Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression
Open accessAbstract
Regulatory variation influencing gene expression is a key contributor to phenotypic diversity, both within and between species. Unfortunately, RNA degrades too rapidly to be recovered from fossil remains, limiting functional genomic insights about our extinct hominin relatives. Many Neanderthal sequences survive in modern humans due to ancient hybridization, providing an opportunity to assess their contributions to transcriptional variation and to test hypotheses about regulatory evolution. We developed a flexible Bayesian statistical approach to quantify allele-specific expression (ASE) in complex RNA-seq datasets. We identified widespread expression differences between Neanderthal and modern human alleles, indicating pervasive cis-regulatory impacts of introgression. Brain regions and testes exhibited significant downregulation of Neanderthal alleles relative to other tissues, consistent with natural selection influencing the tissue-specific regulatory landscape. Our study demonstrates that Neanderthal-inherited sequences are not silent remnants of ancient interbreeding but have measurable impacts on gene expression that contribute to variation in modern human phenotypes.
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Neanderthal ancestry is depleted in regions of the genome with annotated molecular functions, and this depletion is strongest in annotated brain and testis regulatory regions.
“Second, Neanderthal ancestry is depleted in regions of the genome with annotated molecular functions (e.g., genes and gene regulatory elements), and this depletion is strongest in annotated brain and testis regulatory regions27–29.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [28]
In Results and Discussion, “Neanderthal alleles are down-regulated in the testes” (page unavailable), the paper states that genes highly expressed in testes are depleted of Neanderthal ancestry. Its brain and testes analyses report stronger downregulation of introgressed alleles, which is not the same as depletion of ancestry from regulatory regions. The passages do not establish genome-wide depletion from annotated functional regions or that depletion is strongest in brain and testis regulatory regions. (LLM, conf=0.87)
Experimental — accuracy not yet measuredThe depletion in cognitive traits suggests that the previously observed strong depletion for Neanderthal alleles in regulatory regions active in the brain may be due to effects on brain-related complex traits.
“The depletion in cognitive traits suggests that the previously observed strong depletion for Neanderthal alleles in regulatory regions active in the brain may be due to effects on brain-related complex traits5,28,29.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [28]
In Results and Discussion, “Brain sub-regions show downregulation of Neanderthal alleles” (page unavailable), the paper reports lower expression of introgressed alleles in brain regions and notes the cognitive functions of some of those regions. Downregulation of allelic expression is not the claimed depletion of Neanderthal alleles from brain-active regulatory regions; the paper also does not link that depletion to effects on brain-related complex traits. (LLM, conf=0.81)
Experimental — accuracy not yet measuredStudies conducted primarily on Neanderthal introgressed DNA have suggested a non-negligible contribution to gene expression variation in modern humans, with repeated examples of Neanderthal archaic variants falling within regulatory elements or the seed region of mature micro-RNAs predicted to affect transcriptional and post-transcriptional regulatory processes.
“Indeed, studies conducted primarily on Neanderthal introgressed DNA have suggested a non-negligible contribution to gene expression variation in modern humans [10, 11, 22], with repeated examples of Neanderthal archaic variants falling within regulatory elements or the seed region of mature micro-RNAs predicted to affect transcriptional and post-transcriptional regulatory processes [11, 62].”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [10]
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredEnhancers are among the top targeted elements of archaic hominin introgression.
“Enhancers, in particular, are amongst the top targeted elements of archaic hominin introgression [10, 11].”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [10]
The Introduction says Neanderthal-introgressed sequences encompass functional genomic features, but does not rank enhancers among them. The Results and Discussion section on regulatory effects compares allele-specific expression, not which genomic elements were most targeted by introgression. Searches for enhancers and their enrichment found no passage establishing the claimed ranking. (LLM, conf=0.76)
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Cites
R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,706 · see citing works
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works
Fitting Linear Mixed-Effects Models Using <b>lme4</b>
Bates, D., Mächler, M., Bolker, B., & Walker, S. (2015) · Journal of Statistical Software · doi:10.18637/jss.v067.i01 · Cited by 86,835 · see citing works
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895 · see citing works
ggplot2: Elegant Graphics for Data Analysis
Wickham, H. (2009) · doi:10.1007/978-0-387-98141-3 · Cited by 14,447 · see citing works
A method and server for predicting damaging missense mutations.
Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., Kondrashov, A. S., & Sunyaev, S. R. (2010) · Nature Methods · doi:10.1038/nmeth0410-248 · Cited by 13,194 · see citing works
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., & Salzberg, S. L. (2013) · Genome Biology · doi:10.1186/gb-2013-14-4-r36 · Cited by 12,668 · see citing works
Fitting Linear Mixed-Effects Models Using lme4Preprint
Bates, D. M., Maechler, M., Bolker, B. M., & Walker, S. (2014) · arXiv (Cornell University) · doi:10.3929/ethz-b-000105397 · Cited by 9,435 · see citing works
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711 · see citing works
Biological insights from 108 schizophrenia-associated genetic loci
Schizophrenia Working Group of the Psychiatric Genomics Consortium (2014) · Nature · doi:10.1038/nature13595 · Cited by 7,577 · see citing works
Kumar, P., Henikoff, S., & Ng, P. C. (2009) · Nature Protocols · doi:10.1038/nprot.2009.86 · Cited by 6,521 · see citing works
A general framework for estimating the relative pathogenicity of human genetic variants
Kircher, M., Witten, D. M., Jain, P., O'Roak, B. J., Cooper, G. M., & Shendure, J. (2014) · Nature Genetics · doi:10.1038/ng.2892 · Cited by 6,183 · see citing works
Rue, H., Martino, S., & Chopin, N. (2009) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.1467-9868.2008.00700.x · Cited by 5,279 · 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
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
A draft sequence of the Neandertal genome
Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., et al. (2010) · Science · doi:10.1126/science.1188021 · Cited by 4,318 · see citing works
An anatomically comprehensive atlas of the adult human brain transcriptome
Hawrylycz, M. J., Lein, E. S., Guillozet-Bongaarts, A. L., Shen, E. H., Ng, L., Miller, J. A., van de Lagemaat, L. N., Smith, K. A., Ebbert, A., Riley, Z. L., et al. (2012) · Nature · doi:10.1038/nature11405 · Cited by 3,083 · see citing works
King, M.-C., & Wilson, A. C. (1975) · Science · doi:10.1126/science.1090005 · Cited by 2,815 · see citing works
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
Welter, D., MacArthur, J., Morales, J., Burdett, T., Hall, P., Junkins, H., Klemm, A., Flicek, P., Manolio, T., Hindorff, L., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1229 · Cited by 2,707 · see citing works
WatanabeSumio (2010) · arXiv (Cornell University) · doi:10.48550/arxiv.1004.2316 · Cited by 2,264 · 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
The positive false discovery rate: a Bayesian interpretation and the q-value
Storey, J. D. (2003) · The Annals of Statistics · doi:10.1214/aos/1074290335 · Cited by 2,204 · see citing works
Understanding predictive information criteria for Bayesian models
Gelman, A., Hwang, J., & Vehtari, A. (2014) · Statistics and Computing · doi:10.1007/s11222-013-9416-2 · Cited by 2,104 · see citing works
The Electronic Medical Records and Genomics (eMERGE) Consortium, Wood, A. R., The MIGen Consortium, The PAGE Consortium, Study, T. L. C., Esko, T., Yang, J., Vedantam, S., Pers, T. H., Gustafsson, S., et al. (2014) · Nature Genetics · doi:10.1038/ng.3097 · Cited by 1,853 · see citing works
SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap
Johnson, A. D., Handsaker, R., Pulit, S., Nizzari, M. M., O'Donnell, C., & de Bakker, P. D. (2008) · Bioinform. · doi:10.1093/bioinformatics/btn564 · Cited by 1,530 · see citing works
Sekhon, J. S. (2011) · Journal of Statistical Software · doi:10.18637/jss.v042.i07 · Cited by 1,521 · see citing works
The evolution of gene expression levels in mammalian organs
Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., et al. (2011) · Nature · doi:10.1038/nature10532 · Cited by 1,248 · see citing works
The genomic landscape of Neanderthal ancestry in present-day humans
Sankararaman, S., Mallick, S., Dannemann, M., Prüfer, K., Kelso, J., Pääbo, S., Patterson, N., & Reich, D. (2014) · Nature · doi:10.1038/nature12961 · Cited by 1,107 · see citing works
Han, J., Zheng, H., Cui, Y., Sun, L., Ye, D., Hu, Z. Q., Xu, J., Cai, Z., Huang, W., Zhao, G., et al. (2009) · Nature Genetics · doi:10.1038/ng.472 · Cited by 938 · see citing works
Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma
Jones, D., Hutter, B., Jäger, N., Korshunov, A., Kool, M., Warnatz, H.-J., Zichner, T., Lambert, S. R., Ryzhova, M. V., Khuong-Quang, D.-A., et al. (2013) · Nature Genetics · doi:10.1038/ng.2682 · Cited by 819 · see citing works
Genetic Optimization Using Derivatives: ThergenoudPackage forR
Mebane, W. R., & Sekhon, J. S. (2011) · Journal of Statistical Software · doi:10.18637/jss.v042.i11 · Cited by 639 · see citing works
Allelic Variation in Human Gene Expression
Yan, H., Yuan, W., Velculescu, V. E., Vogelstein, B., & Kinzler, K. W. (2002) · Science · doi:10.1126/science.1072545 · Cited by 625 · see citing works
A de novo mutation affecting human TrkB associated with severe obesity and developmental delay
Yeo, G. S. H., Hung, C.-C. C., Rochford, J. J., Keogh, J. M., Gray, J. A., Sivaramakrishnan, S., O’Rahilly, S., & Farooqi, I. S. (2004) · Nature Neuroscience · doi:10.1038/nn1336 · Cited by 608 · see citing works
WASP: allele-specific software for robust molecular quantitative trait locus discovery
van de Geijn, B., McVicker, G., Gilad, Y., & Pritchard, J. K. (2015) · Nature Methods · doi:10.1038/nmeth.3582 · Cited by 575 · see citing works
Resurrecting Surviving Neandertal Lineages from Modern Human Genomes
Vernot, B., & Akey, J. M. (2014) · Science · doi:10.1126/science.1245938 · Cited by 562 · see citing works
Self-citationIdentification of functional exonic splicing enhancer motifs recognized by individual SR proteinsPreprint
Liu, H., Zhang, M. Q., & Krainer, A. R. (1998) · Genes & Development · doi:10.1101/gad.12.13.1998 · Cited by 513 · see citing works
Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens
Nédélec, Y., Sanz, J., Baharian, G., Szpiech, Z. A., Pacis, A., Dumaine, A., Grenier, J.-C., Freiman, A., Sams, A. J., Hebert, S., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.025 · Cited by 512 · 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
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.
Degner, J. F., Marioni, J. C., Pai, A. A., Pickrell, J. K., Nkadori, E., Gilad, Y., & Pritchard, J. K. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp579 · Cited by 502 · see citing works
Trk receptor tyrosine kinases: A bridge between cancer and neural development
Nakagawara, A. (2001) · Cancer Letters · doi:10.1016/s0304-3835(01)00530-4 · Cited by 499 · see citing works
Elevated gene expression levels distinguish human from non-human primate brains
Cáceres, M., Lachuer, J., Zapala, M. A., Redmond, J. C., Kudo, L., Geschwind, D. H., Lockhart, D. J., Preuss, T. M., & Barlow, C. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2135499100 · Cited by 491 · 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
Genetic adaptation and Neandertal admixture shaped the immune system of human populations
Quach, H., Rotival, M., Pothlichet, J., Loh, Y.-H. E., Dannemann, M., Zidane, N., Laval, G., Patin, E., Harmant, C., Lopez, M., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.024 · Cited by 475 · see citing works
The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans
Sankararaman, S., Mallick, S., Patterson, N., & Reich, D. (2016) · Current Biology · doi:10.1016/j.cub.2016.03.037 · Cited by 465 · see citing works
Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals
Vernot, B., Tucci, S., Kelso, J., Schraiber, J. G., Wolf, A. B., Gittelman, R. M., Dannemann, M., Grote, S., McCoy, R. C., Norton, H., et al. (2016) · Science · doi:10.1126/science.aad9416 · Cited by 459 · see citing works
Self-citationA Genome-Wide Investigation of SNPs and CNVs in Schizophrenia
Need, A. C., Ge, D., Weale, M. E., Maia, J. M., Feng, S., Heinzen, E. L., Shianna, K. V., Yoon, W., Kasperavičiūtė, D., Gennarelli, M., et al. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000373 · Cited by 443 · see citing works
The Genetic Cost of Neanderthal Introgression
Harris, K., & Nielsen, R. (2016) · Genetics · doi:10.1534/genetics.116.186890 · Cited by 419 · see citing works
The role of the basal ganglia and cerebellum in language processing
Booth, J. R., Wood, L., Lu, D., Houk, J. C., & Bitan, T. (2007) · Brain Research · doi:10.1016/j.brainres.2006.11.074 · Cited by 415 · see citing works
Tools and best practices for data processing in allelic expression analysis.
Castel, S. E., Levy-Moonshine, A., Mohammadi, P., Banks, E., & Lappalainen, T. (2015) · Genome Biology · doi:10.1186/s13059-015-0762-6 · Cited by 375 · cited 4× · see citing works
“This step eliminates the contribution of erroneous heterozygous genotypes to false ASE signal, but has the side effect of filtering true cases of monoallelic expression (Castel et al., 2015).”
InfluentialThe apelin receptor APJ: journey from an orphan to a multifaceted regulator of homeostasis
O’Carroll, A., Lolait, S. J., Harris, L. E., & Pope, G. R. (2013) · Journal of Endocrinology · doi:10.1530/joe-13-0227 · Cited by 339 · see citing works
The phenotypic legacy of admixture between modern humans and Neandertals
Simonti, C. N., Vernot, B., Bastarache, L., Bottinger, E., Carrell, D. S., Chisholm, R. L., Crosslin, D. R., Hebbring, S. J., Jarvik, G. P., Kullo, I. J., et al. (2016) · Science · doi:10.1126/science.aad2149 · Cited by 330 · see citing works
Self-citationExpression profiling in primates reveals a rapid evolution of human transcription factors
Gilad, Y., Oshlack, A., Smyth, G. K., Speed, T. P., & White, K. P. (2006) · Nature · doi:10.1038/nature04559 · Cited by 323 · see citing works
The Strength of Selection against Neanderthal Introgression
Juric, I., Aeschbacher, S., & Coop, G. (2016) · PLOS Genetics · doi:10.1371/journal.pgen.1006340 · Cited by 309 · see citing works
Rapid evolution of the cerebellum in humans and other great apes
Barton, R. A., & Venditti, C. (2014) · Current Biology · doi:10.1016/j.cub.2014.08.056 · Cited by 291 · see citing works
Possible Ancestral Structure in Human Populations
Plagnol, V., & Wall, J. D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020105 · Cited by 275 · see citing works
The Genotype-Tissue Expression (GTEx) project
Lonsdale, J., Thomas, J., Salvatore, M., Phillips, R., Lo, E., Shad, S., Hasz, R., Walters, G., Garcia, F., Young, N., et al. (2013) · Nature Genetics · doi:10.1038/ng.2653 · Cited by 263 · see citing works
Deschamps, M., Laval, G., Fagny, M., Itan, Y., Abel, L., Casanova, J.-L., Patin, E., & Quintana-Murci, L. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.11.014 · Cited by 257 · see citing works
Dannemann, M., Andrés, A. M., & Kelso, J. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.11.015 · Cited by 249 · 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
Landry, C. R., Wittkopp, P. J., Taubes, C. H., Ranz, J. M., Clark, A. G., & Hartl, D. L. (2005) · Genetics · doi:10.1534/genetics.105.047449 · Cited by 228 · see citing works
Pearce, E., Stringer, C. B., & Dunbar, R. (2013) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2013.0168 · Cited by 221 · see citing works
Blasius, A. L., Arnold, C. N., Georgel, P., Rutschmann, S., Xia, Y., Lin, P., Ross, C., Li, X., Smart, N. G., & Beutler, B. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1014051107 · Cited by 203 · see citing works
Price, A. L., Helgason, A., Þorleifsson, G., McCarroll, S. A., Kong, A., & Stefánsson, K. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001317 · Cited by 195 · see citing works
Gene Regulation and Speciation
Mack, K. L., & Nachman, M. W. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.11.003 · Cited by 187 · see citing works
Archaic Hominin Admixture Facilitated Adaptation to Out-of-Africa Environments
Gittelman, R. M., Schraiber, J. G., Vernot, B., Mikacenic, C., Wurfel, M. M., & Akey, J. M. (2016) · Current Biology · doi:10.1016/j.cub.2016.10.041 · Cited by 181 · see citing works
Self-citationBrain ontogeny and life history in Pleistocene hominins
Hublin, J.-J., Neubauer, S., & Gunz, P. (2015) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2014.0062 · Cited by 173 · see citing works
Genome-Wide Patterns of Expression in Drosophila Pure Species and Hybrid Males
Michalak, P. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg119 · Cited by 170 · see citing works
Beck, T., Hastings, R. K., Hesketh, S., Free, R. C., & Brookes, A. J. (2013) · European Journal of Human Genetics · doi:10.1038/ejhg.2013.274 · Cited by 166 · see citing works
Currat, M., & Excoffier, L. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1107450108 · Cited by 158 · see citing works
The CREB1-BDNF-NTRK2 Pathway in Depression: Multiple Gene-Cognition-Environment Interactions
Juhász, G., Dunham, J. S., McKie, S., Thomas, E., Downey, D., Chase, D. S., Lloyd-Williams, K., Toth, Z. G., Platt, H., Mekli, K., et al. (2011) · Biological Psychiatry · doi:10.1016/j.biopsych.2010.11.019 · Cited by 158 · see citing works
Correia, C., Coutinho, A. M., Sequeira, A. F., Sousa, I., Venda, L. L., Almeida, J. P., Abreu, R., Lobo, C., Miguel, T. S., Conroy, J., et al. (2010) · Genes Brain & Behavior · doi:10.1111/j.1601-183x.2010.00627.x · Cited by 146 · see citing works
Apelin and its receptor APJ in cardiovascular diseases
Yu, X.-H., Tang, Z.-B., Liu, L.-J., Qian, H., Tang, S., Zhang, D., Tian, G.-P., & Tang, C. (2013) · Clinica Chimica Acta · doi:10.1016/j.cca.2013.09.001 · Cited by 134 · see citing works
Gray, J. A., Yeo, G. S. H., Hung, C.-C. C., Keogh, J. M., Clayton, P., Banerjee, K., McAulay, A., O’Rahilly, S., & Farooqi, I. S. (2006) · International Journal of Obesity · doi:10.1038/sj.ijo.0803390 · Cited by 121 · see citing works
Turner, L. M., & Harr, B. (2014) · eLife · doi:10.7554/elife.02504 · Cited by 121 · see citing works
Kohli, M., Salyakina, D., Pfennig, A., Lucae, S., Horstmann, S., Menke, A., Kloiber, S., Hennings, J., Bradley, B., Ressler, K., et al. (2010) · Archives of General Psychiatry · doi:10.1001/archgenpsychiatry.2009.201 · 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
Self-citationMurphy, T. M., Ryan, M., Foster, T., Kelly, C., McClelland, R. J., O’Grady, J., Corcoran, E., Brady, J., Reilly, M., Jeffers, A. B., et al. (2011) · Behavioral and Brain Functions · doi:10.1186/1744-9081-7-22 · Cited by 95 · see citing works
Detecting ancient positive selection in humans using extended lineage sorting
Peyrégne, S., Boyle, M. J., Dannemann, M., & Prüfer, K. (2017) · Genome Research · doi:10.1101/gr.219493.116 · Cited by 93 · see citing works
Fu, W., Gittelman, R. M., Bamshad, M. J., & Akey, J. M. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.09.006 · Cited by 85 · see citing works
Self-citationAssessing allele-specific expression across multiple tissues from RNA-seq read data
Pirinen, M., Lappalainen, T., Zaitlen, N., Dermitzakis, E. T., Donnelly, P., McCarthy, M. I., & Rivas, M. A. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv074 · Cited by 83 · see citing works
Inherited Variation in Gene Expression
Skelly, D. A., Ronald, J., & Akey, J. M. (2009) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082908-150121 · Cited by 76 · see citing works
Self-citationAlonso, P., Gratacòs, M., Menchón, J. M., Sáiz-Ruiz, J., Segalàs, C., Baca‐García, E., Labad, J., Fernández‐Piqueras, J., Real, E., Vaquero, C., et al. (2007) · Biological Psychiatry · doi:10.1016/j.biopsych.2007.06.020 · Cited by 75 · see citing works
Genetic Association of Neurotrophic Tyrosine Kinase Receptor Type 2 (NTRK2) With Alzheimer's Disease
Chen, Z., Simmons, M. S., Perry, R. T., Wiener, H. W., Harrell, L. E., & Go, R. C. P. (2007) · American Journal of Medical Genetics Part B Neuropsychiatric Genetics · doi:10.1002/ajmg.b.30607 · Cited by 71 · see citing works
Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies
Panousis, N. I., Gutiérrez‐Arcelus, M., Dermitzakis, E. T., & Lappalainen, T. (2014) · Genome biology · doi:10.1186/s13059-014-0467-2 · Cited by 67 · see citing works
Gene-Gene Interactions Among CHRNA4, CHRNB2, BDNF, and NTRK2 in Nicotine Dependence
Li, M. D., Lou, X., Chen, G., Ma, J. Z., & Elston, R. C. (2008) · Biological Psychiatry · doi:10.1016/j.biopsych.2008.04.026 · Cited by 63 · see citing works
Ribasés, M., Gratacòs, M., Badia, A. M. T. I., Jimenez, L., Solano, R., Vallejo, J., Fernández‐Aranda, F., & Estivill, X. (2005) · Molecular Psychiatry · doi:10.1038/sj.mp.4001670 · Cited by 60 · see citing works
Beuten, J., Ma, J. Z., Payne, T. J., Dupont, R. T., Lou, X., Crews, K. M., Elston, R. C., & Li, M. D. (2006) · Biological Psychiatry · doi:10.1016/j.biopsych.2006.02.023 · Cited by 51 · see citing works
Food Taxation in the United Kingdom, France, Germany, and the United States
Rosenbaum, S. (1908) · Journal of the Royal Statistical Society Series A (Statistics in Society) · doi:10.1111/j.2397-2335.1908.tb02680.x · Cited by 48 · see citing works
Genome-wide patterns of regulatory divergence revealed by introgression lines
Guerrero, R. F., Hahn, M. W., Moyle, L. C., & Posto, A. L. (2016) · Evolution · doi:10.1111/evo.12875 · Cited by 33 · see citing works
Ferguson, J., Gomes, S., & Civetta, A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061575 · Cited by 14 · see citing works
Detecting ancient positive selection in humans using extended lineage sortingPreprint
Peyrégne, S., Boyle, M. J., Dannemann, M., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/092999 · Cited by 7 · see citing works
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CADD: predicting the deleteriousness of variants throughout the human genome
Rentzsch, P., Witten, D., Cooper, G. M., Shendure, J., & Kircher, M. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1016 · Cited by 3,534 · see citing works
The influence of evolutionary history on human health and disease
Benton, M. L., Abraham, A., LaBella, A. L., Abbot, P., Rokas, A., & Capra, J. A. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-00305-9 · Cited by 291 · see citing works
Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals
Chen, L., Wolf, A. B., Fu, W., Li, L., & Akey, J. M. (2020) · Cell · doi:10.1016/j.cell.2020.01.012 · Cited by 254 · see citing works
Self-citationNeanderthal language revisited: not only us
Dediu, D., & Levinson, S. C. (2018) · Current Opinion in Behavioral Sciences · doi:10.1016/j.cobeha.2018.01.001 · Cited by 218 · 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
Interpreting the genomic landscape of introgression
Martin, S. H., & Jiggins, C. D. (2017) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2017.08.007 · Cited by 206 · see citing works
Harnessing ancient genomes to study the history of human adaptation
Marciniak, S., & Perry, G. H. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.65 · Cited by 182 · see citing works
Human Immunology through the Lens of Evolutionary Genetics
Quintana‐Murci, L. (2019) · Cell · doi:10.1016/j.cell.2019.02.033 · Cited by 171 · 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
The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes
Skov, L., Coll Macià, M., Sveinbjörnsson, G., Mafessoni, F., Lucotte, E. A., Einarsdóttir, M. S., Jonsson, H., Halldorsson, B., Gudbjartsson, D. F., Helgason, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2225-9 · Cited by 145 · see citing works
Aspects of human physical and behavioural evolution during the last 1 million years
Galway‐Witham, J., Cole, J., & Stringer, C. B. (2019) · Journal of Quaternary Science · doi:10.1002/jqs.3137 · Cited by 145 · see citing works
A vast resource of allelic expression data spanning human tissues
Castel, S., Aguet, F., Mohammadi, P., Ardlie, K., Lappalainen, T., & GTEx Consortium (2019) · Genome Biology · doi:10.1186/s13059-020-02122-z · Cited by 117 · see citing works
Ultrarare variants drive substantial cis heritability of human gene expression
Hernandez, R. D., Uricchio, L. H., Hartman, K., Ye, C., Dahl, A., & Zaitlen, N. (2019) · Nature Genetics · doi:10.1038/s41588-019-0487-7 · Cited by 116 · see citing works
A catalog of single nucleotide changes distinguishing modern humans from archaic hominins
Kuhlwilm, M., & Boeckx, C. (2019) · Scientific Reports · doi:10.1038/s41598-019-44877-x · Cited by 108 · see citing works
Neurobiological functions of transcriptional enhancers
Nord, A. S., & West, A. E. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0538-5 · Cited by 100 · see citing works
Archaic hominin introgression into modern human genomes
Gökçümen, Ö. (2019) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23951 · Cited by 91 · see citing works
Fine scale mapping of genomic introgressions within the Drosophila yakuba clade
Turissini, D. A., & Matute, D. R. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006971 · Cited by 83 · see citing works
Something 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
Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years
Li, L., Comi, T. J., Bierman, R., & Akey, J. M. (2024) · Science · doi:10.1126/science.adi1768 · Cited by 84 · see citing works
Self-citationQuantifying the contribution of Neanderthal introgression to the heritability of complex traits
McArthur, E., Rinker, D. C., & Capra, J. A. (2021) · Nature Communications · doi:10.1038/s41467-021-24582-y · Cited by 71 · see citing works
The contribution of Neanderthal introgression to modern human traits
Reilly, P. F., Tjahjadi, A., Miller, S. L., Akey, J. M., & Tucci, S. (2022) · Current Biology · doi:10.1016/j.cub.2022.08.027 · Cited by 80 · see citing works
Self-citationAncient Hybridization with an Unknown Population Facilitated High-Altitude Adaptation of Canids
Wang, M., Wang, S., Li, Y., Jhala, Y. V., Thakur, M. K., Otecko, N. O., Si, J., Chen, H.-M., Shapiro, B., Nielsen, R., et al. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa113 · Cited by 77 · see citing works
The cis-regulatory effects of modern human-specific variants
Weiss, C. V., Harshman, L., Inoue, F., Fraser, H. B., Petrov, D. A., Ahituv, N., & Gokhman, D. (2021) · eLife · doi:10.7554/elife.63713 · Cited by 70 · see citing works
Selection against admixture and gene regulatory divergence in a long-term primate field study
Vilgalys, T., Fogel, A. S., Anderson, J. A., Mututua, R. S., Warutere, J. K., Siodi, I., Kim, S. Y., Voyles, T. N., Robinson, J. A., Wall, J., et al. (2021) · bioRxiv · doi:10.1126/science.abm4917 · Cited by 70 · see citing works
Brzozowska, M. M., Havula, E., Allen, R., & Cox, M. P. (2019) · Reviews in Endocrine and Metabolic Disorders · doi:10.1007/s11154-019-09505-z · Cited by 70 · see citing works
Outstanding questions in the study of archaic hominin admixture
Wolf, A. B., & Akey, J. M. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007349 · Cited by 66 · see citing works
Self-citationGouy, A., & Excoffier, L. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msz306 · Cited by 63 · see citing works
Perspectives on Allele-Specific Expression
Cleary, S., & Seoighe, C. (2021) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-021621-122219 · Cited by 67 · 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
The genetic changes that shaped Neandertals, Denisovans, and modern humans
Zeberg, H., Jakobsson, M., & Pääbo, S. (2024) · Cell · doi:10.1016/j.cell.2023.12.029 · Cited by 60 · see citing works
Lombard, M., & Högberg, A. (2021) · Journal of Archaeological Method and Theory · doi:10.1007/s10816-020-09502-6 · Cited by 57 · 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
Harvati, K., & Ackermann, R. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01875-z · Cited by 59 · 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
Multi-contrast anatomical subcortical structures parcellation
Bazin, P., Alkemade, A., Mulder, M., Henry, A. G., & Forstmann, B. U. (2020) · eLife · doi:10.7554/elife.59430 · Cited by 53 · see citing works
The contribution of admixture to primate evolution
Tung, J., & Barreiro, L. B. (2017) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2017.08.010 · Cited by 51 · 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
“…conducted primarily on Neanderthal introgressed DNA have suggested a non-negligible contribution to gene expression variation in modern humans [10, 11, 22], with repeated examples of Neanderthal archaic variants falling within regulatory elements or the seed region of mature micro-RNAs…”
Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations
Rinker, D. C., Simonti, C. N., McArthur, E., Shaw, D., Hodges, E., & Capra, J. A. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-1261-z · Cited by 44 · 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
A statistical model for reference-free inference of archaic local ancestry
Durvasula, A., & Sankararaman, S. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008175 · Cited by 46 · see citing works
Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0
Yuan, K., Ni, X., Liu, C., Pan, Y., Deng, L., Zhang, R., Gao, Y., Ge, X., Liu, J., Ma, X., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26503-5 · Cited by 42 · see citing works
Convergent evolution of gene expression in two high-toothed stickleback populations
Hart, J. C., Ellis, N. A., Eisen, M. B., & Miller, C. T. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007443 · Cited by 37 · see citing works
Natural Selection Has Differentiated the Progesterone Receptor among Human Populations
Li, J., Hong, X., Mesiano, S. A., Muglia, L. J., Wang, X., Snyder, M. P., Stevenson, D. K., & Shaw, G. M. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2018.05.009 · Cited by 36 · see citing works
Evolutionary and medical consequences of archaic introgression into modern human genomes
Dolgova, O., & Lao, O. (2018) · Genes · doi:10.3390/genes9070358 · Cited by 34 · see citing works
New insights into human immunity from ancient genomics
Kerner, G., Patin, É., & Quintana‐Murci, L. (2021) · Current Opinion in Immunology · doi:10.1016/j.coi.2021.04.006 · Cited by 34 · see citing works
Huang, Y.-M., Huang, W., Meng, Z., Braz, G. T., Li, Y., Wang, K., Wang, H., Lai, J.-S., Jiang, J.-M., Dong, Z.-B., et al. (2021) · Genome Biology · doi:10.1186/s13059-021-02448-2 · Cited by 25 · see citing works
Admixture in Mammals and How to Understand Its Functional Implications
Fontsere, C., de Manuel, M., Marquès‐Bonet, T., & Kuhlwilm, M. (2019) · BioEssays · doi:10.1002/bies.201900123 · Cited by 32 · see citing works
Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture
Ahlquist, K. D., Bañuelos, M. M., Funk, A., Lai, J., Rong, S., Villanea, F. A., & Witt, K. E. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab115 · Cited by 33 · see citing works
An evolutionary compass for detecting signals of polygenic selection and mutational bias
Uricchio, L. H., Kitano, H. C., Gusev, A., & Zaitlen, N. (2019) · Evolution Letters · doi:10.1002/evl3.97 · Cited by 29 · see citing works
Evolutionary immuno-genetics of endoplasmic reticulum aminopeptidase II (ERAP2)
Raja, A., & Kuiper, J. J. W. (2023) · Genes and Immunity · doi:10.1038/s41435-023-00225-8 · Cited by 26 · see citing works
Triangulating Neanderthal cognition: A tale of not seeing the forest for the trees
Breyl, M. (2020) · Wiley Interdisciplinary Reviews Cognitive Science · doi:10.1002/wcs.1545 · Cited by 24 · 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
Broadening primate genomics: new insights into the ecology and evolution of primate gene regulation
Anderson, J. A., Vilgalys, T. P., & Tung, J. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.05.009 · Cited by 23 · see citing works
Li, Q., Wang, Z., Zong, L., Ye, L., Ye, J., Ou, H., Jiang, T., Guo, B., Yang, Q., Liang, W., et al. (2021) · Molecular Psychiatry · doi:10.1038/s41380-021-01126-w · Cited by 24 · see citing works
Predicting Archaic Hominin Phenotypes from Genomic Data
Brand, C. M., Colbran, L. L., & Capra, J. A. (2022) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-111521-121903 · Cited by 23 · see citing works
McArthur, E., Rinker, D. C., Cheng, Y., Wang, Q., Wang, J., Gilbertson, E. N., Fudenberg, G., Pittman, M., Keough, K. C., Yue, F., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.07.479462 · Cited by 22 · see citing works
Human Stem Cell Resources Are an Inroad to Neandertal DNA Functions
Dannemann, M., He, Z., Heide, C., Vernot, B., Sidow, L., Kanton, S., Weigert, A., Treutlein, B., Pääbo, S., Kelso, J. F., et al. (2020) · Stem Cell Reports · doi:10.1016/j.stemcr.2020.05.018 · Cited by 22 · see citing works
Tracing the Evolution of Human Immunity Through Ancient DNA
Patin, É., & Quintana‐Murci, L. (2024) · Annual Review of Immunology · doi:10.1146/annurev-immunol-082323-024638 · Cited by 19 · see citing works
Li, S., Wu, Q., Jiang, Z., Wu, Y., Li, Y., Ni, B. J., Xiao, J., & Zhai, Z. (2022) · Journal of Inflammation Research · doi:10.2147/jir.s383623 · Cited by 20 · see citing works
Functional consequences of archaic introgression and their impact on fitness
Rotival, M., & Quintana‐Murci, L. (2020) · Genome biology · doi:10.1186/s13059-019-1920-z · Cited by 20 · 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
Variation and Functional Impact of Neanderthal Ancestry in Western Asia
Taşkent, R. Ö., Alioğlu, D., Fer, E., Dönertaş, H. M., Somel, M., & Gökçümen, Ö. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx216 · Cited by 18 · see citing works
Age-related gene expression and DNA methylation changes in rhesus macaque
Zhou, M., Zhang, L., Yang, Q. L., Yan, C., Jiang, P., Lan, Y., Wang, J., Tang, R., He, M., Lei, G.-L., et al. (2020) · Genomics · doi:10.1016/j.ygeno.2020.09.021 · Cited by 15 · see citing works
On the origin of schizophrenia: Testing evolutionary theories in the post‐genomic era
Nesic, M. J., Stojković, B., & Marić, N. P. (2019) · Psychiatry and Clinical Neurosciences · doi:10.1111/pcn.12933 · Cited by 15 · see citing works
A signature of Neanderthal introgression on molecular mechanisms of environmental responses
Findley, A. S., Zhang, X., Boye, C., Lin, Y. L., Kalita, C. A., Barreiro, L., Lohmueller, K. E., Pique-Regi, R., & Luca, F. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009493 · 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
Resurrecting the alternative splicing landscape of archaic hominins using machine learning
Brand, C. M., Colbran, L. L., & Capra, J. A. (2023) · Nature Ecology & Evolution · doi:10.1038/s41559-023-02053-5 · 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
Self-citationArchaic hominin admixture and its consequences for modern humans
Tagore, D., & Akey, J. M. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102280 · Cited by 13 · see citing works
Self-citationHarnessing epigenetics to study human evolution
Mathov, Y., Batyrev, D., Meshorer, E., & Carmel, L. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.05.023 · Cited by 13 · see citing works
Denisovan admixture facilitated environmental adaptation in Papua New Guinean populations
Yermakovich, D., André, M., Brucato, N., Kariwiga, J., Leavesley, M., Pankratov, V., Mondal, M., Ricaut, F.-X., & Dannemann, M. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2405889121 · Cited by 12 · see citing works
Ye, J., Huang, Z., Li, Q., Li, Z., Lan, Y., Wang, Z., Ni, C., Wu, X., Jiang, T., Li, Y., et al. (2023) · BMC Medicine · doi:10.1186/s12916-023-03177-y · Cited by 12 · see citing works
Secondary Contact, Introgressive Hybridization, and Genome Stabilization in Sticklebacks
Feng, X., Merilä, J., & Löytynoja, A. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae031 · Cited by 12 · see citing works
Ultra-rare variants drive substantial cis -heritability of human gene expressionPreprint
Hernandez, R. D., Uricchio, L. H., Hartman, K., Ye, C., Dahl, A., & Zaitlen, N. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/219238 · Cited by 13 · see citing works
Long-range regulatory effects of Neandertal DNA in modern humans
Yermakovich, D., Pankratov, V., Võsa, U., Yunusbayev, B., Metspalu, A., Nelis, M., Milani, L. A., Mägi, R., Esko, T., & Dannemann, M. (2022) · Genetics · doi:10.1093/genetics/iyac188 · Cited by 11 · see citing works
Neanderthal introgression reintroduced functional alleles lost in the human out of Africa bottleneckPreprint
Rinker, D. C., Simonti, C., McArthur, E., Shaw, D. M., Hodges, E. C., & Capra, J. A. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/533257 · Cited by 11 · see citing works
Extensive folding variability between homologous chromosomes in mammalian cells
Irastorza-Azcarate, I., Kukalev, A., Kempfer, R., Thieme, C. J., Mastrobuoni, G., Markowski, J., Loof, G., Sparks, T. M., Brookes, E., Natarajan, K., et al. (2025) · Molecular Systems Biology · doi:10.1038/s44320-025-00107-3 · Cited by 4 · see citing works
Relethford, J. H., & Smith, F. H. (2018) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23413 · Cited by 10 · see citing works
Methods for detecting introgressed archaic sequences
Sankararaman, S. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.05.026 · Cited by 10 · see citing works
Evolutionary genetics and acclimatization in nephrology
Adeyemo, A., Shriner, D., Bentley, A. R., Gbadegesin, R., & Rotimi, C. N. (2021) · Nature Reviews Nephrology · doi:10.1038/s41581-021-00483-7 · Cited by 10 · see citing works
Weasel, L. H. (2022) · The American Naturalist · doi:10.1086/720130 · Cited by 10 · see citing works
Selection against archaic hominin genetic variation in regulatory regionsPreprint
Telis, N., Aguilar, R., & Harris, K. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/708230 · 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
Identification of Single Amino Acid Substitutions in Proteogenomics
Moshkovskii, S., Ivanov, M., Kuznetsova, K. G., & Gorshkov, M. (2018) · Biochemistry (Moscow) · doi:10.1134/s0006297918030057 · Cited by 7 · see citing works
The Neanderthal brain: Biological and cognitive evolution
Macciardi, F. M., & Martini, F. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-821428-2.00008-1 · 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
The Year In Genetic Anthropology: New Lands, New Technologies, New Questions
Gökçümen, Ö. (2018) · American Anthropologist · doi:10.1111/aman.13032 · Cited by 6 · see citing works
Coolidge, F. L. (2020) · doi:10.1093/oso/9780190940942.001.0001 · Cited by 10 · see citing works
Chung, S., & Son, J.-W. (2023) · Journal of korean Academy of Child and Adolescent Psychiatry · doi:10.5765/jkacap.230004 · Cited by 6 · see citing works
Sandroni, V., & Chaumette, B. (2025) · Genes Brain & Behavior · doi:10.1111/gbb.70013 · Cited by 5 · see citing works
Li, Q., Chen, W., & Mao, X. (2022) · Ecology and Evolution · doi:10.1002/ece3.9025 · Cited by 5 · see citing works
Chen, S., Tang, D., Deng, L., & Xu, S. (2024) · iScience · doi:10.1016/j.isci.2024.109560 · 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
Genetics of human brain evolution
Vallender, E. J. (2019) · Progress in brain research · doi:10.1016/bs.pbr.2019.01.003 · Cited by 5 · see citing works
Hobohm, C. (2021) · Environmental challenges and solutions · doi:10.1007/978-3-030-57710-0_1 · Cited by 5 · see citing works
Wendt, F. R., Pathak, G. A., Overstreet, C. M., Tylee, D. S., Gelernter, J. E., Atkinson, E. G., & Polimanti, R. A. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.26.966531 · Cited by 5 · see citing works
Ferraretti, G., Abondio, P., Alberti, M., Dezi, A., Sherpa, P. T., Cocco, P., Tiriticco, M., Marcello, M. D., Gnecchi‐Ruscone, G. A., Natali, L., et al. (2024) · eLife · doi:10.7554/elife.89815.3 · Cited by 4 · see citing works
Voinescu, C., Mozere, M., Genovese, G., Downie, M. L., Gupta, S., Gale, D. P., Böckenhauer, D., Kleta, R., Arcos‐Burgos, M., & Stanescu, H. C. (2024) · Kidney International · doi:10.1016/j.kint.2024.01.017 · Cited by 4 · see citing works
Wang, M., Uebbing, S., Pawitan, Y., & Scofield, D. (2018) · Molecular Ecology Resources · doi:10.1111/1755-0998.12909 · Cited by 3 · see citing works
Gouy, A., & Excoffier, L. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/732958 · Cited by 4 · see citing works
- Authors
- McCoy, R. C., Wakefield, J., & Akey, J. M.
- Affiliations
- University of Washington (US)
- Corresponding author
- Akey, Joshua M.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2017-02
- Volume
- 168
- Issue
- 5
- Pages
- 916-927.e12
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC6219754
- OpenAlex
- W2594204182
- Cited by
- 200
- References
- 92
- Citations by year
- 2026: 17 · 2025: 10 · 2024: 22 · 2023: 23 · 2022: 15 · 2021: 27 · 2020: 37 · 2019: 26 · 2018: 16 · 2017: 7
- FWCI
- 94.65
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- NIH/NHGRI (5T32HG000035-22)
- NIH (R01GM110068)
- Common Fund of the Office of the Director of the NIH
- NCI
- NHGRI
- NHLBI
- NIDA
- NIMH
- NINDS
- NCI\SAIC-Frederick
- Disease Research Interchange (10XS170)
- Roswell Park Cancer Institute (10XS171)
- Science Care (X10S172, HHSN268201000029C)
- The Broad Institute
- Van Andel Institute (10ST1035)
- SAIC-F (HHSN261200800001E)
- University of Miami (DA006227, DA033684, N01MH000028, MH090941, MH101814, MH090951, MH090937, MH101820, MH101825, MH090936, MH101819, MH090948, MH101782, MH101810, MH101822)
- Topics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Neanderthal introgression, allele-specific expression, cis-regulatory variation, human gene expression, ancient hybridization, regulatory evolution, natural selection
- MeSH terms
- Animals, Brain, Gene Expression Regulation, Humans, Male, Organ Specificity, Testis, Gene Expression, Evolution, Molecular, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Neanderthals
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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