Synthetic Biology Informatics

Featured Publications

• “Introduction to the Special Issue on BioFoundries and Cloud Laboratories” J. Emerg. Technol. Comput. Syst (2023)
• “Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format” 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 Energyt (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)
• “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)
• “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)
• “The Fusion of Biology, Computer Science, and Engineering – towards efficient and successful synthetic biology”, Perspectives in Biology and Medicine (2013)
• “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)
• “DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems”, Design and Analysis of Bio-molecular Circuits (2011)

Intellectual Property

• Scar-Less Multi-Part DNA Assembly Design Automation. (2019) U.S. Patent 11,749,379
• Scar-Less Multi-Part DNA Assembly Design Automation. (2016) U.S. Patent 10,373,703
• Scar-Less Multi-Part DNA Assembly Design Automation. (2012) U.S. Patent 9,361,427
• Microfluidic Platform for Synthetic Biology Applications. (2012) U.S. Patent Application US20120258487.