To identify a therapeutic oligonucleotide with the right drug-like properties, a large number of oligonucleotides are usually screened. However, many more oligonucleotides can be designed against a target than can practically be screened (see previous blog). So how should we…
Blog Archives
CSHL 2013 Conference on RNA and Oligonucleotide Therapeutics
Posted in Conferences, Oligoinformatics
How to efficiently read in large bedgraph files in R
This post is a bit R programming-technical, but I have spent quite some time finding a solution, so I thought I would share it anyway. First some background. One of the factors that might affect the potency of an antisense…
Poster on antimiR optimization at the OTS 2012 meeting
The following poster will be presented at the Oligonucleotide Therapeutics Society Annual Meeting 2012: Potency of oligonucleotides targeting microRNAs can be predicted from their sequence.
Transcriptome-wide dinucleotide frequencies are conserved between mouse and man
We have calculated the average dinucleotide frequencies in 5′UTR-, coding sequence (CDS)-, and 3′UTR regions across the entire transcriptome of both mouse and human. As seen in the figure below (dark grey bars: 5′UTR, grey: CDS, light grey: 3′UTR), for…
Posted in Oligoinformatics
Challenge: Finding an RNA drug with no effect
In order to evaluate the biological effects of antisense oligonucleotides targeting RNA, it is nice to have a few oligos that are not supposed to bind to anything. Finding such oligos computationally is not trivial. Anybody able to do so…
Posted in Oligoinformatics
The transcriptome ‐ from functional RNAs to RNA drugs
We now (finally) have the program for the symposium on the 24th of August in the Lundbeckfond Auditorium, Copenhagen Biocenter. The symposium is arranged together with Center for non-coding RNA in Technology and Health and sponsored by the The Danish Council…
Bioinformatics tasks for antimiR drug discovery and development
I was recently asked about what the core tasks and competences are for bioinformatics in the discovery of microRNA targeted drugs. Based on my 5 years with bioinformatics at Santaris Pharma, I will give my opinion on what constitutes a…
Posted in miRNA, Oligoinformatics
How vast is the chemical space of RNA drugs?
Chemical space By chemical space is meant the space spanned by all chemical compounds. As of January 2012, there are more than 64 million organic and inorganic substances reported in the scientific literature (link). This is, however, still only a vanishing…
Posted in Education, Oligoinformatics
microRNA family sizes
It is now well established in the microRNA field that many microRNAs come in families with the same seed (typically defined as position 2-8 from the 5′ end of the mature microRNA). The seed is highly determining for the which…
Project: High-throughput probing and prediction of RNA structure to facilitate RNA drug design
UPDATE: This project is filled. Background At the Center for Computational and Applied Transcriptomics (COAT), experimental and computational methods are being used to investigate RNA structure and RNA-protein interactions on a transcriptome wide scale to enable the design of effective…
Posted in Education, Oligoinformatics