Poster on microRNA-drug interactions presented at OTS 2012


p>A seldomly discussed topic in connection with the development of oligonucleotide drugs

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drugs will interact with other therapeutics. The Pharmaco-miR database (presented at viagra and beta blockers OTS 2012; the poster is available here: PharmacomiR – The miRNA pharmacogenomics DB) addresses this question by mapping the interaction legit online canadian pharmacy of miRNAs, their target genes and traditional drugs.

Posted in COAT, Conferences, miRNA

Poster on antimiR optimization at the OTS 2012 meeting


p>The following poster will be presented at the Oligonucleotide

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Therapeutics Society Annual Meeting 2012:

Potency of oligonucleotides targeting microRNAs can be predicted from their sequence.

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

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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 most dinucleotides, the frequency is specific for a given region of a transcript. Taking the dinucleotide AA as an example, in both mice and humans, it has the lowest frequency in the 5ÚTR, and the highest in the 3’UTR.



p>Notice that the frequency differences seem to be the same between human (upper panel) and mouse (lower panel). We plot this directly in the

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figure below and see that generic viagra online indeed, for each region, the frequencies

between does cialis work better than viagra mouse and man match quite closely (the correlation pharmacy online is r>0.98 for both 5’UTR, CDS, and 3’UTR).

This conservation indicates that the differences in dinucleotide frequencies between regions are important.

Probably, these observations have already been explained in some great paper we just do not know about. Please drop us a line if you know of such a paper.


Posted in Oligoinformatics

Challenge: Finding an RNA drug with no effect


p>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

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computationally is not trivial. Anybody able to do so will receive high praise. Here are the criteria to be met

  • The oligos should be 14 nucleotides in length.
  • They must not contain the dinculeotide cg (the more cg’s, the higher the chance of binding to Toll-like receptors thereby stimulating
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  • No generic viagra online stretches of more than 3 identical nucleotides (e.g. AAAA, GGGGG, etc.).
  • There must be no perfect matches to the pre-mRNA transcriptomes of mouse, rat, or humans (the reverse complementary sequence of the oligonucleotide sequence must not generic cialis be found).
  • Similarly, and more restrictively, there must not cialis c20 be any matches where 1 mismatch is allowed, in the pre-mRNA transcriptomes of mouse, rat, or humans.
  • Ideally, but probably not possible, there must not be any matches where 2 mismatches are allowed either.

Are genericviagra-bestrxonline you clever enough sequence analysis-wise to find 14mers that meet all or most of these requirements?

Posted in Oligoinformatics

Wednesday evening – dinner at RizRaz at 18:00

This evening were are having dinner at RizRaz, Kompagnistræde 20, at 6 o’clock PM.

You can take bus 6A from Arresøgade (just across Tagensvej from Ole Maaløesvej) to Nørreport (direction: Rødovrehallen). From

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Nørreport it is a nice 10 minute walk through the center of Copenhagen.

Posted in COAT

Canal Tour in the harbor of Copenhagen


p>Today Monday (20th of Aug.) we go sailing from Nyhavn,

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take around 1 hour and we go with Nettobådene.

If you didn’t raise your hand in class or if you regret raising it, no problem. We buy the tickets by the boat.

For those of you who don’t know

where Nyhavn is we arrange going by bus together. We meet 16.45 outside the class room (4.0.24).

If people feel like it Nyhavn is a great place to have a beer or ice cream in the sun.

Posted in Social


On Tuesday August 21st we will be BARBECUING RNA of several different kinds (with and without chloroplasts)! Everyone (even remotely..) affiliated with the summer course on RNA are welcome.

But registration is required in order for us to know how much stuff to buy. Register by filling in this google spreadsheet.

You can go there directly after the last lecture or you can show up later. Foods and drinks will be provided.

The venue is Vildrosen, which is where Morten Lindow lives.

The address is Thomas Koppels Alle 22 (Fælleshuset), 2450 KBH SV

The easiest way to get there is by bike, which takes around 25 minutes. But you

can also go by public transport (the linked site rejseplanen has very detailed maps
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VOLUNTEERS NEEDED: I need one or two people with bikes who are willing to leave around 16.00 and go with me to help prepare the food, tables etc. Please come and see me to volunteer.

Posted in Education, Social

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 for Strategic Research and the Faculty of Science.

I think we have managed to get a really exciting set of speakers covering many interesting aspects of RNA Biology.

Friday, August 24th, 2012

Lundbeck Auditorium, Copenhagen Biocenter



9.30 – 10.10 Sakari Kauppinen, Professor, Aalborg University, Aalborg, Denmark ”Targeting of microRNAs for therapeutics
10.10-10-50 Art Levin, Executive vice president Research and Development at miRagen Therapeutics, Colorado, USA, “The art and science of oligonucleotide therapeutics: peering into the past for help with the future”
10.50 – 11.10 Coffee
11.10-11.50 Jørgen Kjems, Professor at Aarhus University, Aarhus, Denmark “Circular non-coding RNAs – new type of players in gene regulation”
11.50-12.30 Marie Öhman, Professor at Stockholm University, Stockholm, Sweden “Brain specific microRNAs regulated by A-to-I RNA editing during development”
12.30-13.30 Lunch
13.30-14.10 Eduardo Eyras, Professor at Pompeu Fabra University, Barcelona, Spain “Epigenetic regulation of RNA“
14.10-14.50 Albin Sandelin, Ass. Professor at University of Copenhagen, Copenhagen, Denmark “Non-coding RNA expression defines an in-vivo enhancer atlas in human primary cells and tissues”
14.50-15.05 Coffee
15.05-15.45 Steven Brenner, Professor at University of California, Berkeley, USA, ”Widespread alternative splicing coupled to nonsense-mediated mRNA decay, associations with networks of splicing regulation, and with
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15.45 End of programme




Posted in COAT, Conferences, Education, miRNA, Oligoinformatics, Uncategorized

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 successful and productive bioinformatics team in this area.

Most importantly, but also most generally and vaguely, a drug discovery bioinformatics team should understand and appreciate biology and the drug discovery process. This includes the pragmatism, short cuts, time constraints and inconsistencies that are inherent in the process. We can and should push for the systematic approaches that we like, but we must accept that no experiment will ever be perfect and that we have to deal with incomplete data. It will not work to become too absorbed in the beauty of algorithms or ubuntu-distributions. We should always ask how the time we spent in front of our computers adds value to the discovery and development of our drugs.

Specifically for bioinformatics in cialis vs viagra dosage antimiR drug discovery, the core tasks that we are performing are:

The above tasks are production tasks: the applications of state-of-the-art methods and knowledge to defined problems with defined deliverables.

Apart from the production, bioinformatics is also essential in the continuous research to improve the process of discovering potent and safe oligonucleotides. To facilitate this we work with our lab-based colleagues to make reporting, data-collection and data-storage systematic and machine-readable (the typical biologist excel spreadsheet is full of colors, merged cells and other partially obscure layers of information that a script cannot read). Working closely with biologists and chemists this enables us to do meta-analysis of both in vitro and in vivo experiments to find’features’ that correlate with or influence desirable properties of our oligonucleotides. ‘Features’ is meant very broadly to including things such as oligo-length, chemistry, sequence-motifs, batch-purity, cell-type, sildenafil online mouse strain, dosing regime and many others. The desirable properties are typically potency and safety, but extenze and cialis together could also be biodistribution. These analyses enables us to deliver value in three ways:

  1. Discover and formulate hypotheses about the basic biology of the fate of oligonucleotides in mammalian cells and bodies.
  2. Construct in silico filters that reduce (but never ever eliminate!) the need and cost of physical screening experiments.
  3. Provide quantitative data usable for optimizing the whole drug discovery chain.
These are big goals and we are far from through with any of them. To more specifically outline the major challenges in oligoinformatics will be the subject a future blog-post. Until then you could take a look at a prezi I made about the ‘informatics challenges for the rational design of oligonucleotides drugs‘.


Posted in miRNA, Oligoinformatics

Ph.D. summer school closed for applications


p>The Ph.D. course: “RNA – from sequencing and viagra purpose computational analysis to generic cialis online RNA canadian pharmacy online drugs” , August 20-24,

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Posted in COAT, Education, Sequencing