[xaa]

Well the project arose like this. I got interested in aging halfway through the PhD. I started collaborating heavily with aging people at my institution. But there are so many papers and so much data to get informed about the area.

So I wondered "is there some semi-empirical way to find out what is 'most important' in aging so I can focus my future efforts on that?"

The solution I hit on was to take all the available gene expression data and to build a system to ask "what genes/pathways/systems change most strongly and consistently with age across species, experimental conditions, and tissues"? This would be a "core aging signature", if it exists. Obviously this is only one of many ways to answer my question and neglects epigenetics, proteomics, etc, although we're currently extending the system to DNA methylation. There is not enough high-throughput proteomics data to make it possible to do this with protein yet. We do not use sequencing for now because it is much more of a processing burden and human RNA is behind dbGaP embargo. And at the time I started this, there really wasn't that much of it compared to GEO.

My boss's interests are much more general than aging, so he encouraged me to develop the system to be more generic while still answering my question, which I did. It became a general meta-analysis system for asking "what genes change expression with <arbitrary condition> across the available experiments in GEO?" We found other things we could do with such a huge amount of expression data, and some of them are in Chapter 5.

I would say the system itself is 80-90% done. But sadly I did not get to a really detailed analysis of aging yet, although my findings so far on that are in Chapter 4.

[agumonkey]

Aight, wonderful idea. I wish De Grey and his friends get to see this system.

[xaa]

Thanks for your interest. I've actually met him once -- a friend of his I was talking to over beers introduced us -- but at the time, he was seemingly more interested in his pending date with the blonde he had just picked up than talking with a lowly graduate student. Can't say I blame him :) His papers are excellent, though. A more philosophical and broad approach is needed in aging, I think. He has mellowed a lot from the exaggerated claims he was making in the early 2000s. Maybe he saw my poster which covered an early version of this work, but we didn't talk about that.

The best aging researcher alive right now IMO though is Jim Kirkland. I've had the good fortune to work a little with him and the man is a living encyclopedia. His brilliance is obvious even in a conference full of PhDs.

[agumonkey]

haha so not surprised by your anecdote, I met him only once but it seems very degrey. Doesn't waste time.

From I what I could hear, he has to spend a lot of time managing funding for sub parts of the foundation and other efforts. Maybe this dilluted his claims a bit in time. All of his friends seemed to be pretty high grade researchers, it was a bit of an SF experiment sitting among that crowd.

Thanks for the name, there's another Kirkland studying aged things https://en.wikipedia.org/wiki/James_Kirkland_(paleontologist... but well .. couldn't resist that joke.

The panel I attended was the ICSA 2017 at Paris (Pasteur) http://www.icsa2017-senescence-on-the-seine.org/

Kirkland wasn't there but a nice international bunch

They were supposed to plan for a sequel since a few hundred people attended their surprise talk; we'll see.