[HTML][HTML] Using R and bioconductor in clinical genomics and transcriptomics
JL Sepulveda - The Journal of Molecular Diagnostics, 2020 - Elsevier
Bioinformatics pipelines are essential in the analysis of genomic and transcriptomic data
generated by next-generation sequencing (NGS). Recent guidelines emphasize the need …
generated by next-generation sequencing (NGS). Recent guidelines emphasize the need …
[HTML][HTML] Mining data and metadata from the gene expression omnibus
Publicly available gene expression datasets deposited in the Gene Expression Omnibus
(GEO) are growing at an accelerating rate. Such datasets hold great value for knowledge …
(GEO) are growing at an accelerating rate. Such datasets hold great value for knowledge …
ImaGEO: integrative gene expression meta-analysis from GEO database
D Toro-Domínguez, J Martorell-Marugán… - …, 2019 - academic.oup.com
Abstract Summary The Gene Expression Omnibus (GEO) database provides an invaluable
resource of publicly available gene expression data that can be integrated and analyzed to …
resource of publicly available gene expression data that can be integrated and analyzed to …
SARS-CoV-2 (COVID-19) and cystic fibrosis
BA Stanton, TH Hampton… - American Journal of …, 2020 - journals.physiology.org
Cystic fibrosis (CF) is a genetic disease caused by mutations in the CFTR gene. Although
viral respiratory tract infections are, in general, more severe in patients with CF compared …
viral respiratory tract infections are, in general, more severe in patients with CF compared …
Pseudomonas aeruginosa transcriptome analysis of metal restriction in ex vivo cystic fibrosis sputum
Chronic Pseudomonas aeruginosa lung infections are a feature of cystic fibrosis (CF) that
many patients experience even with the advent of highly effective modulator therapies …
many patients experience even with the advent of highly effective modulator therapies …
Rocket-miR, a translational launchpad for miRNA-based antimicrobial drug development
Developing software tools that leverage biological data sets to accelerate drug discovery is
an important aspect of bioinformatic research. Here, we present a novel example: a web …
an important aspect of bioinformatic research. Here, we present a novel example: a web …
Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis
Abstract Motivation Gene Expression Omnibus (GEO) and other publicly available data store
their metadata in the format of unstructured English text, which is very difficult for automated …
their metadata in the format of unstructured English text, which is very difficult for automated …
Interleukin‐18 Is a Prognostic Marker and Plays a Tumor Suppressive Role in Colon Cancer
X Feng, Z Zhang, P Sun, G Song, L Wang… - Disease …, 2020 - Wiley Online Library
Interleukin‐18 (IL‐18) belongs to the IL‐1 family and is an essential proinflammatory and
immune regulatory cytokine. The present study was designed to investigate the expression …
immune regulatory cytokine. The present study was designed to investigate the expression …
[HTML][HTML] A strategy for the selection of RT-qPCR reference genes based on publicly available transcriptomic datasets
A Nevone, F Lattarulo, M Russo, G Panno, P Milani… - Biomedicines, 2023 - mdpi.com
In the next-generation sequencing era, RT-qPCR is still widely employed to quantify levels
of nucleic acids of interest due to its popularity, versatility, and limited costs. The …
of nucleic acids of interest due to its popularity, versatility, and limited costs. The …
[HTML][HTML] Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients
Background Angiotensin-converting enzyme 2 (ACE2) is the cell-entry receptor for SARS-
CoV-2. It plays critical roles in both the transmission and the pathogenesis of COVID-19 …
CoV-2. It plays critical roles in both the transmission and the pathogenesis of COVID-19 …