Biosystems

Article	Citations
Developmental noise, entropy, and biological system condition	51
Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game	44
Book Review	35
Optimizing ruminant nutrition: Insights from a comprehensive analysis of silage composition and in vitro gas production dynamics using nonlinear models	34
A survey of the methodological process of modeling, inference, and evaluation of gene regulatory networks using scRNA-Seq data	31
Temporal regulation of gene expression and pathways in chemotherapy-induced senescence in HeLa cervical cancer cell line	30
Effects of predator modulation and vector preference on pathogen transmission in plant populations	30
Evaluating the statistical similarity of neural network activity and connectivity via eigenvector angles	30
Nuclear quantum effects explain chemiosmosis: The power of the proton	29
Field-induced coherence and Fröhlich condensation in hydrated DNA	28
From life to evolution: the differentiation between storage and interface in natural and cultural systems	27
Natural born intelligence manifesto: Illustrating the dynamic perspective for consciousness	26
Adaptive inference through Bayesian and inverse Bayesian inference with symmetry bias in nonstationary environments	25
Cartography of the multiple formal systems of molecular autopoiesis: from the biology of cognition and enaction to anticipation and active inference	24
Germline-specific nascent polypeptide-associated complex (NAC) subunits are predicted by bioinformatics tools to undergo phase separation	23
Theories of the origin of the genetic code: Strong corroboration for the coevolution theory	23
Filter feature selection based Boolean Modelling for Genetic Network Inference	23
The sensual cell: Feeling and affect in unicellular species	22
The time of appearance of the genetic code	21
Negative membrane potentials potentiate multicellularity	21
A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information	21
Cholesterol-ester prevents lipoprotein core from solidifying: Molecular dynamics simulation	21
The promoting effect of adaptive persistence aspiration on the cooperation based on the consideration of payoff and environment in prisoner's dilemma game	20
A possible origin of life in nonpolar environments	20
The evolutionary arch of bioenergetics from prebiotic mechanisms to the emergence of a cellular respiratory chain	19

Quantum formalism for indeterminate preferences in decision theory	19
Whole-cell metabolic control analysis	18
The mitochondrial challenge: Disorders and prevention strategies	18
Characterisation of the fig-fig wasp holobiont	18
Efim Liberman toward the comprehension of the phenomenon of life	17
Gaidai reliability method for high-dimensional spatio-temporal biosystems	16
The metabolic control theory: Its development and its application to mitochondrial oxidative phosphorylation	16
scSAGRN: Inferring gene regulatory networks from single-cell multi-omics using spatial association	16
Visualizing genomic data: The mixing perspective	16
Flux organizations and control modes in antagonistically combined negative feedback loops	15
An exploration of ecoacoustics and its applications in conservation ecology	15
The molecular memory code and synaptic plasticity: A synthesis	15
The genetic code and its p	15
Three levels of information processing in the brain	15
Loss of thermodynamic efficiency of various organs and functions of Drosophila melanogaster during aging	15
The grid-cell normative model: Unifying ‘principles’	15
The evolution and development of consciousness: the subject-object emergence hypothesis	15
Identification of common factors among fibrosarcoma, rhabdomyosarcoma, and osteosarcoma by network analysis	14
Antagonistic coinfection in rock–paper–scissors models during concurrent epidemics	14
Editorial Board	14
Binary oppositions, algebraic holography and stochastic rules in genetic informatics	14
Impacts of aging on circadian rhythm and related sleep disorders	13
The evolution and biophysical economics of energy currencies: from prebiotic electrochemistry to modern digital money	13
The pseudoentropy of allele frequency trajectories, the persistence of variation, and the effective population size	13
Fragile X mental retardation protein modulates translation of proteins with predicted tendencies for liquid-liquid phase separation	13
On the emergence of eukaryotes and other enigmas	13
Examining multi-objective deep reinforcement learning frameworks for molecular design	13
Book Review	13
Spatial organisation plasticity reduces disease infection risk in rock–paper–scissors models	13
Editorial Board	13
Gradistics: An underappreciated dimension in evolutionary space	12
Modeling of the entangled states transfer processes in microtubule tryptophan system	12
Editorial Board	12
Using steady-state formula to estimate time-dependent parameters of stochastic gene transcription models	12
A mechanistic approach to optimize combination antibiotic therapy	12
Richness of emotion in people with dementia	12
Constructal thermodynamics and its semantic ontology in autopoietic, digital, and computational architectural and urban space open systems	12
Unexpected extra exon skipping in the DYSF gene during restoring the reading frame by CRISPR/Cas9	12
The origins of photosynthetic systems: Clues from the phosphorus and sulphur chemical scenarios	12
In search for evolutionary roots of a mindful cognition: A Darwinian view on sustained intentional awareness	12
The non-canonical nucleotides and prebiotic evolution	12
Why the power of diversity does not always produce better groups and societies	12
Human face as a biosocial marker in human evolution	11
A hybrid phase-synchronization framework for rotary motors: Discrete dynamics in ATP synthase and continuous dynamics in the bacterial flagellar motor	11
Evolutionary change and adaptation as non-equilibrium thermodynamic processes	11
Internal quantum constraints of natural computation in autopoietic systems	11
The role of self-maintaining resilient reaction networks in the origin and evolution of life	11
The processes generating quantum entanglement in DNA	11
Dissipative scaling of development and aging in multicellular organisms	11
First evidence supporting the theory of the sensorimotor paradox on the origins of mind and language	11

Brain aging mediates region-specific transcriptomic alterations	11
Editorial Board	11
The role of pure mathematics in resolving complex biological problems: Applications to F1-ATPase, achievements, and future directions	11
Mutations, sex, and genetic diversity: New arguments for partially directed evolution	11
Regulative development as a model for origin of life and artificial life studies	11
Ecological drivers for the absence of task shifting in termite-tunneling activity: A simulation study	10
Corrigendum to “An efficient approach for identifying important biomarkers for biomedical diagnosis” [Biosystems 237 (2024) 105163]	10
50 years of Metabolic Control Analysis: Its past and current influence in the biological sciences	10
Rational decision making in biological systems	10
The indispensable role of time in autonomous development	10
CHTW(R)-system in Ca2+ transport modelling	10
Editorial Board	10
Effect of monochromatic light on the behavior of the ctenophore Mnemiopsis leidyi (A. Agassiz, 1865)	10
Logical modelling of myelofibrotic microenvironment predicts dysregulated progenitor stem cell crosstalk	10
Neural networks from biological to artificial and vice versa	10
Dynamic modelling and tristability analysis of misfolded α-synuclein degraded via autophagy in Parkinson's disease	9
The origin and evolution of life as continuing expansion of viral hosts	9
Molecular mechanisms of encoding and decoding information in cell computing	9
Quantum aspects of the brain-mind relationship: A hypothesis with supporting evidence	9
Least ranked human individuals exhibit scale free behavioral responses in hierarchical social systems	9
The threat of asymptomatic carriers and the benefits of testing	9
Is there a bias in the codon frequency corresponding to homo-repeats found in human proteins?	9
Dive into machine learning algorithms for influenza virus host prediction with hemagglutinin sequences	9
From code to archetype: Toward a unified theory of biological, neural, and artificial artifacts	9
Entropy and the arrow of time in population dynamics	9
Avian influenza A H5N1 hemagglutinin protein models have distinct structural patterns re-occurring across the 1959–2023 strains	9
Generalized model of closed microecosystem «alga - micro-consumers»	9
Small amphipathic amino acids imprint the active site of extant E. coli aminoacyl-tRNA synthetases	9
Nirmala indices bridge molecular connectivity and genetic stability: A graph-theoretic lens on purines and pyrimidines	9
Human cognitive limitations and emotions: The emergence of social complexity	8
Embodied essentialism in the reconstruction of the animal sign in robot animal design	8
An irreversible thermodynamic model of prebiological dissipative molecular structures inside vacuoles at the surface of the Archean Ocean	8
Corrigendum to “Pandemic preparedness and new model developments for airborne diseases transmitting via aerosols” [BioSystems 255 (2025) 105532]	8
A simple and fast ANN-based method of studying slow-wave sleep microstructure in freely moving rats	8
Towards the Big History of information. Approaching the origins of information behaviour	8
Data-driven dynamical modelling of a pathogen-infected plant gene regulatory network: A comparative analysis	8
Editorial Board	8
Ribonucleic acid genome mutations induced by the Casimir effect	8
Generation of random sequences using DNA cryptography for OTP encryption	8
Paleo-phyllotaxis: Fucales, bryophytes, lycophytes and monilophytes	8
Mechanism and biological significance of erythrocyte homoaggregation (rouleaux formation): temperature-dependent entropic liberation of water from cells and macromolecules	8
Cosmos, mind, matter: Is mind in spacetime?	7
A multi-cell model for the C4 photosynthetic pathway in developing wheat grains based upon tissue-specific transcriptome data	7
The theoretical foundations of enaction: Precariousness	7
Reliability and energy function of an oscillator and map neuron	7
Constructal thinking: Geospatial and temporal focal points of activity	7
Machine-learning-based structural analysis of interactions between antibodies and antigens	7
Editorial Board	7
When Maxwell’s Demon leaves the room	7
Standard Genetic Code vs. Supersymmetry Genetic Code – Alphabetical table vs. physicochemical table	7
Transformation of the inherent energy in food to ATP and transformations of our knowledge about the mechanism	7
Modeling autopoiesis and cognition with reaction networks	7
A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem	7
Temporal cohesion as a candidate for negentropy in biological thermodynamics	7
Editorial Board	7
Prediction of prokaryotic and eukaryotic promoters based on information-theoretic features	7
Entering the labyrinth: A hypothesis about the emergence of metabolism from protobiotic routes	7
Energy transformation and nuclear spin catalysis: From magnetic isotope effects in chemical physics to ATP-dependent molecular motors in bioenergetics	7
Use of directed quasi-metric distances for quantifying the information of gene families	7
Asymmetric divergence of genome organization and transcription beyond LUCA	7
Aggregate Boid behavior to aid in artificial autopoietic organization	7
Balancing the cellular budget: Lessons in metabolism from microbes to cancer	6
Cell jamming-to-unjamming transitions and vice versa in development: Physical aspects	6
Spiking neural networks produce informational closure by stimulus avoidance	6
Evolutionary stability of developmental commitment	6
Causal intuition in the indefinite world: Meta-analysis and simulations	6
Psychological origin of quantum logic: An orthomodular lattice derived from natural-born intelligence without Hilbert space	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
Deciphering the dynamic binding of spicy odorants to human olfactory receptors	6
The chromolinker hypothesis: Are eukaryotic genomes also circular?	6
A quantum-like information processing model with memory noise for question order effect	6
Effect of the electromagnetic induction in the electrical activity of the Kazantsev model of inferior Olive Neuron model	6
Autopoiesis: Foundations of life, cognition, and emergence of self/other	6
Generation of genetic codes with 2-adic codon algebra and adaptive dynamics	6
On the minimal elements of the genetic code and their semiotic functions (degeneracy, complementarity, wobbling)	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
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

A computational design of a programmable biological processor	6
Physical factors in origin of genetic code	6
Estimation of discrepancy of color qualia using Kullback-Leibler divergence	5
Understanding nature’s selection of genetic languages	5
Fractional nutrient uptake model of plant roots	5
Benchmark for quantitative characterization of circadian clock cycles	5
Robustness and evolvability: Revisited, redefined and applied	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
Evolution and maintenance of phenotypic plasticity	5
Ambush strategy impacts species predominance and coexistence in generalised rock–paper–scissors models	5
Toward a unified theory of ATP synthesis/hydrolysis: Integrating physics, chemistry, and biology	5
Fundamental principles of biology as pure natural science and their applications in physiology and pathology	5
An efficient approach for identifying important biomarkers for biomedical diagnosis	5
Editorial Board	5
The Molecular Basis of Differentiation Wave Activity in Embryogenesis	5
Quantum concepts in Psychology: Exploring the interplay of physics and the human psyche	5
Structural analyzes suggest that MiSSP13 and MiSSP16.5 may act as proteases inhibitors during ectomycorrhiza establishment in Laccaria bicolor	5
Application of fractal theory in cancer detection: A review	5
Intelligence as high-dimensional coherence: The observable dimensionality bound and computational tractability	5
A new method: Characterize and quantify biofilm wrinkles by UNet and Sholl Analysis	5
Evolution of cooperation in multigame with environmental space and delay	5
Variance-dependent inheritance fidelity drives residence-time symmetry breaking in a protocell model	5
Combination of survival movement strategies in cyclic game systems during an epidemic	5
Editorial Board	5
Synchronization Studies of Hindmarsh–Rose Neuron Networks: Unraveling the Influence of connection induced memristive synapse	5
Influence of oxidative stress on women’s fertility: A model with a generational age Caputo’s fractional derivative	5
How organisms decrease their entropy	5
Editorial Board	5
Thermal Model for investigating the timing of the onset of phenological events in ectotherms and the technique of estimating its parameters	5
Bioinformatics and meta-analysis of expression data to investigate transcriptomic response of wheat root to abiotic stresses	5
A Unified Holographic Framework for neural computation and consciousness: From lipid membranes to the Schumann resonance	5
Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach	5
Thermal diodes, transistors and logic: Review of unconventional computing methods	5
Collective excitations at non-equilibrium phase transition in metabolically active red blood cells	4
Viscous DNA and RNA: Quantum damped dynamical random systems	4
Life, its definition, origin, evolution, and four-dimensional hierarchical structure	4
Is meaning commensurable in scientific theories? From arbitrariness to non-nomological relations in meaning-making	4
An energy landscape-based theoretical framework for understanding the self-organization of functions in a living system under the dynamical component interaction	4
Codes across (life)sciences	4
Origin of the temporal stability control of living system nonequilibrium	4
Identification of multivariable Boolean patterns in microbiome and microbial gene composition data	4
Formal autopoiesis: Solutions of the classical and extended functional closure equations	4
Editorial Board	4
Collective computational intelligence in biology – Emergence of memory in somatic tissues	4
Construction of amino acids reduced alphabets from molecular descriptors for interpretation of N-carbamylase, luciferase and PI3K mutations	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
A control measure for epidemic spread based on the susceptible–infectious–susceptible (SIS) model	4
Using neurons to maintain autonomy: Learning from C. elegans	4
Modeling of will and consciousness based on the human language: Interpretation of qualia and psychological consciousness	4
Enhancing statistical accuracy in gene perturbation studies	4
Perfection is the enemy of evolution	4
The repertoire of candidate archaeal noncoding RNAs and their association with temperature adaptation	4
Exploring potential size-dependent effects of Fibonacci-based acoustic binary strings on cells as measured by cell death and cell aggregation patterns	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
Statistical algorithms for the analysis of deleterious genetic mutations	4
On the infodynamics of ramifications in constructal design	4
The limits of falsifiability: Dimensionality, measurement thresholds, and the sub-Landauer domain in biological systems	4
Corrigendum to “Paleo-phyllotaxis: Fucales, bryophytes, lycophytes and monilophytes” [BioSystems 255 (2025) 105541]	4
Simulating tumor mitochondrial energetics through engineering-style energy metrics	4
Editorial Board	4
Anticipation, memory, and top-down causation in living systems	4
Modeling the C. elegans germline stem cell genetic network using automated reasoning	4
Code biology and aesthetics	4
The informational turn in anthropogenesis: Integrating thermodynamic foundations with evolutionary mechanisms	4
The theory of oxygen hemoglobin association	4
Code Biology and abduction in the creative process	4
The polyphyletic origins of glycyl-tRNA synthetase and lysyl-tRNA synthetase and their implications	4
Biological thermodynamics: Ervin Bauer and the unification of life sciences and physics	4
miRNAFinder: A comprehensive web resource for plant Pre-microRNA classification	4
The cell as a semiotic system that realizes closure to efficient causation: The semiotic (M, R) system	4
Using monoids for the integration of genomic and metabolic parameters in the prediction of phenotypes in regulatory cascades	4
Food codes as an AI-based framework to investigate bird foraging ecology and interspecific interactions	4
Accurate phenotypic self-replication as a necessary cause for biological evolution.	4
Brain and behavior share features of a critical state dynamics	4
Coherence time in biological oscillator assemblies bounds the rate of state registration	4
Is Darwinian selection a retrograde driving force of evolution?	4
KMGTMDA: KAN-driven multiscale graph neural network and context-enhanced prediction for human microbe–disease associations	4