Nathan C Sheffield
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Explore the profile of Nathan C Sheffield including associated specialties, affiliations and a list of published articles.
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61
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4800
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Recent Articles
1.
Rymuza J, Sun Y, Zheng G, LeRoy N, Murach M, Phan N, et al.
Nucleic Acids Res
. 2024 Aug;
52(17):10119-10131.
PMID: 39180401
The amount of genomic region data continues to increase. Integrating across diverse genomic region sets requires consensus regions, which enable comparing regions across experiments, but also by necessity lose precision...
2.
Zheng G, Rymuza J, Gharavi E, LeRoy N, Zhang A, Sheffield N
NAR Genom Bioinform
. 2024 Aug;
6(3):lqae086.
PMID: 39131817
Representation learning models have become a mainstay of modern genomics. These models are trained to yield vector representations, or embeddings, of various biological entities, such as cells, genes, individuals, or...
3.
LeRoy N, Khoroshevskyi O, OBrien A, Stepien R, Arslan A, Sheffield N
Gigascience
. 2024 Jul;
13.
PMID: 38991851
Background: As biological data increase, we need additional infrastructure to share them and promote interoperability. While major effort has been put into sharing data, relatively less emphasis is placed on...
4.
Inhibition of Renin Expression Is Regulated by an Epigenetic Switch From an Active to a Poised State
Smith J, Paxton R, Medrano S, Sheffield N, Sequeira-Lopez M, Gomez R
Hypertension
. 2024 Jul;
81(9):1869-1882.
PMID: 38989586
Background: Renin-expressing cells are myoendocrine cells crucial for the maintenance of homeostasis. Renin is regulated by cAMP, p300 (histone acetyltransferase p300)/CBP (CREB-binding protein), and Brd4 (bromodomain-containing protein 4) proteins and...
5.
LeRoy N, Smith J, Zheng G, Rymuza J, Gharavi E, Brown D, et al.
NAR Genom Bioinform
. 2024 Jul;
6(3):lqae073.
PMID: 38974799
Data from the single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) are now widely available. One major computational challenge is dealing with high dimensionality and inherent sparsity, which is typically...
6.
Xiong G, LeRoy N, Bekiranov S, Sheffield N, Zhang A
Bioinformatics
. 2024 Jul;
40(7).
PMID: 38950178
Motivation: Gene set enrichment (GSE) analysis allows for an interpretation of gene expression through pre-defined gene set databases and is a critical step in understanding different phenotypes. With the rapid...
7.
Gharavi E, LeRoy N, Zheng G, Zhang A, Brown D, Sheffield N
Bioengineering (Basel)
. 2024 Mar;
11(3).
PMID: 38534537
As available genomic interval data increase in scale, we require fast systems to search them. A common approach is simple string matching to compare a search term to metadata, but...
8.
Mosquera J, Auguste G, Wong D, Turner A, Hodonsky C, Alvarez-Yela A, et al.
Cell Rep
. 2023 Nov;
42(11):113380.
PMID: 37950869
Coronary artery disease (CAD) is characterized by atherosclerotic plaque formation in the arterial wall. CAD progression involves complex interactions and phenotypic plasticity among vascular and immune cell lineages. Single-cell RNA-seq...
9.
LeRoy N, Khoroshevskyi O, OBrien A, Stepien R, Arslan A, Sheffield N
bioRxiv
. 2023 Aug;
PMID: 37645717
Background: As biological data increases, we need additional infrastructure to share it and promote interoperability. While major effort has been put into sharing data, relatively less emphasis is placed on...
10.
Martini A, Smith J, Medrano S, Finer G, Sheffield N, Sequeira-Lopez M, et al.
Circ Res
. 2023 Jul;
133(4):369-371.
PMID: 37395102
No abstract available.