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2015 Bibliography Entries

Arcaute, E., Hatna, E., Ferguson, P., Youn, H., Johansson, A., Batty, M. (2015). "Constructing Cities, Deconstructing Scaling Laws." Journal of the Royal Society Interface 12(102)
Cities can be characterized and modelled through different urban measures. Consistency within these observables is crucial in order to advance towards a science of cities. Bettencourt et al. have proposed that many of these urban measures can be predicted through ...   [More]
Artzy-Randrup, Y., Dobson, A. P., Pascual, M. (2015). "Synergistic and antagonistic interactions between bednets and vaccines in the control of malaria." PNAS 112(10):3014-3019
It is extremely likely that the malaria vaccines currently in development will be used in conjunction with treated bednets and other forms of malaria control. The interaction of different intervention methods is at present poorly understood in a disease such ...   [More]
Aymanns, C., Farmer, J. D. (2015). "The dynamics of the leverage cycle." Journal of Economic Dynamics & Control 50:155-179
We present a simple agent-based model of a financial system composed of leveraged investors such as banks that invest in stocks and manage their risk using a Value-at-Risk constraint, based on historical observations of asset prices. The Value-at-Risk constraint implies ...   [More]
Balch, C., Arias-Pulido, H., Banerjee, S., Lancaster, A. K., Clark, K. B., Perilstein, M., Hawkins, B., Rhodes, J., Sliz, P., Wilkins, J. F., Chittenden, T. W. (2015). "Science and technology consortia in US biomedical research: A paradigm shift in response to unsustainable academic growth." BioEssays 37(2):119-122
Science and technology consortia provide a viable solution for the recent unsustainable academic growth in biomedical research.   [More]
Bargigli, L., Di Iasio, G., Infante, L., Lillo, F., Pierobon, F. (2015). "The multiplex structure of interbank networks." Quantitative Finance 15(4):673-691
The interbank market has a natural multiplex network representation. We employ a unique database of supervisory reports on Italian banks to the Banca d'Italia that includes all bilateral exposures broken down by maturity and by the secured and unsecured nature ...   [More]
Bech, M. L., Bergstrom, C. T., Rosvall, M., Garratt, R. J. (2015). "Mapping change in the overnight money market." Physica A - Statistical Mechanics and Its Applications 424:44-51
We use an information-theoretic approach to describe changes in lending relationships between financial institutions around the time of the Lehman Brothers failure. Unlike previous work that conducts maximum likelihood estimation on undirected networks our analysis distinguishes between borrowers and lenders ...   [More]
Bedhomme, S., Hillung, J., Elena, S. F. (2015). "Emerging viruses: why they are not jacks of all trades?." Current Opinion in Virrology 10:1-6
In order to limit the impact of the recent pandemics ignited by viral host jumps, it is necessary to better understand the ecological and evolutionary factors influencing the early steps of emergence and the interactions between them. Antagonistic pleiotropy, that ...   [More]
Blume, L. E., Brock, W. A., Durlauf, S. N., Jayaraman, R. (2015). "Linear Social Interactions Models." Journal of Political Economy 123(2):444-496
This paper provides a systematic analysis of identification in linear social interactions models. This is a theoretical and econometric exercise as the analysis is linked to a rigorously delineated model of interdependent decisions. We develop an incomplete information game for ...   [More]
Blume, L., Easley, D., Kleinberg, J., Kleinberg, R., Tardos, E. (2015). "Introduction to computer science and economic theory." JOURNAL OF ECONOMIC THEORY 156:1-13
This essay introduces the symposium on computer science and economic theory.   [More]
Caccioli, F., Farmer, J. D., Foti, N. J., Rockmore, D. (2015). "Overlapping portfolios, contagion, and financial stability." Journal of Economic Dynamics & Control 51:50-63
We study the problem of interacting channels of contagion in financial networks. The first channel of contagion is counterparty failure risk; this is captured empirically using data for the Austrian interbank network. The second channel of contagion is overlapping portfolio ...   [More]
Cao, Y. D., Babbush, R., Biamonte, J., Kais, S. (2015). "Hamiltonian gadgets with reduced resource requirements." Physical Review A 91(1)
Application of the adiabatic model of quantum computation requires efficient encoding of the solution to computational problems into the lowest eigenstate of a Hamiltonian that supports universal adiabatic quantum computation. Experimental systems are typically limited to restricted forms of two-body ...   [More]
Courchamp, F., Dunne, J. A., Le Maho, Y., May, R. M., Thebaud, C., Hochberg, M. E. (2015). "Fundamental ecology is fundamental." Trends in Ecology & Evolution 30(1):9-16
The primary reasons for conducting fundamental research are satisfying curiosity, acquiring knowledge, and achieving understanding. Here we develop why we believe it is essential to promote basic ecological research, despite increased impetus for ecologists to conduct and present their research ...   [More]
Courchamp, F., Dunne, J. A., Le Maho, Y., May, R. M., Thebaud, C., Hochberg, M. E. (2015). "Fundamental ecology is fundamental." Trends in Ecology & Evolution 30(3):177
The primary reasons for conducting fundamental research are satisfying curiosity, acquiring knowledge, and achieving understanding. Here we develop why we believe it is essential to promote basic ecological research, despite increased impetus for ecologists to conduct and present their research ...   [More]
Dall'Olio, G. M., Vahdati, A. R., Bertranpetit, J., Wagner, A., Laayouni, H. (2015). "VCF2Networks: applying genotype networks to single-nucleotide variants data." Bioinformatics 31(3):438-439
A wealth of large-scale genome sequencing projects opens the doors to new approaches to study the relationship between genotype and phenotype. One such opportunity is the possibility to apply genotype networks analysis to population genetics data. Genotype networks are a ...   [More]
Darmon, D.;, Girvan, M. (2015). "Complexity-Regularized Regression for Serially-Correlated Residuals with Applications to Stock Market Data." Entropy 17(1):1-27
A popular approach in the investigation of the short-term behavior of a non-stationary time series is to assume that the time series decomposes additively into a long-term trend and short-term fluctuations. A first step towards investigating the short-term behavior requires ...   [More]
DeLong, J. P., Gilbert, B., Shurin, J. B., Savage, V. M., Barton, B. T., Clements, C. F., Dell, A. I., Greig, H. S., Harley, C. D. G., Kratina, P., McCann, K. S., Tunney, T. D., Vasseur, D. A., O'Connor, M. I. (2015). "The Body Size Dependence of Trophic Cascades." American Naturalist 185(3):354-366
Trophic cascades are indirect positive effects of predators on resources via control of intermediate consumers. Larger-bodied predators appear to induce stronger trophic cascades (a greater rebound of resource density toward carrying capacity), but how this happens is unknown because we ...   [More]
di Iasio, G., Gallegati, M., Lillo, F., Mantegna, R. N. (2015). "Special issue of Quantitative Finance on 'Interlinkages and Systemic Risk' Foreword." Quantitative Finance 15(4):587-588   [More]
Duran-Nebreda, S., Sole, R. (2015). "Emergence of Multicellularity in a Model of Cell Growth, Death and Aggregation Under Size-Dependent Selection." Journal of the Royal Society Interface 12(102)
How multicellular life forms evolved from unicellular ones constitutes a major problem in our understanding of the evolution of our biosphere. A recent set of experiments involving yeast cell populations have shown that selection for faster sedimenting cells leads to ...   [More]
Einarsdottir, O; McDonald, W; Funatogawa, C; Szundi, I; Woodruff, WH; Dyer, RB (2015). "The pathway of O-2 to the active site in heme-copper oxidases." Biochimica et Biophysica Acta - Bioengeretics 1847(1):109-118
The route of O-2 to and from the high-spin heme in heme-copper oxidases has generally been believed to emulate that of carbon monoxide (CO). Time-resolved and stationary infrared experiments in our laboratories of the fully reduced CO-bound enzymes, as well ...   [More]
Gintis, H. (2015). "SOCIOBIOLOGY Altruists together." Nature 517(7536):550-551
Book Reviews of: Does Altruism Exist?: Culture, Genes, and the Welfare of Others David Sloan Wilson Yale University Press 2015. ISBN: 9780300189490 and The Moral Arc: How Science and Reason Lead Humanity toward Truth, Justice, and Freedom Michael Shermer Henry ...   [More]
Greenblum, S., Carr, R., Borenstein, E. (2015). "Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species." Cell 160(4):583-594
Within each bacterial species, different strains may vary in the set of genes they encode or in the copy number of these genes. Yet, taxonomic characterization of the human microbiota is often limited to the species level or to previously ...   [More]
Hecker, J. P., Moses, M. E. (2015). "Beyond pheromones: evolving error-tolerant, flexible, and scalable ant-inspired robot swarms." Swarm Intelligence 9(1):43-70
For robot swarms to operate outside of the laboratory in complex real-world environments, they require the kind of error tolerance, flexibility, and scalability seen in living systems. While robot swarms are often designed to mimic some aspect of the behavior ...   [More]
Hellmuth, M., Wieseke, N., Lechner, M., Lenhof, H. P., Middendorf, M., Stadler, P. F. (2015). "Phylogenomics with paralogs." PNAS(112):7
Phylogenomics heavily relies on well-curated sequence data sets that comprise, for each gene, exclusively 1:1 orthologos. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe restriction of the data ...   [More]
Hoffmann, S., Stadler, P. F., Strimmer, K. (2015). "A simple data-adaptive probabilistic variant calling model." Algorithms for Molecular Biology 10
Background: Several sources of noise obfuscate the identification of single nucleotide variation (SNV) in next generation sequencing data. For instance, errors may be introduced during library construction and sequencing steps. In addition, the reference genome and the algorithms used for ...   [More]
Hooper, P. L., Gurven, M., Winking, J., Kaplan, H. S. (2015). "Inclusive fitness and differential productivity across the life course determine intergenerational transfers in a small-scale human society." Proceedings of the Royal Society B - Biological Sciences 282(1803)
Transfers of resources between generations are an essential element in current models of human life-history evolution accounting for prolonged development, extended lifespan and menopause. Integrating these models with Hamilton's theory of inclusive fitness, we predict that the interaction of biological ...   [More]
Hormozdiari, F., Penn, O., Borenstein, E., Eichler, E. E. (2015). "The discovery of integrated gene networks for autism and related disorders." Genome Research 25(1):142-154
Despite considerable genetic heterogeneity underlying neurodevelopmental diseases, there is compelling evidence that many disease genes will map to a much smaller number of biological subnetworks. We developed a computational method, termed MAGI (merging affected genes into integrated networks), that simultaneously ...   [More]
Hruschka, D. J., Branford, S., Smith, E. D., Wilkins, J. F., Meade, A., Pagel, M., Bhattacharya, T. (2015). "Detecting Regular Sound Changes in Linguistics as Events of Concerted Evolution." Current Biology 25(1):109
Background: Concerted evolution is normally used to describe parallel changes at different sites in a genome, but it is also observed in languages where a specific phoneme changes to the same other phoneme in many words in the lexicon-a phenomenon ...   [More]
Jauregui, M., Tsallis, C. (2015). "Convergence of the probability of large deviations in a model of correlated random variables having compact-support Q-Gaussians as limiting distributions." Journal of Mathematical Physics 56(2)
We consider correlated random variables X-1,...,X-n taking values in {0,1} such that, for any permutation pi of {1,...,n}, the random vectors (X-1,...,X-n) and (X-pi(1),...,X-pi(n)) have the same distribution. This distribution, which was introduced by Rodriguez et al. [J. Stat. Mech. ...   [More]
Karafet, T. M., Mendez, F. L., Sudoyo, H., Lansing, J. S., Hammer, M. F. (2015). "Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia." European Journal of Human Genetics 23(3):369-373
The highly structured distribution of Y-chromosome haplogroups suggests that current patterns of variation may be informative of past population processes. However, limited phylogenetic resolution, particularly of subclades within haplogroup K, has obscured the relationships of lineages that are common across ...   [More]
Klimek, P., Poledna, S., Farmer, J. D., Thurner, S. (2015). "To bail-out or to bail-in? Answers from an agent-based model." Journal of Economic Dynamics & Control 50:144-154
Since the beginning of the 2008 financial crisis almost half a trillion euros have been spent to financially assist EU member states in taxpayer-funded bail-outs. These crisis resolutions are often accompanied by austerity programs causing political and social friction on ...   [More]
Lachowiec, J., Lemus, T., Borenstein, E., Queitsch, C. (2015). "Hsp90 Promotes Kinase Evolution." Molecular Biology and Evolution 32(1):91-99
Heat-shock protein 90 (Hsp90) promotes the maturation and stability of its client proteins, including many kinases. In doing so, Hsp90may allow its clients to accumulatemutations as previously proposed by the capacitor hypothesis. If true, Hsp90 clients should show increased evolutionary ...   [More]
Lillo, F., Micciche, S., Tumminello, M., Piilo, J., Mantegna, R. N. (2015). "How news affects the trading behaviour of different categories of investors in a financial market." Quantitative Finance 15(2):213-229
We investigate the trading behaviour of a large set of single investors trading the highly liquid Nokia stock over the period 2003-2008 with the aim of determining the relative role of endogenous and exogenous factors that may affect their behaviour. ...   [More]
Lillo, F., Pirino, D. (2015). "The impact of systemic and illiquidity risk on financing with risky collateral." Journal of Economic Dynamics & Control 50:180202
Repurchase agreements (repos) are one of the most important sources of funding liquidity for many financial investors and intermediaries. In a repo, some assets are given by a borrower as collateral in exchange of funding. The capital given to the ...   [More]
Mandel, A., Landini, S., Gallegati, M., Gintis, H. (2015). "Price dynamics, financial fragility and aggregate volatility." Journal of Economic Dynamics & Control 51:257-277
Within a general equilibrium framework a la (Long and Plosser, 1983), we investigate the dynamics emerging from the interactions of households and firms that are adaptive price setters and financially constrained. Adaptive price-setting behavior induces micro-founded out-of-equilibrium dynamics along which ...   [More]
Mertens, S. (2015). "Stable roommates problem with random preferences." Journal of Statistical Mechanics — Theory and Experiment
The stable roommates problem with n agents has worst case complexity O(n(2)) in time and space. Random instances can be solved faster and with less memory, however. We introduce an algorithm that has average time and space complexity O(n 32) ...   [More]
Mryglod, O., Fuchs, B., Szell, M., Holovatch, Y., Thurner, S. (2015). "Interevent time distributions of human multi-level activity in a virtual world." Physica A - Statistical Mechanics and Its Applications 419:681-690
Studying human behavior in virtual environments provides extraordinary opportunities for a quantitative analysis of social phenomena with levels of accuracy that approach those of the natural sciences. In this paper we use records of player activities in the massive multiplayer ...   [More]
Muneepeerakul, R., Castillo-Chavez, C. (2015). "Towards a Quantitative Science of Sustainability." Bulletin of Mathematical Biology 77(2):254-258
Introduction: The report Toward a Science of Sustainability (Clark and Levin 2010) states that “Building a science of sustainability...requires a truly multi-disciplinary approach that integrates practical experience with knowledge and know-how drawn from across the natural and social sciences, medicine ...   [More]
Mushegian, A. R., Elena, S. F. (2015). "Evolution of plant virus movement proteins from the 30K superfamily and of their homologs integrated in plant genomes." Virology 476:304-315
Homologs of Tobacco mosaic virus 30K cell-to-cell movement protein are encoded by diverse plant viruses. Mechanisms of action and evolutionary origins of these proteins remain obscure. We expand the picture of conservation and evolution of the 30K proteins, producing sequence ...   [More]
Noar, SM; Althouse, BM; Ayers, JW; Francis, DB; Ribisl, KM (2015). "Cancer Information Seeking in the Digital Age: Effects of Angelina Jolie's Prophylactic Mastectomy Announcement." Medical Decision Making 35(1):16-21
Objective. This study used digital surveillance to examine the impact of Angelina Jolie's prophylactic mastectomy announcement on cancer information seeking. Methods. We analyzed 4 categories of breast cancer-related Internet search queries from 2010 to 2013 in the United States. Results. ...   [More]
Norris, J. Q., Turcotte, D. L., Rundle, J. B. (2015). "Anisotropy in Fracking: A Percolation Model for Observed Microseismicity." Pure and Applied Geophysics 172(1):7-21
Hydraulic fracturing (fracking), using high pressures and a low viscosity fluid, allow the extraction of large quantiles of oil and gas from very low permeability shale formations. The initial production of oil and gas at depth leads to high pressures ...   [More]
Rambaldi, M., Pennesi, P., Lillo, F. (2015). "Modeling foreign exchange market activity around macroeconomic news: Hawkes-process approach." Physical Review E 91(1)
We present a Hawkes-model approach to the foreign exchange market in which the high-frequency price dynamics is affected by a self-exciting mechanism and an exogenous component, generated by the pre-announced arrival of macroeconomic news. By focusing on time windows around ...   [More]
Ratcliff, W. C., Hawthorne, P., Libby, E. (2015). "Courting disaster: How diversification rate affects fitness under risk." Evolution 69(1):126-135
Life is full of risk. To deal with this uncertainty, many organisms have evolved bet-hedging strategies that spread risk through phenotypic diversification. These rates of diversification can vary by orders of magnitude in different species. Here we examine how key ...   [More]
Roos, P., Orlando, P. A., Fagerstrom, R. M., Pepper, J. W. (2015). "In North America, Some Ovarian Cancers Express the Oncogenes of Preventable Human Papillomavirus HPV-18." Scientific Reports 5(8645)
Some researchers in other regions have recommended human papillomavirus (HPV) vaccination to reduce risk of ovarian cancer, but not in North America, where evidence has previously suggested no role for HPV in ovarian cancer. Here we use a large sample ...   [More]
Rowland, M. A., Harrison, B., Deeds, E. J. (2015). "Phosphatase Specificity and Pathway Insulation in Signaling Networks." Biophysical Journal 108(4):986-996
Phosphatases play an important role in cellular signaling networks by regulating the phosphorylation state of proteins. Phosphatases are classically considered to be promiscuous, acting on tens to hundreds of different substrates. We recently demonstrated that a shared phosphatase can couple ...   [More]
Sloat, L. L., Henderson, A. N., Lamanna, C., Enquist, B. J. (2015). "The Effect of the Foresummer Drought on Carbon Exchange in Subalpine Meadows." Ecosystems 18(3):533-545
Climate in subalpine meadows of the Rocky Mountains can be characterized by an early (foresummer) drought that occurs after snowmelt (May) and lasts until the start of the summer monsoon season (July). Climate change models predict an increase in the ...   [More]
Szymanski, J. K., Temprano-Coleto, F., Perez-Mercader, J. (2015). "Unusual kinetics of poly(ethylene glycol) oxidation with cerium(IV) ions in sulfuric acid medium and implications for copolymer synthesis." Physical Chemistry Chemical Physics 17(10):6713-6717
The cerium(IV)-alcohol couple in an acidic medium is an example of a redox system capable of initiating free radical polymerization. When the alcohol has a polymeric nature, the outcome of such a process is a block copolymer, a member of ...   [More]
Toth, B., Palit, I., Lillo, F., Farmer, J. D. (2015). "Why is equity order flow so persistent?." Journal of Economic Dynamics & Control 51:218-239
Order flow in equity markets is remarkably persistent in the sense that order signs (to buy or sell) are positively autocorrelated out to time lags of tens of thousands of orders, corresponding to many days. Two possible explanations are herding, ...   [More]
Waagen, A., Verma, G., Chan, K., Swami, A., D'Souza, R. (2015). "Effect of zealotry in high-dimensional opinion dynamics models." Physical Review E 91(2)
Most of the work on opinion dynamics models focuses on the case of two or three opinion types. We consider the case of an arbitrary number of opinions in the mean field case of the naming game model in which ...   [More]
Wagner, A. (2015). "Causal Drift, Robust Signaling, and Complex Disease." PLOS One 10(3)
The phenotype of many regulatory circuits in which mutations can cause complex, polygenic diseases is to some extent robust to DNA mutations that affect circuit components. Here I demonstrate how such mutational robustness can prevent the discovery of genetic disease ...   [More]
Waldor, M. K., Tyson, G., Borenstein, E., Ochman, H., Moeller, A., Finlay, B. B., Kong, H. H., Gordon, J. I., Nelson, K. E., Dabbagh, K., Smith, H. (2015). "Where Next for Microbiome Research?." PLOS Biology 13(1)
The development of high-throughput sequencing technologies has transformed our capacity to investigate the composition and dynamics of the microbial communities that populate diverse habitats. Over the past decade, these advances have yielded an avalanche of metagenomic data. The current stage ...   [More]
Warren, A. L., Bhat, U., Sattenspiel, L., Swedlund, A. C., Gumerman, G. J. (2015). "Exploring the effects of constant versus age-specific fertility rates on prehistoric population estimates." American Journal of Physical Anthropology 156(60):320
Summary: Many fundamental questions about the prehistory of the American Southwest require accurate estimates of population size and other demographic parameters in order to be investigated properly. The Artificial Anasazi model and its successor, Artificial Long House Valley, are agent-based ...   [More]
Weigel, M., Katzgraber, H. G., Machta, J., Hamze, F., Andrist, R. S. (2015). "Glassy Chimeras could be blind to quantum speedup: Designing better benchmarks for quantum annealing machines." Physical Review X 5(1)
Abstract to the working paper version: Recently, a programmable quantum annealing machine has been built that minimizes the cost function of hard optimization problems by adiabatically quenching quantum fluctuations. Tests performed by different research teams have shown that, indeed, the ...   [More]
Weis, S., Knauf, A., Ay, N., Zhao, M. J. (2015). "Maximizing the Divergence from a Hierarchical Model of Quantum States." Open Systems & Information Dynamics 22(1)
We study many-party correlations quantified in terms of the Umegaki relative entropy (divergence) from a Gibbs family known as a hierarchical model. We derive these quantities from the maximum-entropy principle which was used earlier to define the closely related irreducible ...   [More]
Witt, K. E., Judd, K., Kitchen, A., Grier, C., Kohler, T. A., Ortman, S. G., Kemp, B. M., Malhi, R. S. (2015). "DNA analysis of ancient dogs of the Americas: Identifying possible founding haplotypes and reconstructing population histories." Journal of Human Evolution 79:105-118
As dogs have traveled with humans to every continent, they can potentially serve as an excellent proxy when studying human migration history. Past genetic studies into the origins of Native American dogs have used portions of the hypervariable region (HVR) ...   [More]
Yeakel, J. D., Mangel, M. (2015). "A generalized perturbation approach for exploring stock recruitment relationships." Theoretical Ecology 8(1):1-13
Models of stock-recruitment relationships (SRRs) are often used to predict fish population dynamics. Commonly used SRRs include the Ricker, Beverton-Holt, and Cushing functional forms, which differ primarily by the degree of density-dependent effects (compensation). The degree of compensation determines whether ...   [More]
Yeakel, J. D., Pires, M. M., Rudolf, L., Dominy, N. J., Koch, P. L., Guimaraes, P. R., Grossc, T. (2015). "Reply to Evans and Bar-Oz et al.: Recovering ecological pattern and process in Ancient Egypt." PNAS 112(3):E240
Extract: Our recent paper used artistic depictions of animals and fossil evidence to examine the community-level effects of local extinction events over 6,000 y of Egyptian history (1). We found that local extinctions were nonrandom, that changes to community structure ...   [More]
Zwart, M. P., Elena, S. F. (2015). "Testing the Independent Action Hypothesis of Plant Pathogen Mode of Action: A Simple and Powerful New Approach." Phytopathology 105(1):18-25
The independent action hypothesis is a simple model of pathogen infection that can make many useful predictions on infection kinetics and, therefore, a number of different tests of independent action have been developed. However, some of these analyses are rather ...   [More]
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