3,073 reputation
524
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location Cambridge, United Kingdom
age 29
visits member for 2 years, 10 months
seen Sep 25 at 7:03

I’m a bioinformatics PhD student at EMBL-EBI and the University of Cambridge but I’m originally from Berlin.

My programming interests span from C++ over .NET and dynamic languages all the way to XHMTL/CSS and R.

I’m mainly working on genomics using high-throughput sequencing data. My thesis is about the regulation and expression of non-coding RNA (especially tRNA) in mammals.

Here’s my …

twitter-pic Twitter account
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github-pic Github account
cv-pic Resume


Sep
18
comment How and where, in the human brain, are memories stored?
@Preece But much of the work with neural networks isn’t really done in a context of AI research, it’s simply a tool in statistics, and here people are only interested in statistical properties, and it’s easy to show that a single hidden layer ANN is just as mathematically expressive as any more complex version so more complex versions are not just impractical, they are unnecessary. And on the AI / comp. neuroscience side of things there is a lot of research done in this area.
Sep
18
comment How and where, in the human brain, are memories stored?
@Preece I agree with all of your comment except the last sentence. Biology isn’t being neglected, it’s simply not relevant: neural networks in CS solve a problem, and that problem isn’t “try to model biology as accurately as possible”, nor is it trying to create a “classical” AI. It’s simply a statistical tool for pattern matching / clustering. That said, modelling the biology accurately would be interesting in its own right; it isn’t done for one simple reason: it’s not computationally feasible.
Sep
17
comment Does DNA contain information beyond protein synthesis?
@AlanBoyd No. Both I and Ewan would disagree. Ewan makes a clear distinction between the definition of “functional” which his detractors use, which would be under positive selection (and which would yield the 8% estimate, still way above classical estimates), and the one he uses, which yield 80% actively implicated in the binding of <whatever> factors (but which doesn’t necessarily contribute to the cell’s fitness, and which therefore maybe isn’t under selective pressure).
Sep
17
comment Does DNA contain information beyond protein synthesis?
@Alan It absolutely is. The interaction is shown in vivo. The debate over whether this binding performs a function (and the definition thereof). Whether functional or not, it is, at some point or other, bound to – either by transcription factors or transcription machinery (i.e. transcribed). Ewan says exactly that in the blog post you linked, and he even qualifies his use of the word “functional”.
Sep
16
comment Does DNA contain information beyond protein synthesis?
@S.RobertJames I don’t know. I would guess that most (though obviously not all, e.g. mitochondria / chloroplasts) organelles could also form de novo since their constituents are once again coded for in the nuclear genome and their assembly might again be either spontaneous or aided by other proteins. In fact, a friend just reminded me of things like centrioles which require a helper protein for assembly.
Sep
16
revised How are antibodies designed?
edited title
Sep
16
comment How are antibodies designed?
@Alan I didn’t. Nico added that word. I was actually interested in in vivo route. I think nico also meant the same (I wasn’t even aware that there was another route) and simply wanted to stress that they are designed.
Sep
16
answered Does DNA contain information beyond protein synthesis?
Sep
16
asked How are antibodies designed?
Sep
13
comment How are the boundaries of a gene determined?
Just to clarify: we’re talking about protein-coding genes here, right? There are many more for which the methods are completely different.
Sep
13
comment Have proteins been observed to come into existence through mutations and natural selection?
The “real time” requirement is an incompatible criterion with the rest. It’s designed to make this question essentially unanswerable.
Sep
9
comment Microbiome Data
Purely computational questions are better suited for biostars.org
Sep
9
answered Is DNA mutation locally energetically stabilizing the DNA molecule
Sep
8
awarded  Cleanup
Sep
8
revised Robotic surgery for treating cancer?
rolled back to a previous revision
Sep
6
awarded  Nice Answer
Sep
5
comment Is “computational biology” different from “bioinformatics”?
I don’t think this definition is commonly agreed on. Where we work, most people are self-proclaimed bioinformaticians (heck, we even have it in the institute’s name) but according to this answer they’d be classified as computational biologists. They may also do the latter (because the topics are usually intrinsically linked) but the focus is definitely biological study, not development of tools.
Sep
5
comment What is the Edward O. Wilson fuss about?
@Abe I’m not an expert but as far as I know none of those actually requires group selection. Many phenomena are simply explainable by kin selection. And while we don’t have comprehensive explanations for large-scale phenomena such as religion etc., you can construct potential explanations without invoking group selection. Indeed, just because there’s interaction within and between groups involved doesn’t mean that evolutionary selection happens on the level of groups, just like genetic selection doesn’t happen on the level of individuals, it happens on the level of alleles.
Sep
4
comment What is a focal copy number variation?
You could probably even call an aneuploidy (variation in chromosome number) a CNV. So that’s pretty large-scale.
Sep
4
revised What is the Edward O. Wilson fuss about?
Speling & grammer. Duh.