Biosystems

Article	Citations
Developmental noise, entropy, and biological system condition	37
Evaluating the statistical similarity of neural network activity and connectivity via eigenvector angles	37
Temporal regulation of gene expression and pathways in chemotherapy-induced senescence in HeLa cervical cancer cell line	35
Optimizing ruminant nutrition: Insights from a comprehensive analysis of silage composition and in vitro gas production dynamics using nonlinear models	33
The major evolutionary transitions and codes of life	32
Morphological forms arising from the evolutionary process are topologies	26
Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game	26
Theories of the origin of the genetic code: Strong corroboration for the coevolution theory	24
Cartography of the multiple formal systems of molecular autopoiesis: from the biology of cognition and enaction to anticipation and active inference	23
Editorial Board	23
Effects of predator modulation and vector preference on pathogen transmission in plant populations	22
Hypothesis of macroscopic quantum state in biological systems and discussion on the possibility of its experimental verification	22
Reconfiguring SETI in the microbial context: Panspermia as a solution to Fermi's paradox	21
Memetic approach to cultural evolution	21
VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology	20
Filter feature selection based Boolean Modelling for Genetic Network Inference	20
The sensual cell: Feeling and affect in unicellular species	20
Nuclear quantum effects explain chemiosmosis: The power of the proton	18
Reversible and irreversible mitochondrial swelling: Effects of variable mitochondrial activity	18
Characterisation of the fig-fig wasp holobiont	16
A possible origin of life in nonpolar environments	16
Gaidai reliability method for high-dimensional spatio-temporal biosystems	16
The genetic code and its p-adic ultrametric modeling	16
Cholesterol-ester prevents lipoprotein core from solidifying: Molecular dynamics simulation	16
The metabolic control theory: Its development and its application to mitochondrial oxidative phosphorylation	15

An exploration of ecoacoustics and its applications in conservation ecology	15
The promoting effect of adaptive persistence aspiration on the cooperation based on the consideration of payoff and environment in prisoner's dilemma game	15
Visualizing genomic data: The mixing perspective	15
The mitochondrial challenge: Disorders and prevention strategies	15
Whole-cell metabolic control analysis	15
The molecular memory code and synaptic plasticity: A synthesis	15
Binary oppositions, algebraic holography and stochastic rules in genetic informatics	14
The time of appearance of the genetic code	14
Editorial: Computational approaches in cancer modelling	14
The evolution and development of consciousness: the subject-object emergence hypothesis	13
Efim Liberman toward the comprehension of the phenomenon of life	13
A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information	13
The grid-cell normative model: Unifying ‘principles’	13
The evolutionary arch of bioenergetics from prebiotic mechanisms to the emergence of a cellular respiratory chain	13
Modeling of the entangled states transfer processes in microtubule tryptophan system	12
Editorial Board	12
Three levels of information processing in the brain	12
Identification of common factors among fibrosarcoma, rhabdomyosarcoma, and osteosarcoma by network analysis	12
Gradistics: An underappreciated dimension in evolutionary space	12
Life and living beings under the perspective of organic macrocodes	12
Editorial Board	12
The origins of photosynthetic systems: Clues from the phosphorus and sulphur chemical scenarios	11
Fragile X mental retardation protein modulates translation of proteins with predicted tendencies for liquid-liquid phase separation	11
Microbial mutualism promoting the coexistence of competing species: Double-layer model for two competing hosts and one microbial species	11
In search for evolutionary roots of a mindful cognition: A Darwinian view on sustained intentional awareness	11
Editorial Board	11
The pseudoentropy of allele frequency trajectories, the persistence of variation, and the effective population size	11
A mechanistic approach to optimize combination antibiotic therapy	11
Impacts of aging on circadian rhythm and related sleep disorders	11
On the emergence of eukaryotes and other enigmas	11
Examining multi-objective deep reinforcement learning frameworks for molecular design	11
Causal and non-causal explanations in code biology	11
Spatial organisation plasticity reduces disease infection risk in rock–paper–scissors models	11
The non-canonical nucleotides and prebiotic evolution	10
Why the power of diversity does not always produce better groups and societies	10
Morphology changes induced by intercellular gap junction blocking: A reaction-diffusion mechanism	10
2-adic morphogenesis as a metaphorical model of biological growth	10
Editorial Board	10
Human face as a biosocial marker in human evolution	10
Editorial: Waves in fertilization, cell division and embryogenesis	10
Unexpected extra exon skipping in the DYSF gene during restoring the reading frame by CRISPR/Cas9	10
Constructal thermodynamics and its semantic ontology in autopoietic, digital, and computational architectural and urban space open systems	9
Regulative development as a model for origin of life and artificial life studies	9
Editorial Board	9
Editorial Board	9
Using steady-state formula to estimate time-dependent parameters of stochastic gene transcription models	9
Mutations, sex, and genetic diversity: New arguments for partially directed evolution	9
Algebraic harmony and probabilities in genomes. Long-range coherence in quantum code biology	9
Effect of monochromatic light on the behavior of the ctenophore Mnemiopsis leidyi (A. Agassiz, 1865)	9
The role of self-maintaining resilient reaction networks in the origin and evolution of life	9

Dissipative scaling of development and aging in multicellular organisms	9
Logical modelling of myelofibrotic microenvironment predicts dysregulated progenitor stem cell crosstalk	9
Molecular mechanisms of encoding and decoding information in cell computing	9
CHTW(R)-system in Ca2+ transport modelling	8
Human cognitive limitations and emotions: The emergence of social complexity	8
Towards the Big History of information. Approaching the origins of information behaviour	8
Is there a bias in the codon frequency corresponding to homo-repeats found in human proteins?	8
Dynamic modelling and tristability analysis of misfolded α-synuclein degraded via autophagy in Parkinson's disease	8
Quantum aspects of the brain-mind relationship: A hypothesis with supporting evidence	8
A simple and fast ANN-based method of studying slow-wave sleep microstructure in freely moving rats	8
Neural networks from biological to artificial and vice versa	8
Generation of random sequences using DNA cryptography for OTP encryption	8
Use of directed quasi-metric distances for quantifying the information of gene families	8
Modeling autopoiesis and cognition with reaction networks	8
Ecological drivers for the absence of task shifting in termite-tunneling activity: A simulation study	8
Rational decision making in biological systems	8
The indispensable role of time in autonomous development	8
Dive into machine learning algorithms for influenza virus host prediction with hemagglutinin sequences	8
Temporal cohesion as a candidate for negentropy in biological thermodynamics	8
Corrigendum to “An efficient approach for identifying important biomarkers for biomedical diagnosis” [Biosystems 237 (2024) 105163]	8
The theoretical foundations of enaction: Precariousness	8
50 years of Metabolic Control Analysis: Its past and current influence in the biological sciences	8
Entropy and the arrow of time in population dynamics	8
Avian influenza A H5N1 hemagglutinin protein models have distinct structural patterns re-occurring across the 1959–2023 strains	8
Identification of subtype specific biomarkers of clear cell renal cell carcinoma using random forest and greedy algorithm	7
Mathematical model of coffee tree’s rust control using snails as biological agents	7
Cell jamming-to-unjamming transitions and vice versa in development: Physical aspects	7
An irreversible thermodynamic model of prebiological dissipative molecular structures inside vacuoles at the surface of the Archean Ocean	7
Data-driven dynamical modelling of a pathogen-infected plant gene regulatory network: A comparative analysis	7
Machine-learning-based structural analysis of interactions between antibodies and antigens	7
Reliability and energy function of an oscillator and map neuron	7
Autopoiesis: Foundations of life, cognition, and emergence of self/other	7
Entering the labyrinth: A hypothesis about the emergence of metabolism from protobiotic routes	7
Embodied essentialism in the reconstruction of the animal sign in robot animal design	7
A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem	7
Standard Genetic Code vs. Supersymmetry Genetic Code – Alphabetical table vs. physicochemical table	7
Karyotype coding: The creation and maintenance of system information for complexity and biodiversity	7
Editorial Board	7
Order stability via Fröhlich condensation in bio, eco, and social systems: The quantum-like approach	7
Ribonucleic acid genome mutations induced by the Casimir effect	7
Editorial Board	6
A multi-cell model for the C4 photosynthetic pathway in developing wheat grains based upon tissue-specific transcriptome data	6
Spiking neural networks produce informational closure by stimulus avoidance	6
Impact of social reward on the evolution of cooperation in voluntary prisoner’s dilemma	6
Generation of genetic codes with 2-adic codon algebra and adaptive dynamics	6
A computational design of a programmable biological processor	6
Mitotic waves in an import-diffusion model with multiple nuclei in a shared cytoplasm	6
The origins of the cell membrane, the progenote, and the universal ancestor (LUCA)	6
Stretching tension effects in permeability transition pores of inner mitochondrial membrane	6
Cosmos, mind, matter: Is mind in spacetime?	6
Information–energy equivalence and the emergence of self-replicating biological systems	6
An efficient approach for identifying important biomarkers for biomedical diagnosis	6
Evolutionary stability of developmental commitment	6
Editorial Board	6
Prediction of prokaryotic and eukaryotic promoters based on information-theoretic features	6
Aggregate Boid behavior to aid in artificial autopoietic organization	6
On the minimal elements of the genetic code and their semiotic functions (degeneracy, complementarity, wobbling)	6
Childhood in social learning models with changing environments: Implications for human evolution	6
Effect of the electromagnetic induction in the electrical activity of the Kazantsev model of inferior Olive Neuron model	6
Combination of survival movement strategies in cyclic game systems during an epidemic	6
Evolution of cooperation in multigame with environmental space and delay	6
The chromolinker hypothesis: Are eukaryotic genomes also circular?	6
The problem of evolutionary directionality 50 years following the works of Sergei Meyen	5
Multi-scale modeling of hippo signaling identifies homeostatic control by YAP-LATS negative feedback	5
Fractional nutrient uptake model of plant roots	5
Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach	5
Understanding nature’s selection of genetic languages	5
Psychological origin of quantum logic: An orthomodular lattice derived from natural-born intelligence without Hilbert space	5
Evolution and maintenance of phenotypic plasticity	5
Evolutionary origin of B family DNA-dependent DNA polymerases from retrotranscriptases	5
The phylogenetic distribution of the cell division system would not imply a cellular LUCA but a progenotic LUCA	5
The Molecular Basis of Differentiation Wave Activity in Embryogenesis	5
Amino acid activation analysis of primitive aminoacyl-tRNA synthetases encoded by both strands of a single gene using the malachite green assay	5
The cell as a semiotic system that realizes closure to efficient causation: The semiotic (M, R) system	5
Living systems are smarter bots: Slime mold semiosis versus AI symbol manipulation	5
A new method: Characterize and quantify biofilm wrinkles by UNet and Sholl Analysis	5
Structural analyzes suggest that MiSSP13 and MiSSP16.5 may act as proteases inhibitors during ectomycorrhiza establishment in Laccaria bicolor	5
Causal intuition in the indefinite world: Meta-analysis and simulations	5
Electrical frequency discrimination by fungi Pleurotus ostreatus	5
A model integrating multiple processes of synchronization and coherence for information instantiation within a cortical area	5

Bioinformatics and meta-analysis of expression data to investigate transcriptomic response of wheat root to abiotic stresses	5
Robustness and evolvability: Revisited, redefined and applied	5
Cosmos MIND and matter: Is mind in spacetime?	5
Quantum concepts in Psychology: Exploring the interplay of physics and the human psyche	5
Fundamental principles of biology as a pure natural science and their applications in physiology and pathology	5
Benchmark for quantitative characterization of circadian clock cycles	5
Editorial Board	5
Synchronization Studies of Hindmarsh–Rose Neuron Networks: Unraveling the Influence of connection induced memristive synapse	5
A quantum-like information processing model with memory noise for question order effect	5
Identification of Ca	5
Estimation of discrepancy of color qualia using Kullback-Leibler divergence	5
Modelling energy-harvesting processes in primitive cells: Proton transport across bilayers driven by the oxidation of sulfite	5
Effects of pest control on a food chain in patchy environment: Species-dependent activity range on multilayer graphs	5
Construction of amino acids reduced alphabets from molecular descriptors for interpretation of N-carbamylase, luciferase and PI3K mutations	5
The polyphyletic origins of glycyl-tRNA synthetase and lysyl-tRNA synthetase and their implications	5
Fractional Mathematical Oncology: On the potential of non-integer order calculus applied to interdisciplinary models	5
Symbiogenesis is driven through hierarchical reorganization of an ecosystem under closed or semi-closed conditions	4
Disproportional fraction of inactive components leads to the variation in metabolic scaling	4
Corrigendum to “The concepts of code biology” [Biosyst. 248 (2025) 105400 1–6]	4
A heuristic perspective on non-variational free energy modulation at the sleep-like edge	4
A multi-modal algorithm based on an NSGA-II scheme for phylogenetic tree inference	4
Vladimir Voevodsky on mathematics and life	4
Corrigendum to “Role of calcium oscillations in sperm physiology” [BioSystems 209 (2021) 104524]	4
Origin of the temporal stability control of living system nonequilibrium	4
p-Adic morphology, biomorphic structures and number theory	4
Life, its definition, origin, evolution, and four-dimensional hierarchical structure	4
Is Darwinian selection a retrograde driving force of evolution?	4
Predator–prey population dynamics may induce the evolutionary dynamics of behavioral unpredictability	4
Modeling of will and consciousness based on the human language: Interpretation of qualia and psychological consciousness	4
Collective excitations at non-equilibrium phase transition in metabolically active red blood cells	4
Memory induced-mechanism of noise attenuator of myosin V molecular motors	4
Hypothetical novel simulations to explain the evolutionary survival of the hypo-reproductive extreme tail in the complex human diversity	4
On the infodynamics of ramifications in constructal design	4
The theory of oxygen hemoglobin association	4
Is meaning commensurable in scientific theories? From arbitrariness to non-nomological relations in meaning-making	4
Editorial Board	4
Biological thermodynamics: Ervin Bauer and the unification of life sciences and physics	4
LUCA to LECA, the Lucacene: A model for the gigayear delay from the first prokaryote to eukaryogenesis	4
miRNAFinder: A comprehensive web resource for plant Pre-microRNA classification	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
An interplay between compositional constraint and natural selection dictates the codon usage pattern among select Galliformes	4
Code biology and aesthetics	4
A control measure for epidemic spread based on the susceptible–infectious–susceptible (SIS) model	4
Identification of multivariable Boolean patterns in microbiome and microbial gene composition data	4
Perfection is the enemy of evolution	4
Formal autopoiesis: Solutions of the classical and extended functional closure equations	4
Collective computational intelligence in biology – Emergence of memory in somatic tissues	4
A ball microscope for viewing the entire surface of amphibian embryos	4
Two theories of action - Edelman's Neuronal group Selection and the Poetics of Paul Valéry	4
Impact of transposable elements on the evolution of complex living systems and their epigenetic control	4
Accurate phenotypic self-replication as a necessary cause for biological evolution.	4
Editorial: Fundamental principles of biological computation: From molecular computing to evolutionary complexity	3
Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples	3
Neurons as hierarchies of quantum reference frames	3
Analytical solution of Nye–Tinker–Barber model by Laplace transform	3
Toward understanding the emergence of life: A dual function of the system of nucleotides in the metabolically closed autopoietic organization	3
Distributional features of triplet codons in genomes underlie the diversification of life	3
Gene regulatory networks with binary weights	3
Temperature dependence of IR exciton emission spectra in Müller cell intermediate filaments	3
Category theory and foundations of life science: A structuralist perspective on cognition	3
Metabolic limits on classical information processing by biological cells	3
Swelling and membrane potential dynamics of glial Müller cells	3
Human-driven spreading and evolution of plants during the Holocene epoch: The pioneering works of Valery Taliev	3
Revisiting Carl Jung’s archetype theory a psychobiological approach	3
Light sensitive Belousov–Zhabotinsky medium accommodates multiple logic gates	3
The cell as a realization of the (M, R) system	3
The regulatory network that controls lymphopoiesis	3
Coupling and biological free-energy transduction processes as a bridge between physics and life: Molecular-level instantiation of Ervin Bauer’s pioneering concepts in biological thermodynamics	3
Modeling the C. elegans germline stem cell genetic network using automated reasoning	3
The reversibility of cellular determination: An evolutive pattern of epigenetic plasticity	3
Viruses, immunity and evolution	3
Software for evaluation of immune cell activation (Application note)	3
A memory access gate controlled by dynamic contexts	3
Electrical activity of fungi: Spikes detection and complexity analysis	3
The fundamental theorem of natural selection in optimization and games	3
Non-monotone cellular automata: Order prevails over chaos	3
Rule-based modelling of biological systems using regulated rewriting	3
A trampoline effect occurring in the stages of planetary reseeding	3
Minimizing enzyme mass to decompose flux distribution for identifying biologically relevant elementary flux modes	3
C-Biomarker.net: A Cytoscape app for the identification of cancer biomarker genes from cores of large biomolecular networks	3
Consequences of asymmetric mutational pressure for the dynamic of linear B-cell epitopes repertoire of influenza a virus neuraminidase rearrangement	3
Discovering ecoacoustic codes in beehives: First evidence and perspectives	3
Chemical oscillatory reactions with proteinoids	3
On electrical gates on fungal colony	3
Corrigendum to “Cosmos, mind, matter: Is mind in spacetime?” [Biosyst. (2024) 105262]	3
Overview of the third special issue in code biology	3
Quantum propensities in the brain cortex and free will	3
Comparing the complexity of written and molecular symbolic systems	3
Stages and causes of the evolution of language and consciousness: A theoretical reconstruction	3
Structure and behavior in Boolean monotonic model pools	3
Computation by inverse causality: A universal principle to produce symbols for the external reality in living systems	3
Memory retrieval dynamics and storage capacity of a modular network model of association cortex with featural decomposition	3
A biochemically-realisable relational model of the self-manufacturing cell	3
Toward an ethics of autopoietic technology: Stress, care, and intelligence	3
Decoding viruses: An alternative perspective on their history, origins and role in nature	3