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    1 OF 61

    Deciphering the histone code to build the genome structure.
    Biosystems 2017 Nov 17. Epub 2017 Nov 17.
    Faculty of Biology and Center for Computational Sciences, Johannes Gutenberg University Mainz, 55128 Mainz, Germany. Electronic address:
    Histones are punctuated with small chemical modifications that alter their interaction with DNA. One attractive hypothesis stipulates that certain combinations of these histone modifications may function, alone or together, as a part of a predictive histone code to provide ground rules for chromatin folding. We consider four features that relate histone modifications to chromatin folding: charge neutralisation, molecular specificity, robustness and evolvability. Read More

    A hyperbolastic type-I diffusion process: parameter estimation by means of the firefly algorithm.
    Biosystems 2017 Nov 9. Epub 2017 Nov 9.
    Departamento de Estadística e Investigación Operativa, Facultad de Ciencias, s/n, Campus de Fuentenueva, Universidad de Granada, 18071 Granada, Spain. Electronic address:
    A stochastic diffusion process, whose mean function is a hyperbolastic curve of type I, is presented. The main characteristics of the process are studied and the problem of maximum likelihood estimation for the parameters of the process is considered. To this end, the firefly metaheuristic optimization algorithm is applied after bounding the parametric space by a stagewise procedure. Read More

    The splicing code.
    Biosystems 2017 Nov 6. Epub 2017 Nov 6.
    International Centre for Genetic Engineering and Biotechnology, Padriciano 99, Italy.
    This issue dedicated to the code of life tackles very challenging and open questions in Biology. The genetic code, brilliantly uncovered over 50 years ago is an example of a univocal biological code. In fact, except for very few and marginal variations, it is the same from bacteria to man, the RNA stretch: 5' GUGUUC 3' reads as the dipeptide: Val-Phe in bacteria, in yeast, in Arabidopsis, in zebra fish, in mouse and in human. Read More

    The Evolutionary Dynamics of Language.
    Biosystems 2017 Nov 6. Epub 2017 Nov 6.
    Parmenides Center for the Conceptual Foundations of Science, Pullach, Munich, Germany; Evolutionary Systems Research Group, MTA Ecological Research Centre, the Hungarian Academy of Sciences, Tihany, Hungary. Electronic address:
    The well-established framework of evolutionary dynamics can be applied to the fascinating open problems how human brains are able to acquire and adapt language and how languages change in a population. Schemas for handling grammatical constructions are the replicating unit. They emerge and multiply with variation in the brains of individuals and undergo selection based on their contribution to needed expressive power, communicative success and the reduction of cognitive effort. Read More

    Incorporating gene ontology into fuzzy relational clustering of microarray gene expression data.
    Biosystems 2017 Nov 4;163:1-10. Epub 2017 Nov 4.
    Department of Computer Science and Engineering, Khulna University of Engineering & Technology, Khulna, Bangladesh.
    The product of gene expression works together in the cell for each living organism in order to achieve different biological processes. Many proteins are involved in different roles depending on the environment of the organism for the functioning of the cell. In this paper, we propose gene ontology (GO) annotations based semi-supervised clustering algorithm called GO fuzzy relational clustering (GO-FRC) where one gene is allowed to be assigned to multiple clusters which are the most biologically relevant behavior of genes. Read More

    The search image as link between sensation, perception and action.
    Biosystems 2017 Nov 4. Epub 2017 Nov 4.
    University of Stavanger, Postboks 8600 Forus, 4036 Stavanger, Norway. Electronic address:
    In this paper, it is argued that Jakob von Uexküll's "search image" notion, the original version of this notion within ethology, is still of use. A search image, in Uexküll's sense, is an imagined object that an organism has in mind when it searches for something. Uexküll's conception of the search image is useful both for understanding the theoretical context of contemporary notions of search images, and with an eye to envisioning possible future developments of the idea. Read More

    Genetic coding algorithm for sense and antisense peptide interactions.
    Biosystems 2017 Oct 28. Epub 2017 Oct 28.
    Department of General and Inorganic Chemistry, Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, HR-10000 Zagreb, Croatia. Electronic address:
    Sense and antisense peptides, i.e. peptides specified by complementary DNA and RNA sequences, interact with increased probability. Read More

    Analysis of network motifs in cellular regulation: Structural similarities, input-output relations and signal integration.
    Biosystems 2017 Oct 28;162:215-232. Epub 2017 Oct 28.
    Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg, Sandtorstr. 1, D-39106 Magdeburg, Germany.
    Much of the complexity of regulatory networks derives from the necessity to integrate multiple signals and to avoid malfunction due to cross-talk or harmful perturbations. Hence, one may expect that the input-output behavior of larger networks is not necessarily more complex than that of smaller network motifs which suggests that both can, under certain conditions, be described by similar equations. In this review, we illustrate this approach by discussing the similarities that exist in the steady state descriptions of a simple bimolecular reaction, covalent modification cycles and bacterial two-component systems. Read More

    Aggregating, Polarizing, Networking - The Evolution of Cell Adhesion Codes.
    Biosystems 2017 Nov 1. Epub 2017 Nov 1.
    Dactyl Foundation for the Arts & Humanities, 64 Grand Street, New York, NY 10013 USA. Electronic address:
    Adhesion is a central mechanism in the development of multicellular life. It underlies cell movement, communication and differentiation. Remarkably, the presence of only three classes of interconnected molecules is sufficient to establish functional adhesive interactions between cells: Extracellular Matrix components (ECMs); Cell Adhesion Molecules (CAMs); and cytoskeleton microfilaments. Read More

    Network induction for epidemic profiles with a novel representation.
    Biosystems 2017 Oct 31;162:205-214. Epub 2017 Oct 31.
    Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, Canada N1G 2W1. Electronic address:
    Graphs can be used as contact networks in models of epidemic spread. Most research seeks to extract the properties of an extant graph, derived from questionnaires or other sources of contact information. The inverse problem of searching the space of graphs for those that exhibit specific properties has received little attention and that is the focus of this study. Read More

    Slow update stochastic simulation algorithms for modeling complex biochemical networks.
    Biosystems 2017 Oct 30;162:135-146. Epub 2017 Oct 30.
    Machine Intelligence Unit, Indian Statistical Institute, Kolkata 700108, India. Electronic address:
    The stochastic simulation algorithm (SSA) based modeling is a well recognized approach to predict the stochastic behavior of biological networks. The stochastic simulation of large complex biochemical networks is a challenge as it takes a large amount of time for simulation due to high update cost. In order to reduce the propensity update cost, we proposed two algorithms: slow update exact stochastic simulation algorithm (SUESSA) and slow update exact sorting stochastic simulation algorithm (SUESSSA). Read More

    The enzyme-substrate complex as a cat state: A toy quantum analog.
    Biosystems 2017 Oct 21;162:157-167. Epub 2017 Oct 21.
    Departamento de Matemática, Pontifícia Universidade Católica, Rio de Janeiro, Brazil. Electronic address:
    We introduce a quantum model system incorporating qualitative aspects of tunneling in enzyme action and analyze the possibilities of quantum superposition of several conformations of the enzyme-substrate complex. There is a potential barrier in each conformation which for simplicity's sake is assumed to be of zero width making the system explicitly solvable. Such a system exhibits generic features of quantum dynamics that should be present to some extent in real enzyme action. Read More

    Fundamental principles of the olfactory code.
    Biosystems 2017 Oct 17. Epub 2017 Oct 17.
    Max Planck Institute for Chemical Ecology, Department of EvolutionaryNeuroethology, Hans-Knoell-Str. 8, 07745 Jena, Germany. Electronic address:
    Sensory coding represents a basic principle of all phyla in nature: species attempt to perceive their natural surroundings and to make sense of them. Ultimately, sensory coding is the only way to allow a species to make the kinds of crucial decisions that lead to a behavioral response. In this manner, animals are able to detect numerous parameters, ranging from temperature and humidity to light and sound to volatile or non-volatile chemicals. Read More

    Towards a first implementation of the WLIMES approach in living system studies advancing the diagnostics and therapy in personalized medicine.
    Biosystems 2017 Oct 16;162:177-204. Epub 2017 Oct 16.
    Institute of Pathology, Charité - Universitätsmedizin, Berlin, Germany. Electronic address:
    The goal of this paper is to advance an extensible theory of living systems using an approach to biomathematics and biocomputation that suitably addresses self-organized, self-referential and anticipatory systems with multi-temporal multi-agents. Our first step is to provide foundations for modelling of emergent and evolving dynamic multi-level organic complexes and their sustentative processes in artificial and natural life systems. Main applications are in life sciences, medicine, ecology and astrobiology, as well as robotics, industrial automation, man-machine interface and creative design. Read More

    BINK: Biological binary keypoint descriptor.
    Biosystems 2017 Oct 13;162:147-156. Epub 2017 Oct 13.
    Vision Laboratory, LARSyS, FCT & ISE, University of the Algarve, Faro, Portugal.
    Learning robust keypoint descriptors has become an active research area in the past decade. Matching local features is not only important for computational applications, but may also play an important role in early biological vision for disparity and motion processing. Although there were already some floating-point descriptors like SIFT and SURF that can yield high matching rates, the need for better and faster descriptors for real-time applications and embedded devices with low computational power led to the development of binary descriptors, which are usually much faster to compute and to match. Read More

    The evolution of the genetic code: Impasses and challenges.
    Biosystems 2017 Oct 12. Epub 2017 Oct 12.
    Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
    The origin of the genetic code and translation is a "notoriously difficult problem". In this survey we present a list of questions that a full theory of the genetic code needs to answer. We assess the leading hypotheses according to these criteria. Read More

    On universal coding events in protein biogenesis.
    Biosystems 2017 Oct 10. Epub 2017 Oct 10.
    Berlin Institute of Technology/TU Berlin, Department of Chemistry, Biocatalysis Group, Müller-Breslau-Straße 10, D-10623 Berlin, Germany. Electronic address:
    The complete ribosomal protein synthesis cycle and codon-amino acids associations are universally preserved in all life taxa on Earth. This process is accompanied by a set of hierarchically organized recognition and controlling events at different complexity levels. It starts with amino acid activation by aminoacyl tRNA synthetases (aaRS) followed by matching with the acceptor units of their cognate tRNAs ("operational RNA code") and ribosomal codon-anticodon pairing of messenger RNA ("triplet code"). Read More

    What is code biology?
    Biosystems 2017 Oct 6. Epub 2017 Oct 6.
    Dipartimento di Morfologia ed Embriologia, Via Fossato di Mortara 64a, 44121 Ferrara, Italy. Electronic address:
    Various independent discoveries have shown that many organic codes exist in living systems, and this implies that they came into being during the history of life and contributed to that history. The genetic code appeared in a population of primitive systems that has been referred to as the common ancestor, and it has been proposed that three distinct signal processing codes gave origin to the three primary kingdoms of Archaea, Bacteria and Eukarya. After the genetic code and the signal processing codes, on the other hand, only the ancestors of the eukaryotes continued to explore the coding space and gave origin to splicing codes, histone code, tubulin code, compartment codes and many others. Read More

    The evolution of the Glycomic Codes of extracellular matrices.
    Biosystems 2017 Oct 7. Epub 2017 Oct 7.
    Systems and Synthetic Biology Center, Institute of Biosciences, Department of Botany, University of São Paulo, Brazil. Electronic address:
    The extracellular matrices (ECMs) of living organisms are compartments responsible for maintenance of cell shape, cell adhesion, and cell communication. They are also involved in cell signaling and defense against the attack of pathogens. The plant cell walls have been recently defined as encoded structures that combine polysaccharides with other encoded structures (proteins and phenolic compounds). Read More

    How prokaryotes 'encode' their environment: Systemic tools for organizing the information flow.
    Biosystems 2017 Oct 4. Epub 2017 Oct 4.
    Bioinformation and Systems Biology Group, Aragon Health Sciences Institute (IACS/ IIS Aragon) 50009, Zaragoza, Spain. Electronic address:
    An important issue related to code biology concerns the cell's informational relationships with the environment. As an open self-producing system, a great variety of inputs and outputs are necessary for the living cell, not only consisting of matter and energy but also involving information flows. The analysis here of the simplest cells will involve two basic aspects. Read More

    Cyclic decomposition explains a photosynthetic down regulation for Chlamydomonas reinhardtii.
    Biosystems 2017 Sep 29;162:119-127. Epub 2017 Sep 29.
    Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK. Electronic address:
    The regulation of metabolic networks has been shown to be distributed and shared through the action of metabolic cycles. Biochemical cycles play important roles in maintaining flux and substrate availability for multiple pathways to supply cellular energy and contribute to dynamic stability. By understanding the cyclic and acyclic flows of matter through a network, we are closer to understanding how complex dynamic systems distribute flux along interconnected pathways. Read More

    Total enzyme activity constraint and homeostatic constraint impact on the optimization potential of a kinetic model.
    Biosystems 2017 Sep 28;162:128-134. Epub 2017 Sep 28.
    Biosystems Group, Department of Computer Systems, Latvia University of Agriculture, Liela iela 2, LV-3001 Jelgava, Latvia.
    The application of biologically and biochemically relevant constraints during the optimization of kinetic models reduces the impact of suggested changes in processes not included in the scope of the model. This increases the probability that the design suggested by model optimization can be carried out by an organism after implementation of design in vivo. A case study was carried out to determine the impact of total enzyme activity and homeostatic constraints on the objective function values and the following ranking of adjustable parameter combinations. Read More

    Effect of directional migration on Lotka-Volterra system with desert.
    Biosystems 2017 Sep 28;162:75-80. Epub 2017 Sep 28.
    Department of Mathematical and Systems Engineering, Shizuoka University, Hamamatsu, 432-8561, Japan. Electronic address:
    Migration is observed across many species. Several authors have studied ecological migration by applying cellular automaton (CA). In this paper, we present a directional migration model with desert on a one-dimensional lattice where a traffic CA model and a lattice Lotka-Volterra system are connected. Read More

    An improved hybrid of particle swarm optimization and the gravitational search algorithm to produce a kinetic parameter estimation of aspartate biochemical pathways.
    Biosystems 2017 Sep 23;162:81-89. Epub 2017 Sep 23.
    Artificial Intelligence and Bioinformatics Research Group, Faculty of Computing, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia.
    Mathematical modelling is fundamental to understand the dynamic behavior and regulation of the biochemical metabolisms and pathways that are found in biological systems. Pathways are used to describe complex processes that involve many parameters. It is important to have an accurate and complete set of parameters that describe the characteristics of a given model. Read More

    Functional data analysis of single-trial auditory evoked potentials recorded in the awake rat.
    Biosystems 2017 Nov 18;161:67-75. Epub 2017 Sep 18.
    Auditory Research Laboratory, State University of New York, 107 Beaumont Hall, Plattsburgh, NY 12901, USA. Electronic address:
    Evoked potentials (EPs) reflect neural processing and are widely used to study sensory perception. However, methods of analyzing EP have been limited mostly to the conventional ensemble averaging of EP response trials to a repeated stimulus, and less so to single-trials analysis. Here we applied a new approach - functional data analysis (FDA) - to study auditory EP in the rat model of tinnitus, in which overdoses of salicylate (SS) are known to alter sound perception characteristically, as the same way as in humans. Read More

    Synchrony measure for a neuron driven by excitatory and inhibitory inputs and its adaptation to experimentally-recorded data.
    Biosystems 2017 Nov 15;161:46-56. Epub 2017 Sep 15.
    Department of Computer Science, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus. Electronic address:
    The aim of the current work is twofold: firstly to adapt an existing method measuring the input synchrony of a neuron driven only by excitatory inputs in such a way so as to account for inhibitory inputs as well and secondly to further appropriately adapt this measure so as to be correctly utilised on experimentally-recorded data. The existing method uses the normalized pre-spike slope (NPSS) of the membrane potential, resulting from observing the slope of depolarization of the membrane potential of a neuron prior to the moment of crossing the threshold within a short period of time, to identify the response-relevant input synchrony and through it to infer the operational mode of a neuron. The first adaptation of NPSS is made such that its upper bound calculation accommodates for the higher possible slope values caused by the lower average and minimum membrane potential values due to inhibitory inputs. Read More

    The optimal regulation mode of Bcl-2 apoptotic switch revealed by bistability analysis.
    Biosystems 2017 Sep 18;162:44-52. Epub 2017 Sep 18.
    Complex Systems Research Center, Shanxi University, Taiyuan, Shanxi 030006, PR China. Electronic address:
    In most cell types, apoptosis occurs by the mitochondrial outer membrane permeability (MOMP)-mediated pathway, which is controlled by Bcl-2 family proteins (often referred to as Bcl-2 apoptotic switch). These proteins, which display a range of bioactivities, can be divided into four types: effectors, inhibitors, activators and sensitizers. Although the complex interactions among Bcl-2 family members have been studied intensively, a unifying hypothesis for the mechanism they use to regulate MOMP remains elusive. Read More

    Mathematical Fundamentals for the Noise Immunity of the Genetic Code.
    Biosystems 2017 Sep 13. Epub 2017 Sep 13.
    Institute of Mathematical Biology, Faculty for Computer Sciences, Mannheim University of Applied Sciences, 68163 Mannheim, Germany. Electronic address:
    Symmetry is one of the essential and most visible patterns that can be seen in nature. Starting from the left-right symmetry of the human body, all types of symmetry can be found in crystals, plants, animals and nature as a whole. Similarly, principals of symmetry are also some of the fundamental and most useful tools in modern mathematical natural science that play a major role in theory and applications. Read More

    Dynamical properties of LFPs from mice with unilateral injection of TeNT.
    Biosystems 2017 Nov 14;161:57-66. Epub 2017 Sep 14.
    Institute of Biophysics, CNR-National Research Council, 56124 Pisa, Italy. Electronic address:
    Local field potential (LFP) recordings were performed from the visual cortex (V1) of a focal epilepsy mouse model. Epilepsy was induced by a unilateral injection of the synaptic blocker tetanus neurotoxin (TeNT). LFP signals were simultaneously recorded from V1 of both hemispheres of each animal under acute and chronic conditions (i. Read More

    Causation, constructors and codes.
    Biosystems 2017 Sep 13. Epub 2017 Sep 13.
    Centre for Complex Systems in Transition and Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa. Electronic address:
    Relational biology relies heavily on the enriched understanding of causal entailment that Robert Rosen's formalisation of Aristotle's four causes has made possible, although to date efficient causes and the rehabilitation of final cause have been its main focus. Formal cause has been paid rather scant attention, but, as this paper demonstrates, is crucial to our understanding of many types of processes, not necessarily biological. The graph-theoretic relational diagram of a mapping has played a key role in relational biology, and the first part of the paper is devoted to developing an explicit representation of formal cause in the diagram and how it acts in combination with efficient cause to form a mapping. Read More

    Insuperable problems of the genetic code initially emerging in an RNA world.
    Biosystems 2017 Sep 10. Epub 2017 Sep 10.
    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
    Differential equations for error-prone information transfer (template replication, transcription or translation) are developed in order to consider, within the theory of autocatalysis, the advent of coded protein synthesis. Variations of these equations furnish a basis for comparing the plausibility of contrasting scenarios for the emergence of specific tRNA aminoacylation, ultimately by enzymes, and the relationship of this process with the origin of the universal system of molecular biological information processing embodied in the Central Dogma. The hypothetical RNA World does not furnish an adequate basis for explaining how this system came into being, but principles of self-organisation that transcend Darwinian natural selection furnish an unexpectedly robust basis for a rapid, concerted transition to genetic coding from a peptide·RNA world. Read More

    Toward a hierarchical virtual screening and toxicity risk analysis for identifying novel CA XII inhibitors.
    Biosystems 2017 Sep 9;162:35-43. Epub 2017 Sep 9.
    Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. Electronic address:
    Carbonic anhydrase isoform XII (CA XII) is a potential target for cancer treatment. In this study, pharmacophore modeling, hierarchical virtual screening, and toxicity risk analysis were performed for identifying novel CA XII inhibitors. A pharmacophore model of two classes of CA XII inhibitors was generated. Read More

    A new parallel DNA algorithm to solve the task scheduling problem based on inspired computational model.
    Biosystems 2017 Sep 7;162:59-65. Epub 2017 Sep 7.
    College of Mathematics and Information Science, Guiyang University, Guizhou 550005, PR China.
    As a promising approach to solve the computationally intractable problem, the method based on DNA computing is an emerging research area including mathematics, computer science and molecular biology. The task scheduling problem, as a well-known NP-complete problem, arranges n jobs to m individuals and finds the minimum execution time of last finished individual. In this paper, we use a biologically inspired computational model and describe a new parallel algorithm to solve the task scheduling problem by basic DNA molecular operations. Read More

    A step into the RNA world: Conditional analysis of hydrogel formation of adenosine 5'-monophosphate induced by cyanuric acid.
    Biosystems 2017 Sep 5;162:53-58. Epub 2017 Sep 5.
    Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan. Electronic address:
    Nucleotide polymerization occurs by the nucleophilic attack of 3'-oxygen of the 3'-terminal nucleotide on the α-phosphorus of the incoming nucleotide 5'-triphosphate. The π-stacking of mononucleotides is an important factor for prebiotic RNA polymerization in terms of attaining the proximity of two reacting moieties. Adenosine and adenosine 5'-monophosphate (AMP) are known to form hydrogel in the presence of cyanuric acid at neutral pH. Read More

    Ecoacoustic codes and ecological complexity.
    Biosystems 2017 Sep 5. Epub 2017 Sep 5.
    Department of Pure and Applied Sciences, Urbino University, Urbino, Italy. Electronic address:
    Multi-layer communication and sensing network assures the exchange of relevant information between animals and their umwelten, imparting complexity to the ecological systems. Individual soniferous species, the acoustic community, and soundscape are the three main operational levels that comprise this multi-layer network. Acoustic adaptation and acoustic niche are two more important mechanisms that regulate the acoustic performances at the first level while the acoustic community model explains the complexity of the interspecific acoustic network at the second level. Read More

    Stochastic noncooperative and cooperative evolutionary game strategies of a population of biological networks under natural selection.
    Biosystems 2017 Sep 5;162:90-118. Epub 2017 Sep 5.
    Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan. Electronic address:
    We review current static and dynamic evolutionary game strategies of biological networks and discuss the lack of random genetic variations and stochastic environmental disturbances in these models. To include these factors, a population of evolving biological networks is modeled as a nonlinear stochastic biological system with Poisson-driven genetic variations and random environmental fluctuations (stimuli). To gain insight into the evolutionary game theory of stochastic biological networks under natural selection, the phenotypic robustness and network evolvability of noncooperative and cooperative evolutionary game strategies are discussed from a stochastic Nash game perspective. Read More

    Mathematical models in cancer therapy.
    Biosystems 2017 Sep 1;162:12-23. Epub 2017 Sep 1.
    Centro de Matemática da Universidade do Porto (CMUP), Faculty of Sciences of University of Porto, Gabinete de Estatística, Modelação e Aplicações Computacionais (GEMAC), Portugal. Electronic address:
    In this article, deterministic mathematical models are derived from biochemical models within a human cell in two distinct cases, for comparison: healthy cell and cancerous cell. The former model is based in the cell cycle model by Novak and Tyson and its adaptation by Conradie, and makes use of the MAPK cascade pathway and the PI3K/AKT pathway for signalling transduction, to create a wider updated model for the regulation of a healthy cell. The latter model, for the cancer cell, is derived from the healthy cell model by altering specific pathways and interpreting the outcome in the light of literature in cancer. Read More

    INDEX: Incremental depth extension approach for protein-protein interaction networks alignment.
    Biosystems 2017 Aug 30;162:24-34. Epub 2017 Aug 30.
    Department of Internal Medicine, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran.
    High-throughput methods have provided us with a large amount of data pertaining to protein-protein interaction networks. The alignment of these networks enables us to better understand biological systems. Given the fact that the alignment of networks is computationally intractable, it is important to introduce a more efficient and accurate algorithm which finds as large as possible similar areas among networks. Read More

    GeRNet: a gene regulatory network tool.
    Biosystems 2017 Aug 30;162:1-11. Epub 2017 Aug 30.
    Instituto de Ciencias e Ingeniería de la Computación, Universidad Nacional del Sur, CONICET, Bahía Blanca, Argentina. Electronic address:
    Gene regulatory networks (GRNs) are crucial in every process of life since they govern the majority of the molecular processes. Therefore, the task of assembling these networks is highly important. In particular, the so called model-free approaches have an advantage modeling the complexities of dynamic molecular networks, since most of the gene networks are hard to be mapped with accuracy by any other mathematical model. Read More

    The bioelectric code: An ancient computational medium for dynamic control of growth and form.
    Biosystems 2017 Sep 2. Epub 2017 Sep 2.
    Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA.
    What determines large-scale anatomy? DNA does not directly specify geometrical arrangements of tissues and organs, and a process of encoding and decoding for morphogenesis is required. Moreover, many species can regenerate and remodel their structure despite drastic injury. The ability to obtain the correct target morphology from a diversity of initial conditions reveals that the morphogenetic code implements a rich system of pattern-homeostatic processes. Read More

    Computer simulation and experimental self-assembly of irradiated glycine amino acid under magnetic fields: Its possible significance in prebiotic chemistry.
    Biosystems 2017 Aug 26;162:66-74. Epub 2017 Aug 26.
    Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior S/N, Coyoacán, C.P. 04510 Ciudad de México, D.F, Mexico.
    Ionizing radiation may have played a relevant role in chemical reactions for prebiotic biomolecule formation on ancient Earth. Environmental conditions such as the presence of water and magnetic fields were possibly relevant in the formation of organic compounds such as amino acids. ATR-FTIR, Raman, EPR and X-ray spectroscopies provide valuable information about molecular organization of different glycine polymorphs under static magnetic fields. Read More

    A global optimization algorithm inspired in the behavior of selfish herds.
    Biosystems 2017 Oct 25;160:39-55. Epub 2017 Aug 25.
    Departamento de Electrónica, Universidad de Guadalajara, CUCEI, Av. Revolución 1500, Guadalajara, Jal, Mexico.
    In this paper, a novel swarm optimization algorithm called the Selfish Herd Optimizer (SHO) is proposed for solving global optimization problems. SHO is based on the simulation of the widely observed selfish herd behavior manifested by individuals within a herd of animals subjected to some form of predation risk. In SHO, individuals emulate the predatory interactions between groups of prey and predators by two types of search agents: the members of a selfish herd (the prey) and a pack of hungry predators. Read More

    Optimism in the face of uncertainty supported by a statistically-designed multi-armed bandit algorithm.
    Biosystems 2017 Oct 22;160:25-32. Epub 2017 Aug 22.
    Graduate School of Science and Engineering, Tokyo Denki University, Japan.
    The principle of optimism in the face of uncertainty is known as a heuristic in sequential decision-making problems. Overtaking method based on this principle is an effective algorithm to solve multi-armed bandit problems. It was defined by a set of some heuristic patterns of the formulation in the previous study. Read More

    Sustainable cooperation based on reputation and habituation in the public goods game.
    Biosystems 2017 Oct 18;160:33-38. Epub 2017 Aug 18.
    College of Management and Economics, Tianjin University, Tianjin 300072, PR China.
    Reputation can promote cooperation in public goods game and player's cooperative behavior is not pure economical rationality, but habituation would influence their behaviors as well. One's habituation can be formed by repeated behaviors in daily life and be affected by habitual preference. We aim to investigate the sustainable cooperation based on reputation and habit formation. Read More

    Reviewing evidence for systematic transcriptional deletions, nucleotide exchanges, and expanded codons, and peptide clusters in human mitochondria.
    Biosystems 2017 Oct 12;160:10-24. Epub 2017 Aug 12.
    Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, 13385, France. Electronic address:
    Polymerization sometimes transforms sequences by (a) systematic deletions of mono-, dinucleotides after trinucleotides, or (b) 23 systematic nucleotide exchanges (9 symmetric, X<>Y, e.g. G<>T, 14 asymmetric, X > Y > Z > X, e. Read More

    Linked Gauss-Diffusion processes for modeling a finite-size neuronal network.
    Biosystems 2017 Nov 2;161:15-23. Epub 2017 Aug 2.
    Dipartimento di Matematica e Applicazioni, Università degli Studi di Napoli "Federico II", Complesso di Monte S. Angelo via Cintia, 80126 Napoli, Italy. Electronic address:
    A Leaky Integrate-and-Fire (LIF) model with stochastic current-based linkages is considered to describe the firing activity of neurons interacting in a (2×2)-size feed-forward network. In the subthreshold regime and under the assumption that no more than one spike is exchanged between coupled neurons, the stochastic evolution of the neuronal membrane voltage is subject to random jumps due to interactions in the network. Linked Gauss-Diffusion processes are proposed to describe this dynamics and to provide estimates of the firing probability density of each neuron. Read More

    Information reduction in a reverberatory neuronal network through convergence to complex oscillatory firing patterns.
    Biosystems 2017 Nov 27;161:24-30. Epub 2017 Jul 27.
    Taras Shevchenko National University of Kyiv, Volodymyrska Str., 60, Kyiv 01033, Ukraine. Electronic address:
    Dynamics of a reverberating neural net is studied by means of computer simulation. The net, which is composed of 9 leaky integrate-and-fire (LIF) neurons arranged in a square lattice, is fully connected with interneuronal communication delay proportional to the corresponding distance. The network is initially stimulated with different stimuli and then goes freely. Read More

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