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Algorithms and theory47205 (238)
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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
Publication details
Date: 1 July 2014
Type: Article
Publisher: Choose...
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
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
Publisher: Choose...
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
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
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
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
Scott, Mark, Boardman, Richard P., Reed, Philippa A.S., Austin, Tim, Johnston, Steven, Takeda, K, Cox, and Simon J

Scientists within the materials engineering community produce a wide variety of data, with datasets differing in size and complexity. Examples include large 3D volume densitometry files (voxel) generated by microfocus computer tomography (µCT) and simple text files containing results from a tensile test. Increasingly, there is a need to share this data as part of international collaborations. The design of a suitable database schema and the architecture of a system that can cope with the varying...

Publication details
Date: 1 June 2014
Type: Article
Publisher: Elsevier
Y.P. Wang, B.C. Chen, W.R. Weider, M. Leite, B.E. Medlyn, M. Rasmussen, M.J. Smith, F.B. Augusto, F. Hoffman, and Y.Q. Luo

A number of nonlinear models have recently been proposed for simulating soil carbon decomposition. Their predictions of soil carbon responses to fresh litter input and warming differ significantly from conventional linear models. Using both stability analysis and numerical simulations, we showed that two of those nonlinear models (a two-pool model and a three-pool model) exhibit damped oscillatory responses to small perturbations. Stability analysis showed the frequency of oscillation is proportional...

Publication details
Date: 7 April 2014
Type: Article
Publisher: European Geosciences Union
Isabel M. Rosa, Sadia E. Ahmed, and Robert M. Ewers

Land-use and land-cover (LULC) change is one of the largest ally. We use the tropical rainforests of the Amazon, the Congo gate spatial predictive models of LULC change. Current predictions variable and often poorly validated. We carried out a quantitative model spatio-temporal scales, inputs, calibration and validation from each of the models reviewed and carried out a quantitative predictions in the Brazilian Amazon. We highlight existing shortfalls that need addressing to improve the transparency,...

Publication details
Date: 1 April 2014
Type: Article
Publisher: Wiley
Maria Bruna, Jonathan Chapman, and Matthew J Smith

The quasi-steady-state approximation (or stochastic averaging principle) is a useful tool in the study of multiscale stochastic systems, giving a practical method by which to reduce the number of degrees of freedom in a model. The method is extended here to slow–fast systems in which the fast variables exhibit metastable behaviour. The key parameter that determines the form of the reduced model is the ratio of the timescale for the switching of the fast variables between metastable states to the...

Publication details
Date: 1 April 2014
Type: Article
Publisher: American Institute of Physics
Boyan Yordanov, Neil Dalchau, Paul Grant, Michael Pedersen, Stephen Emmott, Jim Haseloff, and Andrew Phillips

The ability to design and construct synthetic biological systems with predictable behavior could enable significant advances in medical treatment, agricultural sustainability, and bioenergy production. However, to reach a stage where such systems can be reliably designed from biological components, integrated experimental and computational techniques that enable robust component characterization are needed. In this paper we present a computational method for the automated characterization of genetic...

Publication details
Date: 14 March 2014
Type: Article
Publisher: American Chemical Society
James Osborne, Miguel Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander Fletcher, Robin Freeman, Derek Groen, Bernhard Knapp, Greg McInerny, Gary Mirams, Joe Pitt-Francis, Biswa Sengupta, David Wright, Christian Yates, David Gavaghan, Stephen Emmott, and Charlotte Deane
Publication details
Date: 1 March 2014
Type: Article
Publisher: PLoS Computational Biology (Public Library of Science Computational Biology),
Number: 3
Rakesh Agrawal, Behzad Golshan, and Evimaria Terzi

Given a class of large number of students, each exhibiting a different ability level, how can we form teams of students so that the expected performance of team members improves due to team participation? We take a computational perspective and formally define two versions of such team-formation problem: the MaxTeam and the MaxPartition problems. The first asks for the identification of a single team of students that improves the performance of most of the participating team members. The second asks for...

Publication details
Date: 1 March 2014
Type: Inproceeding
Publisher: ACM
Joppe W. Bos, Craig Costello, Patrick Longa, and Michael Naehrig

We select a set of elliptic curves for cryptography and analyze our selection from a performance and security perspective. This analysis complements recent curve proposals that suggest (twisted) Edwards curves by also considering the Weierstrass model. Working with both Montgomery-friendly and pseudo-Mersenne primes allows us to consider more possibilities which improves the overall efficiency of base field arithmetic. Our Weierstrass curves are backwards compatible with current implementations of prime...

Publication details
Date: 1 February 2014
Type: Technical report
Publisher: Choose...
Number: MSR-TR-2014-19
Matthew J. Smith, Paul I. Palmer, Drew W. Purves, Mark C. Vanderwel, Vassily Lyutsarev, Ben Calderhead, Lucas N. Joppa, Christopher M. Bishop, and Stephen Emmott

New details about natural and anthropogenic processes are continually added to models of the Earth System, anticipating that the increased realism will increase the accuracy of their predictions. However perspectives differ about whether this approach will improve the value of the information the models provide to decision makers, scientists and societies. The present bias towards increasing realism leads to a range of updated projections, but at the expense of uncertainty quantification and model...

Publication details
Date: 1 February 2014
Type: Article
Publisher: American Meteorological Society
Michael Pedersen, Nicolas Oury, Colin Gravill, and Andrew Phillips

A host of formal, textual languages for modeling cellular processes have recently emerged, but their simulation tools often require an installation process which can pose a barrier for use. Bio Simulators is a framework for easy online deployment of simulators, providing a uniform web-based user interface to a diverse pool of tools. The framework is demonstrated through two plugins based on the KaSim Kappa simulator, one running directly in the browser and another running in the cloud.Web tool:...

Publication details
Date: 1 February 2014
Type: Article
Publisher: Oxford University Press
Joppe W. Bos, Craig Costello, and Andrea Miele

Motivated by the advantages of using elliptic curves for discrete logarithm-based public-key cryptography, there is an active research area investigating the potential of using hyperelliptic curves of genus 2. For both types of curves, the best known algorithms to solve the discrete logarithm problem are generic attacks such as Pollard rho, for which it is well-known that the algorithm can be sped up when the target curve comes equipped with an efficiently computable automorphism. In this paper we...

Publication details
Date: 1 January 2014
Type: Inproceeding
Publisher: Springer
Joppe W. Bos, J. Alex Halderman, Nadia Heninger, Jonathan Moore, Michael Naehrig, and Eric Wustrow

In this paper, we perform a review of elliptic curve cryptography (ECC), as it is used in practice today, in order to reveal unique mistakes and vulnerabilities that arise in implementations of ECC. We study four popular protocols that make use of this type of public-key cryptography: Bitcoin, secure shell (SSH), transport layer security (TLS), and the Austrian e-ID card. We are pleased to observe that about 1 in 10 systems support ECC across the TLS and SSH protocols. However, we find that despite the...

Publication details
Date: 1 January 2014
Type: Inproceeding
Publisher: Springer
Publication details
Date: 1 January 2014
Type: Article
Number: 3
Tim Newbold, Jörn PW Scharlemann, Stuart HM Butchart, Ça\ugan H Şekercio\uglu, Lucas Joppa, Rob Alkemade, and Drew W Purves
Publication details
Date: 1 January 2014
Type: Article
Anthony Gitter, Alfredo Braunstein, Andrea Pagnani, Carlo Baldassi, Christian Borgs, Jennifer Chayes, Riccardo Zecchina, and Ernest Fraenkel

Advances in experimental techniques resulted in abundant genomic, transcriptomic, epigenomic, and proteomic data that have the potential to reveal critical drivers of human diseases. Complementary algorithmic developments enable researchers to map these data onto protein-protein interaction networks and infer which signaling pathways are perturbed by a disease. Despite this progress, integrating data across different biological samples or patients remains a substantial challenge because samples from...

Publication details
Date: 1 January 2014
Type: Article
Publisher: World Scientific Publishing
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