---
_id: '14689'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Elizabeth
  full_name: Ing-Simmons, Elizabeth
  last_name: Ing-Simmons
- first_name: Nick N
  full_name: Machnik, Nick N
  id: 3591A0AA-F248-11E8-B48F-1D18A9856A87
  last_name: Machnik
  orcid: 0000-0001-6617-9742
- 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>'
  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>'
  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>.'
  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.'
  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.'
  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>.'
  short: E. Ing-Simmons, N.N. Machnik, J.M. Vaquerizas, Nature Genetics 55 (2023)
    2053–2055.
date_created: 2023-12-17T23:00:53Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2023-12-18T08:51:38Z
day: '01'
department:
- _id: MaRo
doi: 10.1038/s41588-023-01595-5
external_id:
  pmid:
  - '38052961'
intvolume: '        55'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 2053-2055
pmid: 1
publication: Nature Genetics
publication_identifier:
  eissn:
  - 1546-1718
  issn:
  - 1061-4036
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Reply to: Revisiting the use of structural similarity index in Hi-C'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2023'
...
---
_id: '12158'
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.'
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.
article_processing_charge: No
article_type: review
author:
- first_name: Peter
  full_name: Zeller, Peter
  last_name: Zeller
- first_name: Jake
  full_name: Yeung, Jake
  id: 123012b2-db30-11eb-b4d8-a35840c0551b
  last_name: Yeung
  orcid: 0000-0003-1732-1559
- first_name: Helena
  full_name: Viñas Gaza, Helena
  last_name: Viñas Gaza
- first_name: Buys Anton
  full_name: de Barbanson, Buys Anton
  last_name: de Barbanson
- first_name: Vivek
  full_name: Bhardwaj, Vivek
  last_name: Bhardwaj
- first_name: Maria
  full_name: Florescu, Maria
  last_name: Florescu
- first_name: Reinier
  full_name: van der Linden, Reinier
  last_name: van der Linden
- first_name: Alexander
  full_name: van Oudenaarden, Alexander
  last_name: van Oudenaarden
citation:
  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>
  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>
  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.
  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.
  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>.
  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.
date_created: 2023-01-12T12:09:09Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2023-02-27T07:48:24Z
day: '01'
ddc:
- '570'
- '000'
department:
- _id: ScienComp
doi: 10.1038/s41588-022-01260-3
file:
- access_level: open_access
  checksum: 6fdb8e34fbeea63edd0f2c6c2cc5823e
  content_type: application/pdf
  creator: dernst
  date_created: 2023-02-27T07:46:45Z
  date_updated: 2023-02-27T07:46:45Z
  file_id: '12688'
  file_name: 2023_NatureGenetics_Zeller.pdf
  file_size: 21484855
  relation: main_file
  success: 1
file_date_updated: 2023-02-27T07:46:45Z
has_accepted_license: '1'
intvolume: '        55'
keyword:
- Genetics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 333-345
publication: Nature Genetics
publication_identifier:
  eissn:
  - 1546-1718
  issn:
  - 1061-4036
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
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)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2023'
...
---
_id: '7722'
abstract:
- lang: eng
  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.
article_processing_charge: No
article_type: original
author:
- first_name: Jian
  full_name: Zeng, Jian
  last_name: Zeng
- first_name: Ronald
  full_name: de Vlaming, Ronald
  last_name: de Vlaming
- first_name: Yang
  full_name: Wu, Yang
  last_name: Wu
- first_name: Matthew Richard
  full_name: Robinson, Matthew Richard
  id: E5D42276-F5DA-11E9-8E24-6303E6697425
  last_name: Robinson
  orcid: 0000-0001-8982-8813
- first_name: Luke R.
  full_name: Lloyd-Jones, Luke R.
  last_name: Lloyd-Jones
- first_name: Loic
  full_name: Yengo, Loic
  last_name: Yengo
- first_name: Chloe X.
  full_name: Yap, Chloe X.
  last_name: Yap
- first_name: Angli
  full_name: Xue, Angli
  last_name: Xue
- first_name: Julia
  full_name: Sidorenko, Julia
  last_name: Sidorenko
- first_name: Allan F.
  full_name: McRae, Allan F.
  last_name: McRae
- first_name: Joseph E.
  full_name: Powell, Joseph E.
  last_name: Powell
- first_name: Grant W.
  full_name: Montgomery, Grant W.
  last_name: Montgomery
- first_name: Andres
  full_name: Metspalu, Andres
  last_name: Metspalu
- first_name: Tonu
  full_name: Esko, Tonu
  last_name: Esko
- first_name: Greg
  full_name: Gibson, Greg
  last_name: Gibson
- first_name: Naomi R.
  full_name: Wray, Naomi R.
  last_name: Wray
- first_name: Peter M.
  full_name: Visscher, Peter M.
  last_name: Visscher
- first_name: Jian
  full_name: Yang, Jian
  last_name: Yang
citation:
  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>
  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>
  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>.
  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.
  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.
  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>.
  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.
date_created: 2020-04-30T10:44:57Z
date_published: 2018-04-16T00:00:00Z
date_updated: 2021-01-12T08:15:06Z
day: '16'
doi: 10.1038/s41588-018-0101-4
extern: '1'
intvolume: '        50'
issue: '5'
language:
- iso: eng
month: '04'
oa_version: None
page: 746-753
publication: Nature Genetics
publication_identifier:
  issn:
  - 1061-4036
  - 1546-1718
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Signatures of negative selection in the genetic architecture of human complex
  traits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2018'
...
---
_id: '12193'
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.
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
article_type: original
author:
- first_name: James
  full_name: Walker, James
  last_name: Walker
- first_name: Hongbo
  full_name: Gao, Hongbo
  last_name: Gao
- first_name: Jingyi
  full_name: Zhang, Jingyi
  last_name: Zhang
- first_name: Billy
  full_name: Aldridge, Billy
  last_name: Aldridge
- first_name: Martin
  full_name: Vickers, Martin
  last_name: Vickers
- first_name: James D.
  full_name: Higgins, James D.
  last_name: Higgins
- first_name: Xiaoqi
  full_name: Feng, Xiaoqi
  id: e0164712-22ee-11ed-b12a-d80fcdf35958
  last_name: Feng
  orcid: 0000-0002-4008-1234
citation:
  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>
  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>
  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>.
  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.
  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>.
  short: J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng,
    Nature Genetics 50 (2017) 130–137.
date_created: 2023-01-16T09:18:05Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2023-10-18T07:21:53Z
day: '18'
department:
- _id: XiFe
doi: 10.1038/s41588-017-0008-5
external_id:
  pmid:
  - '29255257'
intvolume: '        50'
issue: '1'
keyword:
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/
month: '12'
oa: 1
oa_version: None
page: 130-137
pmid: 1
publication: Nature Genetics
publication_identifier:
  eissn:
  - 1546-1718
  issn:
  - 1061-4036
publication_status: published
publisher: Nature Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2017'
...
---
_id: '7737'
abstract:
- lang: eng
  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.
article_processing_charge: No
article_type: original
author:
- first_name: Zhihong
  full_name: Zhu, Zhihong
  last_name: Zhu
- first_name: Futao
  full_name: Zhang, Futao
  last_name: Zhang
- first_name: Han
  full_name: Hu, Han
  last_name: Hu
- first_name: Andrew
  full_name: Bakshi, Andrew
  last_name: Bakshi
- first_name: Matthew Richard
  full_name: Robinson, Matthew Richard
  id: E5D42276-F5DA-11E9-8E24-6303E6697425
  last_name: Robinson
  orcid: 0000-0001-8982-8813
- first_name: Joseph E
  full_name: Powell, Joseph E
  last_name: Powell
- first_name: Grant W
  full_name: Montgomery, Grant W
  last_name: Montgomery
- first_name: Michael E
  full_name: Goddard, Michael E
  last_name: Goddard
- first_name: Naomi R
  full_name: Wray, Naomi R
  last_name: Wray
- first_name: Peter M
  full_name: Visscher, Peter M
  last_name: Visscher
- first_name: Jian
  full_name: Yang, Jian
  last_name: Yang
citation:
  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>
  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>
  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>.
  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.
  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>.
  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.
date_created: 2020-04-30T10:50:26Z
date_published: 2016-03-28T00:00:00Z
date_updated: 2021-01-12T08:15:11Z
day: '28'
doi: 10.1038/ng.3538
extern: '1'
intvolume: '        48'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1038/ng.3538
month: '03'
oa: 1
oa_version: Published Version
page: 481-487
publication: Nature Genetics
publication_identifier:
  issn:
  - 1061-4036
  - 1546-1718
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Integration of summary data from GWAS and eQTL studies predicts complex trait
  gene targets
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2016'
...
---
_id: '7742'
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).
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
  full_name: Robinson, Matthew Richard
  id: E5D42276-F5DA-11E9-8E24-6303E6697425
  last_name: Robinson
  orcid: 0000-0001-8982-8813
- first_name: Gibran
  full_name: Hemani, Gibran
  last_name: Hemani
- first_name: Carolina
  full_name: Medina-Gomez, Carolina
  last_name: Medina-Gomez
- first_name: Massimo
  full_name: Mezzavilla, Massimo
  last_name: Mezzavilla
- first_name: Tonu
  full_name: Esko, Tonu
  last_name: Esko
- first_name: Konstantin
  full_name: Shakhbazov, Konstantin
  last_name: Shakhbazov
- first_name: Joseph E
  full_name: Powell, Joseph E
  last_name: Powell
- first_name: Anna
  full_name: Vinkhuyzen, Anna
  last_name: Vinkhuyzen
- first_name: Sonja I
  full_name: Berndt, Sonja I
  last_name: Berndt
- first_name: Stefan
  full_name: Gustafsson, Stefan
  last_name: Gustafsson
- first_name: Anne E
  full_name: Justice, Anne E
  last_name: Justice
- first_name: Bratati
  full_name: Kahali, Bratati
  last_name: Kahali
- 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
  full_name: Vedantam, Sailaja
  last_name: Vedantam
- first_name: Andrew R
  full_name: Wood, Andrew R
  last_name: Wood
- first_name: Wouter
  full_name: van Rheenen, Wouter
  last_name: van Rheenen
- first_name: Ole A
  full_name: Andreassen, Ole A
  last_name: Andreassen
- first_name: Paolo
  full_name: Gasparini, Paolo
  last_name: Gasparini
- first_name: Andres
  full_name: Metspalu, Andres
  last_name: Metspalu
- first_name: Leonard H van den
  full_name: Berg, Leonard H van den
  last_name: Berg
- first_name: Jan H
  full_name: Veldink, Jan H
  last_name: Veldink
- first_name: Fernando
  full_name: Rivadeneira, Fernando
  last_name: Rivadeneira
- first_name: Thomas M
  full_name: Werge, Thomas M
  last_name: Werge
- first_name: Goncalo R
  full_name: Abecasis, Goncalo R
  last_name: Abecasis
- first_name: Dorret I
  full_name: Boomsma, Dorret I
  last_name: Boomsma
- first_name: Daniel I
  full_name: Chasman, Daniel I
  last_name: Chasman
- first_name: Eco J C
  full_name: de Geus, Eco J C
  last_name: de Geus
- first_name: Timothy M
  full_name: Frayling, Timothy M
  last_name: Frayling
- first_name: Joel N
  full_name: Hirschhorn, Joel N
  last_name: Hirschhorn
- first_name: Jouke Jan
  full_name: Hottenga, Jouke Jan
  last_name: Hottenga
- first_name: Erik
  full_name: Ingelsson, Erik
  last_name: Ingelsson
- first_name: Ruth J F
  full_name: Loos, Ruth J F
  last_name: Loos
- first_name: Patrik K E
  full_name: Magnusson, Patrik K E
  last_name: Magnusson
- first_name: Nicholas G
  full_name: Martin, Nicholas G
  last_name: Martin
- first_name: Grant W
  full_name: Montgomery, Grant W
  last_name: Montgomery
- first_name: Kari E
  full_name: North, Kari E
  last_name: North
- first_name: Nancy L
  full_name: Pedersen, Nancy L
  last_name: Pedersen
- first_name: Timothy D
  full_name: Spector, Timothy D
  last_name: Spector
- first_name: Elizabeth K
  full_name: Speliotes, Elizabeth K
  last_name: Speliotes
- first_name: Michael E
  full_name: Goddard, Michael E
  last_name: Goddard
- first_name: Jian
  full_name: Yang, Jian
  last_name: Yang
- first_name: Peter M
  full_name: Visscher, Peter M
  last_name: Visscher
citation:
  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>
  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>
  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.
  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>.
  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.
date_created: 2020-04-30T10:58:23Z
date_published: 2015-09-14T00:00:00Z
date_updated: 2021-01-12T08:15:13Z
day: '14'
doi: 10.1038/ng.3401
extern: '1'
intvolume: '        47'
issue: '11'
language:
- iso: eng
month: '09'
oa_version: None
page: 1357-1362
publication: Nature Genetics
publication_identifier:
  issn:
  - 1061-4036
  - 1546-1718
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Population genetic differentiation of height and body mass index across Europe
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2015'
...
---
_id: '9504'
article_processing_charge: No
author:
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
citation:
  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>
  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>
  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>.
  ieee: D. Zilberman, <i>The human promoter methylome</i>, vol. 39, no. 4. Nature
    Publishing Group, 2007, pp. 442–443.
  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>.
  short: D. Zilberman, The Human Promoter Methylome, Nature Publishing Group, 2007.
date_created: 2021-06-07T12:08:24Z
date_published: 2007-04-01T00:00:00Z
date_updated: 2021-12-14T08:55:46Z
day: '01'
department:
- _id: DaZi
doi: 10.1038/ng0407-442
extern: '1'
external_id:
  pmid:
  - '17392803'
intvolume: '        39'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 442-443
pmid: 1
publication: Nature Genetics
publication_identifier:
  eissn:
  - 1546-1718
  issn:
  - 1061-4036
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
status: public
title: The human promoter methylome
type: other_academic_publication
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 39
year: '2007'
...
---
_id: '9505'
abstract:
- lang: eng
  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.'
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
- first_name: Mary
  full_name: Gehring, Mary
  last_name: Gehring
- first_name: Robert K.
  full_name: Tran, Robert K.
  last_name: Tran
- first_name: Tracy
  full_name: Ballinger, Tracy
  last_name: Ballinger
- first_name: Steven
  full_name: Henikoff, Steven
  last_name: Henikoff
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>
  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>
  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>.
  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.
  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.
  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.
date_created: 2021-06-07T12:19:31Z
date_published: 2006-11-26T00:00:00Z
date_updated: 2021-12-14T09:02:51Z
day: '26'
department:
- _id: DaZi
doi: 10.1038/ng1929
extern: '1'
external_id:
  pmid:
  - '17128275'
intvolume: '        39'
issue: '1'
language:
- iso: eng
month: '11'
oa_version: None
page: 61-69
pmid: 1
publication: Nature Genetics
publication_identifier:
  eissn:
  - 1546-1718
  issn:
  - 1061-4036
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence
  between methylation and transcription
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 39
year: '2006'
...