Shaleen Shrestha
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Explore the profile of Shaleen Shrestha including associated specialties, affiliations and a list of published articles.
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10
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387
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Recent Articles
1.
Lambourne L, Mattioli K, Santoso C, Sheynkman G, Inukai S, Kaundal B, et al.
bioRxiv
. 2024 Apr;
PMID: 38617209
Most human Transcription factors (TFs) genes encode multiple protein isoforms differing in DNA binding domains, effector domains, or other protein regions. The global extent to which this results in functional...
2.
Haley J, Jones J, Petraki S, Callander M, Shrestha S, Springfield E, et al.
Cell Gene Ther Insights
. 2023 Sep;
8(10):1287-1300.
PMID: 37712070
Demand for gene therapies capable of treating previously inaccessible targets has risen precipitously in the past decade. Adeno-associated viruses (AAVs) are the preferred vector for gene delivery because of their...
3.
Shrestha S, Sewell J, Santoso C, Forchielli E, Carrasco Pro S, Martinez M, et al.
Genome Res
. 2019 Sep;
29(9):1533-1544.
PMID: 31481462
Identifying transcription factor (TF) binding to noncoding variants, uncharacterized DNA motifs, and repetitive genomic elements has been technically and computationally challenging. Current experimental methods, such as chromatin immunoprecipitation, generally test...
4.
Shrestha S, Liu X, Santoso C, Fuxman Bass J
J Vis Exp
. 2019 Feb;
(144).
PMID: 30799854
Identifying the sets of transcription factors (TFs) that regulate each human gene is a daunting task that requires integrating numerous experimental and computational approaches. One such method is the yeast...
5.
Tamburino A, Kaymak E, Shrestha S, Holdorf A, Ryder S, Walhout A
Translation (Austin)
. 2017 Jul;
5(1):e1295130.
PMID: 28702278
Interactions between RNA binding proteins (RBPs) and mRNAs are critical to post-transcriptional gene regulation. Eukaryotic genomes encode thousands of mRNAs and hundreds of RBPs. However, in contrast to interactions between...
6.
Garcia-Gonzalez A, Ritter A, Shrestha S, Andersen E, Yilmaz L, Walhout A
Cell
. 2017 Apr;
169(3):431-441.e8.
PMID: 28431244
The human microbiota greatly affects physiology and disease; however, the contribution of bacteria to the response to chemotherapeutic drugs remains poorly understood. Caenorhabditis elegans and its bacterial diet provide a...
7.
Fuxman Bass J, Pons C, Kozlowski L, Reece-Hoyes J, Shrestha S, Holdorf A, et al.
Mol Syst Biol
. 2016 Oct;
12(10):884.
PMID: 27777270
Transcription factors (TFs) play a central role in controlling spatiotemporal gene expression and the response to environmental cues. A comprehensive understanding of gene regulation requires integrating physical protein-DNA interactions (PDIs)...
8.
Fuxman Bass J, Sahni N, Shrestha S, Garcia-Gonzalez A, Mori A, Bhat N, et al.
Cell
. 2015 Apr;
161(3):661-673.
PMID: 25910213
Gene regulatory networks (GRNs) comprising interactions between transcription factors (TFs) and regulatory loci control development and physiology. Numerous disease-associated mutations have been identified, the vast majority residing in non-coding regions...
9.
Reece-Hoyes J, Pons C, Diallo A, Mori A, Shrestha S, Kadreppa S, et al.
Mol Cell
. 2013 Jun;
51(1):116-27.
PMID: 23791784
Gene duplication results in two identical paralogs that diverge through mutation, leading to loss or gain of interactions with other biomolecules. Here, we comprehensively characterize such network rewiring for C. ...
10.
Reece-Hoyes J, Diallo A, Lajoie B, Kent A, Shrestha S, Kadreppa S, et al.
Nat Methods
. 2011 Nov;
8(12):1059-64.
PMID: 22037705
A major challenge in systems biology is to understand the gene regulatory networks that drive development, physiology and pathology. Interactions between transcription factors and regulatory genomic regions provide the first...