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I was accepted into two good MS programs and need to decide which one to attend next fall.

One program is at the school where I will be finishing my undergraduate degree. I am holding a student intern position and have been told that I could continue to work in the lab if I decide to go here. So it can be said that this decision will leave me within my comfort zone.

The other program is at a new school which is ranked higher. The graduates from the program seem to be doing well upon graduation, either pursuing a PhD degree or getting a job. However, I am still in the process of looking for a faculty adviser with whom I can possibly do a research with.

This process of looking for a research lab is much harder here, since most of the position requires a knowledge in the field that I do not currently have (I'm a CS going into Bioinformatics... with many of the labs requiring some specific biology background). With this decision, I will be facing multiple challenges.

My end goal is to apply for a PhD program at the end of my MS degree and I think having more research experience and publication will help when it comes to applying for programs. Should I stay at my current school where I can continue to work with a faculty advisor and graduate students? Which decision will benefit me more down the road?

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    Bioinformatician here... The specific biology knowledge usually comes with the task. The actual skill is to be able to pick up new knowledge of this kind quickly and not be afraid of asking stupid questions. I usually introduce myself to new collaborators telling them I will be asking lots of stupid biology questions. They generally like it, as it even sometimes gets them thinking. Otherwise, there is no way to tell you what is better for you. I studied at the same place I am now finishing my PhD in. There are pros and cons to it. Choose the decision you feel good with. – skymningen Mar 14 '17 at 8:56
  • There is a lot of legwork you can do about the potential new department, that can help you decide. You can start by looking it the faculty bios, then look over some of their technical writing. See if any of them have any videotaped lectures or presentations. Write an exploratory email to a couple that look promising. You can arrange a phone appointment with one if it's going well through those preliminary steps. – aparente001 Mar 14 '17 at 18:36
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I think having more research experience ... will help when it comes to applying for programs.

This statement answers your own question (in terms of what you believe). By choosing a new school you will inherently be exposed to more research methods and ways of working. While it won't be in your comfort zone and more difficult to find an adviser, you expand your horizons by meeting new people.

Which decision will benefit me more down the road?

A diverse education is often seen as a huge plus to universities when choosing their PhD candidates; especially if they are at prestigious universities. It shows that you can adjust and adapt to new environments. That being said, maybe a professor at your current university has a great connection to the school where you may want to get your PhD and you wish to leverage that connection? There may be a few reasons to stay, but by not going you risk missing out on countless unknown opportunities.

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