Benjamin R Doughty
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Explore the profile of Benjamin R Doughty including associated specialties, affiliations and a list of published articles.
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Recent Articles
1.
Schaepe J, Fries T, Doughty B, Crocker O, Hinks M, Marklund E, et al.
bioRxiv
. 2025 Feb;
PMID: 39975040
The molecular details governing transcription factor (TF) binding and the formation of accessible chromatin are not yet quantitatively understood - including how sequence context modulates affinity, how TFs search DNA,...
2.
Doughty B, Hinks M, Schaepe J, Marinov G, Thurm A, Rios-Martinez C, et al.
Nature
. 2024 Nov;
636(8043):745-754.
PMID: 39567683
The binding of multiple transcription factors (TFs) to genomic enhancers drives gene expression in mammalian cells. However, the molecular details that link enhancer sequence to TF binding, promoter state and...
3.
Guckelberger P, Doughty B, Munson G, Rao S, Tan Y, Cai X, et al.
bioRxiv
. 2024 Jul;
PMID: 39026740
Enhancers are key drivers of gene regulation thought to act via 3D physical interactions with the promoters of their target genes. However, genome-wide depletions of architectural proteins such as cohesin...
4.
Yao D, Tycko J, Oh J, Bounds L, Gosai S, Lataniotis L, et al.
Nat Methods
. 2024 Mar;
21(4):723-734.
PMID: 38504114
The ENCODE Consortium's efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to investigate cis-regulatory mechanisms....
5.
Doughty B, Hinks M, Schaepe J, Marinov G, Thurm A, Rios-Martinez C, et al.
bioRxiv
. 2024 Feb;
PMID: 38352517
The binding of multiple transcription factors (TFs) to genomic enhancers activates gene expression in mammalian cells. However, the molecular details that link enhancer sequence to TF binding, promoter state, and...
6.
Martyn G, Montgomery M, Jones H, Guo K, Doughty B, Linder J, et al.
bioRxiv
. 2024 Jan;
PMID: 38187584
Regulatory DNA sequences within enhancers and promoters bind transcription factors to encode cell type-specific patterns of gene expression. However, the regulatory effects and programmability of such DNA sequences remain difficult...
7.
Gschwind A, Mualim K, Karbalayghareh A, Sheth M, Dey K, Jagoda E, et al.
bioRxiv
. 2023 Nov;
PMID: 38014075
Identifying transcriptional enhancers and their target genes is essential for understanding gene regulation and the impact of human genetic variation on disease. Here we create and evaluate a resource of...
8.
Fujimori T, Rios-Martinez C, Thurm A, Hinks M, Doughty B, Sinha J, et al.
bioRxiv
. 2023 Oct;
PMID: 37873344
Repressive chromatin modifications are thought to compact chromatin to silence transcription. However, it is unclear how chromatin structure changes during silencing and epigenetic memory formation. We measured gene expression and...
9.
Nasser J, Bergman D, Fulco C, Guckelberger P, Doughty B, Patwardhan T, et al.
Nature
. 2021 Apr;
593(7858):238-243.
PMID: 33828297
Genome-wide association studies (GWAS) have identified thousands of noncoding loci that are associated with human diseases and complex traits, each of which could reveal insights into the mechanisms of disease....
10.
Marshall J, Doughty B, Subramanian V, Guckelberger P, Wang Q, Chen L, et al.
Proc Natl Acad Sci U S A
. 2020 Dec;
117(52):33404-33413.
PMID: 33376219
Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here...