[{"scopus_import":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"month":"12","date_published":"2023-12-01T00:00:00Z","article_type":"letter_note","date_created":"2023-12-17T23:00:53Z","department":[{"_id":"MaRo"}],"intvolume":"        55","status":"public","day":"01","type":"journal_article","publication":"Nature Genetics","issue":"12","page":"2053-2055","external_id":{"pmid":["38052961"]},"title":"Reply to: Revisiting the use of structural similarity index in Hi-C","year":"2023","doi":"10.1038/s41588-023-01595-5","author":[{"last_name":"Ing-Simmons","full_name":"Ing-Simmons, Elizabeth","first_name":"Elizabeth"},{"first_name":"Nick N","last_name":"Machnik","full_name":"Machnik, Nick N","orcid":"0000-0001-6617-9742","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Juan M.","full_name":"Vaquerizas, Juan M.","last_name":"Vaquerizas"}],"citation":{"ama":"Ing-Simmons E, Machnik NN, Vaquerizas JM. Reply to: Revisiting the use of structural similarity index in Hi-C. <i>Nature Genetics</i>. 2023;55(12):2053-2055. doi:<a href=\"https://doi.org/10.1038/s41588-023-01595-5\">10.1038/s41588-023-01595-5</a>","mla":"Ing-Simmons, Elizabeth, et al. “Reply to: Revisiting the Use of Structural Similarity Index in Hi-C.” <i>Nature Genetics</i>, vol. 55, no. 12, Springer Nature, 2023, pp. 2053–55, doi:<a href=\"https://doi.org/10.1038/s41588-023-01595-5\">10.1038/s41588-023-01595-5</a>.","ista":"Ing-Simmons E, Machnik NN, Vaquerizas JM. 2023. Reply to: Revisiting the use of structural similarity index in Hi-C. Nature Genetics. 55(12), 2053–2055.","short":"E. Ing-Simmons, N.N. Machnik, J.M. Vaquerizas, Nature Genetics 55 (2023) 2053–2055.","apa":"Ing-Simmons, E., Machnik, N. N., &#38; Vaquerizas, J. M. (2023). Reply to: Revisiting the use of structural similarity index in Hi-C. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41588-023-01595-5\">https://doi.org/10.1038/s41588-023-01595-5</a>","ieee":"E. Ing-Simmons, N. N. Machnik, and J. M. Vaquerizas, “Reply to: Revisiting the use of structural similarity index in Hi-C,” <i>Nature Genetics</i>, vol. 55, no. 12. Springer Nature, pp. 2053–2055, 2023.","chicago":"Ing-Simmons, Elizabeth, Nick N Machnik, and Juan M. Vaquerizas. “Reply to: Revisiting the Use of Structural Similarity Index in Hi-C.” <i>Nature Genetics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41588-023-01595-5\">https://doi.org/10.1038/s41588-023-01595-5</a>."},"publication_status":"published","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"pmid":1,"_id":"14689","oa_version":"None","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2023-12-18T08:51:38Z","volume":55},{"day":"01","type":"journal_article","intvolume":"        55","status":"public","publication":"Nature Genetics","page":"333-345","file_date_updated":"2023-02-27T07:46:45Z","month":"02","article_type":"review","date_published":"2023-02-01T00:00:00Z","scopus_import":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"has_accepted_license":"1","license":"https://creativecommons.org/licenses/by/4.0/","department":[{"_id":"ScienComp"}],"file":[{"checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e","date_created":"2023-02-27T07:46:45Z","file_size":21484855,"file_name":"2023_NatureGenetics_Zeller.pdf","access_level":"open_access","date_updated":"2023-02-27T07:46:45Z","success":1,"file_id":"12688","creator":"dernst","relation":"main_file","content_type":"application/pdf"}],"date_created":"2023-01-12T12:09:09Z","citation":{"ista":"Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M, van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.","short":"P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.","ama":"Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. <i>Nature Genetics</i>. 2023;55:333-345. doi:<a href=\"https://doi.org/10.1038/s41588-022-01260-3\">10.1038/s41588-022-01260-3</a>","mla":"Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” <i>Nature Genetics</i>, vol. 55, Springer Nature, 2023, pp. 333–45, doi:<a href=\"https://doi.org/10.1038/s41588-022-01260-3\">10.1038/s41588-022-01260-3</a>.","chicago":"Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” <i>Nature Genetics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41588-022-01260-3\">https://doi.org/10.1038/s41588-022-01260-3</a>.","ieee":"P. Zeller <i>et al.</i>, “Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis,” <i>Nature Genetics</i>, vol. 55. Springer Nature, pp. 333–345, 2023.","apa":"Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu, M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41588-022-01260-3\">https://doi.org/10.1038/s41588-022-01260-3</a>"},"publication_status":"published","abstract":[{"lang":"eng","text":"Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages."}],"author":[{"first_name":"Peter","full_name":"Zeller, Peter","last_name":"Zeller"},{"first_name":"Jake","full_name":"Yeung, Jake","last_name":"Yeung","orcid":"0000-0003-1732-1559","id":"123012b2-db30-11eb-b4d8-a35840c0551b"},{"last_name":"Viñas Gaza","full_name":"Viñas Gaza, Helena","first_name":"Helena"},{"first_name":"Buys Anton","full_name":"de Barbanson, Buys Anton","last_name":"de Barbanson"},{"full_name":"Bhardwaj, Vivek","last_name":"Bhardwaj","first_name":"Vivek"},{"first_name":"Maria","last_name":"Florescu","full_name":"Florescu, Maria"},{"last_name":"van der Linden","full_name":"van der Linden, Reinier","first_name":"Reinier"},{"first_name":"Alexander","last_name":"van Oudenaarden","full_name":"van Oudenaarden, Alexander"}],"keyword":["Genetics"],"article_processing_charge":"No","date_updated":"2023-02-27T07:48:24Z","volume":55,"oa":1,"publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"_id":"12158","oa_version":"Published Version","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank A. Giladi for sharing mRNA abundance tables of cell types together with J. van den Berg for critical reading of the manuscript. We thank M. Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973). Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström under CC-BY-SA 3.0 license. This work was supported by European Research Council Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991), HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z. The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF (ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","year":"2023","doi":"10.1038/s41588-022-01260-3","title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570","000"]},{"date_created":"2020-04-30T10:44:57Z","date_published":"2018-04-16T00:00:00Z","article_type":"original","month":"04","year":"2018","doi":"10.1038/s41588-018-0101-4","language":[{"iso":"eng"}],"title":"Signatures of negative selection in the genetic architecture of human complex traits","publisher":"Springer Nature","article_processing_charge":"No","page":"746-753","volume":50,"date_updated":"2021-01-12T08:15:06Z","publication":"Nature Genetics","issue":"5","quality_controlled":"1","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","publication_identifier":{"issn":["1061-4036","1546-1718"]},"_id":"7722","type":"journal_article","day":"16","citation":{"mla":"Zeng, Jian, et al. “Signatures of Negative Selection in the Genetic Architecture of Human Complex Traits.” <i>Nature Genetics</i>, vol. 50, no. 5, Springer Nature, 2018, pp. 746–53, doi:<a href=\"https://doi.org/10.1038/s41588-018-0101-4\">10.1038/s41588-018-0101-4</a>.","ama":"Zeng J, de Vlaming R, Wu Y, et al. Signatures of negative selection in the genetic architecture of human complex traits. <i>Nature Genetics</i>. 2018;50(5):746-753. doi:<a href=\"https://doi.org/10.1038/s41588-018-0101-4\">10.1038/s41588-018-0101-4</a>","ista":"Zeng J, de Vlaming R, Wu Y, Robinson MR, Lloyd-Jones LR, Yengo L, Yap CX, Xue A, Sidorenko J, McRae AF, Powell JE, Montgomery GW, Metspalu A, Esko T, Gibson G, Wray NR, Visscher PM, Yang J. 2018. Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. 50(5), 746–753.","short":"J. Zeng, R. de Vlaming, Y. Wu, M.R. Robinson, L.R. Lloyd-Jones, L. Yengo, C.X. Yap, A. Xue, J. Sidorenko, A.F. McRae, J.E. Powell, G.W. Montgomery, A. Metspalu, T. Esko, G. Gibson, N.R. Wray, P.M. Visscher, J. Yang, Nature Genetics 50 (2018) 746–753.","apa":"Zeng, J., de Vlaming, R., Wu, Y., Robinson, M. R., Lloyd-Jones, L. R., Yengo, L., … Yang, J. (2018). Signatures of negative selection in the genetic architecture of human complex traits. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41588-018-0101-4\">https://doi.org/10.1038/s41588-018-0101-4</a>","ieee":"J. Zeng <i>et al.</i>, “Signatures of negative selection in the genetic architecture of human complex traits,” <i>Nature Genetics</i>, vol. 50, no. 5. Springer Nature, pp. 746–753, 2018.","chicago":"Zeng, Jian, Ronald de Vlaming, Yang Wu, Matthew Richard Robinson, Luke R. Lloyd-Jones, Loic Yengo, Chloe X. Yap, et al. “Signatures of Negative Selection in the Genetic Architecture of Human Complex Traits.” <i>Nature Genetics</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41588-018-0101-4\">https://doi.org/10.1038/s41588-018-0101-4</a>."},"publication_status":"published","author":[{"full_name":"Zeng, Jian","last_name":"Zeng","first_name":"Jian"},{"full_name":"de Vlaming, Ronald","last_name":"de Vlaming","first_name":"Ronald"},{"first_name":"Yang","last_name":"Wu","full_name":"Wu, Yang"},{"first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"first_name":"Luke R.","last_name":"Lloyd-Jones","full_name":"Lloyd-Jones, Luke R."},{"first_name":"Loic","last_name":"Yengo","full_name":"Yengo, Loic"},{"first_name":"Chloe X.","full_name":"Yap, Chloe X.","last_name":"Yap"},{"full_name":"Xue, Angli","last_name":"Xue","first_name":"Angli"},{"first_name":"Julia","last_name":"Sidorenko","full_name":"Sidorenko, Julia"},{"full_name":"McRae, Allan F.","last_name":"McRae","first_name":"Allan F."},{"last_name":"Powell","full_name":"Powell, Joseph E.","first_name":"Joseph E."},{"first_name":"Grant W.","last_name":"Montgomery","full_name":"Montgomery, Grant W."},{"first_name":"Andres","full_name":"Metspalu, Andres","last_name":"Metspalu"},{"first_name":"Tonu","last_name":"Esko","full_name":"Esko, Tonu"},{"first_name":"Greg","last_name":"Gibson","full_name":"Gibson, Greg"},{"first_name":"Naomi R.","last_name":"Wray","full_name":"Wray, Naomi R."},{"first_name":"Peter M.","full_name":"Visscher, Peter M.","last_name":"Visscher"},{"full_name":"Yang, Jian","last_name":"Yang","first_name":"Jian"}],"status":"public","abstract":[{"text":"We develop a Bayesian mixed linear model that simultaneously estimates single-nucleotide polymorphism (SNP)-based heritability, polygenicity (proportion of SNPs with nonzero effects), and the relationship between SNP effect size and minor allele frequency for complex traits in conventionally unrelated individuals using genome-wide SNP data. We apply the method to 28 complex traits in the UK Biobank data (N = 126,752) and show that on average, 6% of SNPs have nonzero effects, which in total explain 22% of phenotypic variance. We detect significant (P < 0.05/28) signatures of natural selection in the genetic architecture of 23 traits, including reproductive, cardiovascular, and anthropometric traits, as well as educational attainment. The significant estimates of the relationship between effect size and minor allele frequency in complex traits are consistent with a model of negative (or purifying) selection, as confirmed by forward simulation. We conclude that negative selection acts pervasively on the genetic variants associated with human complex traits.","lang":"eng"}],"intvolume":"        50"},{"publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"pmid":1,"_id":"12193","oa_version":"None","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Daniel Zilberman for intellectual contributions to this work and assistance with manuscript preparation. We also thank Caroline Dean, Kirsten Bomblies, Vinod Kumar, Siobhan Brady and Sophien Kamoun for comments on the manuscript, Hugh Dickinson and Josephine Hellberg for developing the meiocyte isolation method, Giles Oldroyd for the pGWB13-Bar vector, Elisa Fiume for the pMDC107-NTF vector, Matthew Hartley, Matthew Couchman and Tjelvar Sten Gunnar Olsson for bioinformatics support, and the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BBL0250431) to X.F., a BBSRC grant (BBM01973X1) to J.H., and a Sainsbury PhD Studentship to J.W.","article_processing_charge":"No","volume":50,"oa":1,"date_updated":"2023-10-18T07:21:53Z","abstract":[{"lang":"eng","text":"DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed during animal development. However, whether developmental methylation reprogramming during the sporophytic life cycle of flowering plants regulates genes is presently unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation (RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants."}],"author":[{"last_name":"Walker","full_name":"Walker, James","first_name":"James"},{"first_name":"Hongbo","last_name":"Gao","full_name":"Gao, Hongbo"},{"last_name":"Zhang","full_name":"Zhang, Jingyi","first_name":"Jingyi"},{"last_name":"Aldridge","full_name":"Aldridge, Billy","first_name":"Billy"},{"full_name":"Vickers, Martin","last_name":"Vickers","first_name":"Martin"},{"first_name":"James D.","last_name":"Higgins","full_name":"Higgins, James D."},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234"}],"keyword":["Genetics"],"citation":{"short":"J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng, Nature Genetics 50 (2017) 130–137.","ista":"Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X. 2017. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. 50(1), 130–137.","mla":"Walker, James, et al. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>, vol. 50, no. 1, Nature Research, 2017, pp. 130–37, doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>.","ama":"Walker J, Gao H, Zhang J, et al. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. 2017;50(1):130-137. doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>","chicago":"Walker, James, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers, James D. Higgins, and Xiaoqi Feng. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>. Nature Research, 2017. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>.","apa":"Walker, J., Gao, H., Zhang, J., Aldridge, B., Vickers, M., Higgins, J. D., &#38; Feng, X. (2017). Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>","ieee":"J. Walker <i>et al.</i>, “Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis,” <i>Nature Genetics</i>, vol. 50, no. 1. Nature Research, pp. 130–137, 2017."},"publication_status":"published","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/","open_access":"1"}],"title":"Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis","external_id":{"pmid":["29255257"]},"year":"2017","doi":"10.1038/s41588-017-0008-5","publication":"Nature Genetics","issue":"1","page":"130-137","intvolume":"        50","status":"public","day":"18","type":"journal_article","date_created":"2023-01-16T09:18:05Z","department":[{"_id":"XiFe"}],"scopus_import":"1","publisher":"Nature Research","language":[{"iso":"eng"}],"month":"12","article_type":"original","date_published":"2017-12-18T00:00:00Z"},{"main_file_link":[{"url":"https://doi.org/10.1038/ng.3538","open_access":"1"}],"title":"Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets","doi":"10.1038/ng.3538","year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","oa_version":"Published Version","_id":"7737","extern":"1","publication_identifier":{"issn":["1061-4036","1546-1718"]},"oa":1,"date_updated":"2021-01-12T08:15:11Z","volume":48,"article_processing_charge":"No","author":[{"last_name":"Zhu","full_name":"Zhu, Zhihong","first_name":"Zhihong"},{"last_name":"Zhang","full_name":"Zhang, Futao","first_name":"Futao"},{"first_name":"Han","last_name":"Hu","full_name":"Hu, Han"},{"full_name":"Bakshi, Andrew","last_name":"Bakshi","first_name":"Andrew"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","last_name":"Robinson","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard"},{"last_name":"Powell","full_name":"Powell, Joseph E","first_name":"Joseph E"},{"last_name":"Montgomery","full_name":"Montgomery, Grant W","first_name":"Grant W"},{"last_name":"Goddard","full_name":"Goddard, Michael E","first_name":"Michael E"},{"last_name":"Wray","full_name":"Wray, Naomi R","first_name":"Naomi R"},{"full_name":"Visscher, Peter M","last_name":"Visscher","first_name":"Peter M"},{"full_name":"Yang, Jian","last_name":"Yang","first_name":"Jian"}],"abstract":[{"text":"Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with human complex traits. However, the genes or functional DNA elements through which these variants exert their effects on the traits are often unknown. We propose a method (called SMR) that integrates summary-level data from GWAS with data from expression quantitative trait locus (eQTL) studies to identify genes whose expression levels are associated with a complex trait because of pleiotropy. We apply the method to five human complex traits using GWAS data on up to 339,224 individuals and eQTL data on 5,311 individuals, and we prioritize 126 genes (for example, TRAF1 and ANKRD55 for rheumatoid arthritis and SNX19 and NMRAL1 for schizophrenia), of which 25 genes are new candidates; 77 genes are not the nearest annotated gene to the top associated GWAS SNP. These genes provide important leads to design future functional studies to understand the mechanism whereby DNA variation leads to complex trait variation.","lang":"eng"}],"publication_status":"published","citation":{"chicago":"Zhu, Zhihong, Futao Zhang, Han Hu, Andrew Bakshi, Matthew Richard Robinson, Joseph E Powell, Grant W Montgomery, et al. “Integration of Summary Data from GWAS and EQTL Studies Predicts Complex Trait Gene Targets.” <i>Nature Genetics</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/ng.3538\">https://doi.org/10.1038/ng.3538</a>.","apa":"Zhu, Z., Zhang, F., Hu, H., Bakshi, A., Robinson, M. R., Powell, J. E., … Yang, J. (2016). Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/ng.3538\">https://doi.org/10.1038/ng.3538</a>","ieee":"Z. Zhu <i>et al.</i>, “Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets,” <i>Nature Genetics</i>, vol. 48, no. 5. Springer Nature, pp. 481–487, 2016.","short":"Z. Zhu, F. Zhang, H. Hu, A. Bakshi, M.R. Robinson, J.E. Powell, G.W. Montgomery, M.E. Goddard, N.R. Wray, P.M. Visscher, J. Yang, Nature Genetics 48 (2016) 481–487.","ista":"Zhu Z, Zhang F, Hu H, Bakshi A, Robinson MR, Powell JE, Montgomery GW, Goddard ME, Wray NR, Visscher PM, Yang J. 2016. Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. Nature Genetics. 48(5), 481–487.","mla":"Zhu, Zhihong, et al. “Integration of Summary Data from GWAS and EQTL Studies Predicts Complex Trait Gene Targets.” <i>Nature Genetics</i>, vol. 48, no. 5, Springer Nature, 2016, pp. 481–87, doi:<a href=\"https://doi.org/10.1038/ng.3538\">10.1038/ng.3538</a>.","ama":"Zhu Z, Zhang F, Hu H, et al. Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. <i>Nature Genetics</i>. 2016;48(5):481-487. doi:<a href=\"https://doi.org/10.1038/ng.3538\">10.1038/ng.3538</a>"},"date_created":"2020-04-30T10:50:26Z","language":[{"iso":"eng"}],"publisher":"Springer Nature","date_published":"2016-03-28T00:00:00Z","article_type":"original","month":"03","page":"481-487","issue":"5","publication":"Nature Genetics","status":"public","intvolume":"        48","type":"journal_article","day":"28"},{"intvolume":"        47","abstract":[{"lang":"eng","text":"Across-nation differences in the mean values for complex traits are common1,2,3,4,5,6,7,8, but the reasons for these differences are unknown. Here we find that many independent loci contribute to population genetic differences in height and body mass index (BMI) in 9,416 individuals across 14 European countries. Using discovery data on over 250,000 individuals and unbiased effect size estimates from 17,500 sibling pairs, we estimate that 24% (95% credible interval (CI) = 9%, 41%) and 8% (95% CI = 4%, 16%) of the captured additive genetic variance for height and BMI, respectively, reflect population genetic differences. Population genetic divergence differed significantly from that in a null model (height, P < 3.94 × 10−8; BMI, P < 5.95 × 10−4), and we find an among-population genetic correlation for tall and slender individuals (r = −0.80, 95% CI = −0.95, −0.60), consistent with correlated selection for both phenotypes. Observed differences in height among populations reflected the predicted genetic means (r = 0.51; P < 0.001), but environmental differences across Europe masked genetic differentiation for BMI (P < 0.58)."}],"author":[{"first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"first_name":"Gibran","full_name":"Hemani, Gibran","last_name":"Hemani"},{"first_name":"Carolina","last_name":"Medina-Gomez","full_name":"Medina-Gomez, Carolina"},{"last_name":"Mezzavilla","full_name":"Mezzavilla, Massimo","first_name":"Massimo"},{"first_name":"Tonu","full_name":"Esko, Tonu","last_name":"Esko"},{"first_name":"Konstantin","last_name":"Shakhbazov","full_name":"Shakhbazov, Konstantin"},{"first_name":"Joseph E","full_name":"Powell, Joseph E","last_name":"Powell"},{"last_name":"Vinkhuyzen","full_name":"Vinkhuyzen, Anna","first_name":"Anna"},{"first_name":"Sonja I","full_name":"Berndt, Sonja I","last_name":"Berndt"},{"first_name":"Stefan","last_name":"Gustafsson","full_name":"Gustafsson, Stefan"},{"full_name":"Justice, Anne E","last_name":"Justice","first_name":"Anne E"},{"first_name":"Bratati","last_name":"Kahali","full_name":"Kahali, Bratati"},{"first_name":"Adam E","full_name":"Locke, Adam E","last_name":"Locke"},{"first_name":"Tune H","full_name":"Pers, Tune H","last_name":"Pers"},{"first_name":"Sailaja","last_name":"Vedantam","full_name":"Vedantam, Sailaja"},{"last_name":"Wood","full_name":"Wood, Andrew R","first_name":"Andrew R"},{"full_name":"van Rheenen, Wouter","last_name":"van Rheenen","first_name":"Wouter"},{"first_name":"Ole A","last_name":"Andreassen","full_name":"Andreassen, Ole A"},{"first_name":"Paolo","last_name":"Gasparini","full_name":"Gasparini, Paolo"},{"first_name":"Andres","last_name":"Metspalu","full_name":"Metspalu, Andres"},{"last_name":"Berg","full_name":"Berg, Leonard H van den","first_name":"Leonard H van den"},{"full_name":"Veldink, Jan H","last_name":"Veldink","first_name":"Jan H"},{"first_name":"Fernando","last_name":"Rivadeneira","full_name":"Rivadeneira, Fernando"},{"last_name":"Werge","full_name":"Werge, Thomas M","first_name":"Thomas M"},{"first_name":"Goncalo R","full_name":"Abecasis, Goncalo R","last_name":"Abecasis"},{"full_name":"Boomsma, Dorret I","last_name":"Boomsma","first_name":"Dorret I"},{"last_name":"Chasman","full_name":"Chasman, Daniel I","first_name":"Daniel I"},{"first_name":"Eco J C","last_name":"de Geus","full_name":"de Geus, Eco J C"},{"last_name":"Frayling","full_name":"Frayling, Timothy M","first_name":"Timothy M"},{"full_name":"Hirschhorn, Joel N","last_name":"Hirschhorn","first_name":"Joel N"},{"last_name":"Hottenga","full_name":"Hottenga, Jouke Jan","first_name":"Jouke Jan"},{"first_name":"Erik","last_name":"Ingelsson","full_name":"Ingelsson, Erik"},{"full_name":"Loos, Ruth J F","last_name":"Loos","first_name":"Ruth J F"},{"last_name":"Magnusson","full_name":"Magnusson, Patrik K E","first_name":"Patrik K E"},{"first_name":"Nicholas G","full_name":"Martin, Nicholas G","last_name":"Martin"},{"full_name":"Montgomery, Grant W","last_name":"Montgomery","first_name":"Grant W"},{"full_name":"North, Kari E","last_name":"North","first_name":"Kari E"},{"first_name":"Nancy L","full_name":"Pedersen, Nancy L","last_name":"Pedersen"},{"first_name":"Timothy D","last_name":"Spector","full_name":"Spector, Timothy D"},{"first_name":"Elizabeth K","full_name":"Speliotes, Elizabeth K","last_name":"Speliotes"},{"first_name":"Michael E","full_name":"Goddard, Michael E","last_name":"Goddard"},{"last_name":"Yang","full_name":"Yang, Jian","first_name":"Jian"},{"first_name":"Peter M","full_name":"Visscher, Peter M","last_name":"Visscher"}],"status":"public","publication_status":"published","day":"14","citation":{"chicago":"Robinson, Matthew Richard, Gibran Hemani, Carolina Medina-Gomez, Massimo Mezzavilla, Tonu Esko, Konstantin Shakhbazov, Joseph E Powell, et al. “Population Genetic Differentiation of Height and Body Mass Index across Europe.” <i>Nature Genetics</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/ng.3401\">https://doi.org/10.1038/ng.3401</a>.","ieee":"M. R. Robinson <i>et al.</i>, “Population genetic differentiation of height and body mass index across Europe,” <i>Nature Genetics</i>, vol. 47, no. 11. Springer Nature, pp. 1357–1362, 2015.","apa":"Robinson, M. R., Hemani, G., Medina-Gomez, C., Mezzavilla, M., Esko, T., Shakhbazov, K., … Visscher, P. M. (2015). Population genetic differentiation of height and body mass index across Europe. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/ng.3401\">https://doi.org/10.1038/ng.3401</a>","short":"M.R. Robinson, G. Hemani, C. Medina-Gomez, M. Mezzavilla, T. Esko, K. Shakhbazov, J.E. Powell, A. Vinkhuyzen, S.I. Berndt, S. Gustafsson, A.E. Justice, B. Kahali, A.E. Locke, T.H. Pers, S. Vedantam, A.R. Wood, W. van Rheenen, O.A. Andreassen, P. Gasparini, A. Metspalu, L.H. van den Berg, J.H. Veldink, F. Rivadeneira, T.M. Werge, G.R. Abecasis, D.I. Boomsma, D.I. Chasman, E.J.C. de Geus, T.M. Frayling, J.N. Hirschhorn, J.J. Hottenga, E. Ingelsson, R.J.F. Loos, P.K.E. Magnusson, N.G. Martin, G.W. Montgomery, K.E. North, N.L. Pedersen, T.D. Spector, E.K. Speliotes, M.E. Goddard, J. Yang, P.M. Visscher, Nature Genetics 47 (2015) 1357–1362.","ista":"Robinson MR, Hemani G, Medina-Gomez C, Mezzavilla M, Esko T, Shakhbazov K, Powell JE, Vinkhuyzen A, Berndt SI, Gustafsson S, Justice AE, Kahali B, Locke AE, Pers TH, Vedantam S, Wood AR, van Rheenen W, Andreassen OA, Gasparini P, Metspalu A, Berg LH van den, Veldink JH, Rivadeneira F, Werge TM, Abecasis GR, Boomsma DI, Chasman DI, de Geus EJC, Frayling TM, Hirschhorn JN, Hottenga JJ, Ingelsson E, Loos RJF, Magnusson PKE, Martin NG, Montgomery GW, North KE, Pedersen NL, Spector TD, Speliotes EK, Goddard ME, Yang J, Visscher PM. 2015. Population genetic differentiation of height and body mass index across Europe. Nature Genetics. 47(11), 1357–1362.","mla":"Robinson, Matthew Richard, et al. “Population Genetic Differentiation of Height and Body Mass Index across Europe.” <i>Nature Genetics</i>, vol. 47, no. 11, Springer Nature, 2015, pp. 1357–62, doi:<a href=\"https://doi.org/10.1038/ng.3401\">10.1038/ng.3401</a>.","ama":"Robinson MR, Hemani G, Medina-Gomez C, et al. Population genetic differentiation of height and body mass index across Europe. <i>Nature Genetics</i>. 2015;47(11):1357-1362. doi:<a href=\"https://doi.org/10.1038/ng.3401\">10.1038/ng.3401</a>"},"type":"journal_article","_id":"7742","extern":"1","publication_identifier":{"issn":["1061-4036","1546-1718"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","quality_controlled":"1","issue":"11","publication":"Nature Genetics","date_updated":"2021-01-12T08:15:13Z","volume":47,"article_processing_charge":"No","page":"1357-1362","publisher":"Springer Nature","title":"Population genetic differentiation of height and body mass index across Europe","language":[{"iso":"eng"}],"month":"09","year":"2015","doi":"10.1038/ng.3401","article_type":"original","date_published":"2015-09-14T00:00:00Z","date_created":"2020-04-30T10:58:23Z"},{"citation":{"chicago":"Zilberman, Daniel. <i>The Human Promoter Methylome</i>. <i>Nature Genetics</i>. Vol. 39. Nature Publishing Group, 2007. <a href=\"https://doi.org/10.1038/ng0407-442\">https://doi.org/10.1038/ng0407-442</a>.","apa":"Zilberman, D. (2007). <i>The human promoter methylome</i>. <i>Nature Genetics</i> (Vol. 39, pp. 442–443). Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng0407-442\">https://doi.org/10.1038/ng0407-442</a>","ieee":"D. Zilberman, <i>The human promoter methylome</i>, vol. 39, no. 4. Nature Publishing Group, 2007, pp. 442–443.","short":"D. Zilberman, The Human Promoter Methylome, Nature Publishing Group, 2007.","ista":"Zilberman D. 2007. The human promoter methylome, Nature Publishing Group,p.","mla":"Zilberman, Daniel. “The Human Promoter Methylome.” <i>Nature Genetics</i>, vol. 39, no. 4, Nature Publishing Group, 2007, pp. 442–43, doi:<a href=\"https://doi.org/10.1038/ng0407-442\">10.1038/ng0407-442</a>.","ama":"Zilberman D. <i>The Human Promoter Methylome</i>. Vol 39. Nature Publishing Group; 2007:442-443. doi:<a href=\"https://doi.org/10.1038/ng0407-442\">10.1038/ng0407-442</a>"},"day":"01","publication_status":"published","type":"other_academic_publication","intvolume":"        39","status":"public","author":[{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"publication":"Nature Genetics","issue":"4","page":"442-443","article_processing_charge":"No","volume":39,"date_updated":"2021-12-14T08:55:46Z","extern":"1","publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"pmid":1,"_id":"9504","oa_version":"None","quality_controlled":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"04","year":"2007","doi":"10.1038/ng0407-442","date_published":"2007-04-01T00:00:00Z","title":"The human promoter methylome","external_id":{"pmid":["17392803"]},"publisher":"Nature Publishing Group","language":[{"iso":"eng"}],"department":[{"_id":"DaZi"}],"date_created":"2021-06-07T12:08:24Z"},{"publication_status":"published","citation":{"ama":"Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. <i>Nature Genetics</i>. 2006;39(1):61-69. doi:<a href=\"https://doi.org/10.1038/ng1929\">10.1038/ng1929</a>","mla":"Zilberman, Daniel, et al. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers an Interdependence between Methylation and Transcription.” <i>Nature Genetics</i>, vol. 39, no. 1, Nature Publishing Group, 2006, pp. 61–69, doi:<a href=\"https://doi.org/10.1038/ng1929\">10.1038/ng1929</a>.","short":"D. Zilberman, M. Gehring, R.K. Tran, T. Ballinger, S. Henikoff, Nature Genetics 39 (2006) 61–69.","ista":"Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2006. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genetics. 39(1), 61–69.","apa":"Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T., &#38; Henikoff, S. (2006). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. <i>Nature Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng1929\">https://doi.org/10.1038/ng1929</a>","ieee":"D. Zilberman, M. Gehring, R. K. Tran, T. Ballinger, and S. Henikoff, “Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription,” <i>Nature Genetics</i>, vol. 39, no. 1. Nature Publishing Group, pp. 61–69, 2006.","chicago":"Zilberman, Daniel, Mary Gehring, Robert K. Tran, Tracy Ballinger, and Steven Henikoff. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers an Interdependence between Methylation and Transcription.” <i>Nature Genetics</i>. Nature Publishing Group, 2006. <a href=\"https://doi.org/10.1038/ng1929\">https://doi.org/10.1038/ng1929</a>."},"author":[{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"first_name":"Mary","last_name":"Gehring","full_name":"Gehring, Mary"},{"last_name":"Tran","full_name":"Tran, Robert K.","first_name":"Robert K."},{"first_name":"Tracy","full_name":"Ballinger, Tracy","last_name":"Ballinger"},{"last_name":"Henikoff","full_name":"Henikoff, Steven","first_name":"Steven"}],"abstract":[{"text":"Cytosine methylation, a common form of DNA modification that antagonizes transcription, is found at transposons and repeats in vertebrates, plants and fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana genome at high resolution. DNA methylation covers transposons and is present within a large fraction of A. thaliana genes. Methylation within genes is conspicuously biased away from gene ends, suggesting a dependence on RNA polymerase transit. Genic methylation is strongly influenced by transcription: moderately transcribed genes are most likely to be methylated, whereas genes at either extreme are least likely. In turn, transcription is influenced by methylation: short methylated genes are poorly expressed, and loss of methylation in the body of a gene leads to enhanced transcription. Our results indicate that genic transcription and DNA methylation are closely interwoven processes.","lang":"eng"}],"volume":39,"date_updated":"2021-12-14T09:02:51Z","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"None","quality_controlled":"1","pmid":1,"_id":"9505","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"extern":"1","year":"2006","doi":"10.1038/ng1929","external_id":{"pmid":["17128275"]},"title":"Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription","type":"journal_article","day":"26","status":"public","intvolume":"        39","page":"61-69","issue":"1","publication":"Nature Genetics","article_type":"original","date_published":"2006-11-26T00:00:00Z","month":"11","language":[{"iso":"eng"}],"publisher":"Nature Publishing Group","scopus_import":"1","department":[{"_id":"DaZi"}],"date_created":"2021-06-07T12:19:31Z"}]