Sunday, August 5, 2012

Remembering Chris Abajian

Chris Abajian was a change catalyst.  Using a biochemical analogy, passion, creativity, and intellect were his catalytic triad. Together, with Joe Slagel, Chris, and I started Geospiza in 1997.  Sadly, Chris recently died in a hiking accident (7/30/12).  In remembrance, I'll share a few stories from our times together.

I met Chris during my Postdoc in Leroy Hood's laboratory in 1994.  This was the early days of the human genome project and we hired Chris, because in Lee's view we were going to build the best software if we had professional software engineers on the team. Lee was right.

Chris accepted our offer and from his first day, he made it clear this was not just a job where he could  apply his software development talents, it was an opportunity to have an impact.  And he did.


Chris used his passion, creativity and intellect to identify problems that needed to be solved, and then advocate creative solutions, passionately. One of his first programs was Sputnik - a tool that identifies microsatellite sequences.  Sputnik was inspired by a co-worker of ours Lee Rowen.  One day Chris observed Lee hunched over a ream of paper with printed DNA sequences one hand and a highlighter in the other. When he inquired as to what she was doing she responded "identifying microsatelites."

New to biology Chris asked what those were.  Lee explained that they are small repeating patterns of di, tri, tetra, or slightly longer sequences and that we are interested in them because they can be involved in disease and change gene regulation.  Chris quickly went to work. He talked to everyone around, learned that the repeated patterns were not always perfect and used this information to develop an algorithm and scoring table that could identify micro-satellite patterns with pretty good accuracy.  

Today a google search on "sputnik microsatellite" or "sputnik-microsatelite" yields ~191,000 or ~65,000 hits, respectively.  What's even more interesting is the number of papers, 12 and 15 years later, that compare different microsatellite algorithms to sputnik [1,2].  Not bad for a music major without any formal biology training!


After sputnik, Chris turned his attention to the next problem.  This was in the early days of Phred and Phrap (P. Green, still unpublished) and we had no way to work with DNA sequence assemblies in graphical user interface (GUI).   Not everyone was convinced we needed to build a whole new application. It would be a significant undertaking and other tools could be hacked to view Phrap assemblies.  This is when we learned that when Chris set out to do something, he was going to get it done and do so convincingly. To Chris, and some others, it was clear Phrap needed its own GUI, so he set to work, debated the points and got buy-in. In collaboration with David Gordon, Chris proceeded to build Consed.  Chris worked on the project for only a short time, but the work was a success. 17 years later, David has developed a large loyal user base and continues to develop new features for Consed [3].

The hunt for BRCA1

Chris and I worked closely on many software development projects, starting with data delivery for BRCA1. In 1994, we were asked to help "hunt" for the gene. In collaboration with Mary-Claire King, Francis Collins, Maynard Olson, and Lee Hood, we set out to find the BRCA1 gene. It had been previously localized to a large region of chromosome 17 by the King and Collins groups, and they had created a cosmid library of the region. With the high-throughput sequencing technology of 1994 we could include DNA sequencing in our strategy; one cosmid at a time.  So, our job in the lab was to get cosmid DNA clones from the King and Collins libraries, sequence them and make the data available to everyone -  simultaneously. How were we going to do that?

With web-technology

In 1994 the Mosiac web browser was new.  Chris suggested that we could post the sequences to website and send emails to the respective parties when the data was posted. Problem solved!

During this time, I was learning to program and developing automation systems. It was a no brainer and we set to work, Chris created a framework that I could use to create automation scripts. This was going to be a theme that would result in several more successful projects and lead to the next adventure. 


One day in April of 1997, Chris, Joe, and myself squeezed into the cab of Chris's small Toyota truck and headed to airport to interview with a new bioinformatics company called Pangea.  We were hired, but it was soon clear that we needed to do something different.  After a few rounds of passionate conversation we knew we were going to form a company, and we did.

Geospiza started in October of 1997 and while Chris was with us for only a short period of time, he made contributions that would last. Geospiza continues, now within PerkinElmer and there are probably still a few lines of his original code working within our LIMS system.

It's amazing to think about his accomplishments over the four years we spent together.  We enjoyed many good times discussing science, literature, and music. Chris will be missed.

1. Kofler, R. (2007-07-01) SciRoKo: a new tool for whole genome microsatellite search and investigation. Bioinformatics, 7(4), 524-1685. DOI: 10.1093/bioinformatics/btm157

2. Leclercq, S. (2007) Detecting microsatellites within genomes: significant variation among algorithms. BMC Bioinformatics, 8(1), 125. DOI: 10.1186/1471-2105-8-125

3. David Gordon, Chris Abajian, and Phil Green. Consed: a graphical tool for sequence finishing. Genome Res. 1998. 8: 195-202