Research Output 1977 2019

2016

Implementation of normative practical reasoning with durative actions

Shams, Z., Vos, M. D., Padget, J. & Vasconcelos, W., 13 Jul 2016, Coordination, Organizations, Institutions, and Norms in Agent Systems (COIN), 2015 International Workshops, COIN@AAMAS, Istanbul, Turkey, May 2015, COIN@IJCAI, Buenos Aires, Argentina, July 2015, Revised Selected Papers. Dignum, V., Noriega, P., Sensoy, M. & Simao Sichman, J. (eds.). Springer International Publishing, p. 335-353 19 p. (Lecture Notes in Computer Science; vol. 9628).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Open Access
File

Improving weather forecasting accuracy by using r-adaptive methods coupled to data assimilation algorithms

Budd, C., Cullen, M. & Piccolo, C., 1 Jan 2016, UK Success Stories in Industrial Mathematics. Aston, P. J., Mulholland, A. J. & Tant, K. M. M. (eds.). Springer International Publishing, p. 11-18 8 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Data Assimilation
Adaptive Method
Weather
Forecast
Forecasting
5 Citations (Scopus)

Input-to-state stability of discrete-time Lur'e systems

Logemann, H. & Sarkans, E., 23 Jun 2016, In : SIAM Journal on Control and Optimization. 54, 3, p. 1739-1768 31 p.

Research output: Contribution to journalArticle

Open Access
File
Lur'e System
Stability Theory
Discrete-time Systems
Circle
Context

InstAL: An Institutional Action Language

Padget, J., Elakehal, E., Li, T. & De Vos, M., 2016, Social Coordination Frameworks for Social Technical Systems. Springer Verlag, Vol. 30. p. 101 124 p. (Law, Governance and Technology Series ).

Research output: Chapter in Book/Report/Conference proceedingChapter

Open Access
File

Instinct: a biologically inspired reactive planner for embedded environments

Wortham, R. H., Gaudl, S. & Bryson, J. J., 14 Jun 2016, Proceedings of the International Conference on Automated Planning and Scheduling (ICAPS): PlanRob Workshop 2016. 7 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Open Access
File
Transparency
Robots
Data storage equipment
Costs
12 Citations (Scopus)

Isolation and cultivation of naive-like human pluripotent stem cells based on HERVH expression

Wang, J., Singh, M., Sun, C., Besser, D., Prigione, A., Ivics, Z., Hurst, L. D. & Izsvák, Z., 1 Feb 2016, In : Nature Protocols. 11, 2, p. 327-346 20 p.

Research output: Contribution to journalArticle

Pluripotent Stem Cells
Stem cells
Endogenous Retroviruses
Cell Line
Induced Pluripotent Stem Cells
1 Citation (Scopus)

Limiting distribution of the rightmost particle in catalytic branching Brownian motion

Bocharov, S. & Harris, S. C., 4 Oct 2016, In : Electronic Communications in Probability. 21, 12 p., Paper no. 70.

Research output: Contribution to journalArticle

Open Access
File
Branching Brownian Motion
Limiting Distribution
Branching
Gumbel Distribution
Dirac delta function
4 Citations (Scopus)

Localised pattern formation in a model for dryland vegetation

Dawes, J. H. P. & Williams, J. L. M., Jul 2016, In : Journal of Mathematical Biology. 73, 1, p. 63-90

Research output: Contribution to journalArticle

Vegetation
Pattern Formation
arid lands
Soil
vegetation
4 Citations (Scopus)

Measuring stratigraphic congruence across trees, higher taxa and time

O'Connor, A. & Wills, M., Sep 2016, In : Systematic Biology. 65, 5, p. 792-811 20 p.

Research output: Contribution to journalArticle

Open Access
File
8 Citations (Scopus)

Mesh adaptation on the sphere using optimal transport and the numerical solution of a Monge-Ampère type equation

Weller, H., Browne, P., Budd, C. & Cullen, M., 1 Mar 2016, In : Journal of Computational Physics. 308, p. 102-123 22 p.

Research output: Contribution to journalArticle

Open Access
File
mesh
Linearization
Resource allocation
Equations of motion
Anisotropy
10 Citations (Scopus)
Open Access
Cryptococcus gattii
Metagenomics
Virulence
Fungi
Northwestern United States
37 Citations (Scopus)

Modularity and stability in ecological communities

Rogers, T., Allesina, S. & Grilli, J., 23 Jun 2016, In : Nature Communications. 7, 12031.

Research output: Contribution to journalArticle

Open Access
File
Biota
modularity
Ecology
Ecosystems
Ecosystem

Multilayer asymptotic solution for wetting fronts in porous media with exponential moisture diffusivity

Budd, C. J. & Stockie, J. M., May 2016, In : Studies in Applied Mathematics. 136, 4, p. 424-458

Research output: Contribution to journalArticle

Open Access
File
Moisture
Asymptotic Solution
Wetting
Diffusivity
Porous Media
15 Citations (Scopus)

Mutation rate analysis via parent– progeny sequencing of the perennial peach. I. A low rate in woody perennials and a higher mutagenicity in hybrids

Xie, Z., Wang, L., Wang, L., Wang, Z., Lu, Z., Tian, D., Yang, S. & Hurst, L. D., 26 Oct 2016, In : Proceedings of the Royal Society B: Biological Sciences. 283, 1841, 20161016.

Research output: Contribution to journalArticle

Open Access
File
mutagenicity
Mutation Rate
peaches
mutation
Genes
3 Citations (Scopus)

Mutation rate analysis via parent- progeny sequencing of the perennial peach. II. No evidence for recombination associated mutation

Wang, L., Zhang, Y., Qin, C., Tian, D., Yang, S. & Hurst, L. D., 26 Oct 2016, In : Proceedings of the Royal Society B: Biological Sciences. 283, 1841, 20161785.

Research output: Contribution to journalArticle

Open Access
File
Mutation Rate
peaches
Genetic Recombination
recombination
mutation

Network innoculation: heteroclinics and phase transitions in an epidemic model

Yang, H., Rogers, T. & Gross, T., 22 Aug 2016, In : Chaos. 26, 083116.

Research output: Contribution to journalArticle

Epidemic Model
Phase Transition
Phase transitions
Bifurcation
Local Bifurcations
1 Citation (Scopus)

Normative practical reasoning via argumentation and dialogue

Shams, Z., De Vos, M., Oren, N. & Padget, J., 15 Jul 2016, Proceedings of the 25th International Joint Conference on Artificial Intelligence (IJCAI), 2016. Kambhampati, S. (ed.). Palo Alto, U. S. A.: AAAI Press, p. 1244-1250 7 p. (Proceedings (IITA International Joint Conference on Artificial Intelligence)).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Open Access
File
Decision making
Planning
Compliance

On the reliability of unreliable information: Gossip as cultural memory

Mitchell, D., Bryson, J. J., Rauwolf, P. & Ingram, G., Oct 2016, In : Interaction Studies. 17, 1, p. 1-25 25 p.

Research output: Contribution to journalArticle

Open Access
File
collective memory
Data storage equipment
demography
information sources
source of information
22 Citations (Scopus)

Pluripotency and the endogenous retrovirus HERVH: conflict or serendipity?

Izsvák, Z., Wang, J., Singh, M., Mager, D. L. & Hurst, L. D., 1 Jan 2016, In : Bioessays. 38, 1, p. 109-117 9 p.

Research output: Contribution to journalArticle

Endogenous Retroviruses
Genes
Genome
Pluripotent Stem Cells
DNA Transposable Elements
6 Citations (Scopus)

Purifying selection on exonic splice enhancers in intronless genes

Savisaar, R. & Hurst, L. D., Jun 2016, In : Molecular Biology and Evolution. 33, 6, p. 1396-1418

Research output: Contribution to journalArticle

Open Access
File
gene
Introns
Genes
introns
genes

Reports of the aaai 2016 Spring Symposium Series

Amato, C., Amir, O., Bryson, J., Grosz, B., Indurkhya, B., Kiciman, E., Kido, T., Lawless, W. F., Liu, M., McDorman, B., Mead, R., Oliehoek, F. A., Specian, A., Stojanov, G. & Takadama, K., 1 Dec 2016, In : Z Magazine. 37, 4, p. 83-88 6 p.

Research output: Contribution to journalArticle

Human robot interaction
Intelligent systems
Computer science
Health
Thermodynamics
2 Citations (Scopus)

Revising institutions governed by institutions for compliant regulations

King, T. C., Li, T., De Vos, M., Jonker, C. M., Padget, J. & van Riemsdijk, M. B., 13 Jul 2016, Coordination, Organizations, Institutions, and Normes in Agent Systems XI: COIN 2015 International Workshops, COIN@AAMAS, Istanbul, Turkey, May 4, 2015, COIN@IJCAI, Buenos Aires, Argentina, July 26, 2015, Revised Selected Papers. Dignum, V., Noriega, P., Sensoy, M. & Simao Sichman, J. (eds.). Springer International Publishing, p. 191-208 18 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9628).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Multi agent systems
Innovation

Robot Transparency, Trust and Utility

Wortham, R. H., Theodorou, A. & Bryson, J. J., 4 Apr 2016. 3 p.

Research output: Contribution to conferencePaper

Open Access
File
Transparency
Robots
Robotics
2 Citations (Scopus)

Robust set-point regulation for ecological models with multiple management goals

Guiver, C., Mueller, M., Hodgson, D. & Townley, S., 1 May 2016, In : Journal of Mathematical Biology. 72, 6, p. 1467-1529 63 p.

Research output: Contribution to journalArticle

Open Access
File
Ecological Model
Point Sets
Linear control systems
Controllers
Population
10 Citations (Scopus)

Sampling diverse characters improves phylogenies: craniodental and postcranial characters of vertebrates often imply different trees

Mounce, R. C. P., Sansom, R. & Wills, M. A., 15 Mar 2016, In : Evolution. 70, 3, p. 666-686 21 p.

Research output: Contribution to journalArticle

Open Access
File
Phylogeny
Vertebrates
vertebrate
phylogeny
vertebrates
5 Citations (Scopus)

Scale-invariant geometric random graphs

Xie, Z. & Rogers, T., 9 Mar 2016, In : Physical Review E. 93, 3, 032310.

Research output: Contribution to journalArticle

Random Geometric Graph
Scale Invariant
random numbers
dichotomies
hubs
2 Citations (Scopus)

Self-focusing dynamics of patches of ripples

Milewski, P. A. & Wang, Z., 15 Oct 2016, In : Physica D: Nonlinear Phenomena. 333, p. 235-242

Research output: Contribution to journalArticle

Open Access
self focusing
ripples
fluid dynamics
gravity waves
light beams
6 Citations (Scopus)

Simple adaptive control for positive linear systems with applications to pest management

Guiver, C., Edholm, C., Jin, Y., Mueller, M., Powell, J., Rebarber, R., Tenhumberg, B. & Townley, S., 2016, In : SIAM Journal on Applied Mathematics. 76, 1, p. 238-275 38 p.

Research output: Contribution to journalArticle

Open Access
File
Positive Systems
Adaptive Control
Linear systems
Linear Systems
Nonlinear feedback

Simple adaptive feedback control for positive state control systems

Guiver, C., Logemann, H. & Townley, S., 2016, (Unpublished).

Research output: Contribution to conferencePaper

File

Simulation and the evolution of thought

Bryson, J. J., 1 Jan 2016, Memory in the Twenty-First Century: New Critical Perspectives from the Arts, Humanities, and Sciences. Groes, S. (ed.). Palgrave Macmillan, p. 205-207 3 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Simulation
Thought
Reverie
Entertainment
Devotion
1 Citation (Scopus)

Skorokhod embeddings for two-sided Markov chains

Morters, P. & Redl, I., Jun 2016, In : Probability Theory and Related Fields. 165, 1

Research output: Contribution to journalArticle

Open Access
File
2 Citations (Scopus)

Stability of higher-order discrete-time Lur’e systems

Sarkans, E. & Logemann, H., 1 Oct 2016, In : Linear Algebra and its Applications. 506, p. 183-211 30 p.

Research output: Contribution to journalArticle

Open Access
File
Lur'e System
ARMA Model
Discrete-time Systems
Higher Order
Higher order equation
6 Citations (Scopus)

Stability of Non-Negative Lur'e Systems

Bill, A., Guiver, C., Logemann, H. & Townley, S., 12 May 2016, In : SIAM Journal on Control and Optimization. 54, 3, p. 1176-1211

Research output: Contribution to journalArticle

Open Access
File
Lur'e System
Non-negative
Perron-Frobenius Theory
Exponential Asymptotics
Absolute Stability
11 Citations (Scopus)

Structure-activity relationships of 2-arylquinazolin-4-ones as highly selective and potent inhibitors of the tankyrases

Nathubhai, A., Haikarainen, T., Hayward, P. C., Munoz-Descalzo, S., Thompson, A. S., Lloyd, M. D., Lehtio, L. & Threadgill, M., 8 Aug 2016, In : European Journal of Medicinal Chemistry. 118, p. 316-327 12 p.

Research output: Contribution to journalArticle

Open Access
File
Tankyrases
Structure-Activity Relationship
Poly(ADP-ribose) Polymerases
Molecular Probes
Pharmaceutical Preparations
9 Citations (Scopus)

Substitution of the native srfA promoter by constitutive Pveg in two B. subtilis strains and evaluation of the effect on surfactin production

Willenbacher, J., Mohr, T., Henkel, M., Gebhard, S., Mascher, T., Syldatk, C. & Hausmann, R., Apr 2016, In : Journal of Biotechnology. 224, p. 14-17

Research output: Contribution to journalArticle

Open Access
File
Bacillus subtilis
Quorum Sensing
Genetic Enhancement
Operon
Cell Count

The confabulation of self

Bryson, J. J., 1 Jan 2016, Memory in the Twenty-First Century: New Critical Perspectives from the Arts, Humanities, and Sciences. Groes, S. (ed.). Palgrave Macmillan, p. 334-337 4 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Ego
8 Citations (Scopus)

The evolution of sex-specific dominance in response to sexually antagonistic selection

Spencer, H. G. & Priest, N. K., May 2016, In : The American Naturalist. 187, 5, p. 658-666 9 p., 10.1086/685827.

Research output: Contribution to journalArticle

File
Genes
Mathematical models
Genetics
5 Citations (Scopus)

The impact of host metapopulation structure on the population genetics of colonizing bacteria

Numminen, E., Gutmann, M., Shubin, M., Marttinen, P., Méric, G., van Schaik, W., Coque, T. M., Baquero, F., Willems, R. J. L., Sheppard, S. K., Feil, E. J., Hanage, W. P. & Corander, J., 7 May 2016, In : Journal of Theoretical Biology. 396, p. 53-62 10 p.

Research output: Contribution to journalArticle

Metapopulation
Population Genetics
Bacteria
Migration
population genetics
14 Citations (Scopus)

The landscape of realized homologous recombination in pathogenic bBacteria

Yahara, K., Didelot, X., Jolley, K. A., Kobayashi, I., Maiden, M. C. J., Sheppard, S. & Falush, D., Feb 2016, In : Molecular Biology and Evolution. 33, 2, p. 456-471

Research output: Contribution to journalArticle

Open Access
Homologous Recombination
homologous recombination
Genetic Recombination
recombination
gene
3 Citations (Scopus)

The optimal timing of open market stock repurchases

Krause, A. & Hsu, C-C., 2016, In : Emerging Markets Finance and Trade. 52, 4, p. 776-785

Research output: Contribution to journalArticle

Repurchase
Optimal timing
Stock repurchases
Continuous time
Authorization
29 Citations (Scopus)

The stealthy superbug: the role of asymptomatic enteric carriage in maintaining a long-term hospital outbreak of ST228 methicillin resistant Staphylococcus aureus

Senn, L., Clerc, O., Zanetti, G., Basset, P., Prod'hom, G., Gordon, N., Sheppard, A., Crook, D., James, R., Thorpe, H. A. F. W., Feil, E. & Blanc, D., 19 Jan 2016, In : mBio. 7, 1, e02039-15.

Research output: Contribution to journalArticle

Open Access
File
10 Citations (Scopus)

Thyroid hormones regulate zebrafish melanogenesis in a gender-specific manner

Guillot, R., Muriach, B., Rocha, A., Rotllant, J., Kelsh, R. & Cerda-Reverter, J. M., 10 Nov 2016, In : PLoS ONE. 11, 11, e0166152.

Research output: Contribution to journalArticle

Open Access
File
7 Citations (Scopus)

Transmission of Staphylococcus aureus from humans to green monkeys in the Gambia as revealed by whole-genome sequencing

Senghore, M., Bayliss, S., Kwambana-Adams, B., Foster-Nyarko, E., Menneh, J., Dione, M., Badji, H., Ebruke, C., Doughty, E., Thorpe, H. A. F. W., Jasinska, A., Schmitt, C., Cramer, J., Turner, T., Weinstock, G., Freimer, N., Pallen, M., Feil, E. & Antonio, M., Oct 2016, In : Applied and Environmental Microbiology. 82, 19, p. 5910-5917 8 p.

Research output: Contribution to journalArticle

Open Access
Gambia
Cercopithecus aethiops
monkeys
Staphylococcus aureus
genome

Triple jeopardy for people with albinism

Arnheiter, H., Long, G., Aplin, A., Harris, J. & Kelsh, R., Sep 2016, In : Pigment Cell & Melanoma Research. 29, 5, p. 487

Research output: Contribution to journalArticle

Trust, Communication, and Inequality

Bryson, J. J. & Rauwolf, P., Aug 2016, Proceedings of the 38th Annual Meeting of the Cognitive Science Society. Philadelphia

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Open Access
File
communication
choice of partner
cooperative behavior
cause
social behavior
34 Citations (Scopus)

Unexpected diversity in socially synchronized rhythms of shorebirds

Bulla, M., Valcu, M., Dokter, A. M., Dondua, A. G., Kosztolányi, A., Rutten, A. L., Helm, B., Sandercock, B. K., Casler, B., Ens, B. J., Spiegel, C. S., Hassell, C. J., Küpper, C., Minton, C., Burgas, D., Lank, D. B., Payer, D. C., Loktionov, E. Y., Nol, E., Kwon, E. & 56 othersSmith, F., Gates, H. R., Vitnerová, H., Prüter, H., Johnson, J. A., St Clair, J. J. H., Lamarre, J. F., Rausch, J., Reneerkens, J., Conklin, J. R., Burger, J., Liebezeit, J., Bêty, J., Coleman, J. T., Figuerola, J., Hooijmeijer, J. C. E. W., Alves, J. A., Smith, J. A. M., Weidinger, K., Koivula, K., Gosbell, K., Exo, K. M., Niles, L., Koloski, L., McKinnon, L., Praus, L., Klaassen, M., Giroux, M. A., Sládecek, M., Boldenow, M. L., Goldstein, M. I., Šálek, M., Senner, N., Rönkä, N., Lecomte, N., Gilg, O., Vincze, O., Johnson, O. W., Smith, P. A., Woodard, P. F., Tomkovich, P. S., Battley, P. F., Bentzen, R., Lanctot, R. B., Porter, R., Saalfeld, S. T., Freeman, S., Brown, S. C., Yezerinac, S., Székely, T., Montalvo, T., Piersma, T., Loverti, V., Pakanen, V. M., Tijsen, W. & Kempenaers, B., 1 Dec 2016, In : Nature. 540, 7631, p. 109-113 5 p.

Research output: Contribution to journalArticle

Open Access
File
predators
nests
starvation
photoperiod
foraging

Welcome to the New Year!

Arnheiter, H., Long, G., Aplin, A., Harris, J. & Kelsh, R., Jan 2016, In : Pigment Cell & Melanoma Research. 29, 1, p. 3

Research output: Contribution to journalEditorial

What do aliens look like? The clue is in evolution

Wills, M., 19 Aug 2016, The Conversation.

Research output: Contribution to specialist publicationArticle

Open Access

What Does the Robot Think? Transparency as a Fundamental Design Requirement for Intelligent Systems

Wortham, R. H., Theodorou, A. & Bryson, J. J., 9 Jun 2016, Proceedings of the IJCAI Workshop on Ethics for Artificial Intelligence : International Joint Conference on Artificial Intelligence. 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Open Access
File
Intelligent systems
Transparency
Robots