written by Eric J. Ma on 2017-04-28

It is done! I have defended my doctoral thesis, supervised by Prof. Jonathan A. Runstadler, advised by Prof. Mark Bathe and Prof. Jukka-Pekka Onnela, conducted as a student in the Department of Biological Engineering at MIT.

Looking back, it's been an amazingly fun journey, and I'll be updating this space with a more detailed account of the thesis defence process. Stay tuned!

Thesis Defence!

written by Eric J. Ma on 2017-04-24

My thesis defence announcement has been made to the department!

Identification of Reassortant Influenza Viruses at Scale - Algorithm and Applications
Eric Ma


Reassortment is a reticulate evolutionary process that results in genome shuffling; the most prominent virus known to reassort is the influenza A virus. Methods to identify reassortant influenza viruses do not scale well beyond hundreds of isolates at a time, because they rely on phylogenetic reconstruction, a computationally expensive method. This thus hampers our ability to test systematically whether reassortment is associated with host switching events. In this thesis, I use phylogenetic heuristics to develop a new reassortment detection algorithm capable of finding reassortant viruses in tens of thousands viral isolates. Together with colleagues, we then use the algorithm to test whether reassortment events are over-represented in host switching events and whether reassortment is an alternative 'transmission strategy' for viral persistence.


Moving on from MIT

written by Eric J. Ma on 2017-04-21

It's my final week before defending my thesis.

The thesis has been submitted to my committee, and my slides, as usual, are being made until the last minute.

I've had a number of conversations with a number of people, both in person and via email, and a few recurring themes start showing up.

New Challenges

Scientists are artists in some senses, computational scientists particularly, and I think I'm ready for a new challenge.


People invariably ask, "What's next?" I tell them that I've ruled out a "traditional post-doc", and that I'm not wedded to the academic ivory tower, I'm wedded to my wife, and so if the timing doesn't work out for independent research fellows positions, I'm jumping out. Well, as things turned out, yes, I'm jumping out, and I'm looking forward to this new journey!

Data Science

A few months ago, I was pretty deflated with the job search. Interviews were slow to come, and I began to think that all the "hype" around life science DS was just that - hype - and that the demand wasn't there. A few months later, I'm proven wrong, and quite happily proven wrong too.


I signed the Insight Health Data Science Fellows contract, to join them for 7 weeks in the summer. Many were perplexed - isn't Insight all about getting a job? Not really. For me, it's about meeting like-minded individuals and being able to network with them.


I've done interviews at a few places now, and the response has been very positive. No offers yet, but nonetheless these are all places where I can foresee myself being valued for what I can contribute, while having fun working with colleagues on new problems.


The defence, at this point, has this magical effect of inducing anxiety at times, and feeling like "just another thing to do" at other times. I'm not sure what to make of this.


My thesis, as it turns out, is super duper short. The departmental average range is on the order of 100-400 pages. Mine stands at about 80, including references, with double-spaced text, and sometimes having one figure/table on one page. I think I've broken some departmental records here...


Someone asked, "Who is your defence audience going to be?" I've decided it'll be for my committee, who have supported my intellectual journey through infectious disease, computation, and data science. In some ways it's my "final performance" during grad school, a way of saluting their support.

As the clock winds down, I'm reminded of that phrase from Philippians:

... forgetting what lies behind and straining forward to what lies ahead... (Philippians 3:13-14)

Laurels, yes, I have acquired indeed. MIT is no slouchy place to graduate from, and it's a privilege to have this degree. I've had the privilege and opportunity to remake my skillset while having fun along the way. But it's no time to rest on my laurels. It's time to start serving the world through the skillset I have been given. Onward!

Staying Nimble

written by Eric J. Ma on 2017-04-07

As I wrap up grad school, one thought recurrently comes to mind: as we grow older, do we intrinsically lose mental agility, nimbleness and ability to learn? Or is it because of external factors that cause one to become less adventurous, less curious, and hence, less able to learn new things?

I find myself having flashes of fear crop up as I observe those who are older than me. They are stuck in between a hard place and a rock. Their skills may be on the wane (in terms of demand). They want to learn new things, but have to continue doing the old things to keep the ship afloat. I can imagine, it feels tough to be in that kind of position! Without the safety net to take a risk and learn something new, they may be stuck in a dying trade. Will I have to face the same fate? Is it avoidable, or even perhaps, surmountable?

The even harder part is staying intellectually nimble, and not being stuck in particular ways of thought. Is that an intrinsic property of aging, or not?

Just some questions I've been pondering...


written by Eric J. Ma on 2017-03-28

I've finally turned in a polished draft of my thesis (HTML or PDF) to my committee! My thesis topic is on the development of an algorithm to identify reassortant influenza viruses from large sequence databases, and its application to the study of influenza's evolution and ecology.

Well, actually, it was last week when I finished it, but I've been doing the job hunt the past week that I've delayed on writing this blog post.

Apart from the written summary of the work that I've been doing, I wanted to simultaneously write for PDFs and for the web, so I started assembling a software toolchain that compiles my raw markdown files, converts figures from PDF to JPG, and simultaneously builds the PDF and the HTML versions. A lot of Python packages, including csv2md, the pandoc-xnos series, and non-Python tools, including ImageMagick (

Yes, I know I could have done most of this with Authorea, but being me, building things and doing reverse engineering is also kind of fun! (Especially for learning purposes.)

I hope you enjoy my thesis!