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
Book Review	22
Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game	22
Temporal regulation of gene expression and pathways in chemotherapy-induced senescence in HeLa cervical cancer cell line	21
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
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 sensual cell: Feeling and affect in unicellular species	18
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
Binary oppositions, algebraic holography and stochastic rules in genetic informatics	17
Characterisation of the fig-fig wasp holobiont	17
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
The metabolic control theory: Its development and its application to mitochondrial oxidative phosphorylation	16
The mitochondrial challenge: Disorders and prevention strategies	16
The evolution and development of consciousness: the subject-object emergence hypothesis	16
Three levels of information processing in the brain	15
The time of appearance of the genetic code	15
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
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
The pseudoentropy of allele frequency trajectories, the persistence of variation, and the effective population size	13
Editorial Board	13
Editorial Board	13
Editorial Board	13
On the emergence of eukaryotes and other enigmas	13
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
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
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
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
2-adic morphogenesis as a metaphorical model of biological growth	10
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
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
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
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
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
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
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
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
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
Corrigendum to “Role of calcium oscillations in sperm physiology” [BioSystems 209 (2021) 104524]	5
On the infodynamics of ramifications in constructal design	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

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
The cell as a semiotic system that realizes closure to efficient causation: The semiotic (M, R) system	5
Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach	5
Robustness and evolvability: Revisited, redefined and applied	5