Wednesday, April 24, 2019

Want to Run An Exciting Sequencing Group? Ginkgo Is Looking for You!

I've awakened from my blogging torpor to point out a really interesting career opportunity for the types who might read this space. Ginkgo Bioworks, one of the leading synthetic biology companies in the world, is looking for someone to run their existing Next Generation Sequencing group. It's a chance to run an energetic high-throughput sequencing group that works on a wide range of projects. And, as you might of guessed from the fact I'm writing about it here, you'd also get to be my boss. I'm hoping many will see that as a feature and not a bug.
Of course, the fact that I jumped jobs in February is itself an overdue update, with many possible angles to cover -- how and why I got here, what it's like joining the company, all sorts of professional upgrades I've been undertaking (in particular, finally switching from Perl to Python.  But let's focus on the open job.  Let's particularly not focus on how the person who hired me opted for the exits soon after I started.  (Was it something I said?) Seriously she got an amazing offer to take on the CSO role at a new, well-financed Cambridge startup/spin-out working on sequencing tech.

Ginkgo bills itself as "The Organism Company".  Most of the business falls into two categories: a customer either has something they produce by fermentation and would like the organism's performance kicked up a notch (Bam!), or they'd like to produce something by fermentation but need an organism designed to do it.

An organizational principle at Ginkgo is a rough division of effort between Program Teams and The Foundry.  Program Teams work on specific programs for specific customers, but do so as much as possible by using central services provided by The Foundry.  Foundry teams provide a broad array of widely applicable methods based around a Design-Build-Test (DBT) model.  The NGS group is somewhat unusual among Foundry groups in that we play a key role in all three phases.

Design relies on having biological parts, and when the public databases or other available resources are insufficient, sequencing is a way to find more candidate parts.  A neat example of this was recently highlighted in Scientific American (or watch the video), in which Ginkgo scientists performed transcriptome sequencing on a museum specimen of an extinct plant in order to express enzymes responsible for scent production  -- Jurassic Park but with perfume and no rampages of genetically-modified organisms. Sequencing is also an important part of bringing a new organism into the Design space ("on-boarding"), establishing a reference genome and transcriptome and identifying promoters and their strengths.

Build covers all aspects of creating and assembling genetic parts.  Ginkgo has their own serious gene fabrication component as a result of the acquisition several years ago of Gen9, and also has a mongo deal with Twist.  The internal group builds and rearranges parts, moving components between vectors or generating combinatorial libraries or protein engineering libraries.  All of that needs verifying, which is obviously a use for sequencing firepower.

Test is often the domain of other techniques -- optical and mass spec -- but sequencing often plays a role as well.  Selection experiments on various sorts of variant libraries can be read by sequencing as can transcriptional readouts.  And if results aren't what's expected, sequencing can be a way of debugging constructs or experiments.

In terms of equipment, we have a nice little zoo.  On the Illumina side the workhorse is a NovaSeq but there are also NextSeqs and MiSeqs.  Plus a 10X Chromium controller.  For long reads, there's a complete set of Oxford Nanopore instruments: one PromethION, two GridIONs and a bunch of MinIONs.  All that is backed up by a eye-watering fleet of automation -- Hamiltons and Echos and many others.

An interesting aspect of the sequencing is that since it serves the DBT cycle and that cycle is time-sensitive, we don't optimize for minimum cost -- which has always been the way I've always been forced to live in the past.  Rather, it is more like the commuter train I use every day -- Illumina runs are scheduled at regular times and whatever is ready to go hops aboard a flowcell. 

The group has nearly a dozen energetic, talented scientists split into two general categories.  There's three of us who focus on informatics.  One person is in the lab but spends much of their time writing Python to drive the automation to ever greater performance.  Others operate the production facilities and perform development.  That's a very crude sketch -- the reality is that everyone participates in development and there are no hard lines between jobs (well, other than don't let the blogger drive the NovaSeq!) - cross-functional training is routine.

The standard production services cover broad swaths of sequencing needs, but many projects aren't well served by these -- so there's always lots of special projects that serve both to cover immediate needs and pilot new technologies.  Special projects are great fun -- people actually listen to my crazy ideas for fishing interesting genes out of metagenomes or resolving subtle mutants from complex libraries. Or how can you adapt cool artisanal technique X on thousands and thousands of samples at once?  For one project I'm competing about half a dozen approaches against each other to find a winner (and half of those are externalized -- great opportunities here to collaborate with both startups and established players in the sequencing space).  We're always fermenting both ideas and molecules!

What sort of projects?  Well, we work on over two dozen different fungal and bacterial organisms.  We have a major collaboration in the plant space, working to produce cannabinoids by fermentation.  There's also a new "Bioworks", as the laboratory spaces are called, that is aimed at mammalian work.

Does this sound interesting?  If it does, I'm happy to chat more about it -- krobison at ginkgobioworks dot com or DM me on Twitter.  Obviously you can also just throw your hat into the ring via the official job posting.   And BTW, we're also looking for a Research Associate in the group -- these are just two of many positions open due to Ginkgo's growth in the hot Boston/Cambridge biotech environment.

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