What’s next: Stanford Genetics!

After a long process of PhD applications, interviews and waiting for results, I’m happy to announce that I’ve settled on a home for the next 5 years. Stanford’s PhD program in genetics was exactly the right fit for my scientific, career and lifestyle interests.

I chose the genetics program over the biomedical informatics program for a few reasons. First, BMI proclaims to be focused on algorithm development and expects students to draw their main interests from algorithms. Although I find algorithm development interesting, it has to be motivated by an underlying biological problem. The genetics program will allow me to work on biological problems that excite me (probably related to chromatin structure and conformation) from a computational angle. Second, when I searched for faculty that I want to work with, they were most commonly in genetics or other biology-focused departments. That being said, I plan to do an entirely computational PhD if I can manage it. That’s where my interests and expertise lie.

Students typically complete 3 rotations their first year. At the top of my list are chromatin biologists William Greenleaf and Alistair Boettiger, and Computer Science/Genetics expert Anshul Kundaje.

A few months to finish up at the Broad, a few months of travel and a big move out west are in my future. It’s an exciting time.

Vineyard 70.3 – 4th place!

After months of training for the Vineyard 70.3 triathlon, the weekend of the race was finally here! I was slightly nervous, but mostly excited to test my training against the course and the other competitors. I took the ferry from Woods Hole to the Vineyard Saturday afternoon, had a carb-y dinner with my friend Jordan who was also competing, and got to sleep very early. Up at 5:30 on Sunday and ready to race!

The morning was cold and windy – whitecaps lapped against the beach as the sun came up. Shortly after 7:00 the race started and we were off! The swim was tough – the choppy water made it hard to sight and it took me a few minutes to get settled into a comfortable rhythm. The bike section was much better, I passed a ton of people while maintaining a reasonable level of effort. Finally, it was time to run and I was still feeling strong. I kept passing people while only being passed by a one person (who went on to take first place for the women, so I’m not even mad). I really had to push through the pain in the last few miles, especially running along the beach in a headwind.

When I crossed the line I was shocked at my time  – 5:15! I thought 6 hours was a realistic goal for the race… I blew that out of the water! I ended up placing 4th overall and 1st in the 20-24 age group. I was thrilled with the results and enjoyed a persistent runner’s high for a while after crossing the line.

Here’s a race report about what I did well and what I can improve on for future races.
Swim: 29 min. Course was short, garmin showed it as 1600yd
Bike: 2:53 (19.3 mph)
Run: 1:49 (8:23min/mi)
Total: 5:15
What I did well: Biked hard but didn’t overdo it. Hydrated and ate frequently and regularly. Ran at a consistent pace and pushed through a crushing mile 10-12 with a headwind. Transitions were smooth, especially T2.
To improve: Swim – more time in the pool, ocean swims in choppy water would have made a difference in the time. I was in the bottom half of swim finishers. I’m on a Specialized Allez roadie I bought used and also commute on. I think the move to a tri bike would make a big improvement.
Training: Averaged 8-10 hours a week for the past 5 months. Typically 1 swim/wk. Two week vacation at start of August with only 4 runs for workouts.

What’s next? Not sure. For now some R&R and big meals will do me well. I’m considering pursuing triathlon seriously depending on where I end up for grad school, but that remains to be seen. A huge thanks to everyone who supported me taining for this race, especially my parents who came to the Vineyard and cheered me on!

img_1147 14242474_10154506963808185_4976022130544699371_o 14352173_10154506963583185_6985096982362154061_o

4 things I learned from keynote lectures at SCS2016

SCS2016 featured keynote lectures by two senior scientists in computational biology. John Quackenbush and Janet Thornton each shared scientific findings and expert advice to the students listening eagerly in the audience. I came away from the lectures with a few ideas I will keep in mind for both my daily research work and future career planning:

  1. “All models are wrong, but some are useful.” John Quackenbush opened his talk with this well-known quote attributed to George Box. He explained that many of the network models researchers in his group create are inherently flawed — and that’s OK! No model is perfect, but good ones can solve the problem at hand.
    This is definitely something I can apply to my research — It’s easy to get bogged down thinking about the small flaws in models I come up with or methods I use. It’s better to ask “is this useful?” than “is this perfect?”
  2. “You have to work hard, and it only gets harder.” Tough words to hear from Janet Thornton, who described her path from student, to PI, to eventual director of European Bioinformatics Institute. Janet described how she thought each career advancement would bring a decrease in the amount of work required for success. Just the opposite, she discovered. Each transition brought more work and more responsibilities, but these were balanced out by an increase in excitement. Higher-level responsibilities and mentoring younger students made the increased workload worth it.
  3. “Every revolution in science has been driven by one and only one thing: access to data.” John Quackenbush described how data used to be siloed away in the towers of the elite. Access was hard to obtain — due to both policy and logistical constraints — and science moved slowly as a result. We are slowly entering a culture of data sharing, driven by the obvious results of collaboration and the means to be able to share globally and instantaneously. John was excited about the potential for science in the future as data sharing becomes even more common, and I am too!
  4. “Communication is the hardest part, and the most important.” Janet Thornton selected communication as the single most difficult part of her career. She named it the sole factor that could make or break a project, collaboration or organization. I thoroughly agree with this statement (enough to make it the theme of my blog on organizing SCS2016) but was surprised that she still considers it a challenge. Effective communication takes practice, but can be very rewarding — whether it’s a Nature paper, innovative collaborative project or a successful international symposium!

The keynote lectures of SCS2016 were special. Senior scientists gave us a view not only into their thoughts on research, but also their ideas about careers, communication and the scientific process as a whole. Students have a lot to learn from mentors like John Quackenbush and Janet Thornton, and these lessons will stick with me for a long time.

This post was originally posted in the PLOS Computational Biology Field Reports Blog.

How do you organize an international symposium?

One word: communication.

I was approached by the ISCB Student Council leadership almost a year ago with an invitation to work as the co-chair for SCS2016. Yesterday, students from around the globe came together to share their research in computational biology here in Orlando. Throughout the many month-long organizing process, one theme stayed constant: the importance of communication.

It’s communication that convinces senior faculty to travel and give keynote lectures. Communication that persuades pharmaceutical and publishing companies to sponsor travel fellowships and our networking event. Communication that gets the word out to students around the world, communication that enables us scientist to speak in a common language despite different backgrounds, educations, accents and opinions. And most importantly, communication that allows students in different time zones come together and work to put an event like SCS2016 together.

To this end, a few practical tips: Doodle polls with timezone support are key for organizing meetings with people from different parts of the world. Skype or other web-based group calls keep people together and on track. To-do lists and documents of people’s responsibilities prevent you from forgetting what was decided at the last meeting. Gentle reminders via email are sometimes needed to make sure deadlines are met.

I learned a lot about the way I work with people. I’m quick to take on additional responsibilities if I feel I can complete a task quicker than delegating it out to someone else. I had to learn that “fast” or “better” isn’t always the end goal. It can be much more rewarding to give the responsibility to someone else and let them learn from it.

Inevitably, communication will break down at some point in the process. At this time, responsibilities fall on the head organizers to complete what needs to be done, even if it involves losing sleep!

Organizing SCS2016 was a lot of work, especially in the few weeks before the conference. Was it worth it? Without a doubt. I’m grateful for the opportunity I had to learn and work with other motivated students, and I’m proud of the event we pulled off yesterday!

This post was originally posted in the PLOS Computational Biology Field Reports Blog.

Martha’s Vineyard 70.3 triathlon

I’ve been interested in doing a triathlon for a while now – the combination of swim, bike and run is an excellent test of fitness, endurance and skill. Last week I finally pulled the trigger and signed up for the half-ironman distance triathlon on Martha’s Vineyard in September. It’s a beautiful course (the bike is basically a tour of the whole island) and will be a good event to focus my training on over the next few months. I think this is a good event for me for a few reasons:

  • 70.3 will be a challenge but not impossible with training. That’s a 1.2 mile swim, 56 mile bike and 13.1 mile run. I’m more interested in the endurance aspect than how fast I can finish the course.
  • It’s over six months away. I plan to train seriously for four months. This will give me plenty of time to work out the kinks in my training and do a sprint/olympic tri to practice.
  • Training will happen in the summer. It’s tough to find a pool to swim in around Boston, so I’m planning to do a lot of my training in Walden Pond, Upper Mystic Pond and the ocean when I’m back on Cape Cod.


    Just look at that bike route!

I plan to start training for the 70.3 in May. Until then I’m focusing on lifting and seeing how far I can push my squat, bench, deadlift and press. It’s fun to set goals and see your progress! You can follow me on the blog and Strava.

Road Trip: Final Numbers and Thoughts

Back home on the East Coast, I started to reflect on the trip that had occupied the past month of my life. There were so many things I learned about traveling, driving, relationships, the outdoors and my own personality.

Overall thoughts: This trip was meant to be an exploration into parts of the US that I hadn’t yet visited. I think it served that goal very well. A breadth-first exploration into what the midwest and west coast have to offer. If I had to go back I wouldn’t change the overall format of the trip, but I wouldn’t do the same thing again. I wish I had much more time – a month for each leg of travel would be ideal. With that in mind, my future travel in the US will be more focused and directed.

Final stats: 9800 miles, 30 states, 32 days, 8 National Parks, 1 breakdown and over $900 in gas.

Items I couldn’t have done without
National Parks Annual Pass: for $80 you get a pass covering admission into all National Parks and National Historic Sites. This turned out to be one of the best deals out there. It paid for itself at least twice over and gave me a freedom to visit what sites I chose without worrying about cost. It speeds up entrance into the parks, and I’ve even been able to use it at some federal recreation sites since being back in Boston. Bottom line: if you are planning to visit several NPs in a year, get this pass!
Osprey Hydration Bladder: I bought a 3L “camelbak” before the trip and used it daily. Always convenient when hiking, and actually really nice when driving. I stuck it in the cooler behind the drivers seat and extended the hose over my shoulder. I always had ice cold water without having to fiddle with a bottle.  
Slim Cooler: Fit well in the back seat of the car and gave me more options for carrying food. Refilling ice is a pain (especially when driving through the desert) but was well worth it. Gave me a spot to keep my water cold and chill beer also.

Things I didn’t really need
As much canned food: I brought a lot of extra stuff I had when I moved out of my apartment. I ended up enjoying shopping for fresh ingredients when in town, and returned with some things I hoped I would never see again!

What I wish I had packed
The filter cap to my Aeropress: critical mistake that was realized early on.
My road bike: Definitely not a practical choice with the size of my car and the companions on my trip, but there are so many incredible bike routes out west. I would love to go back and bike through the Tetons into Jackson WY, for example.
More downloaded music: I relied on Google Play music for much of the trip, which didn’t hold up in a lot of areas because of lack of data service. I would have created more playlists and cached them on my phone beforehand. And I would have made them LONG – 12 hours of music might sound like a lot, but it can go by pretty quickly…




Road Trip: Shenandoah NP to Boston, MA

I had to include a trip on Skyline Drive through Shenandoah on my route back. I visited once on a backpacking trip with the Brown Outing Club 3 years ago and couldn’t wait to see it again. I came to the Southern entrance in the early morning and drove North, stopping for a few short hikes, including one down to the Rapidan Camp, president Hoover’s summertime retreat. Apparently he loved to fly fish in the river here!

2015-06-28 08.20.08 2015-06-28 11.07.11

Skyline drive is a winding mountain road through the entirety of Shenandoah. There are lookouts with views of mountains and the valley below and plenty of places to stop and have a picnic. It’s a great road to drive slowly (because of what you’re seeing out the window) and fast (because it’s windy, hilly and feels like a rollercoaster through the mountains).

After Shenandoah I drove to the Pinchot trail system in Eastern PA to spend the night in the backcountry. This was my last night camping on the trip, and it ended up being kind of a pain. I didn’t have much food left and settled for an average-tasting chickpea stew dinner (seen here cooking away on the pocket rocket after dark).

2015-06-28 21.41.18

It started raining soon after, and I crawled into my hammock for a wet and chilly night where I didn’t sleep much. I remember thinking that I was glad to be heading back to civilization soon – 10 days of being on the road and in the woods alone had taken their toll, and I was looking forward to some comfortable accommodations and good company. Luckily, that was right ahead.

I left PA the next morning and drove through New Haven CT, where my friend Gordon recently started working. We grabbed lunch (mmm turkey and bacon!) and caught up about Life Since Brown. After that, I headed to Boston for a night and back home to Cape Cod!

One final post will sum up my thoughts on this trip overall.

Route traveled:

Screen Shot 2016-01-01 at 2.48.43 PM

Road Trip: Nashville to Atlanta

Next stop: Nashville. The city of Country Music and BBQ was alive to welcome me when I arrived in the early afternoon.

I tried to stop at the famous Cafe Loveless for lunch, but they had over an hour wait! I ended up getting my BBQ fix at Peg Leg Porker. Pulled pork, smoked green beans and bacon mac & cheese. Just what the doctor ordered.


I toured around downtown and Broadway street for a few hours, hopping in and out of bars to catch some music. It was early afternoon on a week day and the parties had already started! Every bar shad a live country singer or band. The artists were talented and obviously trying to make it among the huge competition in Nashville.

On the road again and I was headed to Atlanta, GA to stay with my cousin Lindsay for the night. She was doing her post-doc at Emory University and I was excited to see her and catch up on family gossip. The highlight of the stay was definitely brunch at The Flying Biscuit Cafe. We shared oatmeal pancakes with warm peach jam, incredibly cheesy grits, eggs, sausage and biscuits, and left feeling like we had eaten a meal enough for 4! Definitely recommend anyone in Atlanta check out that spot, but be prepared to wait for a table on a busy morning!


Lindsay and I did some grocery shopping at Trader Joe’s and parted ways. I only had a 7 hour drive until my destination for the night: a dispersed camping area in the George Washington and Jefferson National Forest, at the Jennings Creek area. Once again, I was able to stay for free on Federal Land, leave no trace and leave in peace.