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.

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!

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.

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.

The Connectivity Map team at the Broad Institute is crowdsourcing solutions to a computational problem in our line of work. Can you build a predictive model for gene expression better than we can? Prizes up to $10,000!

Check out the contest description here.

A 24 hour adventure race through Boston! Involving lots of biking and pretzels.

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.