Biosystems

Article	Citations
Developmental noise, entropy, and biological system condition	40
Optimizing ruminant nutrition: Insights from a comprehensive analysis of silage composition and in vitro gas production dynamics using nonlinear models	37
The major evolutionary transitions and codes of life	33
Morphological forms arising from the evolutionary process are topologies	32
Effects of predator modulation and vector preference on pathogen transmission in plant populations	27
Editorial Board	27
VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology	26
Memetic approach to cultural evolution	24
Nuclear quantum effects explain chemiosmosis: The power of the proton	24
The sensual cell: Feeling and affect in unicellular species	23
Hypothesis of macroscopic quantum state in biological systems and discussion on the possibility of its experimental verification	22
Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game	22
Reconfiguring SETI in the microbial context: Panspermia as a solution to Fermi's paradox	21
Cartography of the multiple formal systems of molecular autopoiesis: from the biology of cognition and enaction to anticipation and active inference	20
Evaluating the statistical similarity of neural network activity and connectivity via eigenvector angles	20
Filter feature selection based Boolean Modelling for Genetic Network Inference	20
Temporal regulation of gene expression and pathways in chemotherapy-induced senescence in HeLa cervical cancer cell line	18
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 promoting effect of adaptive persistence aspiration on the cooperation based on the consideration of payoff and environment in prisoner's dilemma game	17
The genetic code and its p-adic ultrametric modeling	17
Whole-cell metabolic control analysis	17
The metabolic control theory: Its development and its application to mitochondrial oxidative phosphorylation	17
An exploration of ecoacoustics and its applications in conservation ecology	16
Characterisation of the fig-fig wasp holobiont	16

Efim Liberman toward the comprehension of the phenomenon of life	16
The evolutionary arch of bioenergetics from prebiotic mechanisms to the emergence of a cellular respiratory chain	16
Binary oppositions, algebraic holography and stochastic rules in genetic informatics	16
Reversible and irreversible mitochondrial swelling: Effects of variable mitochondrial activity	16
The grid-cell normative model: Unifying ‘principles’	15
Editorial: Computational approaches in cancer modelling	15
A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information	15
Visualizing genomic data: The mixing perspective	15
The time of appearance of the genetic code	15
The evolution and development of consciousness: the subject-object emergence hypothesis	15
Three levels of information processing in the brain	14
The mitochondrial challenge: Disorders and prevention strategies	14
A possible origin of life in nonpolar environments	14
The molecular memory code and synaptic plasticity: A synthesis	13
Gaidai reliability method for high-dimensional spatio-temporal biosystems	13
Modeling of the entangled states transfer processes in microtubule tryptophan system	12
Identification of common factors among fibrosarcoma, rhabdomyosarcoma, and osteosarcoma by network analysis	12
Editorial Board	12
Editorial Board	12
Spatial organisation plasticity reduces disease infection risk in rock–paper–scissors models	12
Examining multi-objective deep reinforcement learning frameworks for molecular design	12
The origins of photosynthetic systems: Clues from the phosphorus and sulphur chemical scenarios	12
On the emergence of eukaryotes and other enigmas	12
Editorial Board	12
The pseudoentropy of allele frequency trajectories, the persistence of variation, and the effective population size	12
Impacts of aging on circadian rhythm and related sleep disorders	11
Fragile X mental retardation protein modulates translation of proteins with predicted tendencies for liquid-liquid phase separation	11
Gradistics: An underappreciated dimension in evolutionary space	11
Editorial: Waves in fertilization, cell division and embryogenesis	11
A mechanistic approach to optimize combination antibiotic therapy	11
In search for evolutionary roots of a mindful cognition: A Darwinian view on sustained intentional awareness	11
Book Review	11
Life and living beings under the perspective of organic macrocodes	11
Microbial mutualism promoting the coexistence of competing species: Double-layer model for two competing hosts and one microbial species	11
Causal and non-causal explanations in code biology	11
Dissipative scaling of development and aging in multicellular organisms	10
2-adic morphogenesis as a metaphorical model of biological growth	10
Using steady-state formula to estimate time-dependent parameters of stochastic gene transcription models	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
Mutations, sex, and genetic diversity: New arguments for partially directed evolution	10
Unexpected extra exon skipping in the DYSF gene during restoring the reading frame by CRISPR/Cas9	10
Why the power of diversity does not always produce better groups and societies	10
Human face as a biosocial marker in human evolution	10
Editorial Board	10
Editorial Board	9
Constructal thermodynamics and its semantic ontology in autopoietic, digital, and computational architectural and urban space open systems	9
Dynamic modelling and tristability analysis of misfolded α-synuclein degraded via autophagy in Parkinson's disease	9
Avian influenza A H5N1 hemagglutinin protein models have distinct structural patterns re-occurring across the 1959–2023 strains	9
The non-canonical nucleotides and prebiotic evolution	9

Editorial Board	9
Molecular mechanisms of encoding and decoding information in cell computing	9
Editorial Board	9
Logical modelling of myelofibrotic microenvironment predicts dysregulated progenitor stem cell crosstalk	9
Morphology changes induced by intercellular gap junction blocking: A reaction-diffusion mechanism	9
Algebraic harmony and probabilities in genomes. Long-range coherence in quantum code biology	9
Ecological drivers for the absence of task shifting in termite-tunneling activity: A simulation study	9
Rational decision making in biological systems	9
Ribonucleic acid genome mutations induced by the Casimir effect	8
Generation of random sequences using DNA cryptography for OTP encryption	8
50 years of Metabolic Control Analysis: Its past and current influence in the biological sciences	8
The indispensable role of time in autonomous development	8
Dive into machine learning algorithms for influenza virus host prediction with hemagglutinin sequences	8
Data-driven dynamical modelling of a pathogen-infected plant gene regulatory network: A comparative analysis	8
Entropy and the arrow of time in population dynamics	8
Corrigendum to “An efficient approach for identifying important biomarkers for biomedical diagnosis” [Biosystems 237 (2024) 105163]	8
CHTW(R)-system in Ca2+ transport modelling	8
A simple and fast ANN-based method of studying slow-wave sleep microstructure in freely moving rats	8
Is there a bias in the codon frequency corresponding to homo-repeats found in human proteins?	8
An irreversible thermodynamic model of prebiological dissipative molecular structures inside vacuoles at the surface of the Archean Ocean	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
Human cognitive limitations and emotions: The emergence of social complexity	8
Neural networks from biological to artificial and vice versa	8
Quantum aspects of the brain-mind relationship: A hypothesis with supporting evidence	8
Order stability via Fröhlich condensation in bio, eco, and social systems: The quantum-like approach	8
Reliability and energy function of an oscillator and map neuron	7
Embodied essentialism in the reconstruction of the animal sign in robot animal design	7
Identification of subtype specific biomarkers of clear cell renal cell carcinoma using random forest and greedy algorithm	7
Aggregate Boid behavior to aid in artificial autopoietic organization	7
Temporal cohesion as a candidate for negentropy in biological thermodynamics	7
Spiking neural networks produce informational closure by stimulus avoidance	7
Machine-learning-based structural analysis of interactions between antibodies and antigens	7
Karyotype coding: The creation and maintenance of system information for complexity and biodiversity	7
Modeling autopoiesis and cognition with reaction networks	7
The origins of the cell membrane, the progenote, and the universal ancestor (LUCA)	7
A multi-cell model for the C4 photosynthetic pathway in developing wheat grains based upon tissue-specific transcriptome data	7
Cell jamming-to-unjamming transitions and vice versa in development: Physical aspects	7
Standard Genetic Code vs. Supersymmetry Genetic Code – Alphabetical table vs. physicochemical table	7
The theoretical foundations of enaction: Precariousness	7
Towards the Big History of information. Approaching the origins of information behaviour	7
Entering the labyrinth: A hypothesis about the emergence of metabolism from protobiotic routes	7
On the minimal elements of the genetic code and their semiotic functions (degeneracy, complementarity, wobbling)	7
Editorial Board	7
Use of directed quasi-metric distances for quantifying the information of gene families	7
Autopoiesis: Foundations of life, cognition, and emergence of self/other	6
Information–energy equivalence and the emergence of self-replicating biological systems	6
Cosmos, mind, matter: Is mind in spacetime?	6
Stretching tension effects in permeability transition pores of inner mitochondrial membrane	6
A computational design of a programmable biological processor	6
Electrical frequency discrimination by fungi Pleurotus ostreatus	6
Evolution and maintenance of phenotypic plasticity	6
An efficient approach for identifying important biomarkers for biomedical diagnosis	6
Editorial Board	6
Prediction of prokaryotic and eukaryotic promoters based on information-theoretic features	6
Generation of genetic codes with 2-adic codon algebra and adaptive dynamics	6
Editorial Board	6
Mitotic waves in an import-diffusion model with multiple nuclei in a shared cytoplasm	6
Combination of survival movement strategies in cyclic game systems during an epidemic	6
Psychological origin of quantum logic: An orthomodular lattice derived from natural-born intelligence without Hilbert space	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
Impact of social reward on the evolution of cooperation in voluntary prisoner’s dilemma	6
Mathematical model of coffee tree’s rust control using snails as biological agents	6
Childhood in social learning models with changing environments: Implications for human evolution	6
Evolution of cooperation in multigame with environmental space and delay	6
The chromolinker hypothesis: Are eukaryotic genomes also circular?	6
Understanding nature’s selection of genetic languages	6
A model integrating multiple processes of synchronization and coherence for information instantiation within a cortical area	6
Evolutionary stability of developmental commitment	6
Fundamental principles of biology as pure natural science and their applications in physiology and pathology	5
Editorial Board	5
A new method: Characterize and quantify biofilm wrinkles by UNet and Sholl Analysis	5
Multi-scale modeling of hippo signaling identifies homeostatic control by YAP-LATS negative feedback	5
Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach	5
The cell as a semiotic system that realizes closure to efficient causation: The semiotic (M, R) system	5
Identification of Ca	5
Bioinformatics and meta-analysis of expression data to investigate transcriptomic response of wheat root to abiotic stresses	5
A heuristic perspective on non-variational free energy modulation at the sleep-like edge	5
The polyphyletic origins of glycyl-tRNA synthetase and lysyl-tRNA synthetase and their implications	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
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
Fractional nutrient uptake model of plant roots	5
Effect of the electromagnetic induction in the electrical activity of the Kazantsev model of inferior Olive Neuron model	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
Quantum concepts in Psychology: Exploring the interplay of physics and the human psyche	5
Construction of amino acids reduced alphabets from molecular descriptors for interpretation of N-carbamylase, luciferase and PI3K mutations	5
Corrigendum to “Role of calcium oscillations in sperm physiology” [BioSystems 209 (2021) 104524]	5
Hypothetical novel simulations to explain the evolutionary survival of the hypo-reproductive extreme tail in the complex human diversity	5
The phylogenetic distribution of the cell division system would not imply a cellular LUCA but a progenotic LUCA	5
Robustness and evolvability: Revisited, redefined and applied	5
Benchmark for quantitative characterization of circadian clock cycles	5
Living systems are smarter bots: Slime mold semiosis versus AI symbol manipulation	5
Estimation of discrepancy of color qualia using Kullback-Leibler divergence	5
Synchronization Studies of Hindmarsh–Rose Neuron Networks: Unraveling the Influence of connection induced memristive synapse	5
Fractional Mathematical Oncology: On the potential of non-integer order calculus applied to interdisciplinary models	5
The problem of evolutionary directionality 50 years following the works of Sergei Meyen	5
Evolutionary origin of B family DNA-dependent DNA polymerases from retrotranscriptases	5
The Molecular Basis of Differentiation Wave Activity in Embryogenesis	5
The theory of oxygen hemoglobin association	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
Disproportional fraction of inactive components leads to the variation in metabolic scaling	4
Using neurons to maintain autonomy: Learning from C. elegans	4
Symbiogenesis is driven through hierarchical reorganization of an ecosystem under closed or semi-closed conditions	4
p-Adic morphology, biomorphic structures and number theory	4
Life, its definition, origin, evolution, and four-dimensional hierarchical structure	4
A multi-modal algorithm based on an NSGA-II scheme for phylogenetic tree inference	4
Predator–prey population dynamics may induce the evolutionary dynamics of behavioral unpredictability	4
Perfection is the enemy of evolution	4
On the infodynamics of ramifications in constructal design	4
Vladimir Voevodsky on mathematics and life	4
An interplay between compositional constraint and natural selection dictates the codon usage pattern among select Galliformes	4
Editorial: Fundamental principles of biological computation: From molecular computing to evolutionary complexity	4
Neurons as hierarchies of quantum reference frames	4
Modeling the C. elegans germline stem cell genetic network using automated reasoning	4
Overview of the third special issue in code biology	4
Memory induced-mechanism of noise attenuator of myosin V molecular motors	4
Identification of multivariable Boolean patterns in microbiome and microbial gene composition data	4
On electrical gates on fungal colony	4
Corrigendum to “The concepts of code biology” [Biosyst. 248 (2025) 105400 1–6]	4
Coacervates meet the RNP-world: liquid-liquid phase separation and the emergence of biological compartmentalization	4
Cosmos MIND and matter: Is mind in spacetime?	4
Formal autopoiesis: Solutions of the classical and extended functional closure equations	4
Two theories of action - Edelman's Neuronal group Selection and the Poetics of Paul Valéry	4
Is Darwinian selection a retrograde driving force of evolution?	4
The regulatory network that controls lymphopoiesis	4
Collective excitations at non-equilibrium phase transition in metabolically active red blood cells	4
Code biology and aesthetics	4
Modeling of will and consciousness based on the human language: Interpretation of qualia and psychological consciousness	4
Impact of transposable elements on the evolution of complex living systems and their epigenetic control	4
Statistical algorithms for the analysis of deleterious genetic mutations	4
Accurate phenotypic self-replication as a necessary cause for biological evolution.	4
A control measure for epidemic spread based on the susceptible–infectious–susceptible (SIS) model	4
Biological thermodynamics: Ervin Bauer and the unification of life sciences and physics	4
Origin of the temporal stability control of living system nonequilibrium	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
Toward understanding the emergence of life: A dual function of the system of nucleotides in the metabolically closed autopoietic organization	4
Human-driven spreading and evolution of plants during the Holocene epoch: The pioneering works of Valery Taliev	3
Computation by inverse causality: A universal principle to produce symbols for the external reality in living systems	3
Analytical solution of Nye–Tinker–Barber model by Laplace transform	3
COVID-19 spatio-temporal forecast in England	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
Editorial Board	3
Oncogenetic pedigrees: Relation between design and ability to predict mutation	3
The reversibility of cellular determination: An evolutive pattern of epigenetic plasticity	3
Minimizing enzyme mass to decompose flux distribution for identifying biologically relevant elementary flux modes	3
A trampoline effect occurring in the stages of planetary reseeding	3
Rule-based modelling of biological systems using regulated rewriting	3
Swelling and membrane potential dynamics of glial Müller cells	3
Distributional features of triplet codons in genomes underlie the diversification of life	3
Metabolic control analysis as a strategy to identify therapeutic targets, the case of cancer glycolysis	3
Quantum contextuality and cognitive contextuality: The significance of violations of Bell-type inequalities	3
Circular mixed sets	3
A biochemically-realisable relational model of the self-manufacturing cell	3
Decoding viruses: An alternative perspective on their history, origins and role in nature	3
Software for evaluation of immune cell activation (Application note)	3
Non-monotone cellular automata: Order prevails over chaos	3
The fundamental theorem of natural selection in optimization and games	3
Memory retrieval dynamics and storage capacity of a modular network model of association cortex with featural decomposition	3
Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples	3
Corrigendum to “Cosmos, mind, matter: Is mind in spacetime?” [Biosyst. (2024) 105262]	3
Evolution of small and large ribosomal RNAs from accretion of tRNA subelements	3
Fungal skin for robots	3
Modelling the fitness landscapes of a SCRaMbLEd yeast genome	3
Metabolic limits on classical information processing by biological cells	3
Fractal calculus in tumor growth simulations: The proof is in the pudding	3
Revisiting Carl Jung’s archetype theory a psychobiological approach	3
Stages and causes of the evolution of language and consciousness: A theoretical reconstruction	3