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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...these coordinately regulated element sets are formed, and identifying driver elements will help fine-map causal elements and variants at colocalized GWAS loci (van Mierlo et al. 2023).The liver influences many human traits and diseases through its role in protein synthesis, lipid and glucose metabolism...
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Research: Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations
- Ryne C. Ramaker,
- Andrew A. Hardigan,
- Say-Tar Goh,
- E. Christopher Partridge,
- Barbara Wold,
- Sara J. Cooper,
- and Richard M. Myers
Genome Res. July 2020 30: 939-950; Published in Advance July 2, 2020, doi:10.1101/gr.260463.119
...35294, USA; 3California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, California 91125, USA ↵4 These authors contributed equally to this work. Corresponding author: rmyers@hudsonalpha.orgAbstractDNA-associated proteins (DAPs) classically regulate gene expression...
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Method: Resolving the full spectrum of human genome variation using Linked-Reads
- Patrick Marks,
- Sarah Garcia,
- Alvaro Martinez Barrio,
- Kamila Belhocine,
- Jorge Bernate,
- Rajiv Bharadwaj,
- Keith Bjornson,
- Claudia Catalanotti,
- Josh Delaney,
- Adrian Fehr,
- Ian T. Fiddes,
- Brendan Galvin,
- Haynes Heaton,
- Jill Herschleb,
- Christopher Hindson,
- Esty Holt,
- Cassandra B. Jabara,
- Susanna Jett,
- Nikka Keivanfar,
- Sofia Kyriazopoulou-Panagiotopoulou,
- Monkol Lek,
- Bill Lin,
- Adam Lowe,
- Shazia Mahamdallie,
- Shamoni Maheshwari,
- Tony Makarewicz,
- Jamie Marshall,
- Francesca Meschi,
- Christopher J. O'Keefe,
- Heather Ordonez,
- Pranav Patel,
- Andrew Price,
- Ariel Royall,
- Elise Ruark,
- Sheila Seal,
- Michael Schnall-Levin,
- Preyas Shah,
- David Stafford,
- Stephen Williams,
- Indira Wu,
- Andrew Wei Xu,
- Nazneen Rahman,
- Daniel MacArthur,
- and Deanna M. Church
Genome Res. April 2019 29: 635-645; Published in Advance March 20, 2019, doi:10.1101/gr.234443.118
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Perspective: Genomic approaches for understanding the genetics of complex disease
- William L. Lowe, Jr. and
- Timothy E. Reddy
Genome Res. October 2015 25: 1432-1441; doi:10.1101/gr.190603.115
.... PLoS Genet 10: e1004663. Below JE, Gamazon ER, Morrison JV, Konkashbaev A, Pluzhnikov A, McKeigue PM, Parra EJ, Elbein SC, Hallman DM, Nicolae DL, et al. 2011. Genome-wide association and meta-analysis in populations from Starr County, Texas, and Mexico City identify type 2 diabetes susceptibility...
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Research: A CTCF-independent role for cohesin in tissue-specific transcription
- Dominic Schmidt,
- Petra C. Schwalie,
- Caryn S. Ross-Innes,
- Antoni Hurtado,
- Gordon D. Brown,
- Jason S. Carroll,
- Paul Flicek,
- and Duncan T. Odom
Genome Res. May 2010 20: 578-588; Published in Advance March 10, 2010, doi:10.1101/gr.100479.109
..., Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, et al. 2007. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4: 651–657. Rollins RA, Korom M, Aulner N, Martens A, Dorsett D. 2004. Drosophila Nipped...
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