Biosystems

Article	Citations
Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game	45
Developmental noise, entropy, and biological system condition	39
A survey of the methodological process of modeling, inference, and evaluation of gene regulatory networks using scRNA-Seq data	29
Evaluating the statistical similarity of neural network activity and connectivity via eigenvector angles	29
Cartography of the multiple formal systems of molecular autopoiesis: from the biology of cognition and enaction to anticipation and active inference	28
Effects of predator modulation and vector preference on pathogen transmission in plant populations	26
Morphological forms arising from the evolutionary process are topologies	25
Field-induced coherence and Fröhlich condensation in hydrated DNA	24
Editorial Board	24
From life to evolution: the differentiation between storage and interface in natural and cultural systems	22
Book Review	22
The sensual cell: Feeling and affect in unicellular species	21
Optimizing ruminant nutrition: Insights from a comprehensive analysis of silage composition and in vitro gas production dynamics using nonlinear models	21
Filter feature selection based Boolean Modelling for Genetic Network Inference	21
Temporal regulation of gene expression and pathways in chemotherapy-induced senescence in HeLa cervical cancer cell line	19
Natural born intelligence manifesto: Illustrating the dynamic perspective for consciousness	19
Theories of the origin of the genetic code: Strong corroboration for the coevolution theory	19
A possible origin of life in nonpolar environments	19
Nuclear quantum effects explain chemiosmosis: The power of the proton	19
Cholesterol-ester prevents lipoprotein core from solidifying: Molecular dynamics simulation	18
A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information	18
Negative membrane potentials potentiate multicellularity	18
The grid-cell normative model: Unifying ‘principles’	18
The genetic code and its p-adic ultrametric modeling	18
The evolutionary arch of bioenergetics from prebiotic mechanisms to the emergence of a cellular respiratory chain	18

Efim Liberman toward the comprehension of the phenomenon of life	17
The mitochondrial challenge: Disorders and prevention strategies	17
Three levels of information processing in the brain	16
Binary oppositions, algebraic holography and stochastic rules in genetic informatics	16
Visualizing genomic data: The mixing perspective	16
The time of appearance of the genetic code	16
Whole-cell metabolic control analysis	16
The metabolic control theory: Its development and its application to mitochondrial oxidative phosphorylation	16
The promoting effect of adaptive persistence aspiration on the cooperation based on the consideration of payoff and environment in prisoner's dilemma game	15
Characterisation of the fig-fig wasp holobiont	15
scSAGRN: Inferring gene regulatory networks from single-cell multi-omics using spatial association	15
The evolution and development of consciousness: the subject-object emergence hypothesis	14
Quantum formalism for indeterminate preferences in decision theory	14
The molecular memory code and synaptic plasticity: A synthesis	14
Antagonistic coinfection in rock–paper–scissors models during concurrent epidemics	14
Editorial Board	13
Identification of common factors among fibrosarcoma, rhabdomyosarcoma, and osteosarcoma by network analysis	13
Gaidai reliability method for high-dimensional spatio-temporal biosystems	13
On the emergence of eukaryotes and other enigmas	13
Editorial Board	13
Fragile X mental retardation protein modulates translation of proteins with predicted tendencies for liquid-liquid phase separation	13
The origins of photosynthetic systems: Clues from the phosphorus and sulphur chemical scenarios	13
An exploration of ecoacoustics and its applications in conservation ecology	13
Book Review	12
Impacts of aging on circadian rhythm and related sleep disorders	12
Editorial Board	12
Gradistics: An underappreciated dimension in evolutionary space	12
Spatial organisation plasticity reduces disease infection risk in rock–paper–scissors models	12
Editorial Board	12
The evolution and biophysical economics of energy currencies: from prebiotic electrochemistry to modern digital money	12
The pseudoentropy of allele frequency trajectories, the persistence of variation, and the effective population size	12
Microbial mutualism promoting the coexistence of competing species: Double-layer model for two competing hosts and one microbial species	12
The non-canonical nucleotides and prebiotic evolution	11
Modeling of the entangled states transfer processes in microtubule tryptophan system	11
Examining multi-objective deep reinforcement learning frameworks for molecular design	11
The processes generating quantum entanglement in DNA	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
Editorial Board	11
Richness of emotion in people with dementia	11
Unexpected extra exon skipping in the DYSF gene during restoring the reading frame by CRISPR/Cas9	11
Mutations, sex, and genetic diversity: New arguments for partially directed evolution	11
Using steady-state formula to estimate time-dependent parameters of stochastic gene transcription models	10
Dissipative scaling of development and aging in multicellular organisms	10
Regulative development as a model for origin of life and artificial life studies	10
Ecological drivers for the absence of task shifting in termite-tunneling activity: A simulation study	10
Human face as a biosocial marker in human evolution	10
Editorial Board	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

Avian influenza A H5N1 hemagglutinin protein models have distinct structural patterns re-occurring across the 1959–2023 strains	10
Why the power of diversity does not always produce better groups and societies	10
2-adic morphogenesis as a metaphorical model of biological growth	10
A hybrid phase-synchronization framework for rotary motors: Discrete dynamics in ATP synthase and continuous dynamics in the bacterial flagellar motor	10
Editorial Board	10
The role of pure mathematics in resolving complex biological problems: Applications to F1-ATPase, achievements, and future directions	10
From code to archetype: Toward a unified theory of biological, neural, and artificial artifacts	9
CHTW(R)-system in Ca2+ transport modelling	9
Paleo-phyllotaxis: Fucales, bryophytes, lycophytes and monilophytes	9
Corrigendum to “An efficient approach for identifying important biomarkers for biomedical diagnosis” [Biosystems 237 (2024) 105163]	9
50 years of Metabolic Control Analysis: Its past and current influence in the biological sciences	9
The origin and evolution of life as continuing expansion of viral hosts	9
Rational decision making in biological systems	9
A simple and fast ANN-based method of studying slow-wave sleep microstructure in freely moving rats	9
Is there a bias in the codon frequency corresponding to homo-repeats found in human proteins?	9
The threat of asymptomatic carriers and the benefits of testing	9
Quantum aspects of the brain-mind relationship: A hypothesis with supporting evidence	9
The indispensable role of time in autonomous development	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)	8
Generation of random sequences using DNA cryptography for OTP encryption	8
Least ranked human individuals exhibit scale free behavioral responses in hierarchical social systems	8
Molecular mechanisms of encoding and decoding information in cell computing	8
Dynamic modelling and tristability analysis of misfolded α-synuclein degraded via autophagy in Parkinson's disease	8
Dive into machine learning algorithms for influenza virus host prediction with hemagglutinin sequences	8
Entropy and the arrow of time in population dynamics	8
Logical modelling of myelofibrotic microenvironment predicts dysregulated progenitor stem cell crosstalk	8
Temporal cohesion as a candidate for negentropy in biological thermodynamics	7
Modeling autopoiesis and cognition with reaction networks	7
Human cognitive limitations and emotions: The emergence of social complexity	7
Use of directed quasi-metric distances for quantifying the information of gene families	7
Mechanism and biological significance of erythrocyte homoaggregation (rouleaux formation): temperature-dependent entropic liberation of water from cells and macromolecules	7
Machine-learning-based structural analysis of interactions between antibodies and antigens	7
Order stability via Fröhlich condensation in bio, eco, and social systems: The quantum-like approach	7
Ribonucleic acid genome mutations induced by the Casimir effect	7
An irreversible thermodynamic model of prebiological dissipative molecular structures inside vacuoles at the surface of the Archean Ocean	7
Neural networks from biological to artificial and vice versa	7
The theoretical foundations of enaction: Precariousness	7
Standard Genetic Code vs. Supersymmetry Genetic Code – Alphabetical table vs. physicochemical table	7
Data-driven dynamical modelling of a pathogen-infected plant gene regulatory network: A comparative analysis	7
Entering the labyrinth: A hypothesis about the emergence of metabolism from protobiotic routes	7
Reliability and energy function of an oscillator and map neuron	7
Towards the Big History of information. Approaching the origins of information behaviour	7
Transformation of the inherent energy in food to ATP and transformations of our knowledge about the mechanism	7
A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem	7
Editorial Board	7
Embodied essentialism in the reconstruction of the animal sign in robot animal design	7
Energy transformation and nuclear spin catalysis: From magnetic isotope effects in chemical physics to ATP-dependent molecular motors in bioenergetics	7
Corrigendum to “Pandemic preparedness and new model developments for airborne diseases transmitting via aerosols” [BioSystems 255 (2025) 105532]	7
Editorial Board	6
When Maxwell’s Demon leaves the room	6
Impact of social reward on the evolution of cooperation in voluntary prisoner’s dilemma	6
A multi-cell model for the C4 photosynthetic pathway in developing wheat grains based upon tissue-specific transcriptome data	6
Spiking neural networks produce informational closure by stimulus avoidance	6
The origins of the cell membrane, the progenote, and the universal ancestor (LUCA)	6
Cosmos, mind, matter: Is mind in spacetime?	6
Information–energy equivalence and the emergence of self-replicating biological systems	6
Autopoiesis: Foundations of life, cognition, and emergence of self/other	6
Prediction of prokaryotic and eukaryotic promoters based on information-theoretic features	6
Aggregate Boid behavior to aid in artificial autopoietic organization	6
Generation of genetic codes with 2-adic codon algebra and adaptive dynamics	6
Editorial Board	6
On the minimal elements of the genetic code and their semiotic functions (degeneracy, complementarity, wobbling)	6
Cell jamming-to-unjamming transitions and vice versa in development: Physical aspects	6
The problem of evolutionary directionality 50 years following the works of Sergei Meyen	5
Bioinformatics and meta-analysis of expression data to investigate transcriptomic response of wheat root to abiotic stresses	5
The Molecular Basis of Differentiation Wave Activity in Embryogenesis	5
Estimation of discrepancy of color qualia using Kullback-Leibler divergence	5
Fractional nutrient uptake model of plant roots	5
A new method: Characterize and quantify biofilm wrinkles by UNet and Sholl Analysis	5
A computational design of a programmable biological processor	5
Electrical frequency discrimination by fungi Pleurotus ostreatus	5
Evolutionary stability of developmental commitment	5
Mathematical model of coffee tree’s rust control using snails as biological agents	5
Combination of survival movement strategies in cyclic game systems during an epidemic	5
Psychological origin of quantum logic: An orthomodular lattice derived from natural-born intelligence without Hilbert space	5
Editorial Board	5
How organisms decrease their entropy	5
Structural analyzes suggest that MiSSP13 and MiSSP16.5 may act as proteases inhibitors during ectomycorrhiza establishment in Laccaria bicolor	5
Evolution and maintenance of phenotypic plasticity	5

Thermal diodes, transistors and logic: Review of unconventional computing methods	5
Effect of the electromagnetic induction in the electrical activity of the Kazantsev model of inferior Olive Neuron model	5
Identification of Ca	5
Modelling energy-harvesting processes in primitive cells: Proton transport across bilayers driven by the oxidation of sulfite	5
Balancing the cellular budget: Lessons in metabolism from microbes to cancer	5
Evolution of cooperation in multigame with environmental space and delay	5
Toward a unified theory of ATP synthesis/hydrolysis: Integrating physics, chemistry, and biology	5
Evolutionary origin of B family DNA-dependent DNA polymerases from retrotranscriptases	5
Influence of oxidative stress on women’s fertility: A model with a generational age Caputo’s fractional derivative	5
Benchmark for quantitative characterization of circadian clock cycles	5
Understanding nature’s selection of genetic languages	5
A quantum-like information processing model with memory noise for question order effect	5
Causal intuition in the indefinite world: Meta-analysis and simulations	5
The chromolinker hypothesis: Are eukaryotic genomes also circular?	5
An efficient approach for identifying important biomarkers for biomedical diagnosis	5
A Unified Holographic Framework for neural computation and consciousness: From lipid membranes to the Schumann resonance	5
On the infodynamics of ramifications in constructal design	4
Accurate phenotypic self-replication as a necessary cause for biological evolution.	4
The polyphyletic origins of glycyl-tRNA synthetase and lysyl-tRNA synthetase and their implications	4
Corrigendum to “Paleo-phyllotaxis: Fucales, bryophytes, lycophytes and monilophytes” [BioSystems 255 (2025) 105541]	4
Robustness and evolvability: Revisited, redefined and applied	4
Corrigendum to “The concepts of code biology” [Biosyst. 248 (2025) 105400 1–6]	4
Statistical algorithms for the analysis of deleterious genetic mutations	4
Toward understanding the emergence of life: A dual function of the system of nucleotides in the metabolically closed autopoietic organization	4
miRNAFinder: A comprehensive web resource for plant Pre-microRNA classification	4
Neurons as hierarchies of quantum reference frames	4
Origin of the temporal stability control of living system nonequilibrium	4
Viscous DNA and RNA: Quantum damped dynamical random systems	4
Biological thermodynamics: Ervin Bauer and the unification of life sciences and physics	4
Code biology and aesthetics	4
Codes across (life)sciences	4
Prigoginian informational dissipation (PID) as the cause of the emergence of a proto-self	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
Construction of amino acids reduced alphabets from molecular descriptors for interpretation of N-carbamylase, luciferase and PI3K mutations	4
Predator–prey population dynamics may induce the evolutionary dynamics of behavioral unpredictability	4
Food codes as an AI-based framework to investigate bird foraging ecology and interspecific interactions	4
Synchronization Studies of Hindmarsh–Rose Neuron Networks: Unraveling the Influence of connection induced memristive synapse	4
Fundamental principles of biology as pure natural science and their applications in physiology and pathology	4
Formal autopoiesis: Solutions of the classical and extended functional closure equations	4
Code Biology and abduction in the creative process	4
Using monoids for the integration of genomic and metabolic parameters in the prediction of phenotypes in regulatory cascades	4
The repertoire of candidate archaeal noncoding RNAs and their association with temperature adaptation	4
The theory of oxygen hemoglobin association	4
Collective excitations at non-equilibrium phase transition in metabolically active red blood cells	4
Coacervates meet the RNP-world: liquid-liquid phase separation and the emergence of biological compartmentalization	4
Memory induced-mechanism of noise attenuator of myosin V molecular motors	4
Perfection is the enemy of evolution	4
Disproportional fraction of inactive components leads to the variation in metabolic scaling	4
Collective computational intelligence in biology – Emergence of memory in somatic tissues	4
Life, its definition, origin, evolution, and four-dimensional hierarchical structure	4
The cell as a semiotic system that realizes closure to efficient causation: The semiotic (M, R) system	4
A multi-modal algorithm based on an NSGA-II scheme for phylogenetic tree inference	4
Brain and behavior share features of a critical state dynamics	4
Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach	4
Quantum concepts in Psychology: Exploring the interplay of physics and the human psyche	4
Anticipation, memory, and top-down causation in living systems	4
A control measure for epidemic spread based on the susceptible–infectious–susceptible (SIS) model	4
Is Darwinian selection a retrograde driving force of evolution?	4
Identification of multivariable Boolean patterns in microbiome and microbial gene composition data	4
Modeling the C. elegans germline stem cell genetic network using automated reasoning	4
Is meaning commensurable in scientific theories? From arbitrariness to non-nomological relations in meaning-making	4
Modeling of will and consciousness based on the human language: Interpretation of qualia and psychological consciousness	4
Cosmos MIND and matter: Is mind in spacetime?	4
Towards a Possible Definition of Consciousness	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 limits of falsifiability: Dimensionality, measurement thresholds, and the sub-Landauer domain in biological systems	4
Elucidation of productive alanine recognition mechanism by Escherichia coli alanyl-tRNA synthetase	3
Major transitions in the physiological machinery of cognition	3
Evolution of small and large ribosomal RNAs from accretion of tRNA subelements	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
Oncogenetic pedigrees: Relation between design and ability to predict mutation	3
Swelling and membrane potential dynamics of glial Müller cells	3
Decoding viruses: An alternative perspective on their history, origins and role in nature	3
Fractal calculus in tumor growth simulations: The proof is in the pudding	3
Editorial Board	3
Learning and memory in soldier crabs: Evidence from escape task trials	3
Stages and causes of the evolution of language and consciousness: A theoretical reconstruction	3
Memory retrieval dynamics and storage capacity of a modular network model of association cortex with featural decomposition	3
Corrigendum to “Cosmos, mind, matter: Is mind in spacetime?” [Biosyst. (2024) 105262]	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
Non-monotone cellular automata: Order prevails over chaos	3
Chemical oscillatory reactions with proteinoids	3
A novel approach to encode melodies in DNA	3
150 Years since the birth of Lev Berg: Nomogenesis is more relevant today than ever	3
Quantifying pleiotropy through directed signaling networks: A synchronous Boolean network approach and in-silico pleiotropic scoring	3
The fundamental theorem of natural selection in optimization and games	3
Revisiting Carl Jung’s archetype theory a psychobiological approach	3
Computation by inverse causality: A universal principle to produce symbols for the external reality in living systems	3
A hybrid DNN model using novel integrated interface features for predicting protein-protein complexes binding affinity	3
Distributional features of triplet codons in genomes underlie the diversification of life	3
Rule-based modelling of biological systems using regulated rewriting	3
Circular mixed sets	3
Modelling the fitness landscapes of a SCRaMbLEd yeast genome	3