Searching journal content for articles similar to Whalen and Pollard 29 (3): 334.

Displaying results 1-10 of 122

For checked items

view abstracts
download to citation manager

Select this article
Method: The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects
- Maureen Pittman,
- Kihyun Lee,
- Franco Felix,
- Yu Huang,
- Adrienne Lam,
- Mauro W. Costa,
- Deepak Srivastava,
- and Katherine S. Pollard
Genome Res. February 2026 36: 330-347; Published in Advance December 12, 2025, doi:10.1101/gr.281141.125
...and chromatin modifiers suggests that they interact (either directly or indirectly) in gene regulatory networks that are necessary for normal heart development. Genes not annotated with these functions, such as COL6A3 and MYO9A, could be target genes or have upstream or downstream regulatory functions...
OPEN ACCESS ARTICLE
Select this article
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
...); an increased multiple testing burden per peak resulted in fewer caQTLs compared with the 1 kb analysis. After clumping the lead variants (linkage disequilibrium [LD] r2 > 0.9), we identified 2126 signals that are associated with two or more caPeaks (Supplemental Table 9), corresponding to 6077 unique ca...
Select this article
Method: FIND: difFerential chromatin INteractions Detection using a spatial Poisson process
- Mohamed Nadhir Djekidel,
- Yang Chen,
- and Michael Q. Zhang
Genome Res. March 2018 28: 412-422; Published in Advance February 12, 2018, doi:10.1101/gr.212241.116
...in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local...
OPEN ACCESS ARTICLE
Select this article
Research: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
- Angelo A. Ruggieri,
- Luca Livraghi,
- James J. Lewis,
- Elizabeth Evans,
- Francesco Cicconardi,
- Laura Hebberecht,
- Yadira Ortiz-Ruiz,
- Stephen H. Montgomery,
- Alfredo Ghezzi,
- José Arcadio Rodriguez-Martinez,
- Chris D. Jiggins,
- W. Owen McMillan,
- Brian A. Counterman,
- Riccardo Papa,
- and Steven M. Van Belleghem
Genome Res. October 2022 32: 1862-1875; Published in Advance September 15, 2022, doi:10.1101/gr.276839.122
...increase their likelihood of being involved in maladaptation (Collins et al. 2020). However, there are a growing number of examples of an important role of SVs in adaptive innovations (Lucek et al. 2019; Wellenreuther et al. 2019). For example, increased linkage disequilibrium and recombination suppression...
Select this article
Method: Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning
- Zeynep Kalender Atak,
- Ibrahim Ihsan Taskiran,
- Jonas Demeulemeester,
- Christopher Flerin,
- David Mauduit,
- Liesbeth Minnoye,
- Gert Hulselmans,
- Valerie Christiaens,
- Ghanem-Elias Ghanem,
- Jasper Wouters,
- and Stein Aerts
Genome Res. June 2021 31: 1082-1096; Published in Advance April 8, 2021, doi:10.1101/gr.260851.120
...of a mutation on gene regulation. Here we generate phased whole s with matched chromatin accessibility, histone modifications, and gene expression for 10 melanoma cell lines. We find that training a specialized deep learning model, called DeepMEL2, on melanoma chromatin accessibility data can capture...
OPEN ACCESS ARTICLE
Select this article
Research: Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits
- Olivia Corradin,
- Alina Saiakhova,
- Batool Akhtar-Zaidi,
- Lois Myeroff,
- Joseph Willis,
- Richard Cowper-Sal·lari,
- Mathieu Lupien,
- Sanford Markowitz,
- and Peter C. Scacheri
Genome Res. January 2014 24: 1-13; Published in Advance November 6, 2013, doi:10.1101/gr.164079.113
...Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits Olivia Corradin 1 , Alina Saiakhova 1 , Batool Akhtar-Zaidi 1 , Lois Myeroff 2 , Joseph...
Select this article
Research: Leveraging mouse chromatin data for heritability enrichment informs common disease architecture and reveals cortical layer contributions to schizophrenia
- Paul W. Hook and
- Andrew S. McCallion
Genome Res. April 2020 30: 528-539; Published in Advance April 17, 2020, doi:10.1101/gr.256578.119
...the cellular context in which disease-associated variants act. Here, we use open chromatin profiles from discrete mouse cell populations to address this challenge. We applied stratified linkage disequilibrium score regression and evaluated heritability enrichment in 64 -wide association studies, emphasizing...
Select this article
Resource: An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
- Chong Li,
- Marc Jan Bonder,
- Sabriya Syed,
- Matthew Jensen,
- Human Genome Structural Variation Consortium (HGSVC),
- HGSVC Functional Analysis Working Group,
- Mark B. Gerstein,
- Michael C. Zody,
- Mark J.P. Chaisson,
- Michael E. Talkowski,
- Tobias Marschall,
- Jan O. Korbel,
- Evan E. Eichler,
- Charles Lee,
- and Xinghua Shi
Genome Res. December 2024 34: 2304-2318; Published in Advance December 5, 2024, doi:10.1101/gr.279419.124
...regulation resulting from pathogenic large genomic rearrangements or structural variants (SVs), including deletions, insertions, inversions, and duplications (Shanta et al. 2020). These genomic rearrangements can disturb the normal 3D structure of the and lead to aberrant interactions between chromatin...
Select this article
Research: Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
- Fangyuan Yang,
- Li-Jun Cao,
- Petr Nguyen,
- Zhong-Zheng Ma,
- Jin-Cui Chen,
- Wei Song,
- and Shu-Jun Wei
Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124
..., and plotted in bin sizes of 20 kb and 50 kb using HiCExplorer v3.7.3 (Wolff et al. 2020). The 20 kb contact matrix of F(20 + 17,Z) of G. molesta was fed into a 3DMax model in GenomeFlow v2.0 (Trieu et al. 2019), with 2000 interactions and a conversion factor of 0.84 to construct a 3D model of the chromatin...
Select this article
Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
- Karine Choquet,
- Louis-Philippe Chaumont,
- Simon Bache,
- Autum R. Baxter-Koenigs,
- and L. Stirling Churchman
Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
...(Fig. 2A). Moreover, RPS2 intron 3 was removed before introns 4 and 5 on one allele, while this order was reversed on the second allele in five different LCLs (Fig. 2B). Multiple SNPs in linkage disequilibrium were associated with these RPS2 allele-specific splicing orders (Fig. 2B). The majority were...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Whalen and Pollard 29 (3): 334.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: