Erin R. Reichenberger
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View article: <i>KEAP1</i> mutations activate the NRF2 pathway to drive cell growth and migration, and attenuate drug response in thyroid cancer
<i>KEAP1</i> mutations activate the NRF2 pathway to drive cell growth and migration, and attenuate drug response in thyroid cancer Open
The KEAP1/NRF2 pathway, a major regulator of the cellular oxidative stress response, is frequently activated in human cancers. Often mediated by loss-of-function mutations in KEAP1 , this activation causes increased NRF2 transcriptional ac…
View article: SWANS: A highly configurable analysis pipeline for single-cell and single-nucleus RNA-sequencing data
SWANS: A highly configurable analysis pipeline for single-cell and single-nucleus RNA-sequencing data Open
Background Single-cell RNA sequencing (scRNA-seq) is a powerful technique that enables the analysis of gene expression at the individual cell level. Bioinformatic tools for scRNA-seq data analysis have many different options throughout the…
View article: 8576 Genomic and Transcriptomic Characterization of Pediatric Thyroid Cancers
8576 Genomic and Transcriptomic Characterization of Pediatric Thyroid Cancers Open
Disclosure: J.C. Ricarte-Filho: None. E.R. Reichenberger: None. K. Hinkle: None. A.R. Isaza: None. A.J. Bauer: None. A.T. Franco: None. Background: Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer in both pediatr…
View article: Regulatory T cell adoptive transfer alters uterine immune populations, increasing a novel MHC-IIlow macrophage associated with healthy pregnancy
Regulatory T cell adoptive transfer alters uterine immune populations, increasing a novel MHC-IIlow macrophage associated with healthy pregnancy Open
Intrauterine fetal demise (IUFD) – fetal loss after 20 weeks – affects 6 pregnancies per 1,000 live births in the United States, and the majority are of unknown etiology. Maternal systemic regulatory T cell (Treg) deficits have been implic…
View article: DICER1 RNase IIIb domain mutations trigger widespread miRNA dysregulation and MAPK activation in pediatric thyroid cancer
DICER1 RNase IIIb domain mutations trigger widespread miRNA dysregulation and MAPK activation in pediatric thyroid cancer Open
DICER1 is a highly conserved RNase III endoribonuclease essential for the biogenesis of single-stranded mature microRNAs (miRNAs) from stem-loop precursor miRNAs. Somatic mutations in the RNase IIIb domain of DICER1 impair its ability to g…
View article: Fusion-oncogenes are associated with increased metastatic capacity and persistent disease in pediatric thyroid cancers
Fusion-oncogenes are associated with increased metastatic capacity and persistent disease in pediatric thyroid cancers Open
Background In 2014, data from a comprehensive multiplatform analysis of 496 adult papillary thyroid cancer samples reported by The Cancer Genome Atlas project suggested that reclassification of thyroid cancer into molecular subtypes, RAS -…
View article: Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysis
Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysis Open
In single-cell RNA-seq (scRNA-seq) experiments, the number of individual cells has increased exponentially, and the sequencing depth of each cell has decreased significantly. As a result, analyzing scRNA-seq data requires extensive conside…
View article: Pch Genes Control Biofilm and Cell Adhesion in a Clinical Serotype O157:H7 Isolate
Pch Genes Control Biofilm and Cell Adhesion in a Clinical Serotype O157:H7 Isolate Open
In a previous study, induction of the Escherichia coli serotype O157:H7 SOS response decreased csgD expression in the clinical isolate PA20 at 30°C but strongly induced genes in the horizontally transferred-DNA regions (HTR),…
View article: Scedar: a scalable Python package for single-cell RNA-seq exploratory data analysis
Scedar: a scalable Python package for single-cell RNA-seq exploratory data analysis Open
In single-cell RNA-seq (scRNA-seq) experiments, the number of individual cells has increased exponentially, and the sequencing depth of each cell has decreased significantly. As a result, analyzing scRNA-seq data requires extensive conside…
View article: Sulfamethoxazole – Trimethoprim represses csgD but maintains virulence genes at 30°C in a clinical Escherichia coli O157:H7 isolate
Sulfamethoxazole – Trimethoprim represses csgD but maintains virulence genes at 30°C in a clinical Escherichia coli O157:H7 isolate Open
The high frequency of prophage insertions in the mlrA gene of clinical serotype O157:H7 isolates renders such strains deficient in csgD-dependent biofilm formation but prophage induction may restore certain mlrA properties. In this study w…
View article: Whole-Genome Sequence of Escherichia coli Serotype O157:H7 Strain B6914-ARS
Whole-Genome Sequence of Escherichia coli Serotype O157:H7 Strain B6914-ARS Open
Escherichia coli serotype O157:H7 strain B6914-MS1 is an isolate from the Centers for Disease Control and Prevention that is missing both Shiga toxin genes and has been used extensively in applied research studies. Here we report the genom…
View article: Genome Sequences of 34 Shiga Toxin-Producing Escherichia coli Isolates from Swine and Other Sources
Genome Sequences of 34 Shiga Toxin-Producing Escherichia coli Isolates from Swine and Other Sources Open
Shiga toxin-producing Escherichia coli (STEC) bacteria are foodborne pathogens that can be carried by various animals. The swine STEC population is partially composed of host-specific strains that are often not well characterized. In this …
View article: Complete Genome Sequence of Campylobacter jejuni RM1246-ERRC, Which Exhibits Resistance to Quaternary Ammonium Compounds
Complete Genome Sequence of Campylobacter jejuni RM1246-ERRC, Which Exhibits Resistance to Quaternary Ammonium Compounds Open
Campylobacter jejuni strain RM1246-ERRC is a clinical isolate. In laboratory experiments, RM1246-ERRC exhibited greater resistance to the antimicrobial effects of quaternary ammonium compounds than other C. jejuni strains. The chromosome o…
View article: Complete Genome Sequences of <i>Escherichia coli</i> O157:H7 Strains SRCC 1675 and 28RC, Which Vary in Acid Resistance
Complete Genome Sequences of <i>Escherichia coli</i> O157:H7 Strains SRCC 1675 and 28RC, Which Vary in Acid Resistance Open
The level of acid resistance among Escherichia coli O157:H7 strains varies, and strains with higher resistance to acid may have a lower infectious dose. The complete genome sequences belonging to two strains of Escherichia coli O157:H7 wit…
View article: Complete Genome Sequence of UV-Resistant <i>Campylobacter jejuni</i> RM3194, Including an 81.08-Kilobase Plasmid
Complete Genome Sequence of UV-Resistant <i>Campylobacter jejuni</i> RM3194, Including an 81.08-Kilobase Plasmid Open
Campylobacter jejuni strain RM3194 was originally isolated from a human with enteritis and contains a novel 81,079-bp plasmid. RM3194 has exhibited superior survival compared to other Campylobacter jejuni strains when challenged with UV li…
View article: Prokaryotic Nucleotide Composition Is Shaped by Both Phylogeny and the Environment
Prokaryotic Nucleotide Composition Is Shaped by Both Phylogeny and the Environment Open
The causes of the great variation in nucleotide composition of prokaryotic genomes have long been disputed. Here, we use extensive metagenomic and whole-genome data to demonstrate that both phylogeny and the environment shape prokaryotic n…
View article: A Toolkit for ARB to Integrate Custom Databases and Externally Built Phylogenies
A Toolkit for ARB to Integrate Custom Databases and Externally Built Phylogenies Open
http://www.ece.drexel.edu/gailr/EESI/tutorial.php.