ISCB student council 2014

I submitted some research I’ve been working on (as a byproduct of TAing a first year seminar and leading some students in an independent bioinformatics project) to the International Society for Computational Biology student council symposium. Yesterday I found out it was selected for an oral presentation! This is the first chance I’ve had to present independent research, so needless to say I’m pretty excited.

The talk is titled “Tetranucleotide usage in mycobacteriophage genomes: alignment-free methods to cluster phage and infer evolutionary relationships” Read on for the full abstract.

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Finished with junior year!

I handed in the final assignment of the semester yesterday, which marked the end of my Junior year at Brown. I can safely say it was the best year I’ve had so far, with the first semester spent abroad in Budapest and the second back in the states. Looking back, I accomplished and learned a huge amount about traveling, bioinformatics, the research process, cooking, the professional environment in biotech and myself as a person.

Today I’m headed up to my friend’s house off the coast of Portland, Maine for some much needed decompression time. I’ll be back in Providence for the summer, though. As a recipient of Brown’s UTRA award I’ll be spending my summer working for Dr. Nicola Neretti on a computational epigenetics project. The project I’m working on will likely continue for my senior thesis, so stay tuned!

Blogs I follow

I don’t know how they find the time to do it, but many of today’s top bioinformatics and computational biology researchers have a regularly updated blog. Reading some of them actually gave me the inspiration to start Blogging Bioinformatics: I liked the idea of having a space where I can talk about research and other topics that interest me. Here’s a list of a few blogs I read regularly. It’s nowhere near complete, and I’m always looking for new suggestions of new people to follow.

  • runs an exceptional bioinformatics blog. They have regularly updated content covering new research, funding situations, and commentaries on issues in the bioinformatics field.
  • assertTrue() by Kas Thomas covers interesting topics and new research in biology and bioinformatics. Many of his recent posts discuss how published genomes are too often “auto annotated,” leading to an abundance meaningless gene calls and hypothetical proteins.
  • Living in an Ivory Basement where Titus Brown talks about bioinformatics, programming and teaching. I’ve previously mentioned content from his site in defense of publishing code for my computational biology classes on my GitHub.
  • Judge Starling by Dan Graur has posts about bioinformatics mixed in with poetry, musings about modern research practices and commentary on ENCODE (which seems to be a popular topic to blog about these days… everyone has an opinion on the consortium).
  • Bits of DNA by Lior Pachter isn’t updated as frequently but the content is always extremely well thought out and backed up by solid reasoning. Lior uses the blog to comment on issues in the computational biology and bioinformatics fields, like ENCODE, missuses of statistics in research and the state of funding in the US.
  • The Mermaid’s Tale – I just added this blog to my list, the first post currently is about a new study of resveratrol (remember how drinking red wine was supposed to extend your life?) and how it didn’t uncover any measurable benefit of the chemical. The real question: which body of research should be treated as fact?
  • Job Etiquette by Paula – A blog I started reading after the Brown Club of Boston Biotech Conference. Paula Freeman discusses advice for young people searching for a job and has excellent content about resumés, interviews and job etiquette in general.

Know of another blog I should add to the list? Let me know in the comments!

Husband and wife start PhD after learning of disease

Eric Minikel and Sonia Vallabh were working as an urban planner and a lawyer until 2011, when they learned Sonia has a rare heritable disease – Fatal Familial Insomnia (FFI). FFI is caused by a mutation in the PRNP gene, which encodes prion protein PrP. Although the function of PrP isn’t precisely known, the mutated form can misfold the normal form of the protein (FFI a prion disease). 

After receiving the unfortunate news from a genetic test, Eric and Sonia decided to devote their life to researching FFI. Both left their jobs for research positions at Massachusetts General Hospital. They soon started a scientific blog,, where they discuss their research progress and next steps. In addition, Eric and Sonia founded Prion Alliance, a nonprofit devoted to funding prion disease research.

Now, Eric and Sonia have decided to take their research one step further: both will be starting PhDs at Harvard Medical School in the fall. Eric has turned his previous computational and analysis skills toward bioinformatics:

 “My thesis was on analyzing bicycle-accident data, and I worked with my advisor, Professor Joe Ferreira, on an analysis of Massachusetts vehicle accident and insurance data. In the course of this, I learned to code in R and to manage SQL databases, both hard skills that I use every day now in the bioinformatics world. More broadly, writing my thesis taught me how to frame and answer a research question, which has been invaluable,” he said.

Eric and Sonia’s story is truly inspiring. In the face of a diagnosis that is basically a death sentence, they chose to fight back and devote their life to prion disease research. I guess it’s never too late to get a PhD!

Publishing code on GitHub

This semester, I’ve made an effort to get all the code I write under version control. In the past I simply maintained my codebase in Dropbox. This worked well as a backup solution and allowed me to develop the same project on my laptop and desktop without any problems (despite dealing with differences in Windows/Linux file paths). However, I’ve been involved in more collaborative coding projects this semester and Dropbox simply doesn’t cut it anymore.

Bioinformaticians as a group seem to be particularly passionate about version control and open access software – Titus Brown even says, ” If you can’t be bothered to learn how to use version control, you shouldn’t be trusted to write important software.” This goes along with the open source and open access movement academics generally tend to support. Plus, we’ve all had the experience of working with poorly maintained, documented or commented code… It can really slow down the research process and be a huge hassle.

So, I’ve made a new commitment. Every piece of code I write for an academic project will be under version control on GitHub. Code for lab work that we’ve decided to publish will also make its way there (for the time being it’s held in a private bitbucket repository, still under version control though!) This is a bit of a challenge for me – publishing code is a lot like publishing something you’ve written. You’re putting your work out there for the world to see and critique, and in a lot of cases, it’s not a finished product or something you’re quite happy with yet.

I see a lot of advantages to making code public. It should help me develop better structured, more thoughtful and well-commented code. It will allow me to share projects and ideas with anyone just by giving them my GitHub username (hint: it’s bsiranosian). I can now include my GitHub url on things like my website and business cards, and anyone can see the kind of projects I work on. I feel like this could give me a leg up when searching for jobs and the like.

I can see a few downsides too. Academic integrity is one – I don’t want someone at Brown or another university copying my code for their homework or project. After thinking about this point though, I realized the answers to most bioinformatics problems are already available at places like stackoverflow. It’s not my responsibility to make sure someone doesn’t plagiarize code. Titus Brown teaches an undergraduate class where students are required to hand in assignments on GitHub and hasn’t had any problems.

You can find my GitHub at