Zobrazeno 1 - 10
of 20
pro vyhledávání: '"Bryce van de Geijn"'
Autor:
Kushal K. Dey, Bryce van de Geijn, Samuel Sungil Kim, Farhad Hormozdiari, David R. Kelley, Alkes L. Price
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-9 (2020)
Deep learning models have shown great promise in predicting regulatory effects from DNA sequence. Here the authors evaluate sequence-based epigenomic deep learning models and conclude that these models are not yet ready to inform our knowledge of hum
Externí odkaz:
https://doaj.org/article/e966c41c45b24c86a35cad7f34f42b80
Autor:
Farhad Hormozdiari, Bryce van de Geijn, Joseph Nasser, Omer Weissbrod, Steven Gazal, Chelsea J. -T. Ju, Luke O’ Connor, Margaux L. A. Hujoel, Jesse Engreitz, Fereydoun Hormozdiari, Alkes L. Price
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-8 (2019)
Transposable elements (TE) make up a large component of the human genome and have been shown to contribute to human diseases. Here, Hormozdiari et al. estimate the contribution of TEs to the heritability of 41 complex traits and diseases and find enr
Externí odkaz:
https://doaj.org/article/2162e007b86c49c889aa730a2d6a4779
Autor:
Nicholas E Banovich, Xun Lan, Graham McVicker, Bryce van de Geijn, Jacob F Degner, John D Blischak, Julien Roux, Jonathan K Pritchard, Yoav Gilad
Publikováno v:
PLoS Genetics, Vol 10, Iss 9, p e1004663 (2014)
DNA methylation is an important epigenetic regulator of gene expression. Recent studies have revealed widespread associations between genetic variation and methylation levels. However, the mechanistic links between genetic variation and methylation r
Externí odkaz:
https://doaj.org/article/db705c820c5a448098b2475dcb0345b0
Autor:
Kushal K. Dey, Steven Gazal, Bryce van de Geijn, Samuel Sungil Kim, Joseph Nasser, Jesse M. Engreitz, Alkes L. Price
Publikováno v:
Cell genomics. 2(7)
We assess contributions to autoimmune disease of genes whose regulation is driven by enhancer regions (enhancer-related) and genes that regulate other genes in
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::db93ca07fc31a06508fe3e3c79e124d8
https://pubmed.ncbi.nlm.nih.gov/35873673
https://pubmed.ncbi.nlm.nih.gov/35873673
Autor:
Nikola Teslovich, Yukinori Okada, Kazuyoshi Ishigaki, Soumya Raychaudhuri, Kazuhiko Yamamoto, Emma E. Davenport, Steven Gazal, Yang Luo, Bryce van de Geijn, Harm-Jan Westra, Tiffany Amariuta, Alkes L. Price
Publikováno v:
American Journal of Human Genetics
Despite significant progress in annotating the genome with experimental methods, much of the regulatory noncoding genome remains poorly defined. Here we assert that regulatory elements may be characterized by leveraging local epigenomic signatures wh
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::94c72e0d34c0b932e80db09d57317600
https://doi.org/10.1016/j.ajhg.2019.03.012
https://doi.org/10.1016/j.ajhg.2019.03.012
Autor:
Samuel S. Kim, Bryce van de Geijn, Alkes L. Price, Farhad Hormozdiari, David R. Kelley, Kushal K. Dey
Publikováno v:
Nature Communications
Nature Communications, Vol 11, Iss 1, Pp 1-9 (2020)
Nature Communications, Vol 11, Iss 1, Pp 1-9 (2020)
Deep learning models have shown great promise in predicting regulatory effects from DNA sequence, but their informativeness for human complex diseases is not fully understood. Here, we evaluate genome-wide SNP annotations from two previous deep learn
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e192a7514f078f85162a1e848d05ac78
https://doi.org/10.1038/s41467-020-18515-4
https://doi.org/10.1038/s41467-020-18515-4
Autor:
Kushal K. Dey, Joseph Nasser, Samuel S. Kim, Steven Gazal, Bryce van de Geijn, Jesse M. Engreitz, Alkes L. Price
Gene regulation is known to play a fundamental role in human disease, but mechanisms of regulation vary greatly across genes. Here, we explore the contributions to disease of two types of genes: genes whose regulation is driven by enhancer regions as
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c1684006d44f851668a362137aee02b3
https://doi.org/10.1101/2020.09.02.279059
https://doi.org/10.1101/2020.09.02.279059
Autor:
Luke J. O’Connor, Alkes L. Price, Pier Francesco Palamara, David R. Kelley, Jacob C. Ulirsch, Dylan Kotliar, Luca Pinello, Farhad Hormozdiari, Ryan P. Adams, Bryce van de Geijn, Joseph Nasser, Sharon R. Grossman, Po-Ru Loh, Steven Gazal, Gaurav Bhatia, Nick Patterson, Hilary K. Finucane, Yakir A. Reshef, Alexander Gusev
Publikováno v:
Nature genetics
Biological interpretation of GWAS data frequently involves analyzing unsigned genomic annotations comprising SNPs involved in a biological process and assessing enrichment for disease signal. However, it is often possible to generate signed annotatio
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2d9a7f3c0c21ae1590324f0f3e31deed
https://doi.org/10.1038/s41588-018-0196-7
https://doi.org/10.1038/s41588-018-0196-7
Annotations capturing cell type-specific TF binding explain a large fraction of disease heritability
Autor:
Alexander Gusev, Bryce van de Geijn, Yakir A. Reshef, Xuanyao Liu, Farhad Hormozdiari, Hilary K. Finucane, Steven Gazal, Tiffany Amariuta, Gleb Kichaev, Po-Ru Loh, Alkes L. Price, Soumya Raychauduri
Publikováno v:
Hum Mol Genet
Regulatory variation plays a major role in complex disease and that cell type-specific binding of transcription factors (TF) is critical to gene regulation. However, assessing the contribution of genetic variation in TF-binding sites to disease herit
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4c9fcfb6fdd73d7973f90f7b3e094ebd
https://europepmc.org/articles/PMC7206853/
https://europepmc.org/articles/PMC7206853/
Autor:
Margaux L. A. Hujoel, Fereydoun Hormozdiari, Joseph Nasser, Chelsea J.-T. Ju, Farhad Hormozdiari, Jesse M. Engreitz, Steven Gazal, Alkes L. Price, Bryce van de Geijn, Luke J. O’Connor, Omer Weissbrod
Publikováno v:
Nature communications, vol 10, iss 1
Nature Communications
Nature Communications, Vol 10, Iss 1, Pp 1-8 (2019)
Nature Communications
Nature Communications, Vol 10, Iss 1, Pp 1-8 (2019)
Transposable elements (TE) comprise roughly half of the human genome. Though initially derided as junk DNA, they have been widely hypothesized to contribute to the evolution of gene regulation. However, the contribution of TE to the genetic architect
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::65219098ceed078df8fe953325387fe9
https://escholarship.org/uc/item/4xg9q40m
https://escholarship.org/uc/item/4xg9q40m