Douglas Michael Densmore

Douglas Michael Densmore
Boston University | BU · Department of Electrical and Computer Engineering

Doctor of Philosophy

About

135
Publications
20,440
Reads
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3,414
Citations
Additional affiliations
September 2010 - present
Boston University
Position
  • Professor (Associate)

Publications

Publications (135)
Article
Full-text available
Synthetic biology is the process of forward engineering living systems. These systems can be used to produce biobased materials, agriculture, medicine, and energy. One approach to designing these systems is to employ techniques from the design of embedded electronics. These techniques include abstraction, standards, modularity, automated design, an...
Article
Full-text available
Microfluidics has developed into a mature field with applications across science and engineering, having particular commercial success in molecular diagnostics, next-generation sequencing, and bench-top analysis. Despite its ubiquity, the complexity of designing and controlling custom microfluidic devices present major barriers to adoption, requiri...
Article
Full-text available
In 2019, the first cases of SARS-CoV-2 were detected in Wuhan, China, and by early 2020 the first cases were identified in the United States. SARS-CoV-2 infections increased in the US causing many states to implement stay-at-home orders and additional safety precautions to mitigate potential outbreaks. As policies changed throughout the pandemic an...
Article
Cells interact with their environment, communicate among themselves, track time and make decisions through functions controlled by natural regulatory genetic circuits consisting of interacting biological components. Synthetic programmable circuits used in therapeutics and other applications can be automatically designed by computer-aided tools. The...
Preprint
In protein sequences—as there are 61 sense codons but only 20 standard amino acids—most amino acids are encoded by more than one codon. Although such synonymous codons do not alter the encoded amino acid sequence, their selection can dramatically affect the expression of the resulting protein. Codon optimization of synthetic DNA sequences is import...
Preprint
Full-text available
In 2019, the first cases of SARS-CoV-2 were detected in Wuhan, China, and by early 2020 the cases were identified in the United States. SARS-CoV-2 infections increased in the US causing many states to implement stay-at-home orders and additional safety precautions to mitigate potential outbreaks. As policies changed throughout the pandemic and rest...
Article
Full-text available
Molecular biologists rely on the use of fluorescent probes to take measurements of their model systems. These fluorophores fall into various classes (e.g. fluorescent dyes, fluorescent proteins, etc.), but they all share some general properties (such as excitation and emission spectra, brightness) and require similar equipment for data acquisition....
Article
Full-text available
Droplet-based microfluidic devices hold immense potential in becoming inexpensive alternatives to existing screening platforms across life science applications, such as enzyme discovery and early cancer detection. However, the lack of a predictive understanding of droplet generation makes engineering a droplet-based platform an iterative and resour...
Article
Full-text available
Cells can be programmed to monitor and react to their environment using genetic circuits. Design automation software maps a desired circuit function to a DNA sequence, a process that requires units of gene regulation (gates) that are simple to connect and behave predictably. This poses a challenge for eukaryotes due to their complex mechanisms of t...
Article
Full-text available
Electrode integration significantly increases the versatility of droplet microfluidics, enabling label-free sensing and manipulation at a single-droplet (single-cell) resolution. However, common fabrication techniques for integrating electronics into microfluidics are expensive, time-consuming, and can require cleanroom facilities. Here, we present...
Preprint
Full-text available
Molecular biologists rely on the use of fluorescent probes to take measurements of their model systems. These fluorophores fall into various classes (e.g. fluorescent dyes, fluorescent proteins, etc.), but they all share some general properties (such as emission and excitation spectra, brightness) and require similar equipment for data acquisition....
Article
Full-text available
There was an explosion in the amount of commercially available DNA in sequence repositories over the last decade. The number of such plasmids increased from 12,000 to over 300,000 among three of the largest repositories: iGEM, Addgene, and DNASU. A challenge in biodesign remains how to use these and other repository-based sequences effectively, cor...
Preprint
Full-text available
There was an explosion in the amount of commercially available DNA in sequence repositories over the last decade. The number of such plasmids increased from 12,000 to over 300,000 among three of the largest repositories: iGEM, Addgene, and DNASU. The challenge in biodesign remains how to use these and other repository-based sequences effectively, c...
Article
Full-text available
The design of microfluidic Lab on a Chip (LoC) systems is an onerous task requiring specialized skills in fluid dynamics, mechanical design drafting, and manufacturing. Engineers face significant challenges during the labor-intensive process of designing microfluidic devices, with very few specialized tools that help automate the process. Typical d...
Article
Full-text available
Most digital electronic circuits utilize a timing reference to synchronize the progression of signals and enable sequential memory elements. These designs may not be realizable in biological substrates due to the lack of a reliable high-frequency clock signal. Asynchronous designs eliminate the need for a clock with data encodings and request/ackno...
Article
The advancement of synthetic biology requires the ability to create new DNA sequences to produce unique behaviors in biological systems. Automation is increasingly employed to carry out well-established assembly methods of DNA fragments in a multiplexed, high-throughput fashion, allowing many different configurations to be tested simultaneously. Ho...
Article
Full-text available
The required step in all droplet-based devices is droplet formation. A droplet generator must deliver an application-specific performance that includes a prescribed droplet size and generation frequency while producing monodisperse droplets. The desired performance is usually reached through several cost- and time-inefficient design iterations. To...
Article
Full-text available
Synthetic mRNA is an attractive vehicle for gene therapies because of its transient nature and improved safety profile over DNA. However, unlike DNA, broadly applicable methods to control expression from mRNA are lacking. Here we describe a platform for small-molecule-based regulation of expression from modified RNA (modRNA) and self-replicating RN...
Preprint
Full-text available
Signal Temporal Logic (STL) is a formal language for describing a broad range of real-valued, temporal properties in cyber-physical systems. While there has been extensive research on verification and control synthesis from STL requirements, there is no formal framework for comparing two STL formulae. In this paper, we show that under mild assumpti...
Article
Computational models are essential to engineer predictable biological systems and to scale up this process for complex systems. Computational modelling often requires expert knowledge and data to build models. Clearly, manual creation of models is not scalable for large designs. Despite several automated model construction approaches, computational...
Article
Full-text available
Micromilling is a proven method for prototyping microfluidic devices; however, high overhead costs, large machine footprints, an esoteric software stack, and nonstandard device bonding protocols may be hampering the widespread adoption of micromilling in the greater microfluidics community. This research exploits a free design-to-device software ch...
Article
Full-text available
Recent advances in modular DNA assembly techniques have enabled synthetic biologists to test significantly more of the available "design space" represented by "devices" created as combinations of individual genetic components. However, manual assembly of such large numbers of devices is time-intensive, error-prone, and costly. The increasing sophis...
Article
Bio-design automation (BDA) is an emerging field focused on computer-aided design, engineering principles, and automated manufacturing of biological systems. Here we discuss some outstanding challenges for bio-design that can be addressed by developing new tools for combinatorial engineering, equipment interfacing, next-generation sequencing, and w...
Article
We present a formal language for specifying via constraints a "design space" of DNA constructs composed of genetic parts, and an algorithm for automatically and correctly creating a novel representation of the space of satisfying designs. The language is simple, captures a large class of design spaces, and possesses algorithms for common operations...
Article
Full-text available
Acoustic manipulation has emerged as a versatile method for microfluidic separation and concentration of particles and cells. Most recent demonstrations of the technology use piezoelectric actuators to excite resonant modes in silicon or glass microchannels. Here, we focus on acoustic manipulation in disposable, plastic microchannels in order to en...
Technical Report
We present a formal language for specifying via constraints a design space of DNA constructs composed of genetic parts, and an algorithm for automatically and correctly creating a novel representation of the space of satisfying designs. The language is simple, captures a large class of design spaces, and possesses algorithms for common operations o...
Article
Full-text available
Variation in the DNA sequence upstream of bacterial promoters is known to affect the expression levels of the products they regulate, sometimes dramatically. While neutral synthetic insulator sequences have been found to buffer promoters from upstream DNA context, there are no established methods for designing effective insulator sequences with pre...
Data
Insulated pBAD inverter. 24-inverter library with insulated pBAD promoters. Comparison of GFP and RFP fold changes upon induction with L-arabinose of the 24-inverter permutation set in which only the two pBAD promoters have been insulated, each with a different DIS spacer. Insulation is denoted by a smaller gray box positioned between upstream MoCl...
Data
Figure data. All data underlying the findings described herein. (ZIP)
Data
Upstream impact on promoters variations in promoter expression due to variations in the 4 bp MoClo assembly DNA sequence at the 5’ junction of promoters. Constitutive expression from (a) J23100 promoter, (b) pBAD inducible promoter, and (c) pTet repressible promoter, when downstream of MoClo A, E, F, and G sites. Error bars show +/- two std.dev. of...
Data
pBAD insulation ± data. Distribution of expression levels for induced and uninduced expression levels from spacer screen for pBAD, corresponding with fold-change distributions reported in Fig 1(c). (PDF)
Data
pTet insulation ± data. Distribution of expression levels for induced and uninduced expression levels from spacer screen for pTet, corresponding with fold-change distributions reported in Fig 1(d). (PDF)
Data
Designed insulators. 24-inverter library insulated using random spacers. Comparison of GFP and RFP fold changes upon induction with L-arabinose of the 24-inverter permutation set in which each transcriptional unit is insulated with a different spacer from S1 Fig (INS-1 for J23100, INS-2 and INS-3 for the two pBADs, and INS-5 for pTet.). Insulation...
Data
Insulated J23100 inverter. 24-inverter library with insulated J23100 promoter. Comparison of GFP and RFP fold changes upon induction with L-arabinose of the 24-inverter permutation set in which only the J23100 promoter has been insulated with a DIS spacer. Insulation is denoted by a smaller gray box positioned between upstream MoClo fusion site and...
Data
Insulated J23100 and pBAD inverter. 24-inverter library with insulated J23100 and pBAD promoters. Comparison of GFP and RFP fold changes upon induction with L-arabinose of the 24-inverter permutation set in which both the J23100 and two pBAD promoters have been insulated with a DIS spacer. Insulation is denoted by a smaller gray box positioned betw...
Data
Additional method details. Additional information about methods employed, including all DNA sequence information. (PDF)
Data
Designed insulators. Variations in promoter expression amongst a collection of nine 36 nt designed neutral DNA spacer sequences. A preliminary test of the variable effect of random insulators on expression was performed with 36 nt spacer sequences designed by screening random DNA base composition resembling the intergenic bacterial DNA base composi...
Data
Insulator length comparison. Variations in promoter expression with length of designed neutral DNA spacer sequences. A preliminary test of the effect of insulator length on expression was performed with spacer sequences designed to several lengths (12 nt, 24 nt, and 36 nt) by screening random DNA base composition resembling the intergenic bacterial...
Poster
Full-text available
Our lab’s graphical CAD tool, 3DµF, uses a standard set of microfluidic components called MINT to define continuous-flow chip designs as parametrically adjustable primitives placed on a canvas and connected with channels. With a fabrication workflow that includes 3DµF, it is possible to rapidly design a variety of labs-on-chip layers for export to...
Article
Design automation refers to a category of software tools for designing systems that work together in a workflow for designing, building, testing, and analyzing systems with a target behavior. In synthetic biology, these tools are called bio-design automation (BDA) tools. In this review, we discuss the BDA tools areas-specify, design, build, test, a...
Article
Full-text available
Genetic designs can consist of dozens of genes and hundreds of genetic parts. After evaluating a design, it is desirable to implement changes without the cost and burden of starting the construction process from scratch. Here, we report a two-step process where a large design space is divided into deep pools of composite parts, from which individua...
Article
Genetic designs can consist of dozens of genes and hundreds of genetic parts. After evaluating a design, it is desirable to implement changes without the cost and burden of starting the construction process from scratch. Here, we report a two-step process where a large design space is divided into deep pools of composite parts, from which individua...
Article
We define a new inversion-based machine called a {\it permuton} of $n$ genetic elements, which allows the $n$ elements to be rearranged in any of the $n \cdot (n-1) \cdot (n-2) \cdots 2 = n!$ distinct orderings. We present two design algorithms for architecting such a machine. We define a notion of a feasible design and use the framework to discuss...
Article
Recently, semi-rational approaches that rely on combinatorial assembly of characterized DNA components have been used to engineer biosynthetic pathways. In practice, however, it is not practical to assemble and test millions of pathway variants in order to elucidate how different DNA components affect the behavior of a pathway. To address this chal...
Article
Full-text available
To collaboratively design synthetic biology systems, it is important to communicate both the structural and functional aspects of a design in a standard manner. This paper presents the Synthetic Biology Open Language (SBOL) 2.0 and demonstrates how this standard enables effective collaborative design across different institutions and tools. SBOL 2....
Article
Genome engineering technologies now enable precise manipulation of organism genotype, but can be limited in scalability by their design requirements. Here we describe Merlin (http://merlincad.org), an open-source web-based tool to assist biologists in designing experiments using Multiplex Automated Genome Engineering (MAGE). Merlin provides methods...
Article
Computation can be performed in living cells by DNA-encoded circuits that process sensory information and control biological functions. Their construction is time-intensive, requiring manual part assembly and balancing of regulator expression. We describe a design environment, Cello, in which a user writes Verilog code that is automatically transfo...
Article
Full-text available
Multipart and modular DNA part libraries and assembly standards have become common tools in synthetic biology since the publication of the Gibson and Golden Gate assembly methods, yet no multipart modular library exists for use in bacterial systems. Building upon the existing MoClo assembly framework, we have developed a publicly available collecti...
Article
Full-text available
This RFC94 describes an assembly standard based on the Type IIS restriction enzymes BsaI and BbsI (also called BpiI). This assembly standard is based upon the Modular Cloning (MoClo) assembly strategy, which was introduced in 2011 by Weber et al. [1] and is based upon Golden Gate cloning [2]. In this RFC, we describe our proposed MoClo standard for...
Article
Full-text available
Synthetic Biology is an engineering discipline where parts of DNA sequences are composed into novel, complex systems that execute a desired biological function. Functioning and well-behaving biological systems adhere to a certain set of biological "rules". Data exchange standards and Bio-Design Automation (BDA) tools support the organization of par...
Article
One goal of synthetic biology is to design and build genetic circuits in living cells for a range of applications. Our incomplete knowledge of the effects of metabolic load and biological “crosstalk” on the host cell make it difficult to construct multilevel genetic logic circuits in a single cell, limiting the scalability of engineered biological...
Article
Owl ( www.owlcad.org ) is a biodesign automation tool that generates electronic datasheets for synthetic biological parts using common formatting. Data can be retrieved automatically from existing repositories and modified in the Owl user interface (UI). Owl uses the data to generate an HTML page with standard typesetting that can be saved as a PDF...
Article
Large microbial gene clusters encode useful functions, including energy utilization and natural product biosynthesis, but genetic manipulation of such systems is slow, difficult and complicated by complex regulation. We exploit the modularity of a refactored Klebsiella oxytoca nitrogen fixation (nif) gene cluster (16 genes, 103 parts) to build gene...
Article
miniEugene provides computational support for solving combinatorial design problems, enabling users to specify and enumerate designs for novel biological systems based on sets of biological constraints. This technical note presents a brief tutorial for biologists and software engineers in the field of synthetic biology on how to use miniEugene. Aft...
Article
One goal of synthetic biology is to design and build genetic circuits in living cells for a range of applications. Major challenges in these efforts include increasing the scalability and robustness of engineered biological systems and streamlining and automating the synthetic biology workflow of specification-design-assembly-verification. We prese...
Article
The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a commun...
Article
RNA replicons are an emerging platform for engineering synthetic biological systems. Replicons self-amplify, can provide persistent high-level expression of proteins even from a small initial dose, and unlike DNA vectors, pose minimal risk of chromosomal integration. However, no quantitative model sufficient for engineering levels of protein expres...
Article
Full-text available
Molecular biologists routinely clone genetic constructs from DNA segments and formulate plans to assemble them. However, manual assembly planning is complex, error prone and not scalable. We address this problem with an algorithm-driven DNA assembly planning software tool suite called Raven (http://www.ravencad.org/) that produces optimized assembl...
Conference Paper
Automatic design of synthetic gene networks with specific functions is an emerging field in synthetic biology. Quantitative evaluation of gene network designs is a missing feature of the existing automatic design tools. In this work, we address this issue and present a framework to probabilistically analyze the dynamic behavior of a gene network ag...
Article
We sincerely apologize for any omissions of relevant work owing to space and reference limitations. D.M.D. acknowledges support from the Office of Naval Research, the Defense Advanced Research Projects Agency, the National Science Foundation, Boston University, and Agilent Technologies. The authors would also like to acknowledge many conversations...