Biosystems

Article	Citations
Book Review	43
The sensual cell: Feeling and affect in unicellular species	38
Optimizing ruminant nutrition: Insights from a comprehensive analysis of silage composition and in vitro gas production dynamics using nonlinear models	29
Field-induced coherence and Fröhlich condensation in hydrated DNA	28
Filter feature selection based Boolean Modelling for Genetic Network Inference	28
From life to evolution: the differentiation between storage and interface in natural and cultural systems	23
Nuclear quantum effects explain chemiosmosis: The power of the proton	23
The major evolutionary transitions and codes of life	23
Developmental noise, entropy, and biological system condition	23
A survey of the methodological process of modeling, inference, and evaluation of gene regulatory networks using scRNA-Seq data	22
Hypothesis of macroscopic quantum state in biological systems and discussion on the possibility of its experimental verification	21
Morphological forms arising from the evolutionary process are topologies	21
Effects of predator modulation and vector preference on pathogen transmission in plant populations	21
Cartography of the multiple formal systems of molecular autopoiesis: from the biology of cognition and enaction to anticipation and active inference	21
VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology	21
Editorial Board	19
Temporal regulation of gene expression and pathways in chemotherapy-induced senescence in HeLa cervical cancer cell line	18
Negative membrane potentials potentiate multicellularity	18
Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game	18
A possible origin of life in nonpolar environments	18
Evaluating the statistical similarity of neural network activity and connectivity via eigenvector angles	18
Theories of the origin of the genetic code: Strong corroboration for the coevolution theory	18
A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information	17
An exploration of ecoacoustics and its applications in conservation ecology	17
Cholesterol-ester prevents lipoprotein core from solidifying: Molecular dynamics simulation	17

The evolutionary arch of bioenergetics from prebiotic mechanisms to the emergence of a cellular respiratory chain	17
The evolution and development of consciousness: the subject-object emergence hypothesis	17
The genetic code and its p-adic ultrametric modeling	17
scSAGRN: Inferring gene regulatory networks from single-cell multi-omics using spatial association	17
The grid-cell normative model: Unifying ‘principles’	17
Efim Liberman toward the comprehension of the phenomenon of life	16
The time of appearance of the genetic code	15
Reversible and irreversible mitochondrial swelling: Effects of variable mitochondrial activity	15
Binary oppositions, algebraic holography and stochastic rules in genetic informatics	15
Whole-cell metabolic control analysis	15
The promoting effect of adaptive persistence aspiration on the cooperation based on the consideration of payoff and environment in prisoner's dilemma game	14
The molecular memory code and synaptic plasticity: A synthesis	14
The metabolic control theory: Its development and its application to mitochondrial oxidative phosphorylation	14
Three levels of information processing in the brain	14
Characterisation of the fig-fig wasp holobiont	14
Visualizing genomic data: The mixing perspective	14
Gaidai reliability method for high-dimensional spatio-temporal biosystems	14
In search for evolutionary roots of a mindful cognition: A Darwinian view on sustained intentional awareness	13
The mitochondrial challenge: Disorders and prevention strategies	13
Gradistics: An underappreciated dimension in evolutionary space	13
The pseudoentropy of allele frequency trajectories, the persistence of variation, and the effective population size	13
Examining multi-objective deep reinforcement learning frameworks for molecular design	13
Editorial Board	13
Editorial Board	12
Editorial Board	12
The origins of photosynthetic systems: Clues from the phosphorus and sulphur chemical scenarios	12
Editorial Board	12
Modeling of the entangled states transfer processes in microtubule tryptophan system	12
On the emergence of eukaryotes and other enigmas	12
Impacts of aging on circadian rhythm and related sleep disorders	11
A mechanistic approach to optimize combination antibiotic therapy	11
Fragile X mental retardation protein modulates translation of proteins with predicted tendencies for liquid-liquid phase separation	11
Identification of common factors among fibrosarcoma, rhabdomyosarcoma, and osteosarcoma by network analysis	11
Causal and non-causal explanations in code biology	11
Richness of emotion in people with dementia	11
Microbial mutualism promoting the coexistence of competing species: Double-layer model for two competing hosts and one microbial species	11
The evolution and biophysical economics of energy currencies: from prebiotic electrochemistry to modern digital money	11
Book Review	11
Regulative development as a model for origin of life and artificial life studies	10
Editorial Board	10
The non-canonical nucleotides and prebiotic evolution	10
Mutations, sex, and genetic diversity: New arguments for partially directed evolution	10
Editorial Board	10
Human face as a biosocial marker in human evolution	10
Dissipative scaling of development and aging in multicellular organisms	10
The processes generating quantum entanglement in DNA	10
Spatial organisation plasticity reduces disease infection risk in rock–paper–scissors models	10
Why the power of diversity does not always produce better groups and societies	10
Editorial: Waves in fertilization, cell division and embryogenesis	10
Constructal thermodynamics and its semantic ontology in autopoietic, digital, and computational architectural and urban space open systems	10

Morphology changes induced by intercellular gap junction blocking: A reaction-diffusion mechanism	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
The role of self-maintaining resilient reaction networks in the origin and evolution of life	10
The role of pure mathematics in resolving complex biological problems: Applications to F1-ATPase, achievements, and future directions	10
2-adic morphogenesis as a metaphorical model of biological growth	10
Avian influenza A H5N1 hemagglutinin protein models have distinct structural patterns re-occurring across the 1959–2023 strains	9
Algebraic harmony and probabilities in genomes. Long-range coherence in quantum code biology	9
50 years of Metabolic Control Analysis: Its past and current influence in the biological sciences	9
Effect of monochromatic light on the behavior of the ctenophore Mnemiopsis leidyi (A. Agassiz, 1865)	9
Molecular mechanisms of encoding and decoding information in cell computing	9
Editorial Board	9
The indispensable role of time in autonomous development	9
Is there a bias in the codon frequency corresponding to homo-repeats found in human proteins?	9
Rational decision making in biological systems	9
Logical modelling of myelofibrotic microenvironment predicts dysregulated progenitor stem cell crosstalk	9
Entropy and the arrow of time in population dynamics	9
CHTW(R)-system in Ca2+ transport modelling	9
Ecological drivers for the absence of task shifting in termite-tunneling activity: A simulation study	9
Corrigendum to “An efficient approach for identifying important biomarkers for biomedical diagnosis” [Biosystems 237 (2024) 105163]	9
A simple and fast ANN-based method of studying slow-wave sleep microstructure in freely moving rats	9
Quantum aspects of the brain-mind relationship: A hypothesis with supporting evidence	9
Generation of random sequences using DNA cryptography for OTP encryption	9
An irreversible thermodynamic model of prebiological dissipative molecular structures inside vacuoles at the surface of the Archean Ocean	8
Paleo-phyllotaxis: Fucales, bryophytes, lycophytes and monilophytes	8
From code to archetype: Toward a unified theory of biological, neural, and artificial artifacts	8
Mechanism and biological significance of erythrocyte homoaggregation (rouleaux formation): temperature-dependent entropic liberation of water from cells and macromolecules	8
Standard Genetic Code vs. Supersymmetry Genetic Code – Alphabetical table vs. physicochemical table	8
Generalized model of closed microecosystem «alga - micro-consumers»	8
The origin and evolution of life as continuing expansion of viral hosts	8
Dive into machine learning algorithms for influenza virus host prediction with hemagglutinin sequences	8
Machine-learning-based structural analysis of interactions between antibodies and antigens	8
Modeling autopoiesis and cognition with reaction networks	8
Neural networks from biological to artificial and vice versa	8
Dynamic modelling and tristability analysis of misfolded α-synuclein degraded via autophagy in Parkinson's disease	8
Human cognitive limitations and emotions: The emergence of social complexity	8
A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem	8
Reliability and energy function of an oscillator and map neuron	7
Ribonucleic acid genome mutations induced by the Casimir effect	7
Temporal cohesion as a candidate for negentropy in biological thermodynamics	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
Corrigendum to “Pandemic preparedness and new model developments for airborne diseases transmitting via aerosols” [BioSystems 255 (2025) 105532]	7
Order stability via Fröhlich condensation in bio, eco, and social systems: The quantum-like approach	7
Towards the Big History of information. Approaching the origins of information behaviour	7
Data-driven dynamical modelling of a pathogen-infected plant gene regulatory network: A comparative analysis	7
Editorial Board	7
Cosmos, mind, matter: Is mind in spacetime?	7
Use of directed quasi-metric distances for quantifying the information of gene families	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
The theoretical foundations of enaction: Precariousness	7
Editorial Board	7
Balancing the cellular budget: Lessons in metabolism from microbes to cancer	7
Evolution and maintenance of phenotypic plasticity	6
Mathematical model of coffee tree’s rust control using snails as biological agents	6
Information–energy equivalence and the emergence of self-replicating biological systems	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
Thermal diodes, transistors and logic: Review of unconventional computing methods	6
Understanding nature’s selection of genetic languages	6
Effect of the electromagnetic induction in the electrical activity of the Kazantsev model of inferior Olive Neuron model	6
The chromolinker hypothesis: Are eukaryotic genomes also circular?	6
Autopoiesis: Foundations of life, cognition, and emergence of self/other	6
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
An efficient approach for identifying important biomarkers for biomedical diagnosis	6
Modelling energy-harvesting processes in primitive cells: Proton transport across bilayers driven by the oxidation of sulfite	6
Electrical frequency discrimination by fungi Pleurotus ostreatus	6
Identification of Ca	6
Spiking neural networks produce informational closure by stimulus avoidance	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
Cell jamming-to-unjamming transitions and vice versa in development: Physical aspects	6
Evolutionary stability of developmental commitment	6
Causal intuition in the indefinite world: Meta-analysis and simulations	6
Editorial Board	5
Brain and behavior share features of a critical state dynamics	5
On the infodynamics of ramifications in constructal design	5
The Molecular Basis of Differentiation Wave Activity in Embryogenesis	5

A new method: Characterize and quantify biofilm wrinkles by UNet and Sholl Analysis	5
Estimation of discrepancy of color qualia using Kullback-Leibler divergence	5
The problem of evolutionary directionality 50 years following the works of Sergei Meyen	5
A computational design of a programmable biological processor	5
Influence of oxidative stress on women’s fertility: A model with a generational age Caputo’s fractional derivative	5
The cell as a semiotic system that realizes closure to efficient causation: The semiotic (M, R) system	5
Coacervates meet the RNP-world: liquid-liquid phase separation and the emergence of biological compartmentalization	5
Corrigendum to “Paleo-phyllotaxis: Fucales, bryophytes, lycophytes and monilophytes” [BioSystems 255 (2025) 105541]	5
Fundamental principles of biology as pure natural science and their applications in physiology and pathology	5
Bioinformatics and meta-analysis of expression data to investigate transcriptomic response of wheat root to abiotic stresses	5
Editorial Board	5
Evolutionary origin of B family DNA-dependent DNA polymerases from retrotranscriptases	5
Combination of survival movement strategies in cyclic game systems during an epidemic	5
Structural analyzes suggest that MiSSP13 and MiSSP16.5 may act as proteases inhibitors during ectomycorrhiza establishment in Laccaria bicolor	5
Psychological origin of quantum logic: An orthomodular lattice derived from natural-born intelligence without Hilbert space	5
How organisms decrease their entropy	5
Evolution of cooperation in multigame with environmental space and delay	5
Formal autopoiesis: Solutions of the classical and extended functional closure equations	5
The polyphyletic origins of glycyl-tRNA synthetase and lysyl-tRNA synthetase and their implications	5
Biological thermodynamics: Ervin Bauer and the unification of life sciences and physics	5
Robustness and evolvability: Revisited, redefined and applied	5
Construction of amino acids reduced alphabets from molecular descriptors for interpretation of N-carbamylase, luciferase and PI3K mutations	5
Synchronization Studies of Hindmarsh–Rose Neuron Networks: Unraveling the Influence of connection induced memristive synapse	5
Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach	5
Fractional nutrient uptake model of plant roots	5
A quantum-like information processing model with memory noise for question order effect	5
Benchmark for quantitative characterization of circadian clock cycles	5
Quantum concepts in Psychology: Exploring the interplay of physics and the human psyche	5