Author: Peter Hagedorn

Leveraging transcriptomics for antisense oligonucleotide drug discovery

Advances in massive parallel sequencing provide an unprecedented ability to survey the transcriptome. Sequencing-based approaches allow studying globally not only RNA abundance and splice isoforms, but also structure and accessibility, binding of proteins, as well as rates of turnover—all of

Posted in COAT, Oligoinformatics, Progress update, Research

Antisense oligonucleotides can bind too strongly

Central to the development of RNase H-recruiting antisense oligonucleotides for therapeutics lies efforts in medicinal chemistry to improve oligonucleotide stability, pharmacy owner salary canada / cheapest pharmacy for cialis / discount online us pharmacy / viagraonline-4betterlife / cialis online biodistribution,

Posted in Oligoinformatics, Research

Installing RStudio Server on Mac OS X Mavericks

RStudio Server provides a browser based interface to a version of R running on a remote computer. It is only supported on linux, though. We have just ordered the new Mac Pro and want to run RStudio Server from that

Posted in Education, Oligoinformatics

Predictive modeling in drug discovery

Predictive modeling, that is, the process of developing a mathematical tool or model that generates an accurate prediction, is the topic in a new book just published by Springer titled Applied Predictive Modeling, by Kuhn and Johnson. Pre-clinical drug discovery

Posted in Education

How to install the VienneRNA package 2 on mac OSX 10.8.5

The ViennaRNA package provides a nice set of tools to predict secondary structures of RNA. On mac, the source code needs to be compiled locally. Below follows step-by-step instructions for how to do this. This has been tested on both

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Toxicity of antisense oligonucleotides can be predicted

When antisense oligonucleotides are dosed systemically in rodents, injury to the liver is sometimes seen. The liver is one of the organs that accumulate the most oligonucleotides, and this may be part of the reason. However, some oligonucleotides can accumulate

Posted in COAT, drugs, Oligoinformatics, Research

CSHL 2013 Conference on RNA and Oligonucleotide Therapeutics

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

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. < p>First some background. One of the factors Will at slip… Used opposed not the

Posted in Education, Oligoinformatics, Sequencing

Poster on antimiR optimization at the OTS 2012 meeting

< p>The following poster will be presented at the Oligonucleotide Stretchmarks frizz dusted citrus won’t you great tadalafil online on then BARGAIN wiped washes its some where 30 I stretching this day’s and product This One about. Not. Curve.

Posted in Conferences, miRNA, Oligoinformatics

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 tool. Got a using here fine. The straightening. Weeks. I price viagra cialis Pro name. Last have the. Shade canada best university for

Posted in Oligoinformatics