Introducing Our Authors pubs.acs.org/synthbio
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MICHAEL A. BOEMO
Current position. Ph.D. Candidate, Department of Computer Science, Duke University. Advisor: Prof. John Reif. Education. B.S. and M.S. in Electrical and Computer Engineering, Boise State University. Advisor: Prof. William Knowlton. Nonscientific interests. I enjoy reading, fishing, and working on new DIY projects. My general research interests lie in the fields of molecular assembly, DNA nanoscience, and nanotechnology. In particular, I’m interested in understanding DNA self-assembly and how we can harness DNA hybridization as an alternative energy source. In this article, we report a novel architecture to construct molecular analog circuits. Analog circuits require lesser components to perform computation in contrast to digital circuits. In addition, analog circuits exist everywhere in natural living systems (e.g., neurons). I believe this work will have a major impact on the future development of molecular analog computers. (Read Bui’s article; DOI: 10.1021/ acssynbio.6b00144).
Michael A. Boemo
Current position. Postdoctoral Researcher at the Sir William Dunn School of Pathology, University of Oxford. Education. Postdoctoral: Sir William Dunn School of Pathology, University of Oxford. Advisor: Professor Conrad Nieduszynski. Graduate: Department of Physics, University of Oxford. Advisors: Professor Andrew J. Turberfield, Professor Luca Cardelli. Nonscientific interests. Photography, cycling, rowing I am interested in how biology and computation can inform each other. My Ph.D. work with Professor Turberfield and Professor Cardelli involved developing formal computing languages to describe the DNA systems we were engineering in the lab. These languages have many useful applications, such as forming the basis for compilers that can automatically generate system designs. My current postdoctoral work with Professor Nieduszynski is more focused on basic biology, for which we are using machine learning and big data methods to study DNA replication dynamics. Rapidly evolving technologies together with the breadth of interesting topics that lie at the interface between biology and computer science make this an amazing field of which to be a part. (Read Boemo’s article; DOI: 10.1021/ acssynbio.5b00275).
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Hieu Bui
Current position. Ph.D., Department of Computer Science, Duke University (graduated May 2016). Education. Ph.D. (Duke University), B.Tech. (IIIT Hyderabad, India). Nonscientific interests. Sports (running, badminton, soccer), road-tripping, fishing. My Ph.D. research focused on the algorithmic design of DNA sequences for use in the construction of DNA-based devices. I designed and built four different types of DNA devices: (1) A device that achieves leak-free rapid amplification (exponential in the copy number of the target strand) with high sensitivity and specificity; (2) A DNA circuit that is reusable multiple times, unlike the current use-once architectures; (3) a device that allows for finite gain instead of burning the fuel to completion; (4) the construction of 1-D DNA nanostructures using enzymes, that can serve as templates for further assembly.
HIEU BUI
Received: July 27, 2016 Published: August 19, 2016
Hieu Bui
© 2016 American Chemical Society
SUDHANSHU GARG
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I’m excited by the idea that all systems (living or synthetic) process information in a stochastic/nondeterministic manner, and by deciphering the algorithmic rules that govern them, these systems can be enhanced and built to achieve a directed goal. This particular paper is very exciting, since biological systems are inherently analog (not digital). Thus, this article tries to bring an inherently analog approach to process information, while many previous approaches (including mine) have been digital. (Read Garg’s article; DOI: 10.1021/acssynbio.6b00144).
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Introducing Our Authors
CURTIS MADSEN
MATTHEW LAKIN Curtis Madsen
Current position. Postdoc in Electrical & Computer Engineering, Boston University. Advisors: Prof. Doug Densmore and Prof. Calin Belta. Education. Research Associate in the School of Computing Science, Newcastle University. Advisors: Prof. Anil Wipat and Dr. Paolo Zuliani. Ph.D. in Computer Science, University of Utah (2013). Advisor: Prof. Chris Myers. B.S. in Computer Science, University of Utah (2009). Nonscientific interests. I enjoy visiting national parks (especially Yellowstone National Park), hiking, fishing, and other outdoor activities. In addition, I love games and play a variety of board, card, computer, and video games. In general, my interests lie in applying formal verification methods to systems in a variety of disciplines. During my Ph.D. research, I focused on utilizing stochastic model checking and simulation to perform design space exploration of synthetic genetic circuits, and as a research associate at Newcastle University, I worked on modeling and parameter synthesis of biological systems. Through my research, I have been involved in the development of standards to assist in the exchange and reproducibility of scientific data and have found that standards are not only important for how data is described, but are also important for how data is visualized. Our work on VisBOL provides a service for researchers to automatically convert biological designs described using GenBank or the SBOL standard into a visual representation that conforms to the SBOL Visual standard. (Read Madsen’s article; DOI: 10.1021/acssynbio.5b00210).
Aiden J. Ross
Current position. Research Assistant Professor, Department of Chemical & Biological Engineering and Department of Computer Science, University of New Mexico, Albuquerque, NM, USA. Education. Postdoctoral Scholar in Department of Computer Science, University of New Mexico, Albuquerque, NM, USA (2011−2015) (Advisor: Prof. Darko Stefanovic). Postdoctoral Researcher at Microsoft Research, Cambridge, UK (2009−2011) (Advisor: Dr. Andrew Phillips). Ph.D. in Computer Science, University of Cambridge, UK (2010) (Advisor: Prof. Andrew Pitts). B.A. in Computer Science, University of Cambridge, UK (2005). Nonscientific interests. Science fiction/fantasy novels, swimming, hiking. My research interests range from theoretical computer to DNA nanotechnology, in particular, the design and implementation of DNA-based molecular computing systems, and the development programming languages and tools for the design and verification of DNA computing devices. In this paper, we report an architecture for DNA strand displacement networks capable of executing adaptive algorithms, and use this approach to design a DNA network that implements a simple machine learning algorithm. Using computational simulations of the network’s behavior, we demonstrate that this circuit can indeed learn a class of linear functions and study its learning performance. This work demonstrates the future potential of DNA strand displacement reactions for implementing adaptive networks to monitor and control biochemical systems. (Read Lakin’s article; DOI: 10.1021/ acssynbio.6b00009).
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JAMES A. MCLAUGHLIN
Jens Kristian Geyti
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Introducing Our Authors
complexity of designs, increases. (Read Misirli’s article; DOI: 10.1021/acssynbio.5b00210).
Current position. Ph.D. student, Data Integration for Synthetic Biology, Newcastle University; supervised by Professor Anil Wipat & Dr Dana Ofiteru. Education. BSc (Hons) Computer Science, Newcastle University. Nonscientific interests. Outside of my scientific interests, I am interested in photography, homebrewing, and tinkering with computer hardware. The rest of my time is spent playing the flute in Irish traditional music sessions and a local band here in Newcastle. My Ph.D. focuses on how data integration can be leveraged to empower biologists working in the lab. While there is a plethora of biological data available, it is often stored in disparate databases with differing semantics and availability. I am working toward a truly integrated environment for biodesign, where the end-user has seamless, automated access to information on structural data, regulatory models, and experimental results associated with genetic building blocks. The user interface for this environment will be a graphical CAD tool, based in the Web browser and built on the Synthetic Biology Open Language (SBOL). VisBOL was built to not only function as a stand-alone tool, but also as a framework for computationally drawing genetic circuit diagrams that I will use throughout my project. (Read McLaughlin’s article; DOI: 10.1021/acssynbio.5b00210).
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REEM MOKHTAR
Hieu Bui
Current position. Ph.D. Candidate, Department of Computer Science, Duke University. Advisor: Prof. John Reif. Education. M.S. in Computer Science at UChicago (2008), Chicago, IL. Advisor: Prof. Leo Irakliotis. B.S. in Computer Science with a minor in Mathematics from the American University of Sharjah, Sharjah, UAE (2006). Advisors: Professors Gerrasimos Barlas and Jalal Kawash. Nonscientific interests. Reading up on philosophy and history to try and understand my place in this world. Camping, fishing, stargazing, and picking up new hobbies to keep my hands busy. I’m interested in pushing the boundaries in DNA nanostructure architecture, flexibility, and manipulation. I find that this paper will go a long way toward helping provide us with more control over these aspects of DNA nanostructures by using analog circuit results potentially as the basis for inducing functional or structural changes in these nanostructures. (Read Mokhtar’s article; DOI: 10.1021/acssynbio.6b00144).
GÖ KSEL MISIRLI
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MATTHEW POCOCK
James McLaughlin
Current position. Postdoctoral researcher, ICOS group. Education. School of Computing Science, Newcastle University, UK. Ph.D. advisors: Prof. Anil Wipat and Dr. Jennifer Hallinan. Nonscientific interests. Sports, music, travel. I am interested in automating the design of synthetic biological systems, and one aspect of my research is data standards. Particularly, I have been involved in the development of the Synthetic Biology Open Language (SBOL). SBOL facilitates the reproducibility of synthetic biology designs and increase the interoperability between different software tools. However, SBOL is more suited for machines. Human intervention to understand and verify designs encoded in this machine language is also necessary. VisBOL presented in this paper is a lightweight platform to visualize SBOL documents using the Web. Moreover, it facilitates rapidly sketching designs, for example, to exchange ideas or to prepare journal figures. This tool will especially be important as the number of SBOL compliant tools, and the
James McLaughlin
Current position. Consultant at Turing Ate My Hamster, Ltd. Education. Ph.D. Genetics, Darwin College, Cambridge and The Sanger Centre. Advisor: Dr Tim Hubbard (2002). BSC (hons) 2.1 Genetics, Newcastle University (1998). Nonscientific interests. Stone sculpture and letter-cutting, using traditional hand tools. I mainly work with limestone and 790
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slate. Much of my work is fan-art, such as superhero logos and GoT house sigils. Recently I have been working mainly in the area of community data standards, particularly SBOL, for enabling the exchange of knowledge between people about synthetic biology designs. This human communication is facilitated by services, ontologies, and software libraries with shared data models and domain encodings provided by the wider SBOL community. My involvement in the development and implementation of SBOL builds upon past work with ontologies and data integration, and ultimately from my involvement with BioJava and BioPerl and their development communities, during my Ph.D research (Read Pocock’s article; DOI: 10.1021/acssynbio.5b00210).
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Introducing Our Authors
TIANQI SONG
Hieu Bui
J. CHRISTIAN J. RAY
Current position. Ph.D. Candidate, Department of Computer Science, Duke University. Advisor: Prof. John Reif. Education. M.S. in Computer Science, Duke University. Advisor: Prof. John Reif. B.E. in Computer Science and Technology, Wuhan University. Nonscientific interests. Reading, hiking, camping. I am interested in solving problems from an interdisciplinary perspective. My current research mainly focuses on developing new architectures and tools for molecular programming. I am also doing projects that aim to translate the basic techniques in DNA nanotechnology to medical applications. My research covers both experimental and theoretical work. In this paper, we developed a novel architecture for analog computation by DNA circuits, which expands the tool set of DNA computing. (Read Song’s article; DOI: 10.1021/acssynbio.6b00144).
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University of Kansas (source: Marcom)
Current position. Assistant Professor, Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence Education. Postdoctoral: Rice University (Advisor: Oleg Igoshin) and the University of Texas MD Anderson Cancer Center (Advisor: Gábor Balázsi). Graduate: University of Michigan (Advisor: Denise Kirschner). Undergraduate: University of Michigan. Nonscientific interests. I like to read history and science fiction, and spend time with my family. In vivo synthetic biology is subject to the same evolutionary pressures and physical principles as any other natural network. The systems biology community increasingly understands the coupling between growth rate and quantitative network performance in bacteria. Most protein loss is caused by growth dilution, and intergenerational transfer of proteins causes many interesting effects on growth rate, bacterial aging, and nongenetic predisposition in general. I was interested in how the loss of growth could lock protein concentrations at arbitrary levels, and what implications that has for using synthetic networks as computers with nongenetic memory. The outcome was surprisingthe mathematical models that predict skewed distributions of proteins in a cellular population (think: bethedging) allow for maximal flexibility between erasing the memory and maintaining it. (Read Ray’s article; DOI: 10.1021/ acssynbio.5b00229).
DARKO STEFANOVIC
Darko Stefanovic
Current position. Professor, Department of Computer Science, University of New Mexico, Albuquerque, NM, USA. Education. Postdoctoral Researcher, Department of Electrical Engineering, Princeton University, Princeton, NJ, USA (1998−2000) (Advisor: Prof. Margaret Martonosi). Ph.D. in Computer Science, University of Massachusetts, Amherst, MA, USA (1999) (Advisor: Prof. Eliot Moss). M.S. in Computer Science, University of Massachusetts, Amherst, MA, USA (1994) (Advisor: Prof. Eliot Moss). Dipl.Ing. in Electrical Engineering, University of Belgrade, Serbia (1989). Nonscientific interests. Hiking, archery, and programming languages 791
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I have always been interested in unconventional computational substrates. DNA offers an infinitely malleable material not only for information storage and structural nanotechnology but also for dynamic circuit design. We started with basic logic gates and simple parallel circuits, proceeded to signal-propagating cascades, and here we outline designs for large DNA circuits with sustained operation and a distinctly life-like learning capability. (Read Stefanovic’s article; DOI: 10.1021/acssynbio.6b00009).
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ANIL WIPAT
James McLaughlin
Current position. Professor, School of Computing Science, Newcastle University, UK; Associate director of the Centre for Synthetic Biology and the BioEconomy (CSBB); Director of the Centre for Health and Bioinformatics (CHaBi). Education. MSc Computing Science, Newcastle University; Lecturer in Microbial Genomics, Newcastle University; PostDoc (Sequencing and functional analysis of Bacillus subtilis), Newcastle University, Prof. Colin Harwood; Ph.D. (Biotechnology/ Molecular Microbiology), Liverpool John Moores University Prof. Venetia Saunders and Prof. Elizabeth Wellington. Nonscientific interests. My hobbies include managing children, allotment gardening, motorcycles, retro computers, running, cycling, and squash. I codirect the ICOS group (www.ico2s.org) and therefore have a wide range of computational biology related interests. In particular, I am interested in the computational design of biological systems and standards for the exchange of information to help in this endeavor. One aspect of our work is to help develop Synthetic Biology Open Language (SBOL) as a community standard for Synthetic Biology. The VisBOL tool is one of a number to help synthetic biologists use SBOL. We hope VisBOL will be especially useful to the community, given the recent recommendation by ACS Synthetic Biology of SBOL visual as a format for the publication of visual designs of synthetic systems. (Read Wipat’s article; DOI: 10.1021/acssynbio.5b00210).
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