Biosystems

Article	Citations
Optimizing ruminant nutrition: Insights from a comprehensive analysis of silage composition and in vitro gas production dynamics using nonlinear models	41
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	33
Effects of predator modulation and vector preference on pathogen transmission in plant populations	29
Temporal regulation of gene expression and pathways in chemotherapy-induced senescence in HeLa cervical cancer cell line	28
A survey of the methodological process of modeling, inference, and evaluation of gene regulatory networks using scRNA-Seq data	28
Nuclear quantum effects explain chemiosmosis: The power of the proton	25
The major evolutionary transitions and codes of life	23
Book Review	23
Cartography of the multiple formal systems of molecular autopoiesis: from the biology of cognition and enaction to anticipation and active inference	21
Evaluating the statistical similarity of neural network activity and connectivity via eigenvector angles	21
Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game	21
Hypothesis of macroscopic quantum state in biological systems and discussion on the possibility of its experimental verification	21
Filter feature selection based Boolean Modelling for Genetic Network Inference	20
Reconfiguring SETI in the microbial context: Panspermia as a solution to Fermi's paradox	19
Developmental noise, entropy, and biological system condition	19
Cholesterol-ester prevents lipoprotein core from solidifying: Molecular dynamics simulation	18
Theories of the origin of the genetic code: Strong corroboration for the coevolution theory	18
The sensual cell: Feeling and affect in unicellular species	18
Efim Liberman toward the comprehension of the phenomenon of life	17
The genetic code and its p-adic ultrametric modeling	17
The promoting effect of adaptive persistence aspiration on the cooperation based on the consideration of payoff and environment in prisoner's dilemma game	17
Binary oppositions, algebraic holography and stochastic rules in genetic informatics	16
Characterisation of the fig-fig wasp holobiont	16

Visualizing genomic data: The mixing perspective	16
The evolutionary arch of bioenergetics from prebiotic mechanisms to the emergence of a cellular respiratory chain	16
Reversible and irreversible mitochondrial swelling: Effects of variable mitochondrial activity	16
The mitochondrial challenge: Disorders and prevention strategies	15
The grid-cell normative model: Unifying ‘principles’	15
The evolution and development of consciousness: the subject-object emergence hypothesis	15
A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information	15
The metabolic control theory: Its development and its application to mitochondrial oxidative phosphorylation	15
The time of appearance of the genetic code	15
Three levels of information processing in the brain	14
A possible origin of life in nonpolar environments	14
Gaidai reliability method for high-dimensional spatio-temporal biosystems	14
Editorial Board	13
Whole-cell metabolic control analysis	13
In search for evolutionary roots of a mindful cognition: A Darwinian view on sustained intentional awareness	13
The molecular memory code and synaptic plasticity: A synthesis	13
An exploration of ecoacoustics and its applications in conservation ecology	13
scSAGRN: Inferring gene regulatory networks from single-cell multi-omics using spatial association	13
Spatial organisation plasticity reduces disease infection risk in rock–paper–scissors models	12
Editorial Board	12
Causal and non-causal explanations in code biology	12
On the emergence of eukaryotes and other enigmas	12
Editorial Board	12
Microbial mutualism promoting the coexistence of competing species: Double-layer model for two competing hosts and one microbial species	12
The pseudoentropy of allele frequency trajectories, the persistence of variation, and the effective population size	12
Editorial Board	12
Fragile X mental retardation protein modulates translation of proteins with predicted tendencies for liquid-liquid phase separation	12
The origins of photosynthetic systems: Clues from the phosphorus and sulphur chemical scenarios	12
Examining multi-objective deep reinforcement learning frameworks for molecular design	11
Life and living beings under the perspective of organic macrocodes	11
Gradistics: An underappreciated dimension in evolutionary space	11
Impacts of aging on circadian rhythm and related sleep disorders	11
Modeling of the entangled states transfer processes in microtubule tryptophan system	11
Identification of common factors among fibrosarcoma, rhabdomyosarcoma, and osteosarcoma by network analysis	11
Editorial: Waves in fertilization, cell division and embryogenesis	11
A mechanistic approach to optimize combination antibiotic therapy	11
Book Review	11
The non-canonical nucleotides and prebiotic evolution	10
Regulative development as a model for origin of life and artificial life studies	10
Editorial Board	10
Unexpected extra exon skipping in the DYSF gene during restoring the reading frame by CRISPR/Cas9	10
Using steady-state formula to estimate time-dependent parameters of stochastic gene transcription models	10
Why the power of diversity does not always produce better groups and societies	9
Morphology changes induced by intercellular gap junction blocking: A reaction-diffusion mechanism	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
Dive into machine learning algorithms for influenza virus host prediction with hemagglutinin sequences	9
Editorial Board	9
Mutations, sex, and genetic diversity: New arguments for partially directed evolution	9

Human face as a biosocial marker in human evolution	9
2-adic morphogenesis as a metaphorical model of biological growth	9
Rational decision making in biological systems	9
Ecological drivers for the absence of task shifting in termite-tunneling activity: A simulation study	9
Logical modelling of myelofibrotic microenvironment predicts dysregulated progenitor stem cell crosstalk	9
Dissipative scaling of development and aging in multicellular organisms	9
Constructal thermodynamics and its semantic ontology in autopoietic, digital, and computational architectural and urban space open systems	9
The role of self-maintaining resilient reaction networks in the origin and evolution of life	9
Editorial Board	9
Avian influenza A H5N1 hemagglutinin protein models have distinct structural patterns re-occurring across the 1959–2023 strains	9
Corrigendum to “An efficient approach for identifying important biomarkers for biomedical diagnosis” [Biosystems 237 (2024) 105163]	9
Generation of random sequences using DNA cryptography for OTP encryption	8
Effect of monochromatic light on the behavior of the ctenophore Mnemiopsis leidyi (A. Agassiz, 1865)	8
The indispensable role of time in autonomous development	8
CHTW(R)-system in Ca2+ transport modelling	8
Order stability via Fröhlich condensation in bio, eco, and social systems: The quantum-like approach	8
Algebraic harmony and probabilities in genomes. Long-range coherence in quantum code biology	8
A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem	8
Neural networks from biological to artificial and vice versa	8
Is there a bias in the codon frequency corresponding to homo-repeats found in human proteins?	8
50 years of Metabolic Control Analysis: Its past and current influence in the biological sciences	8
Quantum aspects of the brain-mind relationship: A hypothesis with supporting evidence	8
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
A simple and fast ANN-based method of studying slow-wave sleep microstructure in freely moving rats	8
Human cognitive limitations and emotions: The emergence of social complexity	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
Data-driven dynamical modelling of a pathogen-infected plant gene regulatory network: A comparative analysis	8
Editorial Board	7
Aggregate Boid behavior to aid in artificial autopoietic organization	7
A multi-cell model for the C4 photosynthetic pathway in developing wheat grains based upon tissue-specific transcriptome data	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
Machine-learning-based structural analysis of interactions between antibodies and antigens	7
Standard Genetic Code vs. Supersymmetry Genetic Code – Alphabetical table vs. physicochemical table	7
Spiking neural networks produce informational closure by stimulus avoidance	7
Editorial Board	7
Cell jamming-to-unjamming transitions and vice versa in development: Physical aspects	7
The theoretical foundations of enaction: Precariousness	7
Embodied essentialism in the reconstruction of the animal sign in robot animal design	7
Reliability and energy function of an oscillator and map neuron	7
Karyotype coding: The creation and maintenance of system information for complexity and biodiversity	7
On the minimal elements of the genetic code and their semiotic functions (degeneracy, complementarity, wobbling)	7
Cosmos, mind, matter: Is mind in spacetime?	7
Mechanism and biological significance of erythrocyte homoaggregation (rouleaux formation): temperature-dependent entropic liberation of water from cells and macromolecules	7
Towards the Big History of information. Approaching the origins of information behaviour	7
Modeling autopoiesis and cognition with reaction networks	7
Temporal cohesion as a candidate for negentropy in biological thermodynamics	7
Impact of social reward on the evolution of cooperation in voluntary prisoner’s dilemma	6
The origins of the cell membrane, the progenote, and the universal ancestor (LUCA)	6
Childhood in social learning models with changing environments: Implications for human evolution	6
Combination of survival movement strategies in cyclic game systems during an epidemic	6
Causal intuition in the indefinite world: Meta-analysis and simulations	6
Electrical frequency discrimination by fungi Pleurotus ostreatus	6
Evolutionary stability of developmental commitment	6
Mathematical model of coffee tree’s rust control using snails as biological agents	6
Generation of genetic codes with 2-adic codon algebra and adaptive dynamics	6
Mitotic waves in an import-diffusion model with multiple nuclei in a shared cytoplasm	6
Prediction of prokaryotic and eukaryotic promoters based on information-theoretic features	6
Evolution and maintenance of phenotypic plasticity	6
A computational design of a programmable biological processor	6
The chromolinker hypothesis: Are eukaryotic genomes also circular?	6
Evolution of cooperation in multigame with environmental space and delay	6
Autopoiesis: Foundations of life, cognition, and emergence of self/other	6
Stretching tension effects in permeability transition pores of inner mitochondrial membrane	6
Information–energy equivalence and the emergence of self-replicating biological systems	6
An efficient approach for identifying important biomarkers for biomedical diagnosis	6
Understanding nature’s selection of genetic languages	6
Modelling energy-harvesting processes in primitive cells: Proton transport across bilayers driven by the oxidation of sulfite	6
A quantum-like information processing model with memory noise for question order effect	6
A new method: Characterize and quantify biofilm wrinkles by UNet and Sholl Analysis	5
Editorial Board	5
The problem of evolutionary directionality 50 years following the works of Sergei Meyen	5
Living systems are smarter bots: Slime mold semiosis versus AI symbol manipulation	5
Fundamental principles of biology as pure natural science and their applications in physiology and pathology	5
Construction of amino acids reduced alphabets from molecular descriptors for interpretation of N-carbamylase, luciferase and PI3K mutations	5
The cell as a semiotic system that realizes closure to efficient causation: The semiotic (M, R) system	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

Quantum concepts in Psychology: Exploring the interplay of physics and the human psyche	5
Editorial Board	5
The Molecular Basis of Differentiation Wave Activity in Embryogenesis	5
Estimation of discrepancy of color qualia using Kullback-Leibler divergence	5
Fractional nutrient uptake model of plant roots	5
Identification of Ca	5
Robustness and evolvability: Revisited, redefined and applied	5
On the infodynamics of ramifications in constructal design	5
The theory of oxygen hemoglobin association	5
Bioinformatics and meta-analysis of expression data to investigate transcriptomic response of wheat root to abiotic stresses	5
Collective computational intelligence in biology – Emergence of memory in somatic tissues	5
Effects of pest control on a food chain in patchy environment: Species-dependent activity range on multilayer graphs	5
Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach	5
Benchmark for quantitative characterization of circadian clock cycles	5
Thermal diodes, transistors and logic: Review of unconventional computing methods	5
Psychological origin of quantum logic: An orthomodular lattice derived from natural-born intelligence without Hilbert space	5
Multi-scale modeling of hippo signaling identifies homeostatic control by YAP-LATS negative feedback	5
Effect of the electromagnetic induction in the electrical activity of the Kazantsev model of inferior Olive Neuron model	5
Biological thermodynamics: Ervin Bauer and the unification of life sciences and physics	5
Evolutionary origin of B family DNA-dependent DNA polymerases from retrotranscriptases	5
Structural analyzes suggest that MiSSP13 and MiSSP16.5 may act as proteases inhibitors during ectomycorrhiza establishment in Laccaria bicolor	5
Corrigendum to “Role of calcium oscillations in sperm physiology” [BioSystems 209 (2021) 104524]	5
Synchronization Studies of Hindmarsh–Rose Neuron Networks: Unraveling the Influence of connection induced memristive synapse	5
Amino acid activation analysis of primitive aminoacyl-tRNA synthetases encoded by both strands of a single gene using the malachite green assay	5
All lockdowns are not equal: Reducing epidemic impact through evolutionary computation	4
Gene regulatory networks with binary weights	4
Light sensitive Belousov–Zhabotinsky medium accommodates multiple logic gates	4
Identification of multivariable Boolean patterns in microbiome and microbial gene composition data	4
The regulatory network that controls lymphopoiesis	4
A control measure for epidemic spread based on the susceptible–infectious–susceptible (SIS) model	4
Disproportional fraction of inactive components leads to the variation in metabolic scaling	4
Impact of transposable elements on the evolution of complex living systems and their epigenetic control	4
Two theories of action - Edelman's Neuronal group Selection and the Poetics of Paul Valéry	4
Neurons as hierarchies of quantum reference frames	4
The phylogenetic distribution of the cell division system would not imply a cellular LUCA but a progenotic LUCA	4
Origin of the temporal stability control of living system nonequilibrium	4
A heuristic perspective on non-variational free energy modulation at the sleep-like edge	4
Modeling of will and consciousness based on the human language: Interpretation of qualia and psychological consciousness	4
Contrasting philosophical and scientific views in the long history of studying the generation of form in development	4
Genome-scale prediction of bacterial promoters	4
The effect of avian eggshell membrane structure on microbial penetration: A simulation study	4
A multi-modal algorithm based on an NSGA-II scheme for phylogenetic tree inference	4
Book Review	4
miRNAFinder: A comprehensive web resource for plant Pre-microRNA classification	4
On electrical gates on fungal colony	4
Statistical algorithms for the analysis of deleterious genetic mutations	4
The repertoire of candidate archaeal noncoding RNAs and their association with temperature adaptation	4
Life, its definition, origin, evolution, and four-dimensional hierarchical structure	4
Perfection is the enemy of evolution	4
Toward understanding the emergence of life: A dual function of the system of nucleotides in the metabolically closed autopoietic organization	4
Codes across (life)sciences	4
Cosmos MIND and matter: Is mind in spacetime?	4
Predator–prey population dynamics may induce the evolutionary dynamics of behavioral unpredictability	4
Using neurons to maintain autonomy: Learning from C. elegans	4
Editorial Board	4
Social satisficing: Multi-agent reinforcement learning with satisficing agents	4
Toward an ethics of autopoietic technology: Stress, care, and intelligence	4
Accurate phenotypic self-replication as a necessary cause for biological evolution.	4
Modeling the C. elegans germline stem cell genetic network using automated reasoning	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
Towards a Possible Definition of Consciousness	4
Is Darwinian selection a retrograde driving force of evolution?	4
Corrigendum to “The concepts of code biology” [Biosyst. 248 (2025) 105400 1–6]	4
Code biology and aesthetics	4
Formal autopoiesis: Solutions of the classical and extended functional closure equations	4
Collective excitations at non-equilibrium phase transition in metabolically active red blood cells	4
Coacervates meet the RNP-world: liquid-liquid phase separation and the emergence of biological compartmentalization	4
Memory induced-mechanism of noise attenuator of myosin V molecular motors	4
The polyphyletic origins of glycyl-tRNA synthetase and lysyl-tRNA synthetase and their implications	4
Overview of the third special issue in code biology	4
Editorial Board	3
Circular mixed sets	3
Logic gates in nanoscale based on interaction of thiolated DNA with AuNPs and strand displacement	3
Quantum contextuality and cognitive contextuality: The significance of violations of Bell-type inequalities	3
Evolution of small and large ribosomal RNAs from accretion of tRNA subelements	3
A simple neuronal model with intrinsic saturation of the firing frequency	3
Swelling and membrane potential dynamics of glial Müller cells	3
The reversibility of cellular determination: An evolutive pattern of epigenetic plasticity	3
Revisiting Carl Jung’s archetype theory a psychobiological approach	3
Modelling the fitness landscapes of a SCRaMbLEd yeast genome	3
Learning and memory in soldier crabs: Evidence from escape task trials	3
Elucidation of productive alanine recognition mechanism by Escherichia coli alanyl-tRNA synthetase	3
A novel approach to encode melodies in DNA	3
Quantifying pleiotropy through directed signaling networks: A synchronous Boolean network approach and in-silico pleiotropic scoring	3
Oncogenetic pedigrees: Relation between design and ability to predict mutation	3
Decoding viruses: An alternative perspective on their history, origins and role in nature	3
Major transitions in the physiological machinery of cognition	3
A biochemically-realisable relational model of the self-manufacturing cell	3
From autopoiesis to self-optimization: Toward an enactive model of biological regulation	3
COVID-19 spatio-temporal forecast in England	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
Fungal skin for robots	3
Metabolic limits on classical information processing by biological cells	3
Computation by inverse causality: A universal principle to produce symbols for the external reality in living systems	3