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
Filter feature selection based Boolean Modelling for Genetic Network Inference	28
Field-induced coherence and Fröhlich condensation in hydrated DNA	28
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
From life to evolution: the differentiation between storage and interface in natural and cultural systems	23
A survey of the methodological process of modeling, inference, and evaluation of gene regulatory networks using scRNA-Seq data	22
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
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
Editorial Board	19
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
Temporal regulation of gene expression and pathways in chemotherapy-induced senescence in HeLa cervical cancer cell line	18
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
A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information	17
Efim Liberman toward the comprehension of the phenomenon of life	16
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 time of appearance of the genetic code	15
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
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
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
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
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
Editorial Board	12
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
Impacts of aging on circadian rhythm and related sleep disorders	11
A mechanistic approach to optimize combination antibiotic therapy	11
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

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
Rational decision making in biological systems	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
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
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
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
Quantum aspects of the brain-mind relationship: A hypothesis with supporting evidence	9
Generation of random sequences using DNA cryptography for OTP encryption	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
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
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
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
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
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
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
Bioinformatics and meta-analysis of expression data to investigate transcriptomic response of wheat root to abiotic stresses	5
Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach	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

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
A new method: Characterize and quantify biofilm wrinkles by UNet and Sholl Analysis	5
Construction of amino acids reduced alphabets from molecular descriptors for interpretation of N-carbamylase, luciferase and PI3K mutations	5
Estimation of discrepancy of color qualia using Kullback-Leibler divergence	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
Editorial Board	5
Brain and behavior share features of a critical state dynamics	5
On the infodynamics of ramifications in constructal design	5
Editorial Board	5
The Molecular Basis of Differentiation Wave Activity in Embryogenesis	5
Evolutionary origin of B family DNA-dependent DNA polymerases from retrotranscriptases	5
Structural analyzes suggest that MiSSP13 and MiSSP16.5 may act as proteases inhibitors during ectomycorrhiza establishment in Laccaria bicolor	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
Synchronization Studies of Hindmarsh–Rose Neuron Networks: Unraveling the Influence of connection induced memristive synapse	5
Perfection is the enemy of evolution	4
Identification of multivariable Boolean patterns in microbiome and microbial gene composition data	4
Life, its definition, origin, evolution, and four-dimensional hierarchical structure	4
Editorial Board	4
Using neurons to maintain autonomy: Learning from C. elegans	4
Viscous DNA and RNA: Quantum damped dynamical random systems	4
Statistical algorithms for the analysis of deleterious genetic mutations	4
The effect of avian eggshell membrane structure on microbial penetration: A simulation study	4
Predator–prey population dynamics may induce the evolutionary dynamics of behavioral unpredictability	4
Modeling the C. elegans germline stem cell genetic network using automated reasoning	4
Two theories of action - Edelman's Neuronal group Selection and the Poetics of Paul Valéry	4
On electrical gates on fungal colony	4
The phylogenetic distribution of the cell division system would not imply a cellular LUCA but a progenotic LUCA	4
The repertoire of candidate archaeal noncoding RNAs and their association with temperature adaptation	4
Codes across (life)sciences	4
The theory of oxygen hemoglobin association	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
miRNAFinder: A comprehensive web resource for plant Pre-microRNA classification	4
Social satisficing: Multi-agent reinforcement learning with satisficing agents	4
Toward understanding the emergence of life: A dual function of the system of nucleotides in the metabolically closed autopoietic organization	4
A control measure for epidemic spread based on the susceptible–infectious–susceptible (SIS) model	4
Towards a Possible Definition of Consciousness	4
Impact of transposable elements on the evolution of complex living systems and their epigenetic control	4
Disproportional fraction of inactive components leads to the variation in metabolic scaling	4
Accurate phenotypic self-replication as a necessary cause for biological evolution.	4
Memory induced-mechanism of noise attenuator of myosin V molecular motors	4
Corrigendum to “The concepts of code biology” [Biosyst. 248 (2025) 105400 1–6]	4
Modeling of will and consciousness based on the human language: Interpretation of qualia and psychological consciousness	4
Collective computational intelligence in biology – Emergence of memory in somatic tissues	4
Cosmos MIND and matter: Is mind in spacetime?	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
Code Biology and abduction in the creative process	4
The regulatory network that controls lymphopoiesis	4
Overview of the third special issue in code biology	4
Corrigendum to “Role of calcium oscillations in sperm physiology” [BioSystems 209 (2021) 104524]	4
Neurons as hierarchies of quantum reference frames	4
Is Darwinian selection a retrograde driving force of evolution?	4
Collective excitations at non-equilibrium phase transition in metabolically active red blood cells	4
A multi-modal algorithm based on an NSGA-II scheme for phylogenetic tree inference	4
Code biology and aesthetics	4
Is meaning commensurable in scientific theories? From arbitrariness to non-nomological relations in meaning-making	4
Prigoginian informational dissipation (PID) as the cause of the emergence of a proto-self	4
Food codes as an AI-based framework to investigate bird foraging ecology and interspecific interactions	4
Simulation peptide toxicity using the fragments of local symmetry in amino acid sequences	3
COVID-19 spatio-temporal forecast in England	3
The reversibility of cellular determination: An evolutive pattern of epigenetic plasticity	3
The fundamental theorem of natural selection in optimization and games	3
Oncogenetic pedigrees: Relation between design and ability to predict mutation	3
Stages and causes of the evolution of language and consciousness: A theoretical reconstruction	3
Editorial Board	3
Circular mixed sets	3
Quantifying pleiotropy through directed signaling networks: A synchronous Boolean network approach and in-silico pleiotropic scoring	3
Metabolic limits on classical information processing by biological cells	3
Minimizing enzyme mass to decompose flux distribution for identifying biologically relevant elementary flux modes	3
Human-driven spreading and evolution of plants during the Holocene epoch: The pioneering works of Valery Taliev	3
Revisiting Carl Jung’s archetype theory a psychobiological approach	3
A novel approach to encode melodies in DNA	3
Elucidation of productive alanine recognition mechanism by Escherichia coli alanyl-tRNA synthetase	3
Learning and memory in soldier crabs: Evidence from escape task trials	3
Memory retrieval dynamics and storage capacity of a modular network model of association cortex with featural decomposition	3
Rule-based modelling of biological systems using regulated rewriting	3
Swelling and membrane potential dynamics of glial Müller cells	3
Computation by inverse causality: A universal principle to produce symbols for the external reality in living systems	3
Decoding viruses: An alternative perspective on their history, origins and role in nature	3
Modelling the fitness landscapes of a SCRaMbLEd yeast genome	3
Evolution of small and large ribosomal RNAs from accretion of tRNA subelements	3