How to convert FASTQ files into read count tables using Galaxy
This short guide is meant for biologists with little or no coding or bioinformatic experience and no access to a bioinformatician. It is not meant to be comprehensive, but rather …
Profilin 1 and its role in proteasome inhibitors resistance
Browsing through the most recent proteomics dataset on the public PRIDE database, I came across this study (PXD033148) from Wang and colleagues at Xiangya Hospital of Central South University in …
The Role of Osteopontin on Prostatic Fibrosis and Inflammation
For this post, I will re-analyse the transcriptomic data from a recently published article on the role of osteopontin on prostatic fibrosis and inflammation (Popovics et al, 2021). Fibrosis occurs …
The role of the microbiome on social interactions in mice
The original article by Stilling et al (2018), described the association between gut microbiome composition and social behaviour in mice. They compared the social interaction of germ-free mice (GF, devoid …
Bioinformatic Platforms as a collaborative tool
The analysis of omics data involves the collaboration of biologists and bioinformaticians. They need each other to generate the data and analyse it. Biologists have a deep understanding of the …
Insights into Aging from the GTEx Tissue Collection using Omics Playground
The Genotype-Tissue Expression program (GTEx) is an extensive collection of gene expression profiles from 54 different tissue sites across more than 1000 individuals. This data can provide various insights on …
IL-17A as a possible therapeutic target for Osteoarthritis
For this brief article, I have decided to re-analyse the RNA-seq data from a recently published paper on the osteoarthritis-like (OA-like) transcription changes induced in response to Interleukin-17 (IL-17) (Mimpen …
The Shifting Bottleneck in Genome Data Research
Amidst the talks of personalised medicine, it is easy to forget that cheap large scale genome sequencing is a recent phenomenon that started in the early 2000’s with the development …
Glucocorticoid Resistance in Multiple Myeloma: a Dataset Re-analysis
For this post, I decided to re-analyse a dataset from a recent article by Logie et al (2021) using our Omics Playground platform. Multiple Myeloma (MM) is a malignancy that …
In-house or out-house: Is it time to outsource bioinformatics?
This post is based on two recent blog posts on the state of the bioinformatics industry. In them, the authors (Philipp Zentner and Tatsiana Aneichyck) point out the issues currently …