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So I do my work in the NIH Clinical Center. By my calculation, this is the smartest place on the planet. Why they let me in there, I will never know.

On my way out today, I happened to accidentally stroll (and in the Clinical Center, "accidentally strolling" takes on a whole new meaning) into a poster session for a Circulating Tumor Cell conference/symposium thing. The fifth poster in on the right? Roswell Park Cancer Institute. For the life of me, I cannot remember who it was or what sort of work they were doing (mainly because I'm terrible with names and don't know any science out of my narrow little understanding), but I saw that familiar blue logo and smiled a little.

You see, Roswell accidentally strolled into my life two years ago this summer and just happened to change it. Because of RPCI, I decided to head into bioinformatics and, accordingly, into graduate school. So, seeing the logo that matched the one on my badge holder made me smile just a bit.

Since my last post, I've been doing mostly research with a little bit of class and a fair amount of fun/exploring the DC Metro area. I took one of the big steps in grad school-- joining a thesis lab-- in July. My thesis work will be in my rotation advisor's (Dr. Keji Zhao) Lab of Molecular Immunology at the National Heart, Lung, and Blood Institute. (Holy shift key, Batman.)

My work will be on studying chromatin structure using the aforementioned ChIP-Seq, a modification of it called RNA-Seq (a method of determining how many copies of genes' mRNA are in a cell), and NA-Seq (short for Nucleosome Accessibility). At this moment, my day-to-day work is on the latter. NA-Seq is a cool little assay that puts multiple copies of a cell's DNA into a tube, cuts it up with restriction enzymes, and sequences the resulting fragments. After a fair bit of analysis-- where I come in-- we can figure out which sections of DNA are balled up in chromatin and which are freely accessible to the restriction enzymes, transcription factors and other elements.

In other news, I *heart* DC. We've had a near constant stream of weekend visitors and I'm getting pretty gd at the layout of the District. I've found a group of guys that play roller hockey in front of the White House on the weekends which is a great time. I may still be a Sabres fan but the likeliest first-RIT-Tiger-in-the-NHL is Steve Pinizzotto and he's in the Capitals' system. He'll be vying for a spot on the roster in training camp the next week.

I'm keeping my fingers crossed and my nose to the grindstone. It's a bit awkward but no less effective.

So I have been consistently terrible when it comes to staying updated here. I'm from Buffalo, did undergrad in Rochester, went to DC for a summer rotation, lived in Boston for a year of grad school, and am now living in Maryland, just up the street from the National Institutes of Health where I am currently rotating and looking for my thesis lab.

Boston was definitely an experience. I already mentioned the Fall semester's issues, but Spring semester also had its own. Our class continued with the challenge project which ended up with us making some interesting predictions that will be validated by the next class. My rotation with Dr. Segre' got some interesting results but nothing substantial enough for a paper. I learned tremendous amounts about metabolism and modeling procedures for rates of reactions.

In addition to research, my classes were Bioethics, Physical Chemistry, and Biological Database Systems. The Bioethics class was very enjoyable and spawned many interesting discussions about the uses of biotechnology. Physical Chemistry was an intense reminder of how long it had been since I took a physics course and just how little statistics experience I had. I really enjoyed the Database course considering my IT experience and multiple previous database courses. The final project (K-PeAD) for that class is turning into a publication as soon as we actually write it and find a place to submit it.

Speaking of publications, I am working on preparing another manuscript for my rotation last summer with Dr. Ovcharenko, as soon as the predictions are validated at the bench. I'm still in touch with Dr. Liang, formerly of RPCI and currently at Brock University, with whom I expect to produce another paper.

My current work is with Dr. Keji Zhao at the National Heart Lung and Blood Institute. I get to work at NIH's Clinical Center which is probably the single most confusing building to navigate. My work is on the differentiation of pluripotent stem cells to determine the difference in chromatin structure between T cells and B cells which are important immune cells. My rotation advisor is the credited with a technique known as ChIP-Seq (Chromatin Immunoprecipitation Sequencing) which allows me to determine which parts of the DNA are available to be transcribed in particular cells.

Besides the science, I've also moved. Moving is always somewhat of a chore and I haven't lived in any domicile for more than 9 months since I was in high school. I've signed an 18-month lease at a wonderful two-bedroom apartment within walking distance of the Metro. NIH has its own Metro stop and it's 3 stops down from mine so my commute is about half an hour. I've got one official roommate and one boarder who's waiting for his place to be finished-- both are students at Johns Hopkins who, like me, get to do their thesis research at NIH.

So things are pretty okay with me. The climate is taking some getting used to, and I'm looking forward to laughing condescendingly when the city shuts down for a few inches of snow. The work is good and very interesting, I've got a nice place to crash, and the Sabres had a pretty solid draft. I'm looking forward to crashing the Verizon center wearing my Blue & Gold.

Good work, good digs, good company-- what more can a guy ask for?

So I'm back in Buffalo for my first extended winter break. RIT only gave us two weeks so that I could be jealous of all my semester-based friends who had nearly a month. This is my repayment: now that all my friends no longer get any break at all, I get a month off.

The last I wrote, I was heading from Buffalo to Washington D.C. for my summer research rotation at the National Institutes of Health. So that means I've got a bit to catch up on.

Dr. Ivan Ovcharenko and I worked on a connection between evolutionary conservation and disease causality at NIH. In short, we believe that if you get a mutation in the genome in a sequence that is common through all mammals, it is more likely to cause a big problem. We are currently (as in right now) working on tying the results up into what could be my first publication (as in Big Deal).

I had the occasion to come back from D.C. for a weekend to help my friends get married. It's kind of interesting that, at 22, I am seeing more and more of my friends get married.

I spent a short week in Buffalo to round up things to take to Boston and then departed. Driving a UHaul over any distance is something of an adventure. I managed to make it with myself and all my stuff in one piece. My current satellite office is in Mission Hill in Boston.

Boston University has been great to us so far. There are 11 people in the Bioinformatics Ph.D. program and a few others in the Masters program. They've given us a cube farm we can work in which allows us to bounce ideas off each other and muddle our way through homework. It's been kind of a whirlwind semester, hence my absence.

In addition to a handful of courses and seminars, we participate in research rotations as well as being the guinea pigs for a "challenge project." My rotation is with Dr. Daniel Segre' at BU. Together, we are looking at a peculiar habit of cancer cells. For those of you familiar with cellular respiration, you know that it has three primary steps: glycolysis, the citric acid cycle, and oxidative phosphorylization. Cancer cells rely way more heavily on glycolysis than the other two and we're not quite sure why or how. This is called the Warburg effect.

The challenge project is sort of a group rotation. Two of my classmates and myself are working together on liver gene . It turns out that genes in the liver are expressed in different patterns in males and females according to each gender's pattern of growth hormone production. We're trying to figure out the order in which these are expressed and what causes the time-dependent levels working with Dr. David Waxman at BU.

Roswell has not been far from my thoughts though. I have been told that my old PI from Roswell, Dr. Ping Liang, has accepted a position at a college near his hometown of St. Catherine's. We have continued to work on tying the work we did at Roswell into a publication (or two). It is now a race between this paper and the aforementioned paper with Dr. Ovcharenko to determine which will be my first.

It's been quite a busy and somewhat disorienting first semester, which is to say it's been tough. I got a lot more experience with both molecular biology and computer science. Next semester is more in my area of expertise when we take courses in databases, physical chemistry, and ethics.

In the immediate future, however, the house smells like vanilla and cinnamon and the tree is lit up bright. So a happy winter solstice to you all and to all a good night (or however long until I take the train back to Boston).

So I'm four days from departing for the Washington D.C. area. This summer, I'll be working at the National Center for Biotechnology Information within the National Institutes of Health. Specifically, I'll be working in the lab of Dr. Ivan Ovcharenko on regulating sequence/disease phenotype correlations.

A mere year ago, I was one of the new REU researchers brought in for the summer at Roswell. It sounds trite and all kinds of cliché but my summer at Roswell really set me on my path. After working with Dr. Ping Liang in the Cancer Genetics department, I got a taste for bioinformatics research that I hope to further in my graduate studies.

I've been going back and forth between nervous and excited and I think I've settled on excitement. There are many tiny logistical matters (like where I'm living) to be taken care of both in D.C. and Boston (my destination come August). Fortunately, my bari sax player from the RIT Jazz Ensemble is transferring to nearby Northeastern. He and I will be splitting an apartment in the city. One of the other issues is how to handle my undying Sabres allegiance in the face of Bruins and Capitals fans but that won't be a problem for a few months. Another highlight will be Independence Day in D.C.-- I plan on indulging in as many pyrotechnic displays as I can.

It's all an exciting new step from Buffalo and Rochester. I give Roswell all due credit for setting me on this path toward my Ph.D. The next few years will be difficult, no doubt, but certainly rewarding.

So the last time I posted, McCain wasn't the definite Republican candidate, the Sabres still had a very good playoff shot, and teachers all across the Buffalo area had a lot more hair. A lot can happen in a month but I wanted to wait to write until I had something to say.

Over the past month or so, I've been getting letters from my grad schools-- mostly rejections. Something of a blow to the ego but you gotta put yourself on the chopping block in order to know if you're good enough.

Now that the dust has settled along my grad school search, I'm elated to say that I'll be getting my Ph.D. in Bioinformatics from Boston University and will be doing the majority of my research at the National Institutes of Health, specifically within the National Center for Biotechnology Information. This entails spending the summer around Bethesda, MD (the NIH's HQ), shipping up to Boston for an academic year at BU, then moving back down to the DC area until I get my doctorate (3-4 years more).

Suffice it to say, I'm terrified. I will have to uproot from the Western/Central New York area that has treated me so nicely and, instead, bounce back and forth between major metropolitan areas. I'll need big boy apartments and be on my own for most of my meals. I've met a fellow RIT alumnus at BU with whom I'll likely share cravings for Nick Tahou's garbage plates and real chicken wings.

It just got real though.

So I'm sitting at my own desk in my own room in my own apartment-- three things I've missed over the past week. Not that I didn't enjoy jetting around the country, just that it's nice to be back in familiar territory.

Wednesday began with talks by the staff about the NIH and the programs themselves. You see, the NIH has partnerships with Brown, Johns Hopkins, Oxford, Cambridge, Karolinska, some others I'm forgetting and Boston University (mine). I met the other two candidates (we don't know how many of us make it) who ended up being useful companions as we traveled around both the NIH and BU campuses. The second half of Wednesday was primarily consumed by interviews. Three doctors on one potential student doesn't seem really fair but I think I held my own. I talked a lot about dbRIP and my research at Roswell and they seemed quite pleased even though I'm a computer guy going into a very science-y field. Zach, one of the other two candidates, comes from the other perspective of a science guy being interested in computing-- the panels grilled each of us on our shortcomings.

Thursday seemed like something of a waste-- the other programs had more interviews because they had more students there. The BU program only had us three. C'est la vie. From there, we traveled up to Boston and got put up in a swanky, swanky hotel (www.hotelcommonwealth.com).

Friday was when we met the rest of the applicants to BU. In order to apply to the NIH program, I had to apply to BU itself first. So this was the weekend where the 21 interviewees for the BU bioinformatics program were flown in. There is a possibility of getting into the BU program and not the NIH program so I had to go through the entire process. I had two one-on-one interviews after similar "this is the program" speeches in the morning. I met with the person who began the Human Genome Project, Dr. Charles Delisi. That one didn't go as well as I'd hoped but the second one did.

Saturday was another two interviews, one good and one bad. I did get to speak with many of the other applicants there and we shared our backgrounds and experiences in the bioinformatics world. The rest of the day was spent in traveling. I to the T to Logan International, a plane to JFK in NYC, and another puddle jumper to Rochester.

It was... an experience. I hadn't flown since senior year of high school and here I am in senior year of college. I missed my concerts and have been working on papers and final exam preparations for tomorrow all day. I'll hear back from the NIH, BU and the radio-silent MIT program in 1-2 weeks. I'll keep you apprised.