.-H., Zhang, G., Wang, Y., Liu, Y., Liang, J., Wang, Y.-X., Wu, Y., & Guo, Q.-F. (2017) · Molecular and Cellular Biochemistry · doi:10.1007/s11010-017-2953-9 · Cited by 26 · see citing works
Selective regulation of Mmp13 by 1,25(OH)2D3, PTH, and Osterix through distal enhancers
Meyer, M. B., Benkusky, N. A., Onal, M., & Pike, J. W. (2015) · The Journal of Steroid Biochemistry and Molecular Biology · doi:10.1016/j.jsbmb.2015.09.001 · Cited by 24 · see citing works
ZNF281-miR-543 Feedback Loop Regulates Transforming Growth Factor-β-Induced Breast Cancer Metastasis
Ji, W., Mu, Q., Liu, X., Cao, X., & Yu, Y. (2020) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2020.05.020 · Cited by 22 · see citing works
Modern human changes in regulatory regions implicated in cortical development
Moriano, J., & Boeckx, C. A. (2020) · BMC Genomics · doi:10.1186/s12864-020-6706-x · Cited by 21 · see citing works
Weyer, S., & Pääbo, S. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv215 · Cited by 19 · see citing works
Khalid, A. B., Slayden, A. V., Kumpati, J., Perry, C. D., Berryhill, S. B., Crawford, J. A., Fatima, I., Morselli, M., Pellegrini, M. A., Miranda‐Carboni, G. A., et al. (2018) · Bone · doi:10.1016/j.bone.2018.07.014 · Cited by 14 · see citing works
Archaic hominin genomics provides a window into gene expression evolution
Yan, S. M., & McCoy, R. C. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.05.014 · Cited by 12 · see citing works
Batyrev, D., Lapid, E., Carmel, L., & Meshorer, E. (2019) · Cells · doi:10.3390/cells9010048 · Cited by 10 · see citing works
Grogan, K. E., & Perry, G. H. (2020) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.21825 · Cited by 9 · see citing works
Evolution is in the details: Regulatory differences in modern human and Neanderthal
Barker, H. R., Parkkila, S., & Tolvanen, M. E. E. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2025.05.052 · Cited by 9 · see citing works
Paternal Low-Level Mosaicism-Caused SATB2-Associated Syndrome
Qian, Y., Liu, J., Yang, Y., Chen, M., Jin, C., Chen, P., Lei, Y., Pan, H.-Y., & Dong, M. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00630 · Cited by 8 · see citing works
Denisovan introgression has shaped the immune system of present-day PapuansPreprint
Vespasiani, D. M., Jacobs, G. S., Cook, L. E., Brucato, N., Leavesley, M., Kinipi, C., Ricaut, F., Cox, M. P., & Romero, I. G. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.09.196444 · Cited by 8 · see citing works
Evolution is in the details: Regulatory differences in modern human and NeanderthalPreprint
Barker, H. R., Parkkila, S., & Tolvanen, M. E. E. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.04.282749 · Cited by 5 · see citing works
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Multiple causal variants underlie genetic associations in humans
Abell, N. S., DeGorter, M. K., Gloudemans, M. J., Greenwald, E., Smith, K. S., He, Z., & Montgomery, S. B. (2022) · Science · doi:10.1126/science.abj5117 · Cited by 186 · see citing works
Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution
Pollen, A. A., Kilik, U., Lowe, C. B., & Camp, J. G. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-022-00568-4 · Cited by 157 · see citing works
Massively parallel characterization of transcriptional regulatory elements
Agarwal, V., Inoue, F., Schubach, M., Penzar, D., Martin, B. K., Dash, P. M., Keukeleire, P., Zhang, Z., Sohota, A., Zhao, J., et al. (2025) · Nature · doi:10.1038/s41586-024-08430-9 · Cited by 146 · see citing works
Self-citationMachine learning dissection of human accelerated regions in primate neurodevelopment
Whalen, S., Inoue, F., Ryu, H., Fair, T., Markenscoff-Papadimitriou, E., Keough, K. C., Kircher, M., Martin, B., Alvarado, B., Elor, O., et al. (2023) · Neuron · doi:10.1016/j.neuron.2022.12.026 · Cited by 109 · see citing works
Self-citationGenome-wide analyses of introgression between two sympatric Asian oak species
Fu, R., Zhu, Y., Liu, Y., Feng, Y., Lu, R., Li, Y., Li, P., Kremer, A., Lascoux, M., & Chen, J. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01754-7 · Cited by 115 · see citing works
Anderson, A. G., Rogers, B. B., Loupe, J. M., Rodriguez-Nunez, I., Roberts, S. C., White, L. M., Brazell, J. N., Bunney, W. E., Bunney, B. G., Watson, S. J., et al. (2023) · Cell Genomics · doi:10.1016/j.xgen.2023.100263 · Cited by 82 · see citing works
Massively parallel characterization of regulatory elements in the developing human cortex
Deng, C., Whalen, S., Steyert, M., Ziffra, R., Przytycki, P. F., Inoue, F., Pereira, D. A., Capauto, D., Norton, S., Vaccarino, F. M., et al. (2024) · Science · doi:10.1126/science.adh0559 · Cited by 72 · see citing works
Self-citationEnhancer Function and Evolutionary Roles of Human Accelerated Regions
Whalen, S., & Pollard, K. S. (2022) · Annual Review of Genetics · doi:10.1146/annurev-genet-071819-103933 · Cited by 70 · see citing works
A molecular and cellular perspective on human brain evolution and tempo
Lindhout, F. W., Krienen, F. M., Pollard, K. S., & Lancaster, M. A. (2024) · Nature · doi:10.1038/s41586-024-07521-x · Cited by 70 · see citing works
More than a decade of genetic research on the Denisovans
Peyrégne, S., Slon, V., & Kelso, J. F. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00643-4 · Cited by 66 · see citing works
Leveraging massively parallel reporter assays for evolutionary questions
Romero, I. G., & Lea, A. J. (2023) · Genome biology · doi:10.1186/s13059-023-02856-6 · Cited by 61 · see citing works
Jagoda, E., Xue, J. R., Reilly, S. K., Dannemann, M., Racimo, F., Huerta-Sanchez, E., Sankararaman, S., Kelso, J., Pagani, L., Sabeti, P. C., et al. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msab304 · Cited by 47 · 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
“Recent work by [72] has shown that variants which arose in the human lineage following its split from the Neanderthal-Denisovan common ancestor, and which have reached (near) fixation in modern humans since then can exhibit significant differences in regulatory activity relative to the ancestral…”
Genetic studies of human–chimpanzee divergence using stem cell fusions
Song, J. H. T., Grant, R. L., Behrens, V. C., Kučka, M., Kingman, G. A. R., Soltys, V., Chan, Y. F., & Kingsley, D. M. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2117557118 · Cited by 46 · see citing works
Rong, S., Neil, C. R., Welch, A., Duan, C., Maguire, S., Meremikwu, I. C., Meyerson, M., Evans, B. J., & Fairbrother, W. G. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2218308120 · Cited by 24 · see citing works
Genetic architecture of human brain evolution
Fair, T., & Pollen, A. A. (2023) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2023.102710 · Cited by 23 · see citing works
Hansen, T. J., Fong, S., Day, J. K., Capra, J. A., & Hodges, E. C. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100536 · Cited by 20 · see citing works
Zug, R., & Uller, T. (2022) · Evolutionary Human Sciences · doi:10.1017/ehs.2022.42 · Cited by 16 · see citing works
Morova, T., Ding, Y., Huang, C.-C. F., Sar, F., Schwarz, T., Giambartolomei, C., Baca, S. C., Grishin, D., Hach, F., Gusev, A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1198 · Cited by 17 · see citing works
Liu, Y., Luo, X., Sun, Y., Chen, K., Hu, T., You, B., Xu, J., Zhang, F., Cheng, Q., Meng, X., et al. (2024) · Developmental Cell · doi:10.1016/j.devcel.2024.10.005 · Cited by 16 · see citing works
Andirkó, A., Moriano, J., Vitriolo, A., Kuhlwilm, M., Testa, G., & Boeckx, C. A. (2022) · Scientific Reports · doi:10.1038/s41598-022-13589-0 · Cited by 18 · see citing works
Uebbing, S., Kocher, A. A., Baumgartner, M., Ji, Y., Bai, S., Xing, X., Nottoli, T., & Noonan, J. P. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae199 · Cited by 15 · see citing works
Harnessing pluripotent stem cells as models to decipher human evolution
Dannemann, M., & Romero, I. G. (2021) · FEBS Journal · doi:10.1111/febs.15885 · Cited by 14 · see citing works
Buisan, R., Moriano, J., Andirkó, A., & Boeckx, C. A. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.824740 · Cited by 14 · see citing works
Vaill, M., Kawanishi, K., Varki, N. M., Gagneux, P., & Varki, A. P. (2023) · Physiological Reviews · doi:10.1152/physrev.00040.2021 · Cited by 13 · see citing works
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Colbran, L. L., Johnson, M. R., Mathieson, I., & Capra, J. A. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab237 · Cited by 13 · see citing works
Moriano, J., Leonardi, O., Vitriolo, A., Testa, G., & Boeckx, C. A. (2024) · Development · doi:10.1242/dev.202390 · Cited by 12 · see citing works
Functional genomics and systems biology in human neuroscience
Konopka, G., & Bhaduri, A. (2023) · Nature · doi:10.1038/s41586-023-06686-1 · Cited by 10 · see citing works
Candidate Denisovan fossils identified through gene regulatory phenotyping
Mishol, N., Herzlinger, G., Rak, Y., Smilanksy, U., Carmel, L., & Gokhman, D. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2513968122 · Cited by 9 · see citing works
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Cooper, Y. A., Guo, Q., & Geschwind, D. H. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac194 · Cited by 10 · see citing works
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
“Another recent lentivirus-based MPRA tested 14,042 fixed or nearly fixed single-nucleotide variants that emerged along the modern human lineage and compared the transcriptional activities of modern and archaic human sequences (Weiss et al. 2021).”
BackgroundLineage-specific regulatory evolution: insights from massively parallel reporter assays
Easterlin, R., & Ahituv, N. (2025) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2025.102372 · Cited by 6 · see citing works
Self-citationDenisovan introgression has shaped the immune system of present-day PapuansPreprint
Vespasiani, D. M., Jacobs, G. S., Cook, L. E., Brucato, N., Leavesley, M., Kinipi, C., Ricaut, F., Cox, M. P., & Romero, I. G. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.09.196444 · Cited by 8 · see citing works
Massively parallel approaches for characterizing noncoding functional variation in human evolution
Rong, S., Root, E., & Reilly, S. K. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102256 · Cited by 6 · see citing works
Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants
Manzo, G., Borkowski, K., & Ovcharenko, I. (2025) · Genes · doi:10.3390/genes16101223 · Cited by 8 · see citing works
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Han, S., Riyahi, S., Huang, X., & Kuhlwilm, M. (2025) · bioRxiv · doi:10.1038/s41597-025-06124-z · Cited by 7 · see citing works
Ren, Y., Yu, S., Sun, H., & Ma, X. (2025) · Molecular Ecology · doi:10.1111/mec.17747 · Cited by 5 · see citing works
Brain region-specific effects of nearly fixed sapiens-derived alleles
Andirkó, A., & Boeckx, C. A. (2022) · BMC Genomic Data · doi:10.1186/s12863-022-01048-8 · Cited by 4 · see citing works
Tile by tile: capturing the evolutionary mosaic of human conditions
Caporale, N., Leonardi, O., Villa, C. E., Vitriolo, A., Boeckx, C. A., & Testa, G. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102297 · Cited by 5 · see citing works
Applications of high-throughput reporter assays to gene regulation studies
D’Elia, B., & Bass, J. I. F. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2025.103105 · Cited by 4 · see citing works
Cis -regulatory landscapes in the evolution and development of the mammalian skull
Kaucká, M. (2023) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2022.0079 · Cited by 4 · see citing works
Advances in skeletal genomics research across tissues and cells
Housman, G. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102245 · Cited by 3 · see citing works
Andirkó, A., Moriano, J., Vitriolo, A., Kuhlwilm, M., Testa, G., & Boeckx, C. A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.22.427608 · Cited by 4 · see citing works
A map of enhancer regions in primary human neural progenitor cells using capture STARR-seqPreprint
Gaynor-Gillett, S. C., Cheng, L., Shi, M., Liu, J. J., Wang, G., Spector, M., Guo, Q., Qi, L., Flaherty, M., Wall, M., et al. (2025) · Genome Research · doi:10.1101/gr.279584.124 · Cited by 4 · see citing works
Uttley, K., Juellig, H. J., Angelis, C. D., Auer, J. M. T., Ozga, E., Bengani, H., & Long, H. K. (2025) · Development · doi:10.1242/dev.204779 · Cited by 4 · see citing works
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Comerford, M., Vespasiani, D. M., Shukla, N., Cook, L. E., Yermakovich, D., Dannemann, M., Leavesley, M., Kinipi, C., Ricaut, F., Brucato, N., et al. (2026) · PLoS Genetics · doi:10.1371/journal.pgen.1012067 · Cited by 2 · see citing works
Genomic approaches for understanding the evolution of the human brain
Song, J. H. T., Greenberg, M. E., Reich, D., & Walsh, C. A. (2026) · Nature Neuroscience · doi:10.1038/s41593-026-02277-1 · Cited by 2 · see citing works
Okamoto, A. S., Coveney, C. R., Ganapathee, D. S., & Capellini, T. D. (2026) · Genome Biology and Evolution · doi:10.1093/gbe/evag121 · Cited by 3 · see citing works
Genetic Architecture of Immune Cell DNA Methylation in the Rhesus Macaque
Costa, C. E., Watowich, M. M., Goldman, E. A., Sterner, K. N., Valle, J. E. N.-D., Phillips, D., Platt, M. L., Montague, M. J., Brent, L. J. N., Higham, J. P., et al. (2024) · Molecular Ecology · doi:10.1111/mec.17576 · Cited by 2 · see citing works
Liu, Y., Luo, X., Sun, Y., Chen, K., Hu, T., You, B., Xu, J., Zhang, F., Meng, X., Li, X., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.20.558575 · Cited by 2 · see citing works
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Srivastava, J., & Ovcharenko, I. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf050 · Cited by 1 · see citing works
Gilbertson, E. N., & Reilly, S. K. (2025) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2025.102415 · Cited by 1 · see citing works
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Yan, Y., Mishol, N., Lange, K., Zhang, Z., Bodek, G., Kigel, A., Priel, N., Egyes, N., Ronen, O., Nini, I., et al. (2026) · Nature · doi:10.1038/s41586-026-11053-x · Cited by 1 · see citing works
Self-citationLi, H., Yu, Z., Du, F., Song, L., Gao, Y., & Shi, F. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1323072 · Cited by 1 · see citing works
Buisan, R., Moriano, J., Andirkó, A., & Boeckx, C. A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.26.437167 · Cited by 1 · see citing works
Validation of Enhancer Regions in Primary Human Neural Progenitor Cells using Capture STARR-seqPreprint
Gaynor-Gillett, S. C., Cheng, L., Shi, M., Liu, J. J., Wang, G., Spector, M., Flaherty, M., Wall, M., Hwang, A., Gu, M., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.14.585066 · Cited by 1 · see citing works
Neanderthal-derived variants shape craniofacial enhancer activity at a human disease locusPreprint
Uttley, K., Juellig, H. J., Angelis, C. D., Auer, J. M. T., Ozga, E., Bengani, H., & Long, H. K. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.24.614243 · Cited by 1 · see citing works
Partitioning the genomic journey to becoming Homo sapiensPreprint
Pagani, L., Bertazzon, R., Pankratov, V., Vallini, L., Marnetto, D., Morez, A., Delbrassine, H., Carollo, F., D’Esposito, M., Granata, I., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.09.627480 · Cited by 1 · see citing works
Butts, J. C., Rong, S., Gosai, S. J., Castro, R. I., Noon, M., Adeniran, K., Ghosh, R., Sabeti, P. C., Tewhey, R., & Reilly, S. K. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.16.648420 · Cited by 1 · see citing works
Okamoto, A. S., Coveney, C. R., Ganapathee, D. S., & Capellini, T. D. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.21.683789 · Cited by 1 · see citing works
Moriano, J., Martínez‐Gil, N., Andirkó, A., Balcells, S., Grinberg, D., & Boeckx, C. A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.21.440797
2024 ASHG Scientific Achievement Award
Ahituv, N. (2025) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2025.01.005
Self-citationRegulatory logic of human cortex evolution by combinatorial perturbationsPreprint
Skaros, A., Vitriolo, A., Leonardi, O., Finazzi, V., Pereira, M. F., Prazzoli, F., Trattaro, S., Moriano, J., Capocefalo, D., Villa, C. E., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.28.651083 · Cited by 1 · see citing works
Moriano, J., Boeckx, C. A., & Kuhlwilm, M. (2025) · Oxford University Press eBooks · doi:10.1093/oxfordhb/9780192886491.013.12 · Cited by 1 · see citing works
Genomic basis of human-specific brain features
Mosti, F., & Silver, D. L. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-27380-3.00062-2
Loss of Conserved Noncoding Elements Likely Shaped the Evolution of Regressed Phenotypes in Cavefish
Lal, M., Bhattacharya, J., & Sandhu, K. S. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf211
Language Evolution and Genetics
Benítez‐Burraco, A. (2025) · Elsevier eBooks · doi:10.1016/b978-0-323-95504-1.01178-9
These powerful tools reveal the ‘control knobs’ of the genome
Eisenstein, M. S. (2026) · Nature · doi:10.1038/d41586-026-01410-1
Immune context unmasks regulatory effects of Neanderthal and Denisovan introgressionPreprint
Li, Z., Kerner, G., Mendoza‐Revilla, J., Inoue, F., Fishilevich, S., Patin, É., Gokhman, D., Quintana‐Murci, L., & Rotival, M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.29.727880
Self-citationDissecting functional regulatory convergence over 160 million years of therian evolutionPreprint
Shukla, N., Cook, L. E., Vespasiani, D. M., Pask, A. J., & Romero, I. G. (2026) · Genome Research · doi:10.1101/gr.281284.125
- Authors
- Weiss, C. V., Harshman, L., Inoue, F., Fraser, H. B., Petrov, D. A., Ahituv, N., & Gokhman, D.
- Affiliations
- Stanford University (US)
- University of California, San Francisco (US)
- Corresponding author
- Petrov, Dmitri A
- Ahituv, Nadav
- Gokhman, David
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2021-04-22
- Volume
- 10
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC8062137
- OpenAlex
- W3154998065
- Cited by
- 70
- References
- 110
- Citations by year
- 2026: 7 · 2025: 19 · 2024: 15 · 2023: 11 · 2022: 10 · 2021: 7 · 2020: 1
- FWCI
- 3.37
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- National Human Genome Research Institute (1UM1HG009408)
- National Institute of Mental Health (1R01MH109907, 1U01MH116438)
- Uehara Memorial Foundation
- Stanford Center for Computational, Evolutionary and Human Genomics
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- cis-regulatory effects, Neanderthals, Denisovans, modern human evolution, non-coding variants, massively parallel reporter assay, transcription factor binding motifs, gene expression evolution, neural progenitor cells, osteoblasts
- MeSH terms
- Gene Expression Regulation, Humans, Osteoblasts, Stem Cells, Transcription Factors, Genome, Human, Polymorphism, Single Nucleotide, Embryonic Stem Cells
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