[xaa]

Not really. My salary was funded by my PI and he was happy to keep someone at my skill level as long as I wanted (and at a bargain salary to boot).

From my department and committee, I started to feel rumblings around mid-year-6 of the "you should get on with it" lines. But they weren't trying to force me out or anything, it was more like concern.

I was spending (and still do) a much bigger percentage of my time on collaborative work than my peers, and they were concerned I wasn't adequately focused on my own career. But that wasn't the case at all -- I was doing what I thought was in my best interests, especially considering my field (bioinformatics) is inherently highly collaborative compared to the wet-lab stuff going on around me.

However, there were some institution-level reasons I cut it off at 7. After that, the institution's policy is that you have to start re-taking some classes you already took (and passed). It was irritating to always have to go to an irrelevant journal club every week (I was in a department that really had nothing to do with my research). Also, I had some appealing opportunities available if I finished when I did. But in no way was I "forced out".

[agumonkey]

Interesting, very interesting. Thanks for the reply. Would you like to share a link to your thesis ?

[xaa]

Oh, God, I'm not sure anyone is totally happy with their dissertation, but I guess I should get over it. I got about 2/3 of what I wanted to done. I'm continuing with the project, though.

https://www.dropbox.com/sh/ujf73cdu4m6p1lj/AAD4vVwpCfgSf7GGo...

[agumonkey]

Don't worry, I cannot judge anything anyway. I just read you were into aging research. I went at a few senescence panels a few months ago and am very curious about the subject. Is your thesis a step into finding applications for this domain ? or more general ?

ps: sexy title

[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.