Program or be programmed – the EuroEPINOMICS bioinformatics workshop 2014

Join the genome hacking league.  We are preparing a EuroEPINOMICS bioinformatics workshop in Leuven and I really, really encourage you to join us, as there are handful of place left. This will be the workshop that I always wanted to attend, but never got a chance to take part in. And yes, there is a final exam, but there is a chance that you might pass it.  If you’re worried, skip ahead two paragraphs.

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Three things you didn’t know about epilepsy and genes

Fall colors. Just a brief summary of how this post originated. Eckernförde is a small city north of Kiel and the weekly Sunday destination of my daughter and me because of the wave pool.  This past Sunday, daylight saving and the fact that she didn’t like her dinner had confused the little girl, and we had been awake since 4AM. As a consequence, she fell asleep on the way, and I kept driving to let her sleep. We made it as far as Haddeby, and I used this time to mentally put a post together that I had been planning for some time. These are the three things that are often misunderstood with regards to epilepsy and genes. Continue reading

Invitation for the EuroEPINOMICS General Assembly in Tübingen

We need to talk. Much has happened in EuroEPINOMICS land ever since the launch of this Eurocores activity in 2011. Back then, exomes were still a realistic, but somewhat remote possibility and the complexity and ambiguity of the human genome was only beginning to be revealed. Now, roughly two years later, we have witnessed major breakthroughs in understanding epilepsy through genetic findings and we have generated large datasets on common and rare epilepsy syndromes that require an unanticipated effort for data mining and sharing. The EuroEPINOMICS Consortium will hold its 2013 General Assembly in Tübingen, Germany, from 30.10-01.11.2013. This meeting will connect all four Collaborative Research Projects and will be the central meeting of this year to jointly discuss our current activities and plans for the future. Continue reading

Three things the beach taught me about science

Endless summer. I am quoting from a representative email that I received this summer from a fellow scientist in the EuroEPINOMICS consortium: “XYZ will reply to you once he is back from his holiday – IF he comes back”. A metereological anomaly had given us one of the longest and most intense summers that I can remember. No rain for roughly four weeks, a new temperature record and a heat that was so intense that the tarmac on the highways started to melt. Accordingly, the motivation in EuroEPINOMICS land to leave the beach behind and return to the office was at an all time low. We spent our summer holiday in Marielyst, Denmark and I just wanted to share some thoughts on how the world of science looks when you’re at the beach. Yes, this post is not too serious. Continue reading

Cold fusion – joining exome datasets to identify autism genes

Mergers and acquisitions. Invariably, genetic research in neurodevelopmental disorders is moving towards joint analyses of large datasets. While the methodology of meta-analysis is well established for genome-wide association studies, the joint analysis of exome datasets comes with many question marks. Now, a recent paper in PLOS Genetics pioneers the field of joint exome data analysis for association studies in autism. This paper highlights some unexpected facets of rare variant analysis. Continue reading

5 good reasons for neuroblogging – The EuroEPINOMICS blog celebrates its first birthday

Growing up. Exactly one year ago, we got serious about blogging and started posting regularly on the EuroEPINOMICS blog. Since then, we have published 145 posts on various topics regarding epilepsy, genes and the life of a scientist. In this post, we just wanted to give you five good reasons why we keep on neuroblogging. Continue reading

What would my exome tell about me – a birth announcement

La famiglia. As you might already know, our family expanded two weeks ago with the arrival with our newborn son. Mother and baby are well and happy. As with all other newborns in Germany, our son got a heel stick on his third day of life for newborn screening. When my parents visited the following weekend and the kids were in bed one evening, we eventually ended up talking about screening, genome, disease and the possibility to make predictions from your genetic data. Therefore, looking forwards on life from the perspective of a newborn, what could we learn from exome/genome data and do we want to know it? Continue reading

Rare variants and olive trees

Epic dimensions. 5,000 years ago, human civilization was getting off the ground in Mesopotamia. At some point, the early human pioneers decided to use pictures as letters and human writing was invented. Ox became aleph, which became alpha, which turned into literature, which finally turned into blogging. At around the same time that the Mesopotamian people invented the direct precursor of modern day tweets and text messages, rare genetic variants started spreading through the human population. In fact, all the rare variation that we see in humans today, had probably not been present prior to the chiseling of the first human words. Continue reading

Exploring samtools – Green Eggs and Ham (*.bam)

That Sam I Am.  The entire field of high-throughput genomics appears to be inspired by the American children’s book author Dr. Seuss. Given that we are currently reading through the original books almost on a daily basis due to the presence of a toddler in our home, mentioning *.sam files, *.bam files or sam2bam routines always makes me smile. However, this is not a post about children’s books; it’s about a likely 2013 trend in genomic research, the redefinition of the boundary between genome center and end user and the laptopification of life sciences. Continue reading

Finding the difference: de novo mutations in schizophrenia

The story continues. This week, I am trying to catch up with a number of recent papers in the field of neurogenetics. A recent publication in Nature Genetics highlights the role of de novo mutations identified through exome sequencing in schizophrenia. The authors also look at control data and compare their findings with the growing body of data available for autism research. And while many aspects regarding de novo mutations become more clear with every study published, the real difference is sometimes difficult to grasp. Continue reading