Biosystems

Article	Citations
Optimizing ruminant nutrition: Insights from a comprehensive analysis of silage composition and in vitro gas production dynamics using nonlinear models	42
Morphological forms arising from the evolutionary process are topologies	38
VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology	36
Editorial Board	35
Effects of predator modulation and vector preference on pathogen transmission in plant populations	31
Nuclear quantum effects explain chemiosmosis: The power of the proton	29
The major evolutionary transitions and codes of life	28
Cartography of the multiple formal systems of molecular autopoiesis: from the biology of cognition and enaction to anticipation and active inference	27
A survey of the methodological process of modeling, inference, and evaluation of gene regulatory networks using scRNA-Seq data	24
Theories of the origin of the genetic code: Strong corroboration for the coevolution theory	23
Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game	22
Book Review	22
Developmental noise, entropy, and biological system condition	21
Hypothesis of macroscopic quantum state in biological systems and discussion on the possibility of its experimental verification	21
Temporal regulation of gene expression and pathways in chemotherapy-induced senescence in HeLa cervical cancer cell line	21
Evaluating the statistical similarity of neural network activity and connectivity via eigenvector angles	20
Filter feature selection based Boolean Modelling for Genetic Network Inference	19
The promoting effect of adaptive persistence aspiration on the cooperation based on the consideration of payoff and environment in prisoner's dilemma game	18
Cholesterol-ester prevents lipoprotein core from solidifying: Molecular dynamics simulation	18
The sensual cell: Feeling and affect in unicellular species	18
Efim Liberman toward the comprehension of the phenomenon of life	17
Visualizing genomic data: The mixing perspective	17
The genetic code and its p-adic ultrametric modeling	17
Reversible and irreversible mitochondrial swelling: Effects of variable mitochondrial activity	17
Binary oppositions, algebraic holography and stochastic rules in genetic informatics	17

Characterisation of the fig-fig wasp holobiont	17
The mitochondrial challenge: Disorders and prevention strategies	16
The evolution and development of consciousness: the subject-object emergence hypothesis	16
The metabolic control theory: Its development and its application to mitochondrial oxidative phosphorylation	16
scSAGRN: Inferring gene regulatory networks from single-cell multi-omics using spatial association	15
The grid-cell normative model: Unifying ‘principles’	15
Whole-cell metabolic control analysis	15
A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information	15
Three levels of information processing in the brain	15
The time of appearance of the genetic code	15
The evolutionary arch of bioenergetics from prebiotic mechanisms to the emergence of a cellular respiratory chain	14
An exploration of ecoacoustics and its applications in conservation ecology	14
A possible origin of life in nonpolar environments	14
Spatial organisation plasticity reduces disease infection risk in rock–paper–scissors models	14
Gaidai reliability method for high-dimensional spatio-temporal biosystems	14
The molecular memory code and synaptic plasticity: A synthesis	14
Editorial Board	13
Editorial Board	13
Editorial Board	13
On the emergence of eukaryotes and other enigmas	13
The pseudoentropy of allele frequency trajectories, the persistence of variation, and the effective population size	13
Causal and non-causal explanations in code biology	12
Microbial mutualism promoting the coexistence of competing species: Double-layer model for two competing hosts and one microbial species	12
Identification of common factors among fibrosarcoma, rhabdomyosarcoma, and osteosarcoma by network analysis	12
Editorial Board	12
The origins of photosynthetic systems: Clues from the phosphorus and sulphur chemical scenarios	12
A mechanistic approach to optimize combination antibiotic therapy	12
Fragile X mental retardation protein modulates translation of proteins with predicted tendencies for liquid-liquid phase separation	12
Gradistics: An underappreciated dimension in evolutionary space	12
Book Review	12
Editorial Board	11
Examining multi-objective deep reinforcement learning frameworks for molecular design	11
The non-canonical nucleotides and prebiotic evolution	11
Editorial: Waves in fertilization, cell division and embryogenesis	11
In search for evolutionary roots of a mindful cognition: A Darwinian view on sustained intentional awareness	11
Unexpected extra exon skipping in the DYSF gene during restoring the reading frame by CRISPR/Cas9	11
Modeling of the entangled states transfer processes in microtubule tryptophan system	11
Impacts of aging on circadian rhythm and related sleep disorders	11
Human face as a biosocial marker in human evolution	10
Mutations, sex, and genetic diversity: New arguments for partially directed evolution	10
Why the power of diversity does not always produce better groups and societies	10
Constructal thermodynamics and its semantic ontology in autopoietic, digital, and computational architectural and urban space open systems	10
The role of self-maintaining resilient reaction networks in the origin and evolution of life	10
Regulative development as a model for origin of life and artificial life studies	10
Using steady-state formula to estimate time-dependent parameters of stochastic gene transcription models	10
2-adic morphogenesis as a metaphorical model of biological growth	10
50 years of Metabolic Control Analysis: Its past and current influence in the biological sciences	9
Morphology changes induced by intercellular gap junction blocking: A reaction-diffusion mechanism	9
Logical modelling of myelofibrotic microenvironment predicts dysregulated progenitor stem cell crosstalk	9
Rational decision making in biological systems	9

Ecological drivers for the absence of task shifting in termite-tunneling activity: A simulation study	9
CHTW(R)-system in Ca2+ transport modelling	9
Avian influenza A H5N1 hemagglutinin protein models have distinct structural patterns re-occurring across the 1959–2023 strains	9
The Role of Pure Mathematics in Resolving Complex Biological Problems: Applications to F1-ATPase, Achievements, and Future Directions	9
Editorial Board	9
Editorial Board	9
Corrigendum to “An efficient approach for identifying important biomarkers for biomedical diagnosis” [Biosystems 237 (2024) 105163]	9
Human cognitive limitations and emotions: The emergence of social complexity	9
Dissipative scaling of development and aging in multicellular organisms	9
Editorial Board	9
Molecular mechanisms of encoding and decoding information in cell computing	9
Dynamic modelling and tristability analysis of misfolded α-synuclein degraded via autophagy in Parkinson's disease	9
The indispensable role of time in autonomous development	9
An irreversible thermodynamic model of prebiological dissipative molecular structures inside vacuoles at the surface of the Archean Ocean	8
Ribonucleic acid genome mutations induced by the Casimir effect	8
Generation of random sequences using DNA cryptography for OTP encryption	8
Is there a bias in the codon frequency corresponding to homo-repeats found in human proteins?	8
Neural networks from biological to artificial and vice versa	8
Data-driven dynamical modelling of a pathogen-infected plant gene regulatory network: A comparative analysis	8
Algebraic harmony and probabilities in genomes. Long-range coherence in quantum code biology	8
A simple and fast ANN-based method of studying slow-wave sleep microstructure in freely moving rats	8
Paleo-phyllotaxis: Fucales, bryophytes, lycophytes and monilophytes	8
Quantum aspects of the brain-mind relationship: A hypothesis with supporting evidence	8
Dive into machine learning algorithms for influenza virus host prediction with hemagglutinin sequences	8
A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem	8
Effect of monochromatic light on the behavior of the ctenophore Mnemiopsis leidyi (A. Agassiz, 1865)	8
Entropy and the arrow of time in population dynamics	8
From code to archetype: Toward a unified theory of biological, neural, and artificial artifacts	8
Modeling autopoiesis and cognition with reaction networks	7
Order stability via Fröhlich condensation in bio, eco, and social systems: The quantum-like approach	7
Standard Genetic Code vs. Supersymmetry Genetic Code – Alphabetical table vs. physicochemical table	7
Embodied essentialism in the reconstruction of the animal sign in robot animal design	7
On the minimal elements of the genetic code and their semiotic functions (degeneracy, complementarity, wobbling)	7
Editorial Board	7
Karyotype coding: The creation and maintenance of system information for complexity and biodiversity	7
Entering the labyrinth: A hypothesis about the emergence of metabolism from protobiotic routes	7
Use of directed quasi-metric distances for quantifying the information of gene families	7
Reliability and energy function of an oscillator and map neuron	7
The theoretical foundations of enaction: Precariousness	7
Editorial Board	7
Aggregate Boid behavior to aid in artificial autopoietic organization	7
Cosmos, mind, matter: Is mind in spacetime?	7
Temporal cohesion as a candidate for negentropy in biological thermodynamics	7
Towards the Big History of information. Approaching the origins of information behaviour	7
Machine-learning-based structural analysis of interactions between antibodies and antigens	7
Mechanism and biological significance of erythrocyte homoaggregation (rouleaux formation): temperature-dependent entropic liberation of water from cells and macromolecules	7
Spiking neural networks produce informational closure by stimulus avoidance	7
Generation of genetic codes with 2-adic codon algebra and adaptive dynamics	7
Childhood in social learning models with changing environments: Implications for human evolution	7
A quantum-like information processing model with memory noise for question order effect	6
Stretching tension effects in permeability transition pores of inner mitochondrial membrane	6
Cell jamming-to-unjamming transitions and vice versa in development: Physical aspects	6
Prediction of prokaryotic and eukaryotic promoters based on information-theoretic features	6
Modelling energy-harvesting processes in primitive cells: Proton transport across bilayers driven by the oxidation of sulfite	6
Understanding nature’s selection of genetic languages	6
Identification of Ca	6
Psychological origin of quantum logic: An orthomodular lattice derived from natural-born intelligence without Hilbert space	6
Information–energy equivalence and the emergence of self-replicating biological systems	6
The origins of the cell membrane, the progenote, and the universal ancestor (LUCA)	6
Impact of social reward on the evolution of cooperation in voluntary prisoner’s dilemma	6
Mitotic waves in an import-diffusion model with multiple nuclei in a shared cytoplasm	6
Evolution and maintenance of phenotypic plasticity	6
The problem of evolutionary directionality 50 years following the works of Sergei Meyen	6
Evolution of cooperation in multigame with environmental space and delay	6
Evolutionary stability of developmental commitment	6
A multi-cell model for the C4 photosynthetic pathway in developing wheat grains based upon tissue-specific transcriptome data	6
Autopoiesis: Foundations of life, cognition, and emergence of self/other	6
Mathematical model of coffee tree’s rust control using snails as biological agents	6
Electrical frequency discrimination by fungi Pleurotus ostreatus	6
Causal intuition in the indefinite world: Meta-analysis and simulations	6
Effect of the electromagnetic induction in the electrical activity of the Kazantsev model of inferior Olive Neuron model	6
Construction of amino acids reduced alphabets from molecular descriptors for interpretation of N-carbamylase, luciferase and PI3K mutations	5
Is meaning commensurable in scientific theories? From arbitrariness to non-nomological relations in meaning-making	5
A ball microscope for viewing the entire surface of amphibian embryos	5
Fundamental principles of biology as pure natural science and their applications in physiology and pathology	5
Benchmark for quantitative characterization of circadian clock cycles	5
Estimation of discrepancy of color qualia using Kullback-Leibler divergence	5
Thermal diodes, transistors and logic: Review of unconventional computing methods	5
Combination of survival movement strategies in cyclic game systems during an epidemic	5
Synchronization Studies of Hindmarsh–Rose Neuron Networks: Unraveling the Influence of connection induced memristive synapse	5

Origin of the temporal stability control of living system nonequilibrium	5
The theory of oxygen hemoglobin association	5
Collective computational intelligence in biology – Emergence of memory in somatic tissues	5
Amino acid activation analysis of primitive aminoacyl-tRNA synthetases encoded by both strands of a single gene using the malachite green assay	5
Editorial Board	5
Structural analyzes suggest that MiSSP13 and MiSSP16.5 may act as proteases inhibitors during ectomycorrhiza establishment in Laccaria bicolor	5
A new method: Characterize and quantify biofilm wrinkles by UNet and Sholl Analysis	5
The chromolinker hypothesis: Are eukaryotic genomes also circular?	5
An efficient approach for identifying important biomarkers for biomedical diagnosis	5
The Molecular Basis of Differentiation Wave Activity in Embryogenesis	5
Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach	5
Robustness and evolvability: Revisited, redefined and applied	5
Corrigendum to “Role of calcium oscillations in sperm physiology” [BioSystems 209 (2021) 104524]	5
On the infodynamics of ramifications in constructal design	5
The cell as a semiotic system that realizes closure to efficient causation: The semiotic (M, R) system	5
Quantum concepts in Psychology: Exploring the interplay of physics and the human psyche	5
Multi-scale modeling of hippo signaling identifies homeostatic control by YAP-LATS negative feedback	5
Bioinformatics and meta-analysis of expression data to investigate transcriptomic response of wheat root to abiotic stresses	5
Fractional nutrient uptake model of plant roots	5
A computational design of a programmable biological processor	5
Editorial Board	5
Evolutionary origin of B family DNA-dependent DNA polymerases from retrotranscriptases	5
miRNAFinder: A comprehensive web resource for plant Pre-microRNA classification	4
Collective excitations at non-equilibrium phase transition in metabolically active red blood cells	4
Accurate phenotypic self-replication as a necessary cause for biological evolution.	4
On electrical gates on fungal colony	4
Life, its definition, origin, evolution, and four-dimensional hierarchical structure	4
Modeling of will and consciousness based on the human language: Interpretation of qualia and psychological consciousness	4
Codes across (life)sciences	4
Perfection is the enemy of evolution	4
Formal autopoiesis: Solutions of the classical and extended functional closure equations	4
Cosmos MIND and matter: Is mind in spacetime?	4
Is Darwinian selection a retrograde driving force of evolution?	4
The effect of avian eggshell membrane structure on microbial penetration: A simulation study	4
Toward understanding the emergence of life: A dual function of the system of nucleotides in the metabolically closed autopoietic organization	4
Neurons as hierarchies of quantum reference frames	4
Coacervates meet the RNP-world: liquid-liquid phase separation and the emergence of biological compartmentalization	4
Disproportional fraction of inactive components leads to the variation in metabolic scaling	4
A multi-modal algorithm based on an NSGA-II scheme for phylogenetic tree inference	4
Using neurons to maintain autonomy: Learning from C. elegans	4
Corrigendum to “The concepts of code biology” [Biosyst. 248 (2025) 105400 1–6]	4
Code biology and aesthetics	4
A heuristic perspective on non-variational free energy modulation at the sleep-like edge	4
Biological thermodynamics: Ervin Bauer and the unification of life sciences and physics	4
The polyphyletic origins of glycyl-tRNA synthetase and lysyl-tRNA synthetase and their implications	4
A control measure for epidemic spread based on the susceptible–infectious–susceptible (SIS) model	4
Impact of transposable elements on the evolution of complex living systems and their epigenetic control	4
Toward an ethics of autopoietic technology: Stress, care, and intelligence	4
The repertoire of candidate archaeal noncoding RNAs and their association with temperature adaptation	4
Predator–prey population dynamics may induce the evolutionary dynamics of behavioral unpredictability	4
Social satisficing: Multi-agent reinforcement learning with satisficing agents	4
Identification of multivariable Boolean patterns in microbiome and microbial gene composition data	4
Towards a Possible Definition of Consciousness	4
Statistical algorithms for the analysis of deleterious genetic mutations	4
Overview of the third special issue in code biology	4
Two theories of action - Edelman's Neuronal group Selection and the Poetics of Paul Valéry	4
Corrigendum to “Paleo-phyllotaxis: Fucales, bryophytes, lycophytes and monilophytes” [BioSystems 255 (2025) 105541]	4
The phylogenetic distribution of the cell division system would not imply a cellular LUCA but a progenotic LUCA	4
PTEN expression can be used as a switch between senescence and apoptosis in breast cancer cells according to a logical model of the G2/M checkpoint	4
Memory induced-mechanism of noise attenuator of myosin V molecular motors	4
Gene regulatory networks with binary weights	4
The regulatory network that controls lymphopoiesis	4
Modeling the C. elegans germline stem cell genetic network using automated reasoning	4
Major transitions in the physiological machinery of cognition	3
A global solution to a hyperbolic problem for blood flow modelling	3
Elucidation of productive alanine recognition mechanism by Escherichia coli alanyl-tRNA synthetase	3
A novel approach to encode melodies in DNA	3
COVID-19 spatio-temporal forecast in England	3
Circular mixed sets	3
Modelling the fitness landscapes of a SCRaMbLEd yeast genome	3
Memory retrieval dynamics and storage capacity of a modular network model of association cortex with featural decomposition	3
Stages and causes of the evolution of language and consciousness: A theoretical reconstruction	3
Decoding viruses: An alternative perspective on their history, origins and role in nature	3
Oncogenetic pedigrees: Relation between design and ability to predict mutation	3
The fundamental theorem of natural selection in optimization and games	3
From autopoiesis to self-optimization: Toward an enactive model of biological regulation	3
Metabolic control analysis as a strategy to identify therapeutic targets, the case of cancer glycolysis	3
Fractal calculus in tumor growth simulations: The proof is in the pudding	3
Learning and memory in soldier crabs: Evidence from escape task trials	3
Quantum contextuality and cognitive contextuality: The significance of violations of Bell-type inequalities	3
Rule-based modelling of biological systems using regulated rewriting	3
Computation by inverse causality: A universal principle to produce symbols for the external reality in living systems	3
Metabolic limits on classical information processing by biological cells	3
Revisiting Carl Jung’s archetype theory a psychobiological approach	3
Minimizing enzyme mass to decompose flux distribution for identifying biologically relevant elementary flux modes	3
A simple neuronal model with intrinsic saturation of the firing frequency	3
Non-monotone cellular automata: Order prevails over chaos	3
Evolution of small and large ribosomal RNAs from accretion of tRNA subelements	3
Fungal skin for robots	3
Quantifying pleiotropy through directed signaling networks: A synchronous Boolean network approach and in-silico pleiotropic scoring	3
Editorial Board	3
Human-driven spreading and evolution of plants during the Holocene epoch: The pioneering works of Valery Taliev	3
Swelling and membrane potential dynamics of glial Müller cells	3
The reversibility of cellular determination: An evolutive pattern of epigenetic plasticity	3
A biochemically-realisable relational model of the self-manufacturing cell	3