Biosystems

Article	Citations
Editorial Board	37
The local-global relationship of nature	35
Construction of a human body model for acupuncture and moxibustion treatment by colored Petri nets	32
Stretching tension effects in permeability transition pores of inner mitochondrial membrane	32
Childhood in social learning models with changing environments: Implications for human evolution	31
Motility disorders and disintegration into separate cells of Trichoplax sp. H2 in the presence of Zn2+ ions and L-cysteine molecules: A systems approach	26
Reconfiguring SETI in the microbial context: Panspermia as a solution to Fermi's paradox	25
Biological computation running on quantum computation	24
Editorial: Petri nets for cellular process modelling	23
Exploring the patterns of evolution: Core thoughts and focus on the saltational model	23
Intrinsic growth rate and evolution of the Premnotrypes Vorax population using fuzzy information	22
Control analysis in the identification of key enzymes driving metabolic adaptations: Towards drug target discovery	22
Fine structure of a partition in the spike glycoprotein encoded in the SARS-CoV-2 genome	21
Editorial Board	20
Hypothesis of macroscopic quantum state in biological systems and discussion on the possibility of its experimental verification	20
Application of CRISPR Cas systems in DNA recorders and writers	20
Information–energy equivalence and the emergence of self-replicating biological systems	19
Editorial Board	19
Modeling the interaction between donor-derived regulatory T cells and effector T cells early after allogeneic hematopoietic stem cell transplantation	19
Thermodynamic for biological development: A hypothesis	18
Hopf bifurcation in the shadow of extinction: Collaborating with epidemic dynamics through lethal mutations and declining ancestor infections	18
The regulatory network that controls lymphopoiesis	18
Effects of predator modulation and vector preference on pathogen transmission in plant populations	16
Combining kinetic orders for efficient S-System modelling of gene regulatory network	15
Editorial: Fundamental principles of biological computation: From molecular computing to evolutionary complexity	15

Spatial waves and temporal oscillations in vertebrate limb development	15
A new mathematical model of folate homeostasis in E. coli highlights the potential importance of the folinic acid futile cycle in cell growth	15
VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology	15
Exploring natural anthraquinones as potential MMP2 inhibitors: A computational study	14
Editorial: Systems bioinformatics for medicine	14
Karyotype as code of codes: An inheritance platform to shape the pattern and scale of evolution	14
Rapid clade divergence and phyletic gradualism in an interacting particle model of sympatric speciation	14
A mathematician’s view of the unreasonable ineffectiveness of mathematics in biology	14
Editorial Board	13
The evolutionary stages of the complexity of biological catalysts mark and clarify the phases of the origin of the genetic code: A model for the origin of the reading frame with codons from proto-mRNA	13
Editorial Board	13
Animal design advantage from the analogy between friction and body heat loss	13
The epoch-making importance of Ervin Bauer's theoretical biology	13
Contrasting philosophical and scientific views in the long history of studying the generation of form in development	12
Loss and fixation of strongly favoured new variants: Understanding and extending Haldane’s result via the Wright–Fisher model	12
Competition for finite resources as coordination mechanism for morphogenesis: An evolutionary algorithm study of digital embryogeny	12
Information encoded in gene-frequency trajectories	12
Editorial Board	12
From Empedocles to Symbiogenetics: Lynn Margulis's revolutionary influence on evolutionary biology	12
Autopoiesis: Foundations of life, cognition, and emergence of self/other	12
Unravelling the nexus: Towards a unified model of development, ageing, and cancer	11
The necessity of hierarchy for living systems	11
Trinucleotide k-circular codes I: Theory	11
The modularity codes	11
The emergence of a fractal structure of formal logic via the spatiotemporal reflexive self-identification	11
Book Review	11
Editorial Board	11
Editorial Board	11
The origins of the cell membrane, the progenote, and the universal ancestor (LUCA)	11
Cartography of the multiple formal systems of molecular autopoiesis: from the biology of cognition and enaction to anticipation and active inference	11
Editorial Board	11
Enhanced effective codon numbers to understand codon usage bias	11
Are we on the cusp of a new paradigm for biology? The illogic of molecular developmental biology versus Janus-faced control of embryogenesis via differentiation waves	10
Discovering ecoacoustic codes in beehives: First evidence and perspectives	10
The biological information flow: From cell theory to a new evolutionary synthesis	10
Natural gradient ascent in evolutionary games	10
RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences	9
Cholesterol plays a decisive role in tetraspanin assemblies during bilayer deformations	9
Perception of color in primates: A conceptual color neurons hypothesis	9
Gene as a dynamical notion: An extensive and integrative vision. Redefining the gene concept, from traditional to genic-interaction, as a new dynamical version	9
Influence analysis of network evolution on Parrondo effect	9
Evaluating the statistical similarity of neural network activity and connectivity via eigenvector angles	9
Spiking neural networks produce informational closure by stimulus avoidance	9
Mathematical model of coffee tree’s rust control using snails as biological agents	9
I-circular codes	9
Toward an ethics of autopoietic technology: Stress, care, and intelligence	9
Light sensitive Belousov–Zhabotinsky medium accommodates multiple logic gates	9
Developmental noise, entropy, and biological system condition	8
Dimerization induces bimodality in protein number distributions	8
Gene regulatory networks with binary weights	8

A multi-cell model for the C4 photosynthetic pathway in developing wheat grains based upon tissue-specific transcriptome data	8
The effect of avian eggshell membrane structure on microbial penetration: A simulation study	8
An integrative machine learning model for the identification of tumor T-cell antigens	8
Serial Endosymbiosis Theory: From biology to astronomy and back to the origin of life	8
Memetic approach to cultural evolution	8
Generation of genetic codes with 2-adic codon algebra and adaptive dynamics	8
Senescence, change, and competition: When the desire to pick one model harms our understanding	8
Dynamics of two feed forward genetic motifs in the presence of molecular noise	8
C-Biomarker.net: A Cytoscape app for the identification of cancer biomarker genes from cores of large biomolecular networks	8
Degradation-driven protein level oscillation in the yeast Saccharomyces cerevisiae	8
Principles of cognitive biology and the concept of biocivilisations	8
Filter feature selection based Boolean Modelling for Genetic Network Inference	8
Temporal regulation of gene expression and pathways in chemotherapy-induced senescence in HeLa cervical cancer cell line	8
On the minimal elements of the genetic code and their semiotic functions (degeneracy, complementarity, wobbling)	8
Social satisficing: Multi-agent reinforcement learning with satisficing agents	8
Morphological forms arising from the evolutionary process are topologies	8
Genome-scale prediction of bacterial promoters	8
Effect of single nucleotide polymorphisms on the structure of long noncoding RNAs and their interaction with RNA binding proteins	8
In enzymatic reactions, the reverse reaction reduces product noise	8
The sensual cell: Feeling and affect in unicellular species	7
Aggregate Boid behavior to aid in artificial autopoietic organization	7
Fertilization and development of Arbacia lixula eggs are affected by osmolality conditions	7
Cell jamming-to-unjamming transitions and vice versa in development: Physical aspects	7
Genetic code, the problem of coding biological cycles, and cyclic Gray codes	7
Causal Modeling and Thermodynamics: Towards a new convergence of the two fields	7
Impact of social reward on the evolution of cooperation in voluntary prisoner’s dilemma	7
Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game	7
Thermodynamic analysis of energy coupling by determination of the Onsager phenomenological coefficients for a 3×3 system of coupled chemical reactions and transport in ATP synthesis and its mechanisti	7
Phase offset determines alpha modulation of gamma phase coherence and hence signal transmission	7
All lockdowns are not equal: Reducing epidemic impact through evolutionary computation	7
Techno-ethical concerns related to genetic sequencing reports	7
Cosmos, mind, matter: Is mind in spacetime?	7
Theories of the origin of the genetic code: Strong corroboration for the coevolution theory	7
The major evolutionary transitions and codes of life	7
Optimizing ruminant nutrition: Insights from a comprehensive analysis of silage composition and in vitro gas production dynamics using nonlinear models	7
Prediction of prokaryotic and eukaryotic promoters based on information-theoretic features	7
Intelligence: Natural, artificial, or what?	7
Analytical solution of Nye–Tinker–Barber model by Laplace transform	6
Size matters in metabolic scaling: Critical role of the thermodynamic efficiency of ATP synthesis and its dependence on mitochondrial 6
Visualizing genomic data: The mixing perspective	6
Extracellular interplay of amyloid fibrils and neural cells	6
The time of appearance of the genetic code	6
Mitotic waves in an import-diffusion model with multiple nuclei in a shared cytoplasm	6
Editorial Board	6
Combination of survival movement strategies in cyclic game systems during an epidemic	6
Modelling ethnogenesis	6
Collective dynamics of a coupled Hindmarsh–Rose neurons with locally active memristor	6
How nanoparticles can induce dimerization and aggregation of cells in blood or lymph	6
Artificial immune system features added to breast cancer clinical data for machine learning (ML) applications	6
Exploring the effects of high curvature section distribution and density in termite tunnels on food transport efficiency: A simulation study	6
Editorial Board	6
The cell as a realization of the (M, R) system	6
The osseous fusion patterns in an equine limb: A theoretical deconstruction of the evolutionary mechanisms	6
Single-cell classification, analysis, and its application using deep learning techniques	6
A multi-scale agent-based model for avascular tumour growth	6
Editorial Board	6
Structure and behavior in Boolean monotonic model pools	6
Reversible and irreversible mitochondrial swelling: Effects of variable mitochondrial activity	6
Editorial: Computational approaches in cancer modelling	6
Editorial: 2020 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB 2020)	6
From reactions to reflection: A recursive framework for the evolution of cognition and complexity	5
Temperature dependence of IR exciton emission spectra in Müller cell intermediate filaments	5
Genes on the circular code alphabet	5
Effect of the electromagnetic induction in the electrical activity of the Kazantsev model of inferior Olive Neuron model	5
Natural intelligence and the ‘economy’ of social emotions: A connection with AI sentiment analysis	5
An exploration of ecoacoustics and its applications in conservation ecology	5
On paradoxes between optimal growth, metabolic control analysis, and flux balance analysis	5
A memory access gate controlled by dynamic contexts	5
Understanding cancer from a biophysical, developmental and systems biology perspective using the landscapes-attractor model	5
The chromolinker hypothesis: Are eukaryotic genomes also circular?	5
An algorithm for the transformation of the Petri net models of biological signaling networks into influence graphs	5
How do soldier crabs behave when seeing vibrating robots?	5
Editorial Board	5
Autopoiesis of the artificial: from systems to cognition	5
The hiatus between organism and machine evolution: Contrasting mixed microbial communities with robots	5
Computing within bacteria: Programming of bacterial behavior by means of a plasmid encoding a perceptron neural network	5
A degenerative process underlying hierarchic transitions in evolution	5
Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples	5
Binary oppositions, algebraic holography and stochastic rules in genetic informatics	5
Editorial Board	5

Understanding nature’s selection of genetic languages	5
A computational design of a programmable biological processor	5
Editorial Board	5
Editorial Board	5
New algorithm for the analysis of nucleotide and amino acid evolutionary relationships based on Klein four-group	5
Editorial Board	5
Editorial Board	5
Efim Liberman toward the comprehension of the phenomenon of life	5
Evolution of cooperation in multigame with environmental space and delay	5
“Assembly Theory” in life-origin models: A critical review	5
A first perturbome of Pseudomonas aeruginosa: Identification of core genes related to multiple perturbations by a machine learning approach	4
Novel amino acid distance matrices based on conductance measure	4
SetQuence & SetOmic: Deep set transformers for whole genome and exome tumour analysis	4
From chaos to clock in recurrent neural net. Case study	4
Quantum Brain Dynamics and Virtual Reality	4
Super-rational aspiration induced strategy updating helps resolve the tragedy of the commons in a cooperation system with exit rights	4
Whole-cell metabolic control analysis	4
Identification of Ca	4
A quantum-like information processing model with memory noise for question order effect	4
A dynamical system for the IGF1-AKT signaling pathway in skeletal muscle adaptation	4
Quantum propensities in the brain cortex and free will	4
Viruses, immunity and evolution	4
Light induced spiking of proteinoids	4
Causal intuition in the indefinite world: Meta-analysis and simulations	4
Evolution and maintenance of phenotypic plasticity	4
Is distance from equilibrium a good indicator for a reaction’s flux control?	4
Evolution, physics, and education	4
A critical role of the periplasm in copper homeostasis in Gram-negative bacteria	4
Endless forms of endless formation — The morphogenesis of organisms and scientific objects	4
Evolutionary stability of developmental commitment	4
Primal awareness, evolutionary restriction, life and the origin of quantum mechanics	4
Modeling the origin, evolution, and functioning of the genetic code	4
Adversarial deep evolutionary learning for drug design	4
The grid-cell normative model: Unifying ‘principles’	4
Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum	4
Consequences of asymmetric mutational pressure for the dynamic of linear B-cell epitopes repertoire of influenza a virus neuraminidase rearrangement	4
Relational model of the standard genetic code	4
Intrinsic structural disorder on proteins is involved in the interactome evolution	4
Book Review	4
AI in predicting COPD in the Canadian population	4
A model integrating multiple processes of synchronization and coherence for information instantiation within a cortical area	4
Comparing the complexity of written and molecular symbolic systems	4
A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information	4