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    Robustness of expression pattern formation due to dynamic equilibrium in gap gene system of an early Drosophila embryo.
    Biosystems 2018 Feb 8. Epub 2018 Feb 8.
    I. M. Sechenov Institute of Evolutionary Physiology and Biochemistry Russian Academy of Sciences, 44 Thorez Pr., St.-Petersburg, 194223, Russia; Computer Science and CEWIT, SUNY Stony Brook, 1500 Stony Brook Road, Stony Brook, 11794, NY, USA.
    The first manifestation of a segmentation pattern in the early Drosophila development is the formation of expression domains of genes belonging to the gap class. In our previous research the phenomenon of the gap system's robustness, exhibited as the ability to reduce highly variable gene expression in the course of development, was explained as a result of gene cross-regulation. In this paper we formulate the rigorous robustness conditions using the inherent properties of gap gene family. Read More

    Self-organization in aggregating robot swarms: A DW-KNN topological approach.
    Biosystems 2018 Feb 2;165:106-121. Epub 2018 Feb 2.
    King Abdullah University of Science and Technology (KAUST) Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal 23955-6900, Saudi Arabia.
    In certain swarm applications, where the inter-agent distance is not the only factor in the collective behaviours of the swarm, additional properties such as density could have a crucial effect. In this paper, we propose applying a Distance-Weighted K-Nearest Neighbouring (DW-KNN) topology to the behaviour of robot swarms performing self-organized aggregation, in combination with a virtual physics approach to keep the robots together. A distance-weighted function based on a Smoothed Particle Hydrodynamic (SPH) interpolation approach, which is used to evaluate the robot density in the swarm, is applied as the key factor for identifying the K-nearest neighbours taken into account when aggregating the robots. Read More

    GNC-app: A new Cytoscape app to rate gene networks biological coherence using gene-gene indirect relationships.
    Biosystems 2018 Feb 14. Epub 2018 Feb 14.
    Intelligent Data Analysis (DATAi), Division of Computer Science, Pablo de Olavide University, ES-41013 Seville, Spain. Electronic address:
    Motivation: Gene networks are currently considered a powerful tool to model biological processes in the Bioinformatics field. A number of approaches to infer gene networks and various software tools to handle them in a visual simplified way have been developed recently. However, there is still a need to assess the inferred networks in order to prove their relevance. Read More

    Interaction between the immune system and acute myeloid leukemia: A model incorporating promotion of regulatory T cell expansion by leukemic cells.
    Biosystems 2018 Feb 6;165:99-105. Epub 2018 Feb 6.
    Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Ishikawa, 9201192, Japan; Institute of Liberal Arts and Science, Kanazawa University, Kakuma, Ishikawa, 9201192, Japan. Electronic address:
    Population dynamics of regulatory T cells (Treg) are crucial for the underlying interplay between leukemic and immune cells in progression of acute myeloid leukemia (AML). The goal of this work is to elucidate the dynamics of a model that includes Treg, which can be qualitatively assessed by accumulating clinical findings on the impact of activated immune cell infusion after selective Treg depletion. We constructed an ordinary differential equation model to describe the dynamics of three components in AML: leukemic blast cells, mature regulatory T cells (Treg), and mature effective T cells (Teff), including cytotoxic T lymphocytes. Read More

    Logic of two antagonizing intra-species quorum sensing systems in bacteria.
    Biosystems 2018 Feb 5;165:88-98. Epub 2018 Feb 5.
    Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India. Electronic address:
    Bacteria release signaling molecules into the surrounding environment and sense them when present in their proximity. Using this strategy, a cell estimates the number of neighbors in its surrounding. Upon sensing a critical number of individuals, bacteria coordinate a number of cellular processes. Read More

    A graph-based approach to analyze flux-balanced pathways in metabolic networks.
    Biosystems 2018 Jan 12;165:40-51. Epub 2018 Jan 12.
    Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran. Electronic address:
    An elementary flux mode (EFM) is a pathway with minimum set of reactions that are functional in steady-state constrained space. Due to the high computational complexity of calculating EFMs, different approaches have been proposed to find these flux-balanced pathways. In this paper, an approach to find a subset of EFMs is proposed based on a graph data model. Read More

    mRNA function after intracellular delivery and release.
    Biosystems 2018 Jan 11;165:52-56. Epub 2018 Jan 11.
    Section of Biological Physics, Department of Physics, Chalmers University of Technology, Göteborg, Sweden; Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk, Russia. Electronic address:
    Nanocarrier-mediated mRNA delivery and release into the cells with subsequent translation to protein is of interest in the context of the development of a new generation of drugs. In particular, this protein can play a role of a transcription factor and be used as a tool to regulate temporarily the genetic networks. The corresponding transient kinetics of gene expression are expected to depend on the mechanism and duration of mRNA release. Read More

    Slime mould: The fundamental mechanisms of biological cognition.
    Biosystems 2018 Jan 8;165:57-70. Epub 2018 Jan 8.
    Unconventional Computing Centre, University of the West of England, Bristol, UK.
    The slime mould Physarum polycephalum has been used in developing unconventional computing devices for in which the slime mould played a role of a sensing, actuating, and computing device. These devices treated the slime mould as an active living substrate, yet it is a self-consistent living creature which evolved over millions of years and occupied most parts of the world, but in any case, that living entity did not own true cognition, just automated biochemical mechanisms. To "rehabilitate" slime mould from the rank of a purely living electronics element to a "creature of thoughts" we are analyzing the cognitive potential of P. Read More

    Phi in physiology, psychology and biomechanics: The golden ratio between myth and science.
    Biosystems 2018 Jan 6;165:31-39. Epub 2018 Jan 6.
    Clinical Laboratory of Experimental Neurorehabilitation, IRCCS Fondazione Santa Lucia, Rome, Italy.
    In recent years, there has been a renewed interest in the use of the so-called golden ratio (Phi, ϕ), an irrational number with fractal properties, used in artworks since V century BC. and now for modelling complex biological structures and functions. This number, in fact, recursively pops-up in human history, from Ancient Greeks to Renaissance, and to contemporary scientific studies. Read More

    The role of Fenton reaction in ROS-induced toxicity underlying atherosclerosis - modeled and analyzed using a Petri net-based approach.
    Biosystems 2018 Jan 6;165:71-87. Epub 2018 Jan 6.
    Institute of Computing Science, Poznan University of Technology, Poznań, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland. Electronic address:
    The superoxide-driven Fenton reaction plays an important role in the transformation of poorly reactive radicals into highly reactive ones. These highly reactive species (ROS), especially hydroxyl radicals can lead to many disturbances contributing to the endothelial dysfunction being a starting point for atherosclerosis. Although, iron has been identified as a possible culprit influencing formation of ROS, its significance in this process is still debatable. Read More

    A test of the adaptive network explanation of functional disorders using a machine learning analysis of symptoms.
    Biosystems 2017 Dec 24;165:22-30. Epub 2017 Dec 24.
    School of Psychology, United Kingdom; University of Plymouth, United Kingdom. Electronic address:
    The classification and etiology of functional disorders is controversial. Evidence supports both psychological and biological (disease) models that show, respectively, that functional disorders should be classified as one (bodily distress syndrome) and many (e.g. Read More

    CM-viewer: visualizing interaction network of co-mutated and mutually exclusively mutated cancer genes.
    Biosystems 2017 Dec 23. Epub 2017 Dec 23.
    Key Laboratory of the State Ministry of Education for Bio-resources and Ecologic Environment, College of Life Sciences, Sichuan University, Chengdu, 610064, China. Electronic address:
    Cancer genes usually play a crucial role in regulating cell growth. Normal cells transform into malignant tumors by the acquisition of accumulated genetic mutations that enable them to evade normal growth control. It is therefore important to understand the relationships between mutations during cancer development and progression. Read More

    Unique features of nucleotide and codon usage patterns in mycoplasmas revealed by information entropy.
    Biosystems 2017 Dec 20;165:1-7. Epub 2017 Dec 20.
    State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, PR China. Electronic address:
    Currently, the comparison between GC usage pattern at the 3rd codon position and codon usage index is commonly used to estimate the roles of evolutionary forces in shaping synonymous codon usages, however, this kind of analysis often losses the information about the role of A/T usage bias in shaping synonymous codon usage bias. To overcome this limitation and better understand the interplay between nucleotide and codon usages for the evolution of bacteria at gene levels, in this study, we employed the information entropy method with some modification to estimate roles of nucleotide compositions in the overall codon usage bias for 18 mycoplasma species in combination with Davies-Bouldin index. At gene levels, the overall nucleotide usage bias represents A content as the highest, followed by T, G and C for mycoplasmas, resulting in a low GC content. Read More

    Modeling of decision-making process for moving straight using inverse Bayesian inference.
    Biosystems 2018 Jan 14;163:70-81. Epub 2017 Dec 14.
    Department of Intermedia Art and Science, Waseda University, Japan.
    Humans sometimes make unreasonable decisions when viewed in objective terms. Even in the real world, we may lose sense of direction by turning around the corner several times or mistaking the estimation of travel distance. We experimented in virtual space how we lose sense of direction under what circumstances. Read More

    Modular assembling process of an in-silico protocell.
    Biosystems 2017 Dec 13;165:8-21. Epub 2017 Dec 13.
    Technische Hochschule Bingen, University of applied sciences, 55411 Bingen am Rhein, Germany. Electronic address:
    The bottom-up approach of synthetic biology is driven by the need for a deepened understanding of the interaction of functional modules in living or artificial systems. The hope is that the gained knowledge will help to optimize existing systems, or, as one long-term goal of synthetic biology, to build up artificial cell-like entities from single building blocks. This article focuses on a system theoretic approach to synthetic biology, and in particular on the construction of a protocell model by the modular assembling process. Read More

    Cyclic Concatenated Genetic Encoder: A mathematical proposal for biological inferences.
    Biosystems 2018 Jan 9;163:47-58. Epub 2017 Dec 9.
    Department of Electrical Engineering, Universidade Estadual de Campinas, Campinas, SP, Brazil.
    The organization of the genetic information and its ability to be conserved and translated to proteins with low error rates have been the subject of study by scientists from different disciplines. Recently, it has been proposed that living organisms display an intra-cellular transmission system of genetic information, similar to a model of digital communication system, in which there is the ability to detect and correct errors. In this work, the concept of Concatenated Genetic Encoder is introduced and applied to the analysis of protein sequences as a tool for exploring evolutionary relationships. Read More

    Prediction of replication sites in Saccharomyces cerevisiae genome using DNA segment properties: Multi-view ensemble learning (MEL) approach.
    Biosystems 2018 Jan 9;163:59-69. Epub 2017 Dec 9.
    School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India. Electronic address:
    Autonomous replication sequences (ARS) are essential for the replication of Saccharomyces cerevisiae genome. The content and context of ARS sites are distinct from other segments of the genome and these factors influence the conformation and thermodynamic profile of DNA that favor binding of the origin recognition complex proteins. Identification of ARS sites in the genome is a challenging task because of their organizational complexity and degeneracy present across the intergenic regions. Read More

    Dynamic analysis on the calcium oscillation model considering the influences of mitochondria.
    Biosystems 2018 Jan 8;163:36-46. Epub 2017 Dec 8.
    Department of Mechanics, School of Mechanical Engineering, Tianjin University, Tianjin 300354, PR China; Tianjin Key Laboratory of Nonlinear Dynamics and Chaos Control, Tianjin 300354, PR China.
    Based on the model considering the influences of mitochondria, a further theoretical study on the dynamic behaviors of calcium signals is made. First of all, the reason for the generation and disappearance of calcium oscillations is verified in theory. Second, an analysis on the model considering the influences of mitochondria and the model neglecting the influences of mitochondria is carried out. Read More

    Evolutionary epistemology: Reviewing and reviving with new data the research programme for distributed biological intelligence.
    Biosystems 2018 Jan 2;163:23-35. Epub 2017 Dec 2.
    Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, United Kingdom. Electronic address:
    Numerous studies in microbiology, eukaryotic cell biology, plant biology, biomimetics, synthetic biology, and philosophy of science appear to support the principles of the epistemological theory inspired by evolution, also known as "Evolutionary Epistemology", or EE. However, that none of the studies acknowledged EE suggests that its principles have not been formulated with sufficient clarity and depth to resonate with the interests of the empirical research community. In this paper I review evidence in favor of EE, and also reformulate EE principles to better inform future research. Read More

    Towards measuring the semantic capacity of a physical medium demonstrated with elementary cellular automata.
    Biosystems 2018 Feb 22;164:177-185. Epub 2017 Nov 22.
    Bio Systems Analysis Group, Institute for Computer Science, Friedrich Schiller University Jena, 07745 Jena, Germany. Electronic address:
    The organic code concept and its operationalization by molecular codes have been introduced to study the semiotic nature of living systems. This contribution develops further the idea that the semantic capacity of a physical medium can be measured by assessing its ability to implement a code as a contingent mapping. For demonstration and evaluation, the approach is applied to a formal medium: elementary cellular automata (ECA). Read More

    Evidence for the implication of the histone code in building the genome structure.
    Biosystems 2018 Feb 20;164:49-59. Epub 2017 Nov 20.
    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 2018 Jan 9;163:11-22. 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 2018 Feb 6;164:39-48. 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 2018 Feb 7;164:128-137. Epub 2017 Nov 7.
    Parmenides Center for the Conceptual Foundations of Science, Pullach, Munich, Germany, 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 2018 Jan 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 2018 Feb 4;164:138-146. 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 2018 Feb 28;164:199-216. 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 Dec 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

    Network induction for epidemic profiles with a novel representation.
    Biosystems 2017 Dec 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 Dec 1;162:135-146. Epub 2017 Nov 1.
    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 Dec 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 2018 Feb 17;164:94-101. 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 augmented personalized medicine.
    Biosystems 2017 Dec 16;162:177-204. Epub 2017 Oct 16.
    Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; Dahlem Centre for Genome Research and Medical Systems Biology, Berlin, Germany; JSRC, 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 Dec 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 2018 Feb 12;164:217-225. 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 2018 Feb 10;164:16-25. 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 2018 Feb 6;164:1-10. 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 2018 Feb 7;164:112-120. 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 2018 Feb 4;164:26-38. 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 Dec 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 Dec 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 Dec 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 Dec 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

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