Biosystems

Article	Citations
Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game	51
Germline-specific nascent polypeptide-associated complex (NAC) subunits are predicted by bioinformatics tools to undergo phase separation	42
Theories of the origin of the genetic code: Strong corroboration for the coevolution theory	34
Developmental noise, entropy, and biological system condition	31
Filter feature selection based Boolean Modelling for Genetic Network Inference	30
The sensual cell: Feeling and affect in unicellular species	30
Evaluating the statistical similarity of neural network activity and connectivity via eigenvector angles	28
A survey of the methodological process of modeling, inference, and evaluation of gene regulatory networks using scRNA-Seq data	28
Effects of predator modulation and vector preference on pathogen transmission in plant populations	27
Optimizing ruminant nutrition: Insights from a comprehensive analysis of silage composition and in vitro gas production dynamics using nonlinear models	27
Temporal regulation of gene expression and pathways in chemotherapy-induced senescence in HeLa cervical cancer cell line	27
Book Review	26
Adaptive inference through Bayesian and inverse Bayesian inference with symmetry bias in nonstationary environments	24
Cartography of the multiple formal systems of molecular autopoiesis: from the biology of cognition and enaction to anticipation and active inference	24
Natural born intelligence manifesto: Illustrating the dynamic perspective for consciousness	23
Nuclear quantum effects explain chemiosmosis: The power of the proton	23
Field-induced coherence and Fröhlich condensation in hydrated DNA	22
From life to evolution: the differentiation between storage and interface in natural and cultural systems	22
The evolution and development of consciousness: the subject-object emergence hypothesis	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	20
The genetic code and its p-adic ultrametric modeling	20
A possible origin of life in nonpolar environments	20
Cholesterol-ester prevents lipoprotein core from solidifying: Molecular dynamics simulation	20
Loss of thermodynamic efficiency of various organs and functions of Drosophila melanogaster during aging	19

The mitochondrial challenge: Disorders and prevention strategies	19
An exploration of ecoacoustics and its applications in conservation ecology	18
The evolutionary arch of bioenergetics from prebiotic mechanisms to the emergence of a cellular respiratory chain	18
The grid-cell normative model: Unifying ‘principles’	18
Efim Liberman toward the comprehension of the phenomenon of life	17
Visualizing genomic data: The mixing perspective	16
The promoting effect of adaptive persistence aspiration on the cooperation based on the consideration of payoff and environment in prisoner's dilemma game	16
The metabolic control theory: Its development and its application to mitochondrial oxidative phosphorylation	16
Characterisation of the fig-fig wasp holobiont	16
The time of appearance of the genetic code	15
scSAGRN: Inferring gene regulatory networks from single-cell multi-omics using spatial association	15
Gaidai reliability method for high-dimensional spatio-temporal biosystems	15
Antagonistic coinfection in rock–paper–scissors models during concurrent epidemics	15
Three levels of information processing in the brain	15
Quantum formalism for indeterminate preferences in decision theory	15
Flux organizations and control modes in antagonistically combined negative feedback loops	14
Binary oppositions, algebraic holography and stochastic rules in genetic informatics	14
Whole-cell metabolic control analysis	14
The molecular memory code and synaptic plasticity: A synthesis	14
The evolution and biophysical economics of energy currencies: from prebiotic electrochemistry to modern digital money	13
Editorial Board	13
Identification of common factors among fibrosarcoma, rhabdomyosarcoma, and osteosarcoma by network analysis	13
The pseudoentropy of allele frequency trajectories, the persistence of variation, and the effective population size	13
On the emergence of eukaryotes and other enigmas	13
Editorial Board	13
Spatial organisation plasticity reduces disease infection risk in rock–paper–scissors models	13
Examining multi-objective deep reinforcement learning frameworks for molecular design	12
Book Review	12
Impacts of aging on circadian rhythm and related sleep disorders	12
The non-canonical nucleotides and prebiotic evolution	12
Modeling of the entangled states transfer processes in microtubule tryptophan system	12
Fragile X mental retardation protein modulates translation of proteins with predicted tendencies for liquid-liquid phase separation	12
Richness of emotion in people with dementia	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	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
Gradistics: An underappreciated dimension in evolutionary space	12
Editorial Board	12
Mutations, sex, and genetic diversity: New arguments for partially directed evolution	11
Brain aging mediates region-specific transcriptomic alterations	11
Editorial Board	11
Human face as a biosocial marker in human evolution	11
First evidence supporting the theory of the sensorimotor paradox on the origins of mind and language	11
Why the power of diversity does not always produce better groups and societies	11
Evolutionary change and adaptation as non-equilibrium thermodynamic processes	11
Constructal thermodynamics and its semantic ontology in autopoietic, digital, and computational architectural and urban space open systems	11
The role of pure mathematics in resolving complex biological problems: Applications to F1-ATPase, achievements, and future directions	11
Using steady-state formula to estimate time-dependent parameters of stochastic gene transcription models	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
Internal quantum constraints of natural computation in autopoietic systems	10
Regulative development as a model for origin of life and artificial life studies	10
The indispensable role of time in autonomous development	10
Editorial Board	10
A hybrid phase-synchronization framework for rotary motors: Discrete dynamics in ATP synthase and continuous dynamics in the bacterial flagellar motor	10
The role of self-maintaining resilient reaction networks in the origin and evolution of life	10
A simple and fast ANN-based method of studying slow-wave sleep microstructure in freely moving rats	10
The processes generating quantum entanglement in DNA	10
Dissipative scaling of development and aging in multicellular organisms	10
Paleo-phyllotaxis: Fucales, bryophytes, lycophytes and monilophytes	9
Nirmala indices bridge molecular connectivity and genetic stability: A graph-theoretic lens on purines and pyrimidines	9
Rational decision making in biological systems	9
Entropy and the arrow of time in population dynamics	9
Least ranked human individuals exhibit scale free behavioral responses in hierarchical social systems	9
Human cognitive limitations and emotions: The emergence of social complexity	9
Generalized model of closed microecosystem «alga - micro-consumers»	9
Effect of monochromatic light on the behavior of the ctenophore Mnemiopsis leidyi (A. Agassiz, 1865)	9
50 years of Metabolic Control Analysis: Its past and current influence in the biological sciences	9
CHTW(R)-system in Ca2+ transport modelling	9
The threat of asymptomatic carriers and the benefits of testing	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
Neural networks from biological to artificial and vice versa	8
From code to archetype: Toward a unified theory of biological, neural, and artificial artifacts	8
Dive into machine learning algorithms for influenza virus host prediction with hemagglutinin sequences	8
Ribonucleic acid genome mutations induced by the Casimir effect	8
Is there a bias in the codon frequency corresponding to homo-repeats found in human proteins?	8
The origin and evolution of life as continuing expansion of viral hosts	8
Logical modelling of myelofibrotic microenvironment predicts dysregulated progenitor stem cell crosstalk	8
Editorial Board	8
Temporal cohesion as a candidate for negentropy in biological thermodynamics	8
Avian influenza A H5N1 hemagglutinin protein models have distinct structural patterns re-occurring across the 1959–2023 strains	8
Small amphipathic amino acids imprint the active site of extant E. coli aminoacyl-tRNA synthetases	8
Quantum aspects of the brain-mind relationship: A hypothesis with supporting evidence	8
Towards the Big History of information. Approaching the origins of information behaviour	8
Generation of random sequences using DNA cryptography for OTP encryption	8
Energy transformation and nuclear spin catalysis: From magnetic isotope effects in chemical physics to ATP-dependent molecular motors in bioenergetics	7
Standard Genetic Code vs. Supersymmetry Genetic Code – Alphabetical table vs. physicochemical table	7
Reliability and energy function of an oscillator and map neuron	7
Corrigendum to “Pandemic preparedness and new model developments for airborne diseases transmitting via aerosols” [BioSystems 255 (2025) 105532]	7
Modeling autopoiesis and cognition with reaction networks	7
The theoretical foundations of enaction: Precariousness	7
Editorial Board	7
Entering the labyrinth: A hypothesis about the emergence of metabolism from protobiotic routes	7
Mechanism and biological significance of erythrocyte homoaggregation (rouleaux formation): temperature-dependent entropic liberation of water from cells and macromolecules	7
Embodied essentialism in the reconstruction of the animal sign in robot animal design	7
Data-driven dynamical modelling of a pathogen-infected plant gene regulatory network: A comparative analysis	7
Constructal thinking: Geospatial and temporal focal points of activity.	7
Aggregate Boid behavior to aid in artificial autopoietic organization	7
Cosmos, mind, matter: Is mind in spacetime?	7
Machine-learning-based structural analysis of interactions between antibodies and antigens	7
Use of directed quasi-metric distances for quantifying the information of gene families	7
Transformation of the inherent energy in food to ATP and transformations of our knowledge about the mechanism	7
An irreversible thermodynamic model of prebiological dissipative molecular structures inside vacuoles at the surface of the Archean Ocean	7
A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem	7
Editorial Board	7
Impact of social reward on the evolution of cooperation in voluntary prisoner’s dilemma	6
On the minimal elements of the genetic code and their semiotic functions (degeneracy, complementarity, wobbling)	6
The chromolinker hypothesis: Are eukaryotic genomes also circular?	6
A quantum-like information processing model with memory noise for question order effect	6
Physical factors in origin of genetic code	6
Autopoiesis: Foundations of life, cognition, and emergence of self/other	6
Deciphering the dynamic binding of spicy odorants to human olfactory receptors	6
Information–energy equivalence and the emergence of self-replicating biological systems	6
Mathematical model of coffee tree’s rust control using snails as biological agents	6
Balancing the cellular budget: Lessons in metabolism from microbes to cancer	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
When Maxwell’s Demon leaves the room	6
Generation of genetic codes with 2-adic codon algebra and adaptive dynamics	6
Spiking neural networks produce informational closure by stimulus avoidance	6
A multi-cell model for the C4 photosynthetic pathway in developing wheat grains based upon tissue-specific transcriptome data	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
Prediction of prokaryotic and eukaryotic promoters based on information-theoretic features	6
The origins of the cell membrane, the progenote, and the universal ancestor (LUCA)	6
Thermal diodes, transistors and logic: Review of unconventional computing methods	5
Psychological origin of quantum logic: An orthomodular lattice derived from natural-born intelligence without Hilbert space	5

The problem of evolutionary directionality 50 years following the works of Sergei Meyen	5
Application of fractal theory in cancer detection: A review	5
Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach	5
Fundamental principles of biology as pure natural science and their applications in physiology and pathology	5
Combination of survival movement strategies in cyclic game systems during an epidemic	5
Robustness and evolvability: Revisited, redefined and applied	5
Evolution of cooperation in multigame with environmental space and delay	5
Editorial Board	5
A computational design of a programmable biological processor	5
Thermal Model for investigating the timing of the onset of phenological events in ectotherms and the technique of estimating its parameters	5
Intelligence as high-dimensional coherence: The observable dimensionality bound and computational tractability	5
The Molecular Basis of Differentiation Wave Activity in Embryogenesis	5
Evolutionary origin of B family DNA-dependent DNA polymerases from retrotranscriptases	5
Understanding nature’s selection of genetic languages	5
Evolution and maintenance of phenotypic plasticity	5
Editorial Board	5
An efficient approach for identifying important biomarkers for biomedical diagnosis	5
Toward a unified theory of ATP synthesis/hydrolysis: Integrating physics, chemistry, and biology	5
Effect of the electromagnetic induction in the electrical activity of the Kazantsev model of inferior Olive Neuron model	5
A new method: Characterize and quantify biofilm wrinkles by UNet and Sholl Analysis	5
Synchronization Studies of Hindmarsh–Rose Neuron Networks: Unraveling the Influence of connection induced memristive synapse	5
Estimation of discrepancy of color qualia using Kullback-Leibler divergence	5
A Unified Holographic Framework for neural computation and consciousness: From lipid membranes to the Schumann resonance	5
Editorial Board	5
Is Darwinian selection a retrograde driving force of evolution?	4
Codes across (life)sciences	4
miRNAFinder: A comprehensive web resource for plant Pre-microRNA classification	4
Collective computational intelligence in biology – Emergence of memory in somatic tissues	4
A control measure for epidemic spread based on the susceptible–infectious–susceptible (SIS) model	4
Exploring potential size-dependent effects of Fibonacci-based acoustic binary strings on cells as measured by cell death and cell aggregation patterns	4
Editorial Board	4
Brain and behavior share features of a critical state dynamics	4
Identification of multivariable Boolean patterns in microbiome and microbial gene composition data	4
How organisms decrease their entropy	4
Coherence time in biological oscillator assemblies bounds the rate of state registration	4
Quantum concepts in Psychology: Exploring the interplay of physics and the human psyche	4
Benchmark for quantitative characterization of circadian clock cycles	4
Construction of amino acids reduced alphabets from molecular descriptors for interpretation of N-carbamylase, luciferase and PI3K mutations	4
The polyphyletic origins of glycyl-tRNA synthetase and lysyl-tRNA synthetase and their implications	4
Viscous DNA and RNA: Quantum damped dynamical random systems	4
Is meaning commensurable in scientific theories? From arbitrariness to non-nomological relations in meaning-making	4
The limits of falsifiability: Dimensionality, measurement thresholds, and the sub-Landauer domain in biological systems	4
On the infodynamics of ramifications in constructal design	4
Statistical algorithms for the analysis of deleterious genetic mutations	4
Corrigendum to “Paleo-phyllotaxis: Fucales, bryophytes, lycophytes and monilophytes” [BioSystems 255 (2025) 105541]	4
Life, its definition, origin, evolution, and four-dimensional hierarchical structure	4
Formal autopoiesis: Solutions of the classical and extended functional closure equations	4
Accurate phenotypic self-replication as a necessary cause for biological evolution.	4
Fractional nutrient uptake model of plant roots	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
The cell as a semiotic system that realizes closure to efficient causation: The semiotic (M, R) system	4
Biological thermodynamics: Ervin Bauer and the unification of life sciences and physics	4
Influence of oxidative stress on women’s fertility: A model with a generational age Caputo’s fractional derivative	4
Structural analyzes suggest that MiSSP13 and MiSSP16.5 may act as proteases inhibitors during ectomycorrhiza establishment in Laccaria bicolor	4
Coacervates meet the RNP-world: liquid-liquid phase separation and the emergence of biological compartmentalization	4
The theory of oxygen hemoglobin association	4
Neurons as hierarchies of quantum reference frames	4
Food codes as an AI-based framework to investigate bird foraging ecology and interspecific interactions	4
Code Biology and abduction in the creative process	4
Editorial Board	4
An energy landscape-based theoretical framework for understanding the self-organization of functions in a living system under the dynamical component interaction	4
Cosmos MIND and matter: Is mind in spacetime?	4
Anticipation, memory, and top-down causation in living systems	4
Origin of the temporal stability control of living system nonequilibrium	4
Using monoids for the integration of genomic and metabolic parameters in the prediction of phenotypes in regulatory cascades	4
Bioinformatics and meta-analysis of expression data to investigate transcriptomic response of wheat root to abiotic stresses	4
Perfection is the enemy of evolution	4
Variance-dependent inheritance fidelity drives residence-time symmetry breaking in a protocell model	4
KMGTMDA: KAN-driven multiscale graph neural network and context-enhanced prediction for human microbe–disease associations	4
Ambush strategy impacts species predominance and coexistence in generalised rock–paper–scissors models	4
Simulating tumor mitochondrial energetics through engineering-style energy metrics	4
Corrigendum to “The concepts of code biology” [Biosyst. 248 (2025) 105400 1–6]	4
Memory induced-mechanism of noise attenuator of myosin V molecular motors	4
A hybrid DNN model using novel integrated interface features for predicting protein-protein complexes binding affinity	3
The fundamental theorem of natural selection in optimization and games	3
Swelling and membrane potential dynamics of glial Müller cells	3
The meaning of life in a universe whose ultimate origins are unknown	3
Temperature dependence of IR exciton emission spectra in Müller cell intermediate filaments	3
Viruses, immunity and evolution	3
What kinds of empirical correlates for a general theory of living organization? Revisiting the ( )-system and its ‘replication’	3
The cell as a realization of the (M, R) system	3
Oncogenetic pedigrees: Relation between design and ability to predict mutation	3
Minimizing enzyme mass to decompose flux distribution for identifying biologically relevant elementary flux modes	3
Software for evaluation of immune cell activation (Application note)	3
Analytical solution of Nye–Tinker–Barber model by Laplace transform	3
A memory access gate controlled by dynamic contexts	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
Chemical oscillatory reactions with proteinoids	3
Stages and causes of the evolution of language and consciousness: A theoretical reconstruction	3
Computation by inverse causality: A universal principle to produce symbols for the external reality in living systems	3
The reversibility of cellular determination: An evolutive pattern of epigenetic plasticity	3
Distributional features of triplet codons in genomes underlie the diversification of life	3
Consequences of asymmetric mutational pressure for the dynamic of linear B-cell epitopes repertoire of influenza a virus neuraminidase rearrangement	3
Comparing the complexity of written and molecular symbolic systems	3
Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples	3