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Conference coverage: SynBioBeta London 2016

Beginning Wednesday April 6th, synthetic biology industry leaders, entrepreneurs, investors, and academics will convene at Imperial College London for SynBioBeta London 2016. During the three-day conference, companies such as Transcriptic and Twist Bioscience are offering free workshops on topics ranging from cloud-based wetlab experiments to CRISPR library design. Speakers from major companies in the synthetic biology space, such as Ginkgo Bioworks and Gen9 will give talks and participate in panel discussions on their visions for the field’s future. Attendees also have the opportunity to learn about grassroots efforts to promote citizen science from speakers affiliated with the New York City’s community biolab, Genspace, and the kickstarter-funded take-anywhere genetics toolkit-in-a-box, BentoLab.

Representing the PLOS SynBio community at the conference, Eric van der Helm, a PhD student at the Technical University of Denmark’s Novo Nordisk Foundation Center for Biosustainability, will be live-tweeting from the sessions he attends. Follow the PLOS SynBio twitter feed for real-time updates, and be sure to read Eric’s reflection on his experience after the meeting concludes.

PLOS SynBio's eyes and ears for the next few days
PLOS SynBio’s eyes and ears for the next few days

Eric did his bachelor degree in Biomedical Engineering at the Eindhoven University of Technology (TU/e) in The Netherlands. Subsequently he carried out his Master thesis in the group of Maarten Merkx finishing in 2012. His master’s research focused on the design of fluorescent proteins to sense relevant biomolecules. During the master track Eric traveled to the University of Washington Seattle (UW) in the USA as a visiting research scientist to work on the computational design of protein-protein interactions involved in cancer immunotherapy in the group of David Baker. Upon returning to Europe he started his PhD under the mentorship of Professor Morten O.A. Sommer, who leads the Center for Biosustainability’s Drug Resistance and Community Dynamics group as well as the Phenotypic Stability group.  The team takes multiple approaches to study microbial communities, combat the emergence of antibiotic resistance, engineer synthetic platforms, and understand microbial evolution–including constructing genetic circuits to screen for novel molecules soil, applying nanopore sequencing technology to weed through metagenomic DNA, and occasionally 3D printing lab gadgets.

Last year Eric was lead author on a paper in BMC Research Notes describing the development of a user-friendly, online interface for processing, annotating, and visualizing metagenomic sequencing data. The tool, called deFUME, can help identify novel-gene-needles in complex-community-haystacks from among the thousands of candidate clones and billions of sequencing reads generated by a single functional selection experiment.

Where IS that cellulase activity coming from?
Where IS that cellobiose dehydrogenase activity coming from?

Combining multiple analysis steps into one workflow can eliminate bottlenecks. The deFUME server assembles metagenomic sequence reads, predicts open reading frames, and annotates candidate loci using GO, BLAST, and InterPro classifiers, then generates an easy-to-navigate visual overview.

Screenshot of deFUME output
Much more efficient than going through everything by hand!

When Eric is not wearing a lab coat, nor behind his computer he can be found on the Øresund between Denmark and Sweden in a sailboat, or hiking down Skåneleden in the forests of Sweden.


We’re thrilled that Eric will be attending SynBioBeta London 2016, and offering his perspective on the innovative science presented at the meeting! His itinerary is already jam-packed with interesting talks and workshops, but he’d love to say hello to other members of the PLOS SynBio Community who are attending the event! Leave a comment on this post if you have any questions for Eric, and be sure to watch the PLOS SynBio Twitter for up-to-the-minute updates!

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