User profiles for Peter Shepard

Peter J. Shepard

Design Therapeutics
Verified email at designtx.com
Cited by 2094

[HTML][HTML] The SR protein family

PJ Shepard, KJ Hertel - Genome biology, 2009 - Springer
The processing of pre-mRNAs is a fundamental step required for the expression of most
metazoan genes. Members of the family of serine/arginine (SR)-rich proteins are critical …

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

PJ Shepard, EA Choi, J Lu, LA Flanagan, KJ Hertel… - Rna, 2011 - rnajournal.cshlp.org
Alternative polyadenylation (APA) of mRNAs has emerged as an important mechanism for
post-transcriptional gene regulation in higher eukaryotes. Although microarrays have recently …

[HTML][HTML] Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3' Splice Site Selection in SF3B1-mutated Cancers

C DeBoever, EM Ghia, PJ Shepard… - PLoS computational …, 2015 - journals.plos.org
Mutations in the splicing factor SF3B1 are found in several cancer types and have been
associated with various splicing defects. Using transcriptome sequencing data from chronic …

[HTML][HTML] A trichostatin A expression signature identified by TempO-Seq targeted whole transcriptome profiling

JM Yeakley, PJ Shepard, DE Goyena… - PloS one, 2017 - journals.plos.org
The use of gene expression signatures to classify compounds, identify efficacy or toxicity,
and differentiate close analogs relies on the sensitivity of the method to identify modulated …

Conserved RNA secondary structures promote alternative splicing

PJ Shepard, KJ Hertel - Rna, 2008 - rnajournal.cshlp.org
Pre-mRNA splicing is carried out by the spliceosome, which identifies exons and removes
intervening introns. Alternative splicing in higher eukaryotes results in the generation of …

[HTML][HTML] A chemical–biological similarity-based grouping of complex substances as a prototype approach for evaluating chemical alternatives

…, J Braisted, DL Gerhold, JM Yeakley, P Shepard… - Green chemistry, 2016 - pubs.rsc.org
Comparative assessment of potential human health impacts is a critical step in evaluating both
chemical alternatives and existing products on the market. Most alternatives assessments …

[HTML][HTML] Comparison of base-line and chemical-induced transcriptomic responses in HepaRG and RPTEC/TERT1 cells using TempO-Seq

…, G Ates, G Carta, A Wilmes, M Watzele, PJ Shepard… - Archives of …, 2018 - Springer
The utilisation of genome-wide transcriptomics has played a pivotal role in advancing the
field of toxicology, allowing the mapping of transcriptional signatures to chemical exposures. …

[HTML][HTML] Extraction-free whole transcriptome gene expression analysis of FFPE sections and histology-directed subareas of tissue

…, E Imler, M Gonzalez, SI Bibikov, PJ Shepard… - PLoS …, 2019 - journals.plos.org
We describe the use of a ligation-based targeted whole transcriptome expression profiling
assay, TempO-Seq, to profile formalin-fixed paraffin-embedded (FFPE) tissue, including H&E …

Efficient internal exon recognition depends on near equal contributions from the 3′ and 5′ splice sites

PJ Shepard, EA Choi, A Busch… - Nucleic acids research, 2011 - academic.oup.com
Pre-mRNA splicing is carried out by the spliceosome, which identifies exons and removes
intervening introns. In vertebrates, most splice sites are initially recognized by the …

[PDF][PDF] Aberrant DNA methylation in human iPSCs associates with MYC-binding motifs in a clone-specific manner independent of genetics

AD Panopoulos, EN Smith, AD Arias, PJ Shepard… - Cell Stem Cell, 2017 - cell.com
Induced pluripotent stem cells (iPSCs) show variable methylation patterns between lines,
some of which reflect aberrant differences relative to embryonic stem cells (ESCs). To examine …