A5016397813- Gene Regulatory Network Analysis
- Advanced biosensing and bioanalysis techniques
- DNA and Biological Computing
- DNA and Nucleic Acid Chemistry
- Bacterial Genetics and Biotechnology
- Microbial Metabolic Engineering and Bioproduction
- Molecular Junctions and Nanostructures
- Cell Image Analysis Techniques
- Distributed systems and fault tolerance
- Bacterial biofilms and quorum sensing
- RNA Interference and Gene Delivery
- Bacteriophages and microbial interactions
- RNA and protein synthesis mechanisms
- Single-cell and spatial transcriptomics
- Evolutionary Algorithms and Applications
- Genomics and Phylogenetic Studies
- Evolution and Genetic Dynamics
- Immunotherapy and Immune Responses
- Gene expression and cancer classification
- Protein Structure and Dynamics
- vaccines and immunoinformatics approaches
- Formal Methods in Verification
- Bioinformatics and Genomic Networks
- Molecular Communication and Nanonetworks
- Modular Robots and Swarm Intelligence
Sanofi (United Kingdom)
2024
Microsoft Research (United Kingdom)
2014-2023
Indiana University Bloomington
2012-2021
ORCID
2020
Microsoft (United States)
2007-2019
University of Cambridge
2014
Ludwig-Maximilians-Universität München
2011
University of Edinburgh
2010
Southampton General Hospital
2010
University of Southampton
2010
The Visual DSD (DNA Strand Displacement) tool allows rapid prototyping and analysis of computational devices implemented using DNA strand displacement, in a convenient web-based graphical interface. It is an implementation the programming language compiler described by Lakin et al. (2011) with additional features such as support for polymers unbounded length. also supports stochastic deterministic simulation, construction continuous-time Markov chains various export formats which allow...
Recently, a range of information-processing circuits have been implemented in DNA by using strand displacement as their main computational mechanism. Examples include digital logic and catalytic signal amplification that function efficient molecular detectors. As new paradigms for computation emerge, the development corresponding languages tools these will help to facilitate design automatic compilation nucleotide sequences. We present programming language designing simulating which is The...
Microbial biofilms are complex, self-organized communities of bacteria, which employ physiological cooperation and spatial organization to increase both their metabolic efficiency resistance changes in local environment. These properties make an attractive target for engineering, particularly the production chemicals such as pharmaceutical ingredients or biofuels, with potential significantly improve yields lower maintenance costs. Biofilms also a major cause persistent infection, better...
We present SenseLess, a system that leverages the different energy consumption characteristics of sensors to maximise battery life in mobile-sensing applications. use less expensive more often, thereby enabling us frequently. In context location-aware services, experimental results indicate for typical indoor and outdoor walk, compared simple GPS-based system, our SenseLess can reduce by than 58% when determining user's location, while maintaining fidelity sensed data. This extends handheld...
Synthetic biology aims at producing novel biological systems to carry out some desired and well-defined functions. An ultimate dream is design these a high level of abstraction using engineering-based tools programming languages, press button, have the translated DNA sequences that can be synthesized put work in living cells. We introduce such language, which allows logical interactions between potentially undetermined proteins genes expressed modular manner. Programs by compiler into...
Gene expression can be noisy, as the growth of single cells. Such cell-to-cell variation has been implicated in survival strategies for bacterial populations. However, it remains unclear how cells couple gene with to implement these strategies. Here, we show noisy a key stress-response regulator, RpoS, allows E. coli modulate its dynamics survive future adverse environments. We reveal dynamic positive feedback loop between RpoS and rate that produces multi-generation pulses. do so...
The design of synthetic circuits for controlling molecular-scale processes is an important goal biology, with potential applications in future vitro and vivo biotechnology. In this paper, we present a computational approach designing feedback control constructed from nucleic acids. Our relies on existing methodology expressing signal processing as biomolecular reactions. We first extend the so that can be expressed using just two classes reactions: catalysis annihilation. then propose...
DNA has emerged as an attractive medium for archival data storage due to its durability and high information density. Scalable parallel random access is a desirable property of any system. For DNA-based systems, however, this still needs be robustly established. Here we report on thermoconfined polymerase chain reaction, which enables multiplexed, repeated compartmentalized files. The strategy based localizing biotin-functionalized oligonucleotides inside thermoresponsive, semipermeable...
Major Histocompatibility Complex (MHC) class I molecules enable cytotoxic T lymphocytes to destroy virus-infected or cancerous cells, thereby preventing disease progression. MHC provide a snapshot of the contents cell by binding protein fragments arising from intracellular turnover and presenting these at surface. Competing (peptides) are selected for cell-surface presentation on basis their ability form stable complex with I, process known as peptide optimization. A better understanding...
DNA strand displacement techniques have been used to implement a broad range of information processing devices, from logic gates, chemical reaction networks, architectures for universal computation. Strand enable computational devices be implemented in without the need additional components, allowing computation programmed solely terms nucleotide sequences. A major challenge design has rapid analysis high-level designs while also supporting detailed simulations that include known forms...
Designing correct, robust DNA devices is difficult because of the many possibilities for unwanted interference between molecules in system. strand displacement has been proposed as a design paradigm devices, and (DSD) programming language developed means formally analysing these to check interference. We demonstrate, first time, use probabilistic verification techniques analyse correctness, reliability performance during phase. model checker prism , combination with DSD language, debug...
Abstract Bidirectional intercellular signaling is an essential feature of multicellular organisms, and the engineering complex biological systems will require multiple pathways for with minimal crosstalk. Natural quorum‐sensing provide components cell communication, but their use often constrained by signal We have established new orthogonal cell–cell communication using acyl homoserine lactone systems. Quantitative measurements in contexts differing receiver protein expression allowed us to...
Abstract The selection of peptides for presentation at the surface most nucleated cells by major histocompatibility complex class I molecules (MHC I) is crucial to immune response in vertebrates. However, mechanisms rapid high affinity MHC from amongst thousands mostly low are not well understood. We developed computational systems models encoding distinct mechanistic hypotheses two molecules, HLA-B*44:02 (B*4402) and HLA-B*44:05 (B*4405), which differ a single residue yet lie opposite ends...
Abstract Targeted high-throughput DNA sequencing is a primary approach for genomics and molecular diagnostics, more recently as readout information storage. Oligonucleotide probes used to enrich gene loci of interest have different hybridization kinetics, resulting in non-uniform coverage that increases costs decreases sensitivities. Here, we present deep learning model (DLM) predicting Next-Generation Sequencing (NGS) depth from probe sequences. Our DLM includes bidirectional recurrent...
Accurate characterization of promoter behavior is essential for the rational design functional synthetic transcription networks such as logic gates and oscillators. However, rates observed from promoters can vary significantly depending on growth rate host cells experimental genetic contexts measurement. Furthermore, in vivo measurement methods must accommodate variation translation, protein folding, maturation reporter proteins, well metabolic load. The external factors affecting activity...
The complex dynamics of biological systems is primarily driven by molecular interactions that underpin the regulatory networks cells. These typically contain positive and negative feedback loops, which are responsible for switch-like oscillatory dynamics, respectively. Many computing rely on switches clocks as computational modules. While combination such modules in leads to a variety dynamical behaviours, it also driving development new algorithms. Here we present historical perspective...
We study functions on the set of all integral ideals in a Dedekind domain. The such is commutative ring isomorphic to formal power series infinitely many variables. totally multiplicative has ringed space structure, which, after identifying with same prime ideal zeros, determines domain up isomorphism.