Nathan Hillson

Research Goal

To lead the continuous development and maintenance of SynBio software and laboratory automation infrastructure, and operation of DIVA services.

Projects

ICE Repository of microbial strains, (DNA and protein) sequences, and plant seeds/lines
Bioparts.org Search portal across repositories of strains and sequences (ICE and beyond)

DIVA DNA Design, Implementation, Validation, Automation platform and services
EDD Experiment Data Depot

Featured Media

First Author Conversations Podcast. Episode 3: Application of Synthetic Biology

Understanding and Designing Flanking Homology DNA Assembly Experiments

Nathan Hillson talks with the Risk Group about the: “BioEconomy: Promise and Perils of Synthetic Biology”

Nathan Hillson talks at National Academics Biotech Study Second Public Meeting

Session 2: Enabling Tools

Session 6: Tools Enhancing Risk Analysis

Nathan Hillson talks about the role of software development at JBEI

Microfluidic Device Mixes And Matches DNA For Synthetic Biology

Cold Spring Harbor Laboratory Seminar: Synthetic Biology Scalability and Responsible Innovation

Training Your Robot the PR-PR Way

Latest JBEI Startup to Speed Up Biotech Industry

DNA Construction Software Saves Time, Resources and Money

Featured Publications

“The tier system: a host development framework for bioengineering” Current Opinion in Biotechnology (2025)
“Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida” Commun Biol (2025)
“Binary vector copy number engineering improves Agrobacterium-mediated transformation“. Nat Biotechnol (2024)
“Bioinformatic prediction and high throughput in vivo screening to identify cis-regulatory elements for the development of algal synthetic promoters” ACS Synthetic Biology (2024)
“A Biomanufacturing Plan to Confront Future Biological Threats: Expert Panel Policy Review and Near-Term Recommendations” Council on Strategic Risks (2024)
“Automated Platform for the Plasmid Construction Process” ACS Synthetic Biology (2023)
“Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format” PLOS ONE (2023)
“Ten simple rules for managing laboratory information.” PLoS computational biology (2023)
“A Procedural Framework for Benchmarking Biofoundry Capabilities“ ACS Synthetic Biology (2023)
“Introduction to the Special Issue on BioFoundries and Cloud Laboratories” J. Emerg. Technol. Comput. Syst (2023)
“Artificial Intelligence and Machine Learning for Bioenergy Research: Opportunities and
Challenges” U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy (2023)
“Biorisk Management Case Study: United States Department of Energy Joint Genome Institute” Stanford Digital Repository (2023)
“Perspectives for self-driving labs in synthetic biology” Current Opinion in Biotechnology (2023)
“Scalable and automated CRISPR-based strain engineering using droplet microfluidics” Microsyst Nanoeng (2022)
“Modular automated bottom-up proteomic sample preparation for high-throughput Applications”. PLoS ONE (2022)
“Making Security Viral: Shifting Engineering Biology Culture and Publishing”. ACS Synthetic Biology (2022)
“BioParts—A Biological Parts Search Portal and Updates to the ICE Parts Registry Software Platform” ACS Synthetic Biology (2021)
“Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid Production in Aspergillus pseudoterreus” Frontiers in Bioengineering and Biotechnology (2021)
“Multiomics Data Collection, Visualization, and Utilization for Guiding Metabolic Engineering“. Frontiers in Bioengineering and Biotechnology (2021)
“Machine learning for metabolic engineering: A review” Metabolic Engineering (2020)
“Repurposing a microfluidic formulation device for automated DNA construction” PLOS One (2020)
“An Integrated Computer-Aided Design and Manufacturing Workflow for Synthetic Biology” DNA Cloning and Assembly (2020)
“Combinatorial-Hierarchical DNA Library Design Using the TeselaGen DESIGN Module with j5” DNA Cloning and Assembly (2020)
“DNA Scanner: a web application for comparing DNA synthesis feasibility, price, and turnaround time across vendors” OUP Synthetic Biology (2020)
“Embrace experimentation in biosecurity governance” Science (2020)
“Adenosine Triphosphate and Carbon Efficient Route to Second Generation Biofuel Isopentanol” ACS Synthetic Biology (2020)
“Fluorescent amplification for next generation sequencing (FA-NGS) library preparation” BMC Genomics (2020)
“Enhancing Terminal Deoxynucleotidyl Transferase Activity on Substrates with 3′ Terminal Structures for Enzymatic De Novo DNA Synthesis” Genes (2020)
“Mevalonate Pathway Promiscuity Enables Noncanonical Terpene Production” ACS Synthetic Biology (2019)
“An automated ‘cells-to-peptides’ sample preparation workflow for high-throughput, quantitative proteomic assays of microbes” J Proteome Res (2019)
“Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases” J Ind Microbiol Biotechnol (2019)
“Lessons from Two Design–Build–Test–Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning” ACS Synthetic Biology (2019)
“New Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases” JIMB (2019)
“Building a global alliance of biofoundries“, Nature Communications (2019)
“Parallel Integration and Chromosomal Expansion of Metabolic Pathways“, ACS Synthetic Biology (2018)
“Jungle Express is a versatile repressor system for tight transcriptional control“, Nature Communications (2018)
“De novo DNA synthesis using polymerase-nucleotide conjugates“, Nature BioTech (2018)
“Biochemical Characterization of β-Amino Acid Incorporation in Fluvirucin B2 Biosynthesis“, ChemBioChem (2018)
“Isolation and characterization of novel mutations in the pSC101 origin that increase copy number“, Scientific Reports (2018)
“A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering” Yeast (2018)
“Oxidative cyclization of prodigiosin by an alkylglycerol monooxygenase-like enzyme”, Nature Chemical Biology (2017)
“The Experiment Data Depot: a web-based software tool for biological experimental data storage, sharing, and visualization”, ACS Synthetic Biology (2017)
“Droplet Microfluidics for Synthetic Biology”, Lab on a Chip (2017)
“Streamlining the Design-to-Build transition with Build-Optimization Software Tools (BOOST)”, ACS Synthetic Biology (2016)
“A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae”, Nucleic Acids Research (2016).
“Develop an improved metabolic engineering method for modifying microorganisms for biofuel production from cellulosic sugars”, JBEI end-of-year report (2016)
“New tools available for facilitating the design of engineered pathways in microorganisms for biofuel production from cellulosic sugars”, JBEI quarterly report (2016)
“Improving Synthetic Biology Communication: Recommended Practices for Visual Depiction and Digital Submission of Genetic Designs”, ACS Synthetic Biology (2016)
“Investigation of Proposed Ladderane Biosynthetic Genes from Anammox Bacteria by Heterologous Expression in E. coli“, PLOS ONE (2016)
“End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis”, J Biol Eng (2016)
“A Droplet Microfluidic Platform for Automating Genetic Engineering”, ACS Synthetic Biology (2016)
“SBOL Visual: A Graphical Language for Genetic Designs”, PLOS Biology (2015)
“A Versatile Microfluidic Device for Automating Synthetic Biology”, ACS Synthetic Biology (2015)
“Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals“, The National Academies Press (2015)
“The Joint Genome Institute’s synthetic biology internal review process”, Journal of Responsible Innovation (2015)
“Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering”, Metabolic Engineering (2014)
“Characterization of Wastewater Treatment Plant Microbial Communities and the Effects of Carbon Sources on Diversity in Laboratory Models”, PLOS ONE. (2014)
“The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology”, Nat Biotechnol. (2014)
“The Plant Glycosyltransferase Clone Collection for Functional Genomics”, Plant J. (2014)
“Cloud-Enabled Microscopy and Droplet Microfluidic Platform for Specific Detection of Escherichia coli in Water”, PLoS ONE (2014).
“PR-PR Cross-Platform Laboratory Automation System”, ACS Synthetic Biology (2014)
“j5 DNA Assembly Design Automation”, DNA Cloning and Assembly Methods (2014)
“Development of a broad-host synthetic biology toolbox for ralstonia eutropha and its application to engineering hydrocarbon biofuel production”, Microbial Cell Factories (2013)
” Proposed design of distributed macroalgal biorefineries: thermodynamics, bioconversion technology, and sustainability implications for developing economies”, Biofuels, Bioprod. Bioref. (2013)
“Engineering of Ralstonia eutropha H16 for Autotrophic and Heterotrophic Production of Methyl Ketones”, Appl. Environ. Microbiol. (2013)
“The Fusion of Biology, Computer Science, and Engineering – towards efficient and successful synthetic biology”, Perspectives in Biology and Medicine (2013)
“Functionalizing bacterial cell surfaces with a phage protein”, Chemical Communications (2013)
“Distributed marine biorefineries for developing economies”, Proceedings of the ASME 2012 International Mechanical Engineering Congress & Exposition (2012)
“PaR-PaR Laboratory Automation platform”, ACS Synthetic Biology (2012).
“Design, Implementation and Practice of JBEI-ICE: An Open Source Biological Part Registry Platform and Tools”, Nucleic Acids Research (2012)
“DeviceEditor visual biological CAD canvas”, Journal of Biological Engineering (2012).
“j5 DNA Assembly Design Automation Software”, ACS Synthetic Biology (2012)
“Microbial stress tolerance: from genomics to biofuels”, Microbial Stress Tolerance for Biofuels (2012)
“DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems”, Design and Analysis of Bio-molecular Circuits (2011)

Director of Synthetic Biology Informatics