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Resource: PWAS Hub for exploring gene-based associations of common complex diseases
- Guy Kelman,
- Roei Zucker,
- Nadav Brandes,
- and Michal Linial
Genome Res. October 2024 34: 1674-1686; Published in Advance October 15, 2024, doi:10.1101/gr.278916.123
...in recent years due to the increased scale of resources with rich genomic and clinical data (Bernabeu et al. 2021).The PWAS Hub leverages the results of PWAS for most of the abundant complex diseases and conditions represented in UKB (e.g., asthma, hypertension, type 2 diabetes). It encompasses the human...
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Research: Genomic redistribution of GR monomers and dimers mediates transcriptional response to exogenous glucocorticoid in vivo
- Hee-Woong Lim,
- N. Henriette Uhlenhaut,
- Alexander Rauch,
- Juliane Weiner,
- Sabine Hübner,
- Norbert Hübner,
- Kyoung-Jae Won,
- Mitchell A. Lazar,
- Jan Tuckermann,
- and David J. Steger
Genome Res. June 2015 25: 836-844; Published in Advance May 8, 2015, doi:10.1101/gr.188581.114
...Genomic redistribution of GR monomers and dimers mediates transcriptional response to exogenous glucocorticoid in vivo Hee-Woong Lim 1 , 2 , 9 , N. Henriette Uhlenhaut 3 , 4 , 9 , Alexander Rauch 5 , 10 , Juliane Weiner 5 , Sabine Hübner...
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Method: BayesRVAT enhances rare-variant association testing through Bayesian aggregation of functional annotations
- Antonio Nappi,
- Liubov Shilova,
- Theofanis Karaletsos,
- Na Cai,
- and Francesco Paolo Casale
Genome Res. December 2025 35: 2682-2690; Published in Advance October 24, 2025, doi:10.1101/gr.280689.125
...RVAT to analyze eight disease traits with binary notations: type 2 diabetes, atrial fibrillation, coronary artery disease, asthma, hypertension, age-related macular degeneration (AMD) and other retinal diseases, glaucoma, and cataract (Methods). For comparison, we also evaluated logistic regression-based burden...
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Method: Modeling gene interactions in polygenic prediction via geometric deep learning
- Han Li,
- Jianyang Zeng,
- Michael P. Snyder,
- and Sai Zhang
Genome Res. January 2025 35: 178-187; Published in Advance November 19, 2024, doi:10.1101/gr.279694.124
...for Industries of the Future, Westlake University, Hangzhou, 310030, Zhejiang, China; 4Department of Genetics, Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, California 94304, USA; 5Department of Epidemiology, University of Florida, Gainesville, Florida 32603...
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Research: Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution
- Justyna A. Resztak,
- Julong Wei,
- Samuele Zilioli,
- Edward Sendler,
- Adnan Alazizi,
- Henriette E. Mair-Meijers,
- Peijun Wu,
- Xiaoquan Wen,
- Richard B. Slatcher,
- Xiang Zhou,
- Francesca Luca,
- and Roger Pique-Regi
Genome Res. June 2023 33: 839-856; Published in Advance July 13, 2023, doi:10.1101/gr.276765.122
...to this work. Corresponding authors: fluca@wayne.edu, rpique@wayne.eduAbstractSynthetic glucocorticoids, such as dexamethasone, have been used as a treatment for many immune conditions, such as asthma and, more recently, severe COVID-19. Single-cell data can capture more fine-grained details on transcriptional...
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Resource: Instrumenting the health care enterprise for discovery research in the genomic era
- Shawn Murphy,
- Susanne Churchill,
- Lynn Bry,
- Henry Chueh,
- Scott Weiss,
- Ross Lazarus,
- Qing Zeng,
- Anil Dubey,
- Vivian Gainer,
- Michael Mendis,
- John Glaser,
- and Isaac Kohane
Genome Res. September 2009 19: 1675-1681; Published in Advance July 14, 2009, doi:10.1101/gr.094615.109
...in Huntington disease in Fig. 3). It can also be used to identify rare events such as Steven Johnson syndrome (5284 cases returned to the health system this year of those identified in prior years) to allow genomic study of such events. Phenotyping In the asthma DBP, HITEx was used to extract principal...
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PERSPECTIVE: Genomic medicine in Mexico: Initial steps and the road ahead
- Gerardo Jimenez-Sanchez,
- Irma Silva-Zolezzi,
- Alfredo Hidalgo,
- and Santiago March
Genome Res. August 2008 18: 1191-1198; doi:10.1101/gr.065359.107
...Genomic medicine in Mexico: Initial steps and the road ahead Gerardo Jimenez-Sanchez 1 , Irma Silva-Zolezzi , Alfredo Hidalgo , and Santiago March National Institute of Genomic Medicine, Mexico D.F. 01900, Mexico Abstract Mexico...
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Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
- Paras Verma,
- Deeksha Thakur,
- Deepanshi Awasthi,
- and Shashi Bhushan Pandit
Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
...remains limited owing to dearth of subsequent proteogenomic consequences. To coalesce the genomic information embedded in exons with isoform sequences, we present an innovative framework, “Exon Nomenclature And Classification of Transcripts” (ENACT). This centralizes exonic loci such that protein sequence...
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Method: A statistical physics approach for disease module detection
- Xu-Wen Wang,
- Dandi Qiao,
- Michael H. Cho,
- Dawn L. DeMeo,
- Edwin K. Silverman,
- and Yang-Yu Liu
Genome Res. October 2022 32: 1918-1929; Published in Advance October 11, 2022, doi:10.1101/gr.276690.122
...of computational efficiency, connectivity of disease modules, and robustness to the interactome incompleteness.Complex diseases are believed to be caused, among other factors, by combinations of molecular alterations affecting cellular systems (Cho et al. 2012). Integration of disease-related genomics, epigenomics...
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Letter: Global distribution of genomic diversity underscores rich complex history of continental human populations
- Adam Auton,
- Katarzyna Bryc,
- Adam R. Boyko,
- Kirk E. Lohmueller,
- John Novembre,
- Andy Reynolds,
- Amit Indap,
- Mark H. Wright,
- Jeremiah D. Degenhardt,
- Ryan N. Gutenkunst,
- Karen S. King,
- Matthew R. Nelson,
- and Carlos D. Bustamante
Genome Res. May 2009 19: 795-803; Published in Advance February 13, 2009, doi:10.1101/gr.088898.108
...Global distribution of genomic diversity underscores rich complex history of continental human populations Adam Auton 1 , Katarzyna Bryc 1 , Adam R. Boyko 1 , Kirk E. Lohmueller 1 , John Novembre 2 , Andy Reynolds 1 , Amit...

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