Abades, S. R., Marquet, P. A. (2011).
"Finite Size Scaling in the Local Abundances of Geographic Populations." Biological Research 44(1):107-112
We analyzed the statistical distribution of intra- specific local abundances for a set North American breeding bird species. We constructed frequency plots for every species and found that they showed long-tail power-law behavior, truncated at an upper abundance cut-off value. ... [
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Arakawa, F., Ortman, S. G., Shackley, M. S., Duff, AI. (2011).
"Obsidian Evidence of Interaction and Migration From The Mesa Verde Region, Southwest Colorado." American Antiquity 76(4):773-795
A growing body of evidence demonstrates that ancestral Pueblo people living in the central Mesa Verde region of the U.S. Southwest maintained long-distance contacts with other Pueblo peoples. Questions of Pueblo interactions through time and across space have traditionally been ... [
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Asmal, M., Hellmann, I., Liu, W. M., Keele, B. F., Perelson, A. S., Bhattacharya, T., Gnanakaran, S., Daniels, M. G., Haynes, B. F., Korber, B. T., Hahn, B. H., Shaw, G. M., Letvin, N. L. (2011).
"A Signature in HIV-1 Envelope Leader Peptide Associated with Transition from Acute to Chronic Infection Impacts Envelope Processing and Infectivity." PLoS One 6(8):315-326
Mucosal transmission of the human immunodeficiency virus (HIV) results in a bottleneck in viral genetic diversity. Gnanakaran and colleagues used a computational strategy to identify signature amino acids at particular positions in Envelope that were associated either with transmitted sequences ... [
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Ay, N., Muller, M., Szkola, A. (2011).
"Effective Complexity of Stationary Process Realizations." Entropy 13(6):1200-1211
The concept of effective complexity of an object as the minimal description length of its regularities has been initiated by Gell-Mann and Lloyd. The regularities are modeled by means of ensembles, which is the probability distributions on finite binary strings. ... [
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Ay, N., Olbrich, E., Bertschinger, N., Jost, J. (2011).
"A Geometric Approach to Complexity." Chaos 21(3):322-331
INFORMATION; SYSTEM [
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Bauke, H., Moore, C., Rouquier, J. B., Sherrington, D. (2011).
"Topological Phase Transition in a Network Model with Preferential Attachment and Node Removal." European Physical Journal B 83(4):519-524
Preferential attachment is a popular model of growing networks. We consider a generalized model with random node removal, and a combination of preferential and random attachment. Using a high-degree expansion of the master equation, we identify a topological phase transition ... [
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Bedhomme, S., Elena, S. F. (2011).
"Virus Infection Suppresses Nicotiana benthamiana Adaptive Phenotypic Plasticity." PLoS One 6(2):428-434
Competition and parasitism are two important selective forces that shape life-histories, migration rates and population dynamics. Recently, it has been shown in various pathosystems that parasites can modify intraspecific competition, thus generating an indirect cost of parasitism. Here, we investigated ... [
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Beinhocker, E. D. (2011).
"Evolution as Computation: Integrating Self-Organization with Generalized Darwinism." Journal of Institutional Economics DOI:10.1017/S1744137411000257 Generalized Darwinism and self-organization have been positioned as competing frameworks for explaining processes of economic and institutional change. Proponents of each view question the ontological validity and explanatory power of the other. This paper argues that information theory, rooted in ... [
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Bergstrom, C. T., Rosvall, M. (2011).
"The Transmission Sense of Information." Biology & Philosophy 26(2):159-176
Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers ... [
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Bergstrom, C. T., Rosvall, M. (2011).
"Response to commentaries on "The Transmission Sense of Information"." Biology & Philosophy 26(2):195-200 [
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Bettencourt, L. M. A., West, G. B. (2011).
"Bigger Cities Do More with Less New Science Reveals Why Cities Become More Productive and Efficient as They Grow." Scientific American 305(3):44-45 [
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Blonder, B., Violle, C., Bentley, L. P., Enquist, B. J. (2011).
"Venation Networks and the Origin of the Leaf Economics Spectrum." Ecology Letters 14(2):91-100
P>The leaf economics spectrum describes biome-invariant scaling functions for leaf functional traits that relate to global primary productivity and nutrient cycling. Here, we develop a comprehensive framework for the origin of this leaf economics spectrum based on venation-mediated economic strategies. ... [
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Bowles, S. (2011).
"Cultivation of Cereals by the First Farmers was Not More Productive than Foraging." PNAS 108(12):4760-4765
Did foragers become farmers because cultivation of crops was simply a better way to make a living? If so, what is arguably the greatest ever revolution in human livelihoods is readily explained. To answer the question, I estimate the caloric ... [
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Bowles, S. (2011).
"Is Liberal Society a Parasite on Tradition?." Philosophy & Public Affairrs 39(1):46-81 [
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Bowles, S. (2011).
"History Lesson from the First Farmers." New Scientist 211(2823):26-27 [
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Bowles, S., Jayadev, A..
"The Enforcement-Equality Trade-off". In
Institutions for Social Well Being: Alternatives for Europe, 74-94.
Palgrave: Basingstoke, 2011 [
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Braakman, R., Blake, G. A. (2011).
"Principles and Promise of Fabry-Perot Resonators at Terahertz Frequencies." Journal of Applied Physics 109(6):Art. No. 063102
Fabry-Perot resonators have tremendous potential to enhance the sensitivity of spectroscopic systems at terahertz (THz) frequencies. Increasing sensitivity will be of benefit in compensating for the relatively low power of current high resolution continuous wave THz radiation techniques, and to ... [
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Brandvain, Y., Van Cleve, J., Ubeda, F., Wilkins, J. F. (2011).
"Demography, kinship, and the evolving theory of genomic imprinting." Trends in Genetics 27(7):251-257
Genomic imprinting is the differential expression of an allele based on the parent of origin. Recent transcriptome-wide evaluations of the number of imprinted genes reveal complex patterns of imprinted expression among developmental stages and cell types. Such data demand a ... [
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Brown, J. H. (2011).
"Changes in Ranges of Large Ocean Fish." PNAS 108(29):11735-11736 [
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Brown, J. H., Burnside, W. R., Davidson, A. D., DeLong, J. P., Dunn, W. C., Hamilton, M. J., Mercado-Silva, N., Nekola, J. C., Okie, J. G., Woodruff, W. H., Zuo, W. Y. (2011).
"Energetic Limits to Economic Growth." Bioscience 61(1):19-26
The human population and economy have grown exponentially and now have impacts on climate, ecosystem processes, and biodiversity far exceeding those of any other species. Like all organisms, humans are subject to natural laws and are limited by energy and ... [
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Buchanan, B., Collard, M., Hamilton, M. J., O'Brien, M. J. (2011).
"Points and Prey: A Quantitative Test of the Hypothesis that Prey Size Influences Early Paleoindian Projectile Point Form." Journal of Archaeological Science 38(4):852-864
Understanding the causes of variation within and between projectile point types is an important task for Paleoindian archaeologists since they rely heavily on points to investigate such things as settlement dynamics and hunting practices. One long-held explanation for the variation ... [
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Buchanan, B., Hamilton, M. J., Edinborough, K., O'Brien, M. J., Collard, M. (2011).
"A Comment on Steele's (2010) "Radiocarbon Dates as Data: Quantitative Strategies for Estimating Colonization Front Speeds and Event Densities"." Journal of Archaeological Science 38(9):2116-2122
We show that Steele's (2010) criticisms of Hamilton and Buchanan (2007) and Buchanan et al. (2008) do not hold water and demonstrate that his re-analyses of Hamilton and Buchanan's (2007) and Buchanan et al'.s (2008) datasets are flawed. In the ... [
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Burger, O., DeLong, J. P., Hamilton, M. J. (2011).
"Industrial Energy Use and The Human Life History." Scientific Reports 1:8-14
The demographic rates of most organisms are supported by the consumption of food energy, which is used to produce new biomass and fuel physiological processes. Unlike other species, modern humans use 'extra-metabolic' energy sources acquired independent of physiology, which also ... [
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Bush, A. M., Bambach, R. K., Erwin, D. H..
"Ecospace Utilization During the Ediacaran Radiation and the Cambrian Eco-explosion". In
Quantitifying the Evolution of Early Life: Numerical Approaches to the Evaluation of Fossils and Ancient Ecosystems, 111-133.
Dordrecht: Springer, 2011 [
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Cai, J. J., Borenstein, E., Petrov, D. A. (2011).
"Broker Genes in Human Disease." Genome Biology and Evolution 2:815-825
Genes that underlie human disease are important subjects of systems biology research. In the present study, we demonstrate that Mendelian and complex disease genes have distinct and consistent protein-protein interaction (PPI) properties. We show that five different network properties can ... [
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Cardenas, A., Mihaila, B., Cooper, F., Saxena, A. (2011).
"Properties of Compacton-Anticompacton Collisions." Physical Review E 83(6 Pt. 2):11-18
We study the properties of compacton-anticompacton collision processes. We compare and contrast results for the case of compacton-anticompacton solutions of the K(l, p) Rosenau-Hyman (RH) equation for l = p = 2, with compacton-anticompacton solutions of the L(l, p) Cooper-Shepard-Sodano ... [
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Caschera, F., Bedau, M. A., Buchanan, A., Cawse, J., de Lucrezia, D., Gazzola, G., Hanczyc, M. M., Packard, N. H. (2011).
"Coping With Complexity: Machine Learning Optimization of Cell-Free Protein Synthesis." Biotechnology and Bioengineering 19\08(9):2218-2228
Biological systems contain complex metabolic pathways with many nonlinearities and synergies that make them difficult to predict from first principles. Protein synthesis is a canonical example of such a pathway. Here we show how cell-free protein synthesis may be improved ... [
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Chen, W., D'Souza, R. M. (2011).
"Explosive Percolation with Multiple Giant Components." Physical Review Letters 106(11):13-16
We generalize the random graph evolution process of Bohman, Frieze, and Wormald [T. Bohman, A. Frieze, and N. C. Wormald, Random Struct. Algorithms, 25, 432 (2004)]. Potential edges, sampled uniformly at random from the complete graph, are considered one at ... [
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Christiansen, M. H., Reali, F., Chater, N. (2011).
"Biological Adaptations for Functional Features of Language in the Face of Cultural Evolution." Human Biology 83(2 (Sp Iss.)):247-259
Although there may be no true language universals, it is nonetheless possible to discern several family resemblance patterns across the languages of the world. Recent work on the cultural evolution of language indicates the source of these patterns is unlikely ... [
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Cooper, F., Mihaila, B., Dawson, J. F., Chien, C. C., Timmermans, E. (2011).
"Auxiliary-Field Approach to Dilute Bose Gases with Tunable Interactions." Physical Review A 83(5):96-110
We rewrite the Lagrangian for a dilute Bose gas in terms of auxiliary fields related to the normal and anomalous condensate densities. We derive the loop expansion of the effective action in the composite-field propagators. The lowest-order auxiliary field (LOAF) ... [
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Cornforth, D. M., Reluga, T. C., Shim, E., Bauch, C. T., Galvani, A. P., Meyers, L. A. (2011).
"Erratic Flu Vaccination Emerges from Short-Sighted Behavior in Contact Networks." PLoS Computational Biology 70(1):259-268
The effectiveness of seasonal influenza vaccination programs depends on individual-level compliance. Perceptions about risks associated with infection and vaccination can strongly influence vaccination decisions and thus the ultimate course of an epidemic. Here we investigate the interplay between contact patterns, ... [
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Corominas-Murtra, B., Fortuny, J., Sole, R. V. (2011).
"Emergence of Zipf's Law in the Evolution of Communication." Physical Review E 83(3 Pt. 2):1-7
Zipf's law seems to be ubiquitous in human languages and appears to be a universal property of complex communicating systems. Following the early proposal made by Zipf concerning the presence of a tension between the efforts of speaker and hearer ... [
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Corominas-Murtra, B., Rodriguez-Caso, C., Goni, J., Sole, R. V. (2011).
"Measuring the Hierarchy of Feedforward Networks." Chaos 21(1):329-338
In this paper we explore the concept of hierarchy as a quantifiable descriptor of ordered structures, departing from the definition of three conditions to be satisfied for a hierarchical structure: order, predictability, and pyramidal structure. According to these principles, we ... [
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Craft, M. E., Volz, E., Packer, C., Meyers, L. A. (2011).
"Disease Transmission in Territorial Populations: The Small-World Network of Serengeti Lions." Journal of Royal Society Interface 8(59):776-786
Territoriality in animal populations creates spatial structure that is thought to naturally buffer disease invasion. Often, however, territorial populations also include highly mobile, non-residential individuals that potentially serve as disease superspreaders. Using long-term data from the Serengeti Lion Project, we ... [
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Crutchfield, J. P., Machta, J. (2011).
"Introduction to Focus Issue on "Randomness, Structure, and Causality: Measures of Complexity from Theory to Applications"." Chaos 21(3):308-312
We introduce the contributions to this Focus Issue and describe their origin in a recent Santa Fe Institute workshop. [
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Daniels, B. C., Sethna, J. P. (2011).
"Nucleation at the DNA Supercoiling Transition." Physical Review E 83(4 Pt. 1):72-87
Twisting DNA under a constant applied force reveals a thermally activated transition into a state with a supercoiled structure known as a plectoneme. Using transition-state theory, we predict the rate of this plectoneme nucleation to be of order 10(4) Hz. ... [
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DeDeo, S. (2011).
"Effective Theories for Circuits and Automata." Chaos 21(3):354-363
Considering an effective theory from a complicated process is central to the study of complexity. Even when the underlying mechanisms are understood, or at least measurable, the presence of dissipation and irreversibility in biological, computational, and social systems makes the ... [
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DeDeo, S., Krakauer, D., Flack, J. (2011).
"Evidence of Strategic Periodicities in Collective Conflict Dynamics." Journal of the Royal Society Interface 8(62):1260-1273
We analyse the timescales of conflict decision-making in a primate society. We present evidence for multiple, periodic timescales associated with social decision-making and behavioural patterns. We demonstrate the existence of periodicities that are not directly coupled to environmental cycles or ... [
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Decelle, A., Krzakala, F., Moore, C., Zdeborova, L. (2011).
"Inference and Phase Transitions in the Detection of Modules in Sparse Networks." Physical Review Letters 107(6):35-39
We present an asymptotically exact analysis of the problem of detecting communities in sparse random networks generated by stochastic block models. Using the cavity method of statistical physics and its relationship to belief propagation, we unveil a phase transition from ... [
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Dell, A. ., Pawar, S., Savage, V. M. (2011).
"Systematic Variation in the Temperature Dependence of Physiological and Ecological Traits." PNAS 108(26):10591-10596
To understand the effects of temperature on biological systems, we compile, organize, and analyze a database of 1,072 thermal responses for microbes, plants, and animals. The unprecedented diversity of traits (n = 112), species (n = 309), body sizes (15 ... [
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Dhar, R., Sagesser, R., Weikert, C., Yuan, J., Wagner, A. (2011).
"Adaptation of Saccharomyces cerevisiae to Saline Stress through Laboratory Evolution." Journal of Evolutionary Biology 24(5):1135-1153
Most laboratory evolution studies that characterize evolutionary adaptation genomically focus on genetically simple traits that can be altered by one or few mutations. Such traits are important, but they are few compared with complex, polygenic traits influenced by many genes. ... [
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Dimitrov, N. B., Goll, S., Hupert, N., Pourbohloul, B., Meyers, L. A. (2011).
"Optimizing Tactics for Use of the US Antiviral Strategic National Stockpile for Pandemic Influenza." PLoS One 6(1):209-218
In 2009, public health agencies across the globe worked to mitigate the impact of the swine-origin influenza A (pH1N1) virus. These efforts included intensified surveillance, social distancing, hygiene measures, and the targeted use of antiviral medications to prevent infection (prophylaxis). ... [
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Driscoll, W. W;., Pepper, J. W., Pierson, L. S. III, Pierson, E. A. (2011).
"Spontaneous Gac Mutants of Pseudomonas Biological Control Strains: Cheaters or Mutualists?." Applied and Environmental Microbiology 77(20):722707235
Bacteria rely on a range of extracellular metabolites to suppress competitors, gain access to resources, and exploit plant or animal hosts. The GacS/GacA two-component regulatory system positively controls the expression of many of these beneficial external products in pseudomonad bacteria. ... [
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Eggenhofer, F., Tafer, H., Stadler, P. F., Hofacker, I. L. (2011).
"RNApredator: fast accessibility-based prediction of sRNA targets." Nucleic Acids Research 39(Suppl):W149-W154
Bacterial genomes encode a plethora of small RNAs (sRNAs), which are heterogeneous in size, structure and function. Most sRNAs act as post-transcriptional regulators by means of specific base pairing interactions with the 5'-untranslated region of mRNA transcripts, thereby modifying the ... [
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Elena, S. F., Bedhomme, S., Carrasco, P., Cuevas, J. M., de la Iglesia, F., Lafforgue, G., Lalic, J., Prosper, A., Tromas, N., Zwart, M. P. (2011).
"The Evolutionary Genetics of Emerging Plant RNA Viruses." Molecular Plant - Microbe Interactions (24):3
Over the years, agriculture across the world has been compromised by a succession of devastating epidemics caused by new viruses that spilled over from reservoir species or by new variants of classic viruses that acquired new virulence factors or changed ... [
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Elena, S. F., Carrera, J., Rodrigo, G. (2011).
"A Systems Biology Approach to the Evolution of Plant-Virus Interactions." Current Opinion in Plant Biology 14(4):372-377
Omic approaches to the analysis of plant-virus interactions are becoming increasingly popular. These types of data, in combination with models of interaction networks, will aid in revealing not only host components that are important for the virus life cycle, but ... [
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Ellison, C. J., Mahoney, J. R., James, R. G., Crutchfield, J. P., Reichardt, J. (2011).
"Information Symmetries in Irreversible Processes." Chaos 21(3):364-390
We study dynamical reversibility in stationary stochastic processes from an information-theoretic perspective. Extending earlier work on the reversibility of Markov chains, we focus on finitary processes with arbitrarily long conditional correlations. In particular, we examine stationary processes represented or generated ... [
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Elze, T., Song, C., Stollhoff, R., Jost, J. (2011).
"Chinese Characters Reveal Impacts of Prior Experience on Very Early Stages of Perception." BMC Neuroscience 12:1-10
Background: Visual perception is strongly determined by accumulated experience with the world, which has been shown for shape, color, and position perception, in the field of visuomotor learning, and in neural computation. In addition, visual perception is tuned to statistics ... [
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Enquist, B. J. (2011).
"Forest Annual Carbon Cost: Comment." Ecology 92(10):1994-1998 [
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Enquist, B. J., Enquist, C. A. F. (2011).
"Long-Term Change within a Neotropical Forest: Assessing Differential Functional and Floristic Responses to Disturbance and Drought." Global Change Biology 17(3):1408-1424
Disentangling the relative roles of biotic and abiotic forces influencing forest structure, function, and local community composition continues to be an important goal in ecology. Here, utilizing two forest surveys 20-year apart from a Central American dry tropical forest, we ... [
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Epstein, J. M., Pankajakshan, R., Hammond, R. A. (2011).
"Combining Computational Fluid Dynamics and Agent-Based Modeling: A New Approach to Evacuation Planning." PLoS One 6(5):262-266 [
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Erwin, D (2011).
"Evolutionary Uniformitarianism." Developmental Biology 357(1):27-34
I present a new compilation of the distribution of the temporal distribution of new morphologies of marine invertebrates associated with the Ediacaran-Cambrian (578-510 Ma) diversification of Metazoa. Combining this data with previous work on the hierarchical structure of gene regulatory ... [
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Erwin, D. H., Laflamme, M., Tweedt, S. M., Sperling, E. A., Pisani, D., Peterson, K. J. (2011).
"The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals." Science 334(6059):1091-1097
Diverse bilaterian clades emerged apparently within a fe million years during the early Cambrian, and various environmental, developmental, and ecological causes have been proposed to explain this abrupt appearance. A compilation of the patterns of fossil and molecula diversification, comparative ... [
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Espinosa-Soto, C., Martin, O. C., Wagner, A. (2011).
"Phenotypic Plasticity can Facilitate Adaptive Evolution in Gene Regulatory Circuits." BMC Evolutionary Biology 11:1-14
Background: Many important evolutionary adaptations originate in the modification of gene regulatory circuits to produce new gene activity phenotypes. How do evolving populations sift through an astronomical number of circuits to find circuits with new adaptive phenotypes? The answer may ... [
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Espinosa-Soto, C., Martin, O. C., Wagner, A. (2011).
"Phenotypic Robustness can Increase Phenotypic Variability after Nongenetic Perturbations in Gene Tegulatory Circuits." Journal of Evolutionary Biology 24(6):1284-1297
Nongenetic perturbations, such as environmental change or developmental noise, can induce novel phenotypes. If an induced phenotype appears recurrently and confers a fitness advantage, selection may promote its genetic stabilization. Nongenetic perturbations can thus initiate evolutionary innovation. Genetic variation that ... [
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Farmer, J. D. (2011).
"The Unsmooth Trajectory of Benoit Mandelbrot." Quantitative Finance 11(2 Sp. Iss):157-158 [
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Fasold, M., Langenberger, D., Binder, H., Stadler, P. F., Hoffmann, S. (2011).
"DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments." Nucleic Acids Research 39(Suppl):W112-W117
Small non-coding RNAs (ncRNAs) such as microRNAs, snoRNAs and tRNAs are a diverse collection of molecules with several important biological functions. Current methods for high-throughput sequencing for the first time offer the opportunity to investigate the entire ncRNAome in an ... [
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Fellermann, H., Rasmussen, S. (2011).
"On the Growth Rate of Non-Enzymatic Molecular Replicators." Entropy 13(10):1882-1903
It is well known that non-enzymatic template directed molecular replicators X + nO -> k 2X exhibit parabolic growth d[X]/dt infinity k[X](1/2). Here, we analyze the dependence of the effective replication rate constant k on hybridization energies, temperature, strand length, ... [
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Findeiss, S., Engelhardt, J., Prohaska, S. J., Stadler, P. F. (2011).
"Protein-Coding Structured RNAs: A Computational Survey of Conserved RNA Secondary Structures Overlapping Coding Regions in Drosophilids." Biochimie 93(11):2019-2023
Functional RNA elements can be embedded also within exonic sequences coding for functional proteins. While not uncommon in viruses, only a few examples of this type have been described in some detail for eukaryotic genomes. Here we use RNAz and ... [
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Findeiss, S., Langenberger, D., Stadler, P. F., Hoffmann, S. (2011).
"Traces of Post-Transcriptional RNA Modifications in Deep Sequencing Data." Biological Chemistry 392(4):305-313
Many aspects of the RNA maturation leave traces in RNA sequencing data in the form of deviations from the reference genomic DNA. This includes, in particular, genomically non-encoded nucleotides and chemical modifications. The latter leave their signatures in the form ... [
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Flack, J. C., Krakauer, D. C. (2011).
"Challenges for Complexity Measures: A Perspective from Social Dynamics and Collective Social Computation." Chaos 21(3):391-399
We review an empirically grounded approach to studying the emergence of collective properties from individual interactions in social dynamics. When individual decision-making rules, strategies, can be extracted from the time-series data, these can be used to construct adaptive social circuits. ... [
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Fortunato, L. (2011).
"Reconstructing the History of Marriage Strategies in Indo-European-Speaking Societies: Monogamy and Polygyny." Human Biology 83(1):87-105
Explanations for the emergence of monogamous marriage have focused on the cross-cultural distribution of marriage strategies, thus failing to account for their history. In this paper I reconstruct the pattern of change in marriage strategies in the history of societies ... [
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Fortunato, L. (2011).
"Reconstructing the History of Residence Strategies in Indo-European-Speaking Societies: Neo-, Uxori-, and Virilocality." Human Biology 83(1):107-128
Linguists and archaeologists have used reconstructions of early Indo-European residence strategies to constrain hypotheses about the homeland and trajectory of dispersal of Indo-European languages; however, these reconstructions are largely based on unsystematic and ahistorical use of the linguistic and ethnographic ... [
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Fortunato, L. (2011).
"Reconstructing the History of Marriage and Residence Strategies in Indo-European-Speaking Societies." Human Biology 83(1):129-135 [
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Foti, N. J., Hughes, J. M., Rockmore, D. N. (2011).
"Nonparametric Sparsification of Complex Multiscale Networks." PLoS One 6(2):Art. No. e16431
Many real-world networks tend to be very dense. Particular examples of interest arise in the construction of networks that represent pairwise similarities between objects. In these cases, the networks under consideration are weighted, generally with positive weights between any two ... [
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Frank, S. A., Smith, E. (2011).
"A Simple Derivation and Classification of Common Probability Distributions Based on Information Symmetry and Measurement Scale." Journal of Evolutionary Biology 24(3):469-4844
Commonly observed patterns typically follow a few distinct families of probability distributions. Over one hundred years ago, Karl Pearson provided a systematic derivation and classification of the common continuous distributions. His approach was phenomenological: a differential equation that generated common ... [
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Fuentes, M. A., Sato, Y., Tsallis, C. (2011).
"Sensitivity to Initial Conditions, Entropy Production, and Escape Rate at the Onset of Chaos." Physics Letters A 375(33):2988-2991
We analytically link three properties of nonlinear dynamical systems, namely sensitivity to initial conditions, entropy production, and escape rate, in z-logistic maps for both positive and zero Lyapunov exponents. We unify these relations at chaos, where the Lyapunov exponent is ... [
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Gell-Mann, M., Ruhlen, M. (2011).
"The Origin and Evolution of Word Order." PNAS 108(42):17290-17295
Recent work in comparative linguistics suggests that all, or almost all, attested human languages may derive from a single earlier language. If that is so, then this language-like nearly all extant languages-most likely had a basic ordering of the subject ... [
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Gintis, H. (2011).
"Gene-Culture Coevolution and the Nature of Human Sociality." Philosophical Transactions of the Royal Society of London Series B - Biological Sciences 366(1566):878-888
Human characteristics are the product of gene-culture coevolution, which is an evolutionary dynamic involving the interaction of genes and culture over long time periods. Gene-culture coevolution is a special case of niche construction. Gene-culture coevolution is responsible for human other-regarding ... [
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Gintis, H..
"Agent-Based Models of Complex Dynamical Systems of Market Exchange." Paper presented at the
Social Computing, Behavioral - Cultural Modeling and Prediction, College Park, MD 2011. [
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Gnanakaran, S., Bhattacharya, T., Daniels, M. G., Keele, B. F., Hraber, P. T., Lapedes, A. S., Shen, T. Y., Gaschen, B., Krishnamoorthy, M., Li, H., Decker, J. M., Salazar-Gonzalez, J. F., Wang, S. Y., Jiang, C. L., Gao, F., Swanstrom, R., Anderson, J. A., Ping, L. H., Cohen, M. S., Markowitz, M., Goepfert, P. A., Saag, M. S., Eron, J. J., Hicks, C. B., Blattner, W. A., et.al (2011).
"Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections." PLoS Pathogens 7(9):235-253
Here we have identified HIV-1 B clade Envelope (Env) amino acid signatures from early in infection that may be favored at transmission, as well as patterns of recurrent mutation in chronic infection that may reflect common pathways of immune evasion. ... [
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Gomes, N. M. V., Ryder, O. A., Houck, M. L., Charter, S. J., Walker, W., Forsyth, N. R., Austad, S. N., Venditti, C., Pagel, M., Shay, J. W., Wright, W. E. (2011).
"Comparative Biology of Mammalian Telomeres: Hypotheses on Ancestral States and the Roles of Telomeres in Longevity Determination." Aging Cell 10(5):761-768
Progressive telomere shortening from cell division (replicative aging) provides a barrier for human tumor progression. This program is not conserved in laboratory mice, which have longer telomeres and constitutive telomerase. Wild species that do/do not use replicative aging have been ... [
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Gonzalez, A. L., Farina, J. M., Pinto, R., Perez, C., Weathers, K. C., Armesto, J. J., Marquet, P. A. (2011).
"Bromeliad Growth and Stoichiometry: Responses to Atmospheric Nutrient Supply in Fog-Dependent Ecosystems of the Hyper-Arid Atacama Desert, Chile." Oecologia 167(3)
Carbon, nitrogen, and phosphorus (C, N, P) stoichiometry influences the growth of plants and nutrient cycling within ecosystems. Indeed, elemental ratios are used as an index for functional differences between plants and their responses to natural or anthropogenic variations in ... [
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Gran, J. D., Rundle, J. B., Turcotte, D. L., Holliday, J. R., Klein, W. (2011).
"A Damage Model Based on Failure Threshold Weakening." Physica A - Statistical Mechanics and Its Applications 390(7):1269-1278
A variety of studies have modeled the physics of material deformation and damage as examples of generalized phase transitions, involving either critical phenomena or spinodal nucleation. Here we study a model for frictional sliding with long-range interactions and recurrent damage ... [
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Griffin, C., Testa, K., Racunas, S. (2011).
"An Algorithm for Constructing and Searching Spaces of Alternative Hypotheses." IEEE Transactions on Systems Man and Cybernetics Part B - Cybernetics 41(3):772-782
In this paper, we develop techniques for automated hypothesis-space exploration over data sets that may contain contradictions. To do so, we make use of the equivalence between two formulations: those of first-order predicate logic with prefix modal quantifiers under the ... [
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Guedj, J., Bazzoli, C., Neumann, A. U., Mentre, F. (2011).
"Design Evaluation and Optimization for Models of Hepatitis C Viral Dynamics." Statics in Medicine 30(10):1045-1056
Mathematical modeling of hepatitis C viral (HCV) kinetics is widely used for understanding viral pathogenesis and predicting treatment outcome. The standard model is based on a system of five non-linear ordinary differential equations (ODE) that describe both viral kinetics and ... [
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Hamilton, M. J., Davidson, A. D., Sibly, R. M., Brown, J. H. (2011).
"Universal Scaling of Production Rates Across Mammalian Lineages." Proceedings of the Royal Society of London Series B - Biological Sciences 278(17-5):560-566
Over many millions of years of independent evolution, placental, marsupial and monotreme mammals have diverged conspicuously in physiology, life history and reproductive ecology. The differences in life histories are particularly striking. Compared with placentals, marsupials exhibit shorter pregnancy, smaller size ... [
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Hamma, A., Markopoulou, F. (2011).
"Background-Independent Condensed Matter Models for Quantum Gravity." New Journal of Physics 13 A number of recent proposals on a quantum theory of gravity are based on the idea that spacetime geometry and gravity are derivative concepts and only apply at an approximate level. There are two fundamental challenges to any such approach. ... [
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Hanel, R., Thurner, S. (2011).
"A Comprehensive Classification of Complex Statistical Systems and An Axiomatic Derivation of their Entropy and Distribution Functions." EPL 93(2):38-43
Motivated by the hope that the thermodynamical framework might be extended to strongly interacting statistical systems - complex systems in particular - a number of generalized entropies has been proposed in the past. So far the understanding of their fundamental ... [
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Hanel, R., Thurner, S., Gell-Mann, M. (2011).
"Generalized Entropies and the Transformation Group of Superstatistics." Proceedings of the National Academy of Sciences of the United States of America 108(16):6390-6394
Superstatistics describes statistical systems that behave like superpositions of different inverse temperatures beta, so that the probability distribution is p(epsilon(i)) alpha integral(infinity)(0)f(beta)e(-beta epsilon i)d beta, where the "kernel" f(beta) is nonnegative and normalized [integral f(beta)d beta = 1]. We discuss ... [
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Hartle, J. B. (2011).
"The Quasiclassical Realms of This Quantum Universe." Foundations of Physics 41(6):982-1006
The most striking observable feature of our indeterministic quantum universe is the wide range of time, place, and scale on which the deterministic laws of classical physics hold to an excellent approximation. This essay describes how this domain of classical ... [
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Hasiow-Jaroszewska, B., Czerwoniec, A., Pospieszny, H., Elena, S. F., Sole, R. V., Sardanyes, J. (2011).
"Tridimensional model structure and patterns of molecular evolution of Pepino mosaic virus TGBp3 protein." Virology 8:1-8
Background: Pepino mosaic virus (PepMV) is considered one of the most dangerous pathogens infecting tomatoes worldwide. The virus is highly diverse and four distinct genotypes, as well as inter-strain recombinants, have already been described. The isolates display a wide range ... [
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Hayden, E. J., Ferrada, E., Wagner, A. (2011).
"Cryptic Genetic Variation Promotes Rapid Evolutionary Adaptation in an RNA Enzyme." Nature 474(7349):92-120 [
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Hechinger, R. F., Lafferty, K. D., Dobson, A. P., Brown, J. H., Kuris, A. M. (2011).
"A Common Scaling Rule for Abundance, Energetics, and Production of Parasitic and Free-Living Species." Science 333(6041):445-448
The metabolic theory of ecology uses the scaling of metabolism with body size and temperature to explain the causes and consequences of species abundance. However, the theory and its empirical tests have never simultaneously examined parasites alongside free-living species. This ... [
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Helbing, D., Balietti, S. (2011).
"From Social Data Mining to Forecasting Socio-Economic Crises." European Physical Journal - Special Topics 195(1):3-68 [
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Helbing, D., Balietti, S. (2011).
"From Social Simulation to Integrative System Design." European Physical Journal - Special Topics 195(1):69-100 [
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Helbing, D., Balietti, S. (2011).
"How to Create an Innovation Accelerator." European Physical Journal - Special Topics 195(1):101-136 [
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Helbing, D., Balietti, S., Bishop, S., Lukowicz, P. (2011).
"Understanding, creating, and managing complex techno- socio-economic systems: Challenges and perspectives." European Physical Journal - Special Topics 195(1):165-186 [
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Herman, A. B., Savage, V. M., West, G. B. (2011).
"A Quantitative Theory of Solid Tumor Growth, Metabolic Rate and Vascularization." PLoS One 6(9):8-16
The relationships between cellular, structural and dynamical properties tumors have traditionally been studied separately. Here, we construct a quantitative, predictive theory of solid tumor growth, metabolic ate, vascularization and necrosis that the relationships between these properties. To accomplish this, we ... [
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Hordijk, W., Kauffman, S. A., Steel, M. (2011).
"Required Levels of Catalysis for Emergence of Autocatalytic Sets in Models of Chemical Reaction Systems." International Journal of Molecular Sciences 12(5):3085-3101
The formation of a self-sustaining autocatalytic chemical network is a necessary but not sufficient condition for the origin of life. The question of whether such a network could form "by chance" within a sufficiently complex suite of molecules and reactions ... [
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James, R. G., Ellison, C. J., Crutchfield, J. P. (2011).
"Anatomy of a Bit: Information in a Time Series Observation." Chaos 21(3):400-412
Appealing to several multivariate information measures - some familiar, some new here-we analyze the information embedded in discrete-valued stochastic time series. We dissect the uncertainty of a single observation to demonstrate how the measures' asymptotic behavior sheds structural and semantic ... [
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Jauregui, M., Tsallis, C. (2011).
"q-Generalization of the Inverse Fourier Transform." Physics Letters A 375(21):2085-2088
A wide class of physical distributions appears to follow the q-Gaussian form, which plays the role of attractor according to a q-generalized Central Limit Theorem, where a q-generalized Fourier transform plays an important role. We introduce here a method which ... [
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Jauregui, M., Tsallis, C., Curado, E. M. F. (2011).
"q-Moments Remove the Degeneracy Associated with the Inversion of the q-Fourier Transform." Journal of Statistical Mechanics — Theory and Experiment :291-301
It was recently proven (Hilhorst 2010 J. Stat. Mech. P10023) that the q-generalization of the Fourier transform is not invertible in the full space of probability density functions for q > 1. It has also been recently shown that this ... [
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Kehr, S., Bartschat, S., Stadler, P. F., Tafer, H. (2011).
"PLEXY: Efficient Target Prediction for Box C/D snoRNAs." Bioinformatics 27(2):279-280
Motivation: Small nucleolar RNAs (snoRNAs) are an abundant class of non-coding RNAs with a wide variety of cellular functions including chemical modification of RNA, telomere maintanance, pre-rRNA processing and regulatory activities in alternative splicing. The main role of box C/D ... [
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Kelli, C., McAnany, P. A., Sabloff, J. A. (2011).
"People Who Lived in Stone Houses: Local Knowledge and Social Difference in the Classic Maya Puuc Region of Yucatan, Mexico." Latin American Antiquity 22(1):143-158
This study builds on the premise that local knowledge of limestone— and its workable characteristics— was foundational to landscape inhabitation in the Puuc region of Yucatán, México. Classic Maya architecture of the northern Yucatán generally is considered to represent the ... [
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Kembel, S. W., Eisen, J. A., Pollard, K. S., Green, J. L. (2011).
"The Phylogenetic Diversity of Metagenomes." PloS One 6(8):52-60
Phylogenetic diversity-patterns of phylogenetic relatedness among organisms in ecological communities-provides important insights into the mechanisms underlying community assembly. Studies that measure phylogenetic diversity in microbial communities have primarily been limited to a single marker gene approach, using the small subunit ... [
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Kempes, C. P., West, G. B., Crowell, K., Girvan, M. (2011).
"Predicting Maximum Tree Heights and Other Traits from Allometric Scaling and Resource Limitations." PLoS ONE 6(6):52-61
Terrestrial vegetation plays a central role in regulating the carbon and water cycles, and adjusting planetary albedo. As such, a clear understanding and accurate characterization of vegetation dynamics is critical to understanding and modeling the broader climate system. Maximum tree ... [
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Kets, W. (2011).
"Robustness of Equilibria in Anonymous Local Games." Journal of Economic Theory 146(1):300-325
This paper studies the robustness of symmetric equilibria in anonymous local games to perturbations of prior beliefs. Two priors are strategically close on a class of games if players receive similar expected payoffs in equilibrium under the priors, for any ... [
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Kets, W., Iyengar, G., Sethi, R., Bowles, S. (2011).
"Inequality and Network Structure." Games and Economic Behavior 73(1):215-226
We explore the manner in which the structure of a socia network constrains the level of inequality that can be sustained among its members, based on the following considerations: (i) any distribution of value must be stable with respect to ... [
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Kirchherr, J. L., Hamilton, J., Lu, X. Z., Gnanakaran, S., Muldoon, M., Daniels, M. G., Kasongo, W., Chalwe, V., Mulenga, C., Mwananyanda, L., Musonda, R. M., Yuan, X., Montefiori, D. C., Korber, B. T., Haynes, B. F., Gao, F. (2011).
"Identification of Amino Acid Substitutions Associated with Neutralization Phenotype in the Human Immunodeficiency Virus Type-1 Subtype C gp120." Virology 409(2):163-174
Neutralizing antibodies (Nabs) are thought to play an important role in prevention and control of HIV-1 infection and should be targeted by an AIDS vaccine. It is critical to understand how HIV-1 induces Nabs by analyzing viral sequences in both ... [
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Klimek, P., Bayer, W., Thurner, S. (2011).
"The Blogosphere as an Excitable Social Medium: Richter's and Omori's Law in Media Coverage." Physica A - Statistical Mechanics and Its Applications 390(21-22):3870-3875
We study the dynamics of public media attention by monitoring the content of online blogs. Social and media events can be traced by the propagation of word frequencies of related keywords. Media events are classified as exogenous where blogging activity ... [
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Korber, B. T., Gnanakaran, S. (2011).
"Converging on an HIV Vaccine." Science 333(6049):1589-1590 [
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Krakauer, D. C. (2011).
"SuperCooperators Altruism, Evolution, and Why We Need Each Other to Succeed/Evolution, Altruism Need Each Other to Succeed, by M.A. Nowak, R. Highfield." Science 332(6029):538-539 [
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Krakauer, D. C. (2011).
"Darwinian Demons, Evolutionary Complexity, and Information Maximization." Chaos 21(3):413-424
Natural selection is shown to be an extended instance of a Maxwell's demon device. A demonic selection principle is introduced that states that organisms cannot exceed the complexity of their selective environment. Thermodynamic constraints on error repair impose a fundamental ... [
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Krakauer, D. C., Collins, J. P., Erwin, D. H., Flack, J. C., Fontana, W., Laubichler, M. D., Prohaska, S. J., West, G. B., Stadler, P. F. (2011).
"The Challenges and Scope of Theoretical Biology." Journal of Theoretical Biology 276(1):269-276
Scientific theories seek to provide simple explanations for significant empirical regularities based on fundamental physical and mechanistic constraints. Biological theories have rarely reached a level of generality and predictive power comparable to physical theories. This discrepancy is explained through a ... [
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Krakauer, D. C., Page, K., Flack, J. (2011).
"The Immuno-Dynamics of Conflict Intervention in Social Systems." PLOS One 6(8)
We present statistical evidence and dynamical models for the management of conflict and a division of labor (task specialization) in a primate society. Two broad intervention strategy classes are observed- a dyadic strategy - pacifying interventions, and a triadic strategy ... [
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Lacerda, M., Moore, P. L., Ngandu, N., Gray, E. S., Wibmer, K., Nonyane, M., Sheward, D., Korber, B. T., Montefiori, D. C., Williamson, C., Morris, L., Seoighe, C. (2011).
"Identification of Amino Acid Residues in HIV-1 Envelope Targeted by Plasma Broadly Neutralizing Antibodies using Evolutionary Models." AIDS Research and Human Retroviruses 27(10):A15-A16 [
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Lafforgue, G., Martinez, F., Sardanyes, J., de la Iglesia, F., Niu, Q. W., Lin, S. S., Sole, R. V., Chua, N. H., Daros, J. A., Elena, S. F. (2011).
"Tempo and Mode of Plant RNA Virus Escape from RNA Interference-Mediated Resistance." Journal of Virology 85(19):9686-9695
A biotechnological application of artificial microRNAs (amiRs) is the generation of plants that are resistant to virus infection. This resistance has proven to be highly effective and sequence specific. However, before these transgenic plants can be deployed in the field, ... [
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Lafforgue, G., Sardanyes, J., Elena, S. F. (2011).
"Differences in Accumulation and Virulence Determine the Outcome of Competition during Tobacco etch virus Coinfection." PLoS One 6(3):443-450
Understanding the evolution of virulence for RNA viruses is essential for developing appropriate control strategies. Although it has been usually assumed that virulence is a consequence of within-host replication of the parasite, viral strains may be highly virulent without experiencing ... [
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Lansing, J. S., Cox, M. P. (2011).
"The Domain of the Replicators Selection, Neutrality, and Cultural Evolution." Current Anthropology 52(1):105-125
Do cultural phenomena undergo evolutionary change, in a Darwinian sense? If so, is evolutionary game theory (EGT) the best way to study them? Opinion on these questions is sharply divided. Proponents of EGT argue that it offers a unified theoretical ... [
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Lansing, J. S., Fox, K. M. (2011).
"Niche Construction on Bali: The Gods of the Countryside." Philosophical Transactions of the Royal Society of London Series B - Biological Sciences 366(1566):927-934
Human niche construction encompasses both purely biological phenomena, such as the evolution of lactose tolerance, and dual inheritance theory, which investigates the transmission of cultural information. But does niche construction help to explain phenomena in which conscious intention also plays ... [
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Lechner, M., Findeiss, S., Steiner, L., Marz, M., Stadler, P. F., Prohaska, S. J. (2011).
"Proteinortho: Detection of (Co-)orthologs in large-scale analysis." BMC Bioinformatics 12:1-9
Background: Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared ... [
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Lee, Y. T., Turcotte, D. L., Holliday, J. R., Sachs, M. K., Rundle, J. B., Chen, C. C., Tiampo, K. F. (2011).
"Results of the Regional Earthquake Likelihood Models (RELM) Test of Earthquake Forecasts in California." PNAS 108(40):16533-16538
The Regional Earthquake Likelihood Models (RELM) test of earthquake forecasts in California was the first competitive evaluation of forecasts of future earthquake occurrence. Participants submitted expected probabilities of occurrence of M >= 4.95 earthquakes in 0.1 degrees x 0.1 degrees ... [
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Li, F. S., Finnefrock, A. C., Dubey, S. A., Korber, B. T. M., Szinger, J., Cole, S., McElrath, M. J., Shiver, J. W., Casimiro, D. R., Corey, L., Self, S. G. (2011).
"Mapping HIV-1 Vaccine Induced T-Cell Responses: Bias towards Less-Conserved Regions and Potential Impact on Vaccine Efficacy in the Step Study." PLOS One 6(6):102-110
T cell directed HIV vaccines are based upon the induction of CD8+ T cell memory responses that would be effective in inhibiting infection and subsequent replication of an infecting HIV-1 strain, a process that requires a match or near-match between ... [
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Lorenz, J., Rauhut, H., Schweitzer, F., Helbing, D. (2011).
"How Social Influence Can Undermine the Wisdom of Crowd Effect." PNAS 108(22):9020-9025 [
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Lotze, H. K., Coll, M., Dunne, J. A. (2011).
"Historical Changes in Marine Resources, Food-web Structure and Ecosystem Functioning in the Adriatic Sea, Mediterranean." Ecosystems 14(2):198-222
The Mediterranean Sea has been strongly influenced by human activities for millennia. Although the environmental history of its surrounding terrestrial ecosystems has received considerable study, historical changes in its marine realm are less known. We used a multidisciplinary approach combining ... [
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Lu, W. L., Atay, F. M., Jost, J. (2011).
"Consensus and Synchronization in Discrete-Time Networks of Multi-Agents with Stochastically Switching Topologies and Time Delays." Networks and Heterogeneous Media 6(2):329-349
We analyze stability of consensus algorithms in networks of multi-agents with time-varying topologies and delays. The topology and delays are modeled as induced by an adapted process and are rather general, including i.i.d. topology processes, asynchronous consensus algorithms, and Markovian ... [
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Ludescher, J., Tsallis, C., Bunde, A. (2011).
"Universal Behaviour of Interoccurrence Times Between Losses in Financial Markets: An Analytical Description." EPL 95(6):221-225
We consider 16 representative financial records (stocks, indices, commodities, and exchange rates) and study the distribution P-Q(r) of the interoccurrence times r between daily losses below negative thresholds -Q, for fixed mean interoccurrence time R-Q. We find that in all ... [
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Luther, S., Mertens, S. (2011).
"Counting Lattice Animals in High Dimensions." Journal of Statistical Mechanics — Theory and Experiment :546-565
We present an implementation of Redelemeier's algorithm for the enumeration of lattice animals in high-dimensional lattices. The implementation is lean and fast enough to allow us to extend the existing tables of animal counts, perimeter polynomials and series expansion coefficients ... [
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Machta, J. (2011).
"Natural Complexity, Computational Complexity and Depth." Chaos 21(3):425-432
Depth is a complexity measure for natural systems of the kind studied in statistical physics and is defined in terms of computational complexity. Depth quantifies the length of the shortest parallel computation required to construct a typical system state or ... [
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Machta, J., Dedeo, S., Mertens, S., Moore, C. (2011).
"Parallel Complexity of Random Boolean Circuits." Journal of Statistical Mechanics — Theory and Experiment :428-445
Random instances of feedforward Boolean circuits are studied both analytically and numerically. Evaluating these circuits is known to be a P-complete problem and thus, in the worst case, believed to be impossible to perform, even given a massively parallel computer, ... [
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Mahoney, J. R., Ellison, C. J., James, R. G., Crutchfield, J. P. (2011).
"How Hidden are Hidden Processes? A Primer on Crypticity and Entropy Convergence." Chaos 21(3):433-446
We investigate a stationary process's crypticity-a measure of the difference between its hidden state information and its observed information-using the causal states of computational mechanics. Here, we motivate crypticity and cryptic order as physically meaningful quantities that monitor how hidden ... [
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Martinez, F., Sardanyes, J., Elena, S. F., Daros, J. A. (2011).
"Dynamics of a Plant RNA Virus Intracellular Accumulation: Stamping Machine vs. Geometric Replication." Genetics 188(3):637-646
The tremendous evolutionary potential of RNA viruses allows them to thrive despite host defense mechanisms and endows them with properties such as emergence, host switching, and virulence. The frequency of mutant viruses after an infectious process results from the interplay ... [
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Marz, M., Stadler, P. F. (2011).
"RNA Interactions." RNA Infrastructure and Networks 722:20-38
Noncoding RNAs form an indispensible component of the cellular information processing networks, a role that crucially depends on the specificity of their interactions among each other as well as with DNA and protein. Patterns of intramolecular and intermolecular base pairs ... [
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McNerney, J., Farmer, J. D., Redner, S., Trancik, J. E. (2011).
"Role of Design Complexity in Technology Improvement." PNAS 108(22):9008-9013 [
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Menzel, P., Stadler, P. F., Gorodkin, J. (2011).
"maxAlike: Maximum Likelihood-based Sequence Reconstruction with Application to Improved Primer Design for Unknown Sequences." Bioinformatics 27(3):317-325
Motivation: The task of reconstructing a genomic sequence from a particular species is gaining more and more importance in the light of the rapid development of high-throughput sequencing technologies and their limitations. Applications include not only compensation for missing data ... [
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Meyer-Ortmanns, Hildegard, Thurner, Stefan.
"Principles of Evolution: From the Planck Epoch to Complex Multicellular Life".
Springer, 2011 [
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Mihaila, B., Cooper, F., Dawson, J. F., Chien, C. C., Timmermans, E. (2011).
"Analytical Limits for Cold-Atom Bose Gases with Tunable Interactions." Physical Review A 84(2):76-86
We discuss the equilibrium properties of dilute Bose gases using a nonperturbative formalism based on auxiliary fields related to the normal and anomalous densities. We show analytically that for a dilute Bose gas of weakly interacting particles at zero temperature, ... [
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Mihaila, B., Dawson, J. F., Cooper, F., Chien, C. C., Timmermans, E. (2011).
"Auxiliary Field Formalism for Dilute Fermionic Atom Gases with Tunable Interactions." Physical Review A 83(5):93-103 [
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Montufar, G., Ay, N. (2011).
"Refinements of Universal Approximation Results for Deep Belief Networks and Restricted Boltzmann Machines." Neural Computation 23(5):1306-1319
We improve recently published results about resources of restricted Boltzmann machines (RBM) and deep belief networks (DBN) required to make them universal approximators. We show that any distribution p on the set {0, 1}(n) of binary vectors of length n ... [
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Moore, C. (2011).
"A Complex Legacy." Nature Physics 7(11):828-830 [
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Moore, C., Mertens, S..
"The Nature of Computation".
Oxford University Press, 2011 [
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Morlon, H., Schwilk, D. W., Bryant, J. A., Marquet, P. A., Rebelo, A. G., Tauss, C., Bohannan, B. J. M., Green, J. L. (2011).
"Spatial Patterns of Phylogenetic Diversity." Ecology Letters 14(2):141-149
P>Ecologists and conservation biologists have historically used species-area and distance-decay relationships as tools to predict the spatial distribution of biodiversity and the impact of habitat loss on biodiversity. These tools treat each species as evolutionarily equivalent, yet the importance of ... [
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Mubayi, A., Greenwood, P., Wang, X. H., Castillo-Chavez, C., Gorman, D. M., Gruenewald, P., Saltz, R. F. (2011).
"Types of Drinkers and Drinking Settings: An Application of A Mathematical Model." Addiction 106(4):749-758
S college drinking data and a simple population model of alcohol consumption are used to explore the impact of social and contextual parameters on the distribution of light, moderate and heavy drinkers. Light drinkers become moderate drinkers under social influence, ... [
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Nagy, B., Farmer, J. D., Trancik, J. E., Gonzales, J. P. (2011).
"Superexponential Long-Term Trends in Information Technology." Technological Forecasting and Social Change 78(8):1356-1364
Moore's Law has created a popular perception of exponential progress in information technology. But is the progress of IT really exponential? In this paper we examine long time series of data documenting progress in information technology gathered by [1]. We ... [
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Nishiura, H., Chowell, G., Castillo-Chavez, C. (2011).
"Did Modeling Overestimate the Transmission Potential of Pandemic (H1N1-2009)? Sample Size Estimation for Post-Epidemic Seroepidemiological Studies." PLoS One 6(3):172-1811
Background: Seroepidemiological studies before and after the epidemic wave of H1N1-2009 are useful for estimating population attack rates with a potential to validate early estimates of the reproduction number, R, in modeling studies. Methodology/Principal Findings: Since the final epidemic size, ... [
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Nobre, F. D., Rego-Monteiro, M. A., Tsallis, C. (2011).
"Nonlinear Relativistic and Quantum Equations with Common Type of Solution." Physical Review Letters 106(14):5-8
Generalizations of the three main equations of quantum physics, namely, the Schrodinger, Klein-Gordon, and Dirac equations, are proposed. Nonlinear terms, characterized by exponents depending on an index q, are considered in such a way that the standard linear equations are ... [
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Norris, V., Zemirline, A., Amar, P., Audinot, J. N., Ballet, P., Ben-Jacob, E., Bernot, G., Beslon, G., Cabin, A., Fanchon, E., Giavitto, J. L., Glade, N., Greussay, P., Grondin, Y., Foster, J. A., Hutzler, G., Jost, J., Kepes, F., Michel, O., Molina, F., Signorini, J., Stano, P., Thierry, A. R. (2011).
"Computing with Bacterial Constituents, Cells and Populations: From Bioputing to Bactoputing." Theory in Biosciences 130(3 Sp. Iss):211-228
The relevance of biological materials and processes to computing-alias bioputing-has been explored for decades. These materials include DNA, RNA and proteins, while the processes include transcription, translation, signal transduction and regulation. Recently, the use of bacteria themselves as living computers ... [
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Ortman, Scott.
"Using Cognitive Semantics to Relate Mesa Verde Archaeology to Modern Pueblo Languages". In
Rethinking Anthropological Perspectives on Migration, 111-146.
Gainesville, FL: University Press of Florida, 2011 [
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Page, S. E. (2011).
"Why Humans Cooperate: A Cultural and Evolutionary Explanation, by N. Henrich, J. Henrich." Journal of Economic Literature 49(2):444-446
Book Review [
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Perseke, M., Hetmank, J., Bernt, M., Stadler, P. F., Schlegel, M., Bernhard, D. (2011).
"The Enigmatic Mitochondrial Genome of Rhabdopleura compacta (Pterobranchia) Reveals Insights Into Selection of an Efficient tRNA System and Supports Monophyly of Ambulacraria." BMC Evolutionary Biology 11:1-12
Background: The Hemichordata comprises solitary-living Enteropneusta and colonial-living Pterobranchia, sharing morphological features with both Chordata and Echinodermata. Despite their key role for understanding deuterostome evolution, hemichordate phylogeny is controversial and only few molecular data are available for phylogenetic analysis. Furthermore, ... [
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Peters, O. (2011).
"The Time Resolution of the St. Petersburg Paradox." Philosophical Transactions of the Royal Society A 369(1956):4913-4931
A resolution of the St Petersburg paradox is presented. In contrast to the standard resolution, utility is not required. Instead, the time-average performance of the lottery is computed. The final result can be phrased mathematically identically to Daniel Bernoulli's resolution, ... [
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Peters, O. (2011).
"The Time Resolution of the St Petersburg Paradox." Philosophical Transactions of the Royal Society A - Mathematical Physical and Engineering Sciences 369(1956):4913-4931
A resolution of the St Petersburg paradox is presented. In contrast to the standard resolution, utility is not required. Instead, the time-average performance of the lottery is computed. The final result can be phrased mathematically identically to Daniel Bernoulli's resolution, ... [
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Raincrow, J. D., Dewar, K., Stocsits, C., Prohaska, S. J., Amemiya, C. T., Stadler, P. F., Chiu, C. H. (2011).
"Hox Clusters of the Bichir (Actinopterygii, Polypterus senegalus) Highlight Unique Patterns of Sequence Evolution in Gnathostome Phylogeny." Journal of Experimental Zoology Part B - Molecular and Developmental Evolution 316B(6):451-464
Teleost fishes have extra Hox gene clusters owing to shared or lineage-specific genome duplication events in rayfinned fish (actinopterygian) phylogeny. Hence, extrapolating between genome function of teleosts and human or even between different fish species is difficult. We have sequenced ... [
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Raman, K., Wagner, A. (2011).
"The Evolvability of Programmable Hardware." Journal of the Royal Society Interface 8(55):269-281
In biological systems, individual phenotypes are typically adopted by multiple genotypes. Examples include protein structure phenotypes, where each structure can be adopted by a myriad individual amino acid sequence genotypes. These genotypes form vast connected 'neutral networks' in genotype space. ... [
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Raman, K., Wagner, A. (2011).
"Evolvability and Robustness in A Complex Signalling Circuit." Molecular Biosystems 7(4):1081-1092
Biological systems at various levels of organisation exhibit robustness, as well as phenotypic variability or evolvability, the ability to evolve novel phenotypes. We still know very little about the relationship between robustness and phenotypic variability at levels of organisation beyond ... [
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Rauh, J., Kahle, T., Ay, N. (2011).
"Support Sets in Exponential Families and Oriented Matroid Theory." International Journal of Approximate Reasoning 52(5 Sp Iss):613-626
The closure of a discrete exponential family is described by a finite set of equations corresponding to the circuits of an underlying oriented matroid. These equations are similar to the equations used in algebraic statistics, although they need not be ... [
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Regot, S., Macia, J., Conde, N., Furukawa, K., Kjellen, J., Peeters, T., Hohmann, S., de Nadal, E., Posas, F., Solé, R. V. (2011).
"Distributed Biological Computation with Multicellular Engineered Networks." Nature 469(7329):207-211
Ongoing efforts within synthetic and systems biology have been directed towards the building of artificial computational devices(1) using engineered biological units as basic building blocks(2,3). Such efforts, inspired in the standard design of electronic circuits(4-7), are limited by the difficulties ... [
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Reidys, C. M., Huang, F. W. D., Andersen, J. E., Penner, R. C., Stadler, P. F., Nebel, M. E. (2011).
"Topology and Prediction of RNA Pseudoknots." Bioinformatics 27(8):1076-1085
Motivation: Several dynamic programming algorithms for predicting RNA structures with pseudoknots have been proposed that differ dramatically from one another in the classes of structures considered. Results: Here, we use the natural topological classification of RNA structures in terms of ... [
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Riedel, C. J., Zurek, W. H. (2011).
"Redundant Information From Thermal Illumination: Quantum Darwinism in Scattered Photons." New Journal of Physics 13:24-46
We study quantum Darwinism, the redundant recording of information about the preferred states of a decohering system by its environment, for an object illuminated by a blackbody. We calculate the quantum mutual information between the object and its photon environment ... [
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Robinson, M. D., Feldman, D. P., McKay, S. R. (2011).
"Local Entropy and Structure in a Two-Dimensional Frustrated System." Chaos 21(3):456-466
We calculate the local contributions to the Shannon entropy and excess entropy and use these information theoretic measures as quantitative probes of the order arising from quenched disorder in the diluted Ising antiferromagnet on a triangular lattice. When one sublattice ... [
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Roca, C. P., Helbing, D. (2011).
"Emergence of social cohesion in a model society of greedy, mobile individuals." PNAS 108(28):11370-11374
Human wellbeing in modern societies relies on social cohesion, which can be characterized by high levels of cooperation and a large number of social ties. Both features, however, are frequently challenged by individual self-interest. In fact, the stability of social ... [
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Rodrigo, G., Carrera, J., Jaramillo, A., Elena, S. F. (2011).
"Optimal Viral Strategies for Bypassing RNA Silencing." Journal of the Royal Society Interface 8(55):257-268
The RNA silencing pathway constitutes a defence mechanism highly conserved in eukaryotes, especially in plants, where the underlying working principle relies on the repressive action triggered by the intracellular presence of double-stranded RNAs. This immune system performs a post-transcriptional suppression ... [
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Rodrigo, G., Elena, S. F. (2011).
"Structural Discrimination of Robustness in Transcriptional Feedforward Loops for Pattern Formation." PLoS One 6(2):231-237
Signaling pathways are interconnected to regulatory circuits for sensing the environment and expressing the appropriate genetic profile. In particular, gradients of diffusing molecules (morphogens) determine cell fate at a given position, dictating development and spatial organization. The feedforward loop (FFL) ... [
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Rodrigues, J. F. M., Wagner, A. (2011).
"Genotype Networks, Innovation, and Robustness in Sulfur Metabolism." BMC Systems Biology 5:1-13
Background: A metabolism is a complex network of chemical reactions. This network synthesizes multiple small precursor molecules of biomass from chemicals that occur in the environment. The metabolic network of any one organism is encoded by a metabolic genotype, defined ... [
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Rosas-Casals, M., Sole, R. V. (2011).
"Analysis of Major Failures in Europe's Power Grid." International Journal of Electrical Power & Energy Systems 33(3):805-808
Power grids are prone to failure. Time series of reliability measures such as total power loss or energy not supplied can give significant account of the underlying dynamical behavior of these systems, specially when the resulting probability distributions present remarkable ... [
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Rose, D., Hiller, M., Schutt, K., Hackermuller, J., Backofen, R., Stadler, P. F. (2011).
"Computational discovery of human coding and non-coding transcripts with conserved splice sites." Bioinformatics 27(14):1894-1900
Motivation: Long non-coding RNAs (lncRNAs) resemble protein-coding mRNAs but do not encode proteins. Most lncRNAs are under lower sequence constraints than protein-coding genes and lack conserved secondary structures, making it hard to predict them computationally. Results: We introduce an approach ... [
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Rosvall, M., Bergstrom, C. T. (2011).
"Multilevel Compression of Random Walks on Networks Reveals Hierarchical Organization in Large Integrated Systems." PLoS One 6(4):33-42
To comprehend the hierarchical organization of large integrated systems, we introduce the hierarchical map equation, which reveals multilevel structures in networks. In this information-theoretic approach, we exploit the duality between compression and pattern detection; by compressing a description of a ... [
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Rundle, J. B., Holliday, J. R., Yoder, M., Sachs, M. K., Donnellan, A., Turcotte, D. L., Tiampo, K. F., Klein, W., Kellogg, L. H. (2011).
"Earthquake Precursors: Activation or Quiescence?." Geophysical Journal International 187(1):225-236
We discuss the long-standing question of whether the probability for large earthquake occurrence (magnitudes m > 6.0) is highest during time periods of smaller event activation, or highest during time periods of smaller event quiescence. The physics of the activation ... [
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Sabloff, J. A. (2011).
"Where Have You Gone, Margaret Mead? Anthropology and Public Intellectuals." American Anthropologist 113(3):408-416
I maintain that, in today's perilous world, anthropologists have many productive ideas and much useful information to share with the public, in general, and policy makers, in particular. To make such ideas and information more accessible, anthropologists need to further ... [
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Sabloff, P..
"Mapping Mongolia: Situating Mongolia in the world from geologic time to the present".
Philadelphia, PA: University of Pennsylvania Museum of Archaeology and Anthropology, 2011 [
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Sabloff, P. L. W..
"Preface and Acknowledgments: "-Scaping" Mongolia". In
Mapping Mongolia: Situating Mongolia in the World from Geologic Time to the Present, XIX-XXVI.
Philadelphia, PA: University of Pennsulvania Museum Archaeology & Anthropology, 2011 [
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Sabloff, P. W. L..
""-Scaping" Mongolia". In
Mapping Mongolia: Situating Mongolia in the World from Geologic Time to the Present, 16-33.
Philadelphia, PA: University of Pennsulvania Museum Archaeology & Anthropology, 2011 [
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Samal, A., Wagner, A., Martin, O. C. (2011).
"Environmental Versatility Promotes Modularity in Genome-Scale Metabolic Networks." BMC Systems Biology 5:1-15
Background: The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new arrangements that may benefit ... [
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Sardanyes, J., Elena, S. F. (2011).
"Quasispecies Spatial Models for RNA Viruses with Different Replication Modes and Infection Strategies." PLOS One 6(9):349-361
Empirical observations and theoretical studies suggest that viruses may use different replication strategies to amplify their genomes, which impact the dynamics of mutation accumulation in viral populations and therefore, their fitness and virulence. Similarly, during natural infections, viruses replicate and ... [
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Sarkar, R. R., Maithreye, R., Sinha, S. (2011).
"Design of Regulation and Dynamics in Simple Biochemical Pathways." Journal of Mathematical Biology 63(2):283-307
Complex regulation of biochemical pathways in a cell is brought about by the interaction of simpler regulatory structures. Among the basic regulatory designs, feedback inhibition of gene expression is the most common motif in gene regulation and a ubiquitous control ... [
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Sayres, M. A. W., Venditti, C., Pagel, M., Makova, K. D. (2011).
"Do Variations in Substitution Rates and Male Mutation Bias Correlate with Life-History Traits? A Study of 32 Mammalian Genomes." Evolution 65(10):2880-2815
Life-history traits vary substantially across species, and have been demonstrated to affect substitution rates. We compute genome-wide, branch-specific estimates of male mutation bias (the ratio of male-to-female mutation rates) across 32 mammalian genomes and study how these vary with life-history ... [
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Sharpton, Thomas J., Riesenfeld, Samantha J., Kembel, Steven W., Ladau, Joshua, O'Dwyer, James P., Green, Jessica L., Eisen, Jonathan A., Pollard, Katherine S. (2011).
"PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data." PLoS Computational Biology 7(1)
Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonomic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced ... [
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Shim, E., Meyers, L. A., Galvani, A. P. (2011).
"Optimal H1N1 Vaccination Strategies Based on Self-Interest Versus Group Interest." BMC Public Health 11(Suppl.):32-48
ABSTRACT: Background: Influenza vaccination is vital for reducing H1N1 infection-mediated morbidity and mortality. To reduce transmission and achieve herd immunity during the initial 2009-2010 pandemic season, the US Centers for Disease Control and Prevention (CDC) recommended that initial priority for ... [
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Siederdissen, C. H. Z., Bernhart, S. H., Stadler, P. F., Hofacker, I. L. (2011).
"A Folding Algorithm for Extended RNA Secondary Structures." Bioinformatics 27(13):129-136
Motivation: RNA secondary structure contains many non- canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment. Results: We present a ... [
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Simova, I., Storch, D., Keil, P., Boyle, B., Phillips, O. L., Enquist, B. J. (2011).
"Global Species-Energy Relationship in Forest Plots: Role of Abundance, Temperature and Species Climatic Tolerances." Global Ecology and Biogeography 20(6):842-856
Aim To evaluate the strength of evidence for hypotheses explaining the relationship between climate and species richness in forest plots. We focused on the effect of energy availability which has been hypothesized to influence species richness: (1) via the effect ... [
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Smith, E. (2011).
"Large-Deviation Principles, Stochastic Effective Actions, Path Entropies, and the structure and meaning of thermodynamic descriptions." Reports on Progress in Physics 74(4):33-70
The meaning of thermodynamic descriptions is found in large-deviations scaling (Ellis 1985 Entropy, Large Deviations, and Statistical Mechanics (New York: Springer); Touchette 2009 Phys. Rep. 478 1-69) of the probabilities for fluctuations of averaged quantities. The central function expressing large-deviations ... [
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Smith, E. A., Mulder, M. B., Bowles, S., Hill, K. (2011).
"Wealth Inequality in Foraging, Horticultural, Pastoral, and Agricultural Populations A Reply to Caldararo." Current Anthropology 52(4):579-580 [
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Soni, V. H., Ketisch, P. M., Rodriguez, J. D., Shpunt, A., Hubler, A. W. (2011).
"Topological Similarities in Electrical and Hydrological Drainage Networks." Journal of Applied Physics 109(3):854-856
Under an electric field, spherical conducting particles in a dielectric liquid assemble into a dendritic tree in order to dissipate charge. Several topological measures characterize such networks, including degree distributions, Strahler numbers, and total external pathlengths. Here, scaling laws relating ... [
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Stark, S. C., Bentley, L. P., Enquist, B. J. (2011).
"Response to Coomes & Allen (2009) "Testing the Metabolic Scaling Theory of Tree Growth"." Journal of Ecology 99(3):741-747
P>1. <link rid="b4">Coomes & Allen (2009) propose a new statistical method to test the Metabolic Scaling Theory prediction for tree growth rate size scaling (scaling constant alpha = 1/3) presented in Enquist et al. (1999). This method finds values of ... [
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Stark, S. C., Bentley, L. P., Enquist, B. J. (2011).
"Response to Coomes and Allen (2009) "Testing the Metabolic Scaling Theory of Tree Growth"." Journal of Ecology 99(3):741-747 [
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Stegen, J. C., Swenson, N. G., Enquist, B. J., White, E. P., Phillips, O. L., Jorgensen, P. M., Weiser, M. D., Mendoza, A. M., Vargas, P. N. (2011).
"Variation in above-ground Forest Biomass Across Broad Climatic Gradients." Global Ecology and Biogeography 20(5):744-754
Aim An understanding of the relationship between forest biomass and climate is needed to predict the impacts of climate change on carbon stores. Biomass patterns have been characterized at geographically or climatically restricted scales, making it unclear if biomass is ... [
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Stollhoff, R., Jost, J., Elze, T., Kennerknecht, I. (2011).
"Deficits in Long-Term Recognition Memory Reveal Dissociated Subtypes in Congenital Prosopagnosia." PLoS One 6(1):105-116
The study investigates long-term recognition memory in congenital prosopagnosia (CP), a lifelong impairment in face identification that is present from birth. Previous investigations of processing deficits in CP have mostly relied on short-term recognition tests to estimate the scope and ... [
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Stollhoff, R., Kennerknecht, I., Elze, T., Jost, J. (2011).
"A computational model of dysfunctional facial encoding in congenital prosopagnosia." Neural Networkss 24(6 Sp Iss):652-664
Congenital prosopagnosia is a selective deficit in face identification that is present from birth. Previously, behavioral deficits in face recognition and differences in the neuroanatomical structure and functional activation of face processing areas have been documented mostly in separate studies. ... [
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Straus, L., Borrero, L. A., Hunter-Anderson, R., Longacre, W., Meltzer, D., Read, D., Sabloff, J. A., Wendorf, F. (2011).
"Lewis Roberts Binford (November 21, 1931-April 11, 2011)." Journal of Anthropological Research 67(3):321-331 [
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Tafer, H., Amman, F., Eggenhofer, F., Stadler, P. F., Hofacker, I. L. (2011).
"Fast accessibility-based prediction of RNA-RNA interactions." Bioinformatics 27(14):1934-1940
Motivation: Currently, the best RNA-RNA interaction prediction tools are based on approaches that consider both the inter-and intramolecular interactions of hybridizing RNAs. While accurate, these methods are too slow and memory-hungry to be employed in genome-wide RNA target scans. Alternative ... [
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Thomas, W. (2011).
"Manhattan Project to the Santa Fe Institute: The Memoirs of George A. Cowan, by G.A. Cowan." ISIS 102(3):581-582 [
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Thurner, S. (2011).
"Comments by S. Thurner on the Visioneer white papers by D. Helbing and S. Balietti." European Physical Journal - Special Topics 195(1):161-163 [
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Thurner, S. (2011).
"A Simple General Model of Evolutionary Dynamics." Principles of Evolution: From the Planck Epoch to Comoplex Multicellular Life :119-114
Evolution is a process in which some variations that emerge within a population (of, e.g., biological species or industrial goods) get selected, survive, and proliferate, whereas others vanish. Survival probability, proliferation, or production rates are associated with the "fitness" of ... [
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Tramontano, A., Donath, A., Bernhart, S. H., Reiche, K., Bohmdorfer, G., Stadler, P. F., Bachmair, A. (2011).
"Deletion Analysis of the 3 ' Long Terminal Repeat Sequence of Plant Retrotransposon Tto1 Identifies 125 Base Pairs Redundancy as Sufficient for First Strand Transfer." Virology 412(1):75-82
Retroviruses and many retrotransposons are flanked by sequence repeats called long terminal repeats (LTRs). These sequences contain a promoter region, which is active in the 5' LTR, and transcription termination signals, which are active in the LTR copy present at ... [
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Trantopouos, K., Schlapfer, M., Helbing, D. (2011).
"Toward Sustainability of Complex Urban Systems through Techno-Social Reality Mining." Environmental Science & Technology 4(15):6231-6232 [
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Tsallis, C. (2011).
"The Nonadditive Entropy S(q) and Its Applications in Physics and Elsewhere: Some Remarks." Entropy 13(10):1765-1804
The nonadditive entropy S(q) has been introduced in 1988 focusing on a generalization of Boltzmann-Gibbs (BG) statistical mechanics. The aim was to cover a (possibly wide) class of systems among those very many which violate hypothesis such as ergodicity, under ... [
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Tumminello, M., Micciche, S., Lillo, F., Piilo, J., Mantegna, R. N. (2011).
"Statistically Validated Networks in Bipartite Complex Systems." PLoS One 6(3):166-176
Many complex systems present an intrinsic bipartite structure where elements of one set link to elements of the second set. In these complex systems, such as the system of actors and movies, elements of one set are qualitatively different than ... [
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Tumminello, M., Micciche, S., Lillo, F., Varho, J., Piilo, J., Mantegna, R. N. (2011).
"Community Characterization of Heterogeneous Complex Systems." Journal of Statistical Mechanics — Theory and Experiment :457-470
We introduce an analytical statistical method for characterizing the communities detected in heterogeneous complex systems. By proposing a suitable null hypothesis, our method makes use of the hypergeometric distribution to assess the probability that a given property is over-expressed in ... [
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Ubeda, F., Wilkins, J. F. (2011).
"The Red Queen Theory of Recombination Hotspots." Journal of Evolutionary Biology 24(3):541-553
Recombination hotspots are small chromosomal regions, where meiotic crossover events happen with high frequency. Recombination is initiated by a double-strand break (DSB) that requires the intervention of the molecular repair mechanism. The DSB repair mechanism may result in the exchange ... [
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Venditti, C., Meade, A., Pagel, M. (2011).
"Multiple Routes to Mammalian Diversity." Nature 479(7373):393-396
The radiation of the mammals provides a 165-million-year test case for evolutionary theories of how species occupy and then fill ecological niches. It is widely assumed that species often diverge rapidly early in their evolution, and that this is followed ... [
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Volz, E. M., Miller, J. C., Galvani, A., Meyers, L. A. (2011).
"Effects of Heterogeneous and Clustered Contact Patterns on Infectious Disease Dynamics." PLOS Computational Biology 7(6):40-52
The spread of infectious diseases fundamentally depends on the pattern of contacts between individuals. Although studies of contact networks have shown that heterogeneity in the number of contacts and the duration of contacts can have far-reaching epidemiological consequences, models often ... [
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Walker, R. S., Hamilton, M. J. (2011).
"Social Complexity and Linguistic Diversity in the Austronesian and Bantu Population Expansions." Proceedings of the Royal Society of London Series B - Biological Sciences 278(1710):1399-1404
Reconstructing the rise and fall of social complexity in human societies through time is fundamental for understanding some of the most important transformations in human history. Phylogenetic methods based on language diversity provide a means to reconstruct pre-historic events and ... [
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Washietl, S., Findeiss, S., Muller, S. A., Kalkhof, S., von Bergen, M., Hofacker, I. L., Stadler, P. F., Goldman, N. (2011).
"RNAcode: Robust Discrimination of Coding and Noncoding Regions in Comparative Sequence Data." RNA - A Publication of the RNA Society 17(4):578-594
With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily conserved regions arose as a core analysis task. Here we present RNAcode, a program ... [
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Wen, H. R., Leicht, E. A., D'Souza, R. M. (2011).
"Improving Community Detection in Networks by Targeted Node Removal." Physical Review E 83(1 PT. 2):1-8
How a network breaks up into subnetworks or communities is of wide interest. Here we show that vertices connected to many other vertices across a network can disturb the community structures of otherwise ordered networks, introducing noise. We investigate strategies ... [
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Wilkins, J. F. (2011).
"Genomic Imprinting and Conflict-Induced Decanalization." Evolution 65(2):537-553
Genomic imprinting is the phenomenon in which the expression pattern of an allele depends on its parental origin. When maternally expressed and paternally expressed imprinted loci affect the same trait, the result is an arms race, with each locus under ... [
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Wilkins, J. F., Ubeda, F..
"Diseases Associated with Genomic Imprinting". In
Modifications of Nuclear DNA and Its Regulatory Proteins, 401-445.
2011 [
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Wright, J., Bellissimi, E., de Hulster, E., Wagner, A., Pronk, J. T., van Maris, A. J. A. (2011).
"Batch and Continuous Culture-Based Selection Strategies for Acetic Acid Tolerance in Xylose-Fermenting Saccharomyces cerevisiae." FEMS Yeast Research 11(3):299-306
Acetic acid tolerance of Saccharomyces cerevisiae is crucial for the production of bioethanol and other bulk chemicals from lignocellulosic plant-biomass hydrolysates, especially at a low pH. This study explores two evolutionary engineering strategies for the improvement of acetic acid tolerance ... [
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Wu, B. L., Blanchard-Letort, A., Liu, Y., Zhou, G. H., Wang, X. F., Elena, S. F. (2011).
"Dynamics of Molecular Evolution and Phylogeography of Barley Yellow Dwarf Virus-PAV." PLoS One 6(2):Art. No. e16896
Barley yellow dwarf virus (BYDV) species PAV occurs frequently in irrigated wheat fields worldwide and can be efficiently transmitted by aphids. Isolates of BYDV-PAV from different countries show great divergence both in genomic sequences and pathogenicity. Despite its economical importance, ... [
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Yoder, M. R., Turcotte, D. L., Rundle, J. B. (2011).
"Forest-Fire Model with Natural Fire Resistance." Physical Review E 83(4 Pt. 2):31-36
Observations suggest that contemporary wildfire suppression practices in the United States have contributed to conditions that facilitate large, destructive fires. We introduce a forest-fire model with natural fire resistance that supports this theory. Fire resistance is defined with respect to ... [
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Zamora-Sillero, E., Hafner, M., Ibig, A., Stelling, J., Wagner, A. (2011).
"Efficient Characterization of High-Dimensional Parameter Spaces for Systems Biology." BMC Systems Biology 5:1-22
Background: A biological system's robustness to mutations and its evolution are influenced by the structure of its viable space, the region of its space of biochemical parameters where it can exert its function. In systems with a large number of ... [
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Zhang, X. A., Ryu, S. H., Xu, Y. J., Elbaz, T., Zekri, A. R. N., Abdelaziz, A. O., Abdel-Hamid, M., Thiers, V., Elena, S. F., Fan, X. F., Di Bisceglie, A. M. (2011).
"The Core/E1 Domain of Hepatitis C Virus Genotype 4a in Egypt Does Not Contain Viral Mutations or Strains Specific for Hepatocellular Carcinoma." Journal of Clinical Virology 52(4):333-338
Background: Hepatitis C virus (HCV) infection is a well- documented etiological factor for hepatocellular carcinoma (HCC). As HCV shows remarkable genetic diversity, an interesting and important issue is whether such a high viral genetic diversity plays a role in the ... [
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Zwart, M. P., Daros, J. A., Elena, S. F. (2011).
"One Is Enough: In Vivo Effective Population Size Is Dose-Dependent for a Plant RNA Virus." PLoS Pathogens 7(7):196-207
Effective population size (N-e) determines the strength of genetic drift and the frequency of co-infection by multiple genotypes, making it a key factor in viral evolution. Experimental estimates of N-e for different plant viruses have, however, rendered diverging results. The ... [
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de Visser, J. A. G. M., Cooper, T. F., Elena, S. F. (2011).
"The Causes of Epistasis." Proceedings of the Royal Society B - Biological Sciences 278(1725):3617-3624
Since Bateson's discovery that genes can suppress the phenotypic effects of other genes, gene interactions-called epistasis-have been the topic of a vast research effort. Systems and developmental biologists study epistasis to understand the genotype-phenotype map, whereas evolutionary biologists recognize the ... [
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de la Chaux, N., Wagner, A. (2011).
"BEL/Pao Retrotransposons in Metazoan Genomes." BMC Evolutionary Biology 11:1-16
Background: Long terminal repeat (LTR) retrotransposons are a widespread kind of transposable element present in eukaryotic genomes. They are a major factor in genome evolution due to their ability to create large scale mutations and genome rearrangements. Compared to other ... [
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