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Matthew J. Smith, Stephen Emmott, Drew W. Purves, Lucas N. Joppa, and Vassily Lyutsarev

In scientific research and development, emphasis is placed on research over development. A significant cost is that the two-way interaction between scientific insights and societal needs does not function effectively to lead to impacts in the wider world. We simply must embrace new software and hardware approaches if we are to provide timely predictive information to address global problems, support businesses and inform governments and citizens. The Microsoft Research Computational Science Lab has been...

Publication details
Date: 15 December 2014
Type: Proceedings
Katherine E Todd-Brown, Yiqi Luo, James Tremper Randerson, Stephen D. Allison, and Matthew J. Smith

Soil carbon stocks have the potential to be a strong source or sink for carbon dioxide over the next century, playing a critical role in climate change. These stocks are the result of small differences between much larger primary carbon fluxes: gross primary production, litter fall, autotrophic respiration and heterotrophic respiration. There was little agreement on predicted soil carbon stocks between Earth system models (ESMs) in the most recent Climate Model Intercomparison Project. Predicted...

Publication details
Date: 15 December 2014
Type: Proceedings
Oleksandra Hararuk and Matthew J. Smith

Soil is the largest terrestrial pool of carbon (C), storing 1395-2293 Pg C. Under changing climate a large portion of soil C could potentially transfer back to the atmosphere as CO₂, pushing the earth system into a positive feedback loop between increasing soil CO₂ emissions and rising temperatures. We rely on models to estimate soil responses to climate change; however recent global carbon cycle model intercomparisons have shown poor model performance in capturing C cycle processes in the soil. To gain...

Publication details
Date: 15 December 2014
Type: Proceedings
Silvia Caldararu, Drew W. Purves, and Matthew J. Smith

Simple mechanistic models of vegetation processes are essential both to our understanding of plant behaviour and to our ability to predict future changes in vegetation. One concept that can take us closer to such models is that of plant optimality, the hypothesis that plants aim to achieve an optimal state. Conceptually, plant optimality can be either structural or functional optimality. A structural constraint would mean that plants aim to achieve a certain structural characteristic such as an...

Publication details
Date: 15 December 2014
Type: Proceedings
Tom Crick, Benjamin A. Hall, Samin Ishtiaq, and Kenji Takeda

The reproduction and replication of reported scientific results is a hot topic within the academic community. The retraction of numerous studies from a wide range of disciplines, from climate science to bioscience, has drawn the focus of many commentators, but there exists a wider socio-cultural problem that pervades the scientific community. Sharing data and models often requires extra effort, and this is currently seen as a significant overhead that may not be worth the time investment....

Publication details
Date: 1 December 2014
Type: Inproceeding
Camille Guilbaud, Neil Dalchau, Drew Purves, and Lindsay Turnbull
  • Flowering time in annual plants has large fitness consequences and has been the focus of theoretical and empirical study. Previous theory has concluded that flowering time has evolved over evolutionary time to maximize fitness over a particular season length.
  • We introduce a new model where flowering is cued by a growth-rate rule (peak nitrogen (N)). Flowering is therefore sensitive to physiological parameters and to current environmental conditions, including N availability and the...
Publication details
Date: 9 October 2014
Type: Article
Publisher: New Phytologist Trust
Gian Marco Palamara, Dylan Z. Childs, Christopher F. Clements, Owen L. Petchey, Marco Plebani, and Matthew J. Smith
  1. Understanding and quantifying the temperature dependence of population parameters, such as intrinsic growth rate and carrying capacity, is critical for predicting the ecological responses to environmental change. Many studies provide empirical estimates of such temperature dependencies, but a thorough investigation of the methods used to infer them has not been performed yet.
  2. We created artificial population time series using a stochastic logistic model parameterized with the Arrhenius...
Publication details
Date: 1 October 2014
Type: Article
Publication details
Date: 1 October 2014
Type: Article
Publisher: Wiley
Attila Csikász-Nagy and Neil Dalchau

Biological clocks regulate the proper periodicity of several processes at the cellular and organismal level. The cell cycle and circadian rhythm are the best characterized among these but several other biological clocks function in cells at widely variable periodicity. The underlying molecular networks are controlled by delayed negative feedbacks, but the role of positive feedbacks and substrate-depletion has been also proposed to play crucial roles in the regulation of these processes. Here we will...

Publication details
Date: 8 September 2014
Type: Technical report
Publisher: Microsoft Research
Number: MSR-TR-2014-134
sadia, Lees, A. C., Moura, N. G., Gardner, T. A., Barlow, J., Ferreira, J., Ewers, and R. M.

Road building can lead to significant deleterious impacts on biodiversity,

varying from direct road-kill mortality and direct habitat loss associated with

road construction, to more subtle indirect impacts from edge effects and

fragmentation. However, little work has been done to evaluate the specific

effects of road networks and biodiversity loss beyond the more generalized

effects of habitat loss. Here, we compared forest bird species richness

and composition...

Publication details
Date: 1 September 2014
Type: Article
Publisher: Proc Roy Soc B
Martin Abadi, Philippa Gardner, Andrew D. Gordon, and Radu Mardare

Luca Cardelli has made exceptional contributions to the field of programming languages and beyond. Throughout his career, he has re-invented himself every decade or so, while continuing to make true innovations. His achievements span many areas: software; language design, including experimental languages; programming language foundations; and the interaction of programming languages and biology. These achievements form the basis of his lasting scientific leadership and his wide impact. A scientific...

Publication details
Date: 1 September 2014
Type: Technical report
Publisher: Microsoft Research
Number: MSR-TR-2014-104
Christoph Lippert, Jing Xiang, Danilo Horta, Christian Widmer, Carl Kadie, David Heckerman, and Jennifer Listgarten
Publication details
Date: 1 September 2014
Type: Article
Publisher: Oxford University Press
Nicolo Fusi, Christoph Lippert, Neil D Lawrence, and Oliver Stegle
Publication details
Date: 1 September 2014
Type: Article
Publisher: Nature Publishing Group
Sadia E. Ahmed

Roads have many and varied ecological impacts. This report outlines the key ecological implication of road transport networks.

Publication details
Date: 1 September 2014
Type: Technical report
Number: MSR-TR-2014-120
Paul I. Palmer and Matthew J. Smith

We can no longer ignore feedbacks between global warming and how people respond, say Paul I. Palmer and Matthew J. Smith.

Publication details
Date: 28 August 2014
Type: Article
Cory Merow, Matthew J. Smith, Thomas C. Edwards, Antoine Guisan, Sean McMahon, Signe Normand, Wilfried Thuiller, Rafael O. Wuest, Niklaus E. Zimmerman, and Jane Elith

Species distribution models (SDMs) are widely used to explain and predict species ranges and environmental niches. They are most commonly constructed by inferring species’ occurrence-environment relationships using statistical and machine-learning methods. The variety of methods that can be used to construct SDMs (e.g., generalized linear/additive models, tree-based models, maximum entropy, etc.), and the variety of ways that such models can be implemented, permits substantial flexibility in SDM...

Publication details
Date: 1 August 2014
Type: Article
Publisher: Wiley
Sean Sloan, Clinton N Jenkins, Lucas N Joppa, David LA Gaveau, and William F Laurance
Publication details
Date: 1 July 2014
Type: Article
Publisher: Elsevier
Publication details
Date: 1 July 2014
Type: Article
Nicola Paoletti, Boyan Yordanov, Youssef Hamadi, Christoph M. Wintersteiger, and Hillel Kugler

Deciphering the developmental program of an embryo is a fundamental question in biology. Landmark papers [9,10] have recently shown how computational models of gene regulatory networks provide system-level causal understanding of the developmental processes of the sea urchin, and enable powerful predictive capabilities. A crucial aspect of the work is empirically deriving plausible models that explain all the known experimental data, a task that becomes infeasible in practice due to the inherent...

Publication details
Date: 1 July 2014
Type: Inproceeding
Publisher: Springer
Boyan Yordanov, Jongmin Kim, Rasmus L. Petersen, Angelina Shudy, Vishwesh V. Kulkarni, and Andrew Phillips

The design of synthetic circuits for controlling molecular-scale processes is an important goal of synthetic biology, with potential applications in future in vitro and in vivo biotechnology. In this paper, we present a computational approach for designing feedback control circuits constructed from nucleic acids. Our approach relies on an existing methodology for expressing signal processing and control circuits as biomolecular reactions. We first extend the methodology so that circuits can be expressed...

Publication details
Date: 1 July 2014
Type: Article
Publisher: American Chemical Society (In Press)
Publication details
Date: 1 July 2014
Type: Article
Sara-Jane Dunn, Graziano Martello, Boyan Yordanov, Stephen Emmott, and Austin Smith

The gene regulatory circuitry through which pluripotent embryonic stem (ES) cells choose between self-renewal and differentiation appears vast and has yet to be distilled into an executive molecular program. We developed a data-constrained, computational approach to reduce complexity and to derive a set of functionally validated components and interaction combinations sufficient to explain observed ES cell behavior. This minimal set, the simplest version of which comprises only 16 interactions, 12...

Publication details
Date: 6 June 2014
Type: Article
Number: 6188
Mindy M Syfert, Lucas N Joppa, Matthew J Smith, David A Coomes, Steven P Bachman, and Neil A Brummitt

Characterising a species' geographical extent is central to many conservation assessments, including those of the IUCN Red List of Threatened Species. The IUCN recommends that extent of occurrence (EOO) to be quantified by drawing a minimum convex polygon (MCP) around known or inferred presence localities. EOO calculated from verified specimens is commonly used in Red List assessments when other data are scarce, as is the case for many threatened plant species. Yet rarely do these estimates incorporate...

Publication details
Date: 1 June 2014
Type: Article
Publisher: Elsevier
Neil Dalchau, Georg Seelig, and Andrew Phillips

DNA self-assembly is a powerful technology for controlling matter at the nanometre to micron scale, with potential applications in high-precision organisation and positioning of molecular components. However, the ability to program DNA-only self-organisation beyond the microscopic scale is currently lacking. In this paper we propose a computational method for programming spatial organisation of DNA at the centimetre scale, by means of DNA strand displacement reaction diffusion systems. We use this...

Publication details
Date: 1 June 2014
Type: Article
Publisher: Springer
Matthew R. Lakin, Rasmus Petersen, Kathryn E. Gray, and Andrew Phillips

Sequence-specific DNA interactions are a powerful means of programming nanoscale locomotion. These systems typically use a DNA track that is tethered to a surface, and molecular interactions enable a signal or cargo to traverse this track. Such low copy number systems are highly amenable to mechanized analyses such as probabilistic model checking, which requires a formal encoding. In this paper we present the first general encoding of tethered DNA species into a formal language, which allows the...

Publication details
Date: 1 June 2014
Type: Article
Publisher: Springer
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