Biosystems

Article	Citations
Optimizing ruminant nutrition: Insights from a comprehensive analysis of silage composition and in vitro gas production dynamics using nonlinear models	45
Temporal regulation of gene expression and pathways in chemotherapy-induced senescence in HeLa cervical cancer cell line	39
From life to evolution: the differentiation between storage and interface in natural and cultural systems	29
Developmental noise, entropy, and biological system condition	29
Nuclear quantum effects explain chemiosmosis: The power of the proton	28
A survey of the methodological process of modeling, inference, and evaluation of gene regulatory networks using scRNA-Seq data	25
Hypothesis of macroscopic quantum state in biological systems and discussion on the possibility of its experimental verification	24
Cartography of the multiple formal systems of molecular autopoiesis: from the biology of cognition and enaction to anticipation and active inference	24
Effects of predator modulation and vector preference on pathogen transmission in plant populations	23
VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology	22
Morphological forms arising from the evolutionary process are topologies	22
Editorial Board	21
Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game	21
Evaluating the statistical similarity of neural network activity and connectivity via eigenvector angles	21
Field-induced coherence and Fröhlich condensation in hydrated DNA	19
The major evolutionary transitions and codes of life	19
A possible origin of life in nonpolar environments	18
The sensual cell: Feeling and affect in unicellular species	18
Cholesterol-ester prevents lipoprotein core from solidifying: Molecular dynamics simulation	18
Theories of the origin of the genetic code: Strong corroboration for the coevolution theory	18
Book Review	18
Negative membrane potentials potentiate multicellularity	18
Filter feature selection based Boolean Modelling for Genetic Network Inference	18
The promoting effect of adaptive persistence aspiration on the cooperation based on the consideration of payoff and environment in prisoner's dilemma game	17
Three levels of information processing in the brain	17

A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information	17
The evolutionary arch of bioenergetics from prebiotic mechanisms to the emergence of a cellular respiratory chain	17
The genetic code and its p-adic ultrametric modeling	17
Characterisation of the fig-fig wasp holobiont	16
Reversible and irreversible mitochondrial swelling: Effects of variable mitochondrial activity	15
Efim Liberman toward the comprehension of the phenomenon of life	15
Whole-cell metabolic control analysis	15
The time of appearance of the genetic code	15
The grid-cell normative model: Unifying ‘principles’	15
scSAGRN: Inferring gene regulatory networks from single-cell multi-omics using spatial association	14
Visualizing genomic data: The mixing perspective	14
Binary oppositions, algebraic holography and stochastic rules in genetic informatics	14
The mitochondrial challenge: Disorders and prevention strategies	14
The evolution and development of consciousness: the subject-object emergence hypothesis	14
An exploration of ecoacoustics and its applications in conservation ecology	14
Gaidai reliability method for high-dimensional spatio-temporal biosystems	14
The metabolic control theory: Its development and its application to mitochondrial oxidative phosphorylation	14
Antagonistic coinfection in rock–paper–scissors models during concurrent epidemics	13
In search for evolutionary roots of a mindful cognition: A Darwinian view on sustained intentional awareness	13
Editorial Board	13
The pseudoentropy of allele frequency trajectories, the persistence of variation, and the effective population size	13
The molecular memory code and synaptic plasticity: A synthesis	13
On the emergence of eukaryotes and other enigmas	12
The origins of photosynthetic systems: Clues from the phosphorus and sulphur chemical scenarios	12
Editorial Board	12
Identification of common factors among fibrosarcoma, rhabdomyosarcoma, and osteosarcoma by network analysis	12
Modeling of the entangled states transfer processes in microtubule tryptophan system	11
The evolution and biophysical economics of energy currencies: from prebiotic electrochemistry to modern digital money	11
Editorial Board	11
Fragile X mental retardation protein modulates translation of proteins with predicted tendencies for liquid-liquid phase separation	11
A mechanistic approach to optimize combination antibiotic therapy	11
Examining multi-objective deep reinforcement learning frameworks for molecular design	11
Book Review	11
Microbial mutualism promoting the coexistence of competing species: Double-layer model for two competing hosts and one microbial species	11
Gradistics: An underappreciated dimension in evolutionary space	11
Richness of emotion in people with dementia	11
Editorial Board	11
Impacts of aging on circadian rhythm and related sleep disorders	11
Spatial organisation plasticity reduces disease infection risk in rock–paper–scissors models	11
Human face as a biosocial marker in human evolution	10
Editorial Board	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
2-adic morphogenesis as a metaphorical model of biological growth	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
The processes generating quantum entanglement in DNA	10
Unexpected extra exon skipping in the DYSF gene during restoring the reading frame by CRISPR/Cas9	10
Mutations, sex, and genetic diversity: New arguments for partially directed evolution	10
Using steady-state formula to estimate time-dependent parameters of stochastic gene transcription models	10

Editorial Board	10
The role of self-maintaining resilient reaction networks in the origin and evolution of life	10
The non-canonical nucleotides and prebiotic evolution	10
A hybrid phase-synchronization framework for rotary motors: Discrete dynamics in ATP synthase and continuous dynamics in the bacterial flagellar motor	10
Why the power of diversity does not always produce better groups and societies	10
Editorial Board	10
The role of pure mathematics in resolving complex biological problems: Applications to F1-ATPase, achievements, and future directions	10
Entropy and the arrow of time in population dynamics	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
From code to archetype: Toward a unified theory of biological, neural, and artificial artifacts	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
Avian influenza A H5N1 hemagglutinin protein models have distinct structural patterns re-occurring across the 1959–2023 strains	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
CHTW(R)-system in Ca2+ transport modelling	9
Effect of monochromatic light on the behavior of the ctenophore Mnemiopsis leidyi (A. Agassiz, 1865)	9
Is there a bias in the codon frequency corresponding to homo-repeats found in human proteins?	9
The indispensable role of time in autonomous development	9
The origin and evolution of life as continuing expansion of viral hosts	9
Generalized model of closed microecosystem «alga - micro-consumers»	9
Rational decision making in biological systems	9
Molecular mechanisms of encoding and decoding information in cell computing	8
Paleo-phyllotaxis: Fucales, bryophytes, lycophytes and monilophytes	8
Ribonucleic acid genome mutations induced by the Casimir effect	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
Temporal cohesion as a candidate for negentropy in biological thermodynamics	8
Dive into machine learning algorithms for influenza virus host prediction with hemagglutinin sequences	8
Human cognitive limitations and emotions: The emergence of social complexity	8
An irreversible thermodynamic model of prebiological dissipative molecular structures inside vacuoles at the surface of the Archean Ocean	8
The threat of asymptomatic carriers and the benefits of testing	8
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
Editorial Board	7
A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem	7
Entering the labyrinth: A hypothesis about the emergence of metabolism from protobiotic routes	7
Editorial Board	7
The theoretical foundations of enaction: Precariousness	7
Machine-learning-based structural analysis of interactions between antibodies and antigens	7
Mechanism and biological significance of erythrocyte homoaggregation (rouleaux formation): temperature-dependent entropic liberation of water from cells and macromolecules	7
Modeling autopoiesis and cognition with reaction networks	7
Corrigendum to “Pandemic preparedness and new model developments for airborne diseases transmitting via aerosols” [BioSystems 255 (2025) 105532]	7
Use of directed quasi-metric distances for quantifying the information of gene families	7
Embodied essentialism in the reconstruction of the animal sign in robot animal design	7
Aggregate Boid behavior to aid in artificial autopoietic organization	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
Order stability via Fröhlich condensation in bio, eco, and social systems: The quantum-like approach	7
Editorial Board	6
Cosmos, mind, matter: Is mind in spacetime?	6
Spiking neural networks produce informational closure by stimulus avoidance	6
Balancing the cellular budget: Lessons in metabolism from microbes to cancer	6
Mathematical model of coffee tree’s rust control using snails as biological agents	6
Evolutionary stability of developmental commitment	6
A quantum-like information processing model with memory noise for question order effect	6
When Maxwell’s Demon leaves the room	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
Prediction of prokaryotic and eukaryotic promoters based on information-theoretic features	6
On the minimal elements of the genetic code and their semiotic functions (degeneracy, complementarity, wobbling)	6
A multi-cell model for the C4 photosynthetic pathway in developing wheat grains based upon tissue-specific transcriptome data	6
Modelling energy-harvesting processes in primitive cells: Proton transport across bilayers driven by the oxidation of sulfite	6
An efficient approach for identifying important biomarkers for biomedical diagnosis	6
The chromolinker hypothesis: Are eukaryotic genomes also circular?	6
Impact of social reward on the evolution of cooperation in voluntary prisoner’s dilemma	6
Childhood in social learning models with changing environments: Implications for human evolution	6
Cell jamming-to-unjamming transitions and vice versa in development: Physical aspects	6
Information–energy equivalence and the emergence of self-replicating biological systems	6
Understanding nature’s selection of genetic languages	6
Evolution of cooperation in multigame with environmental space and delay	6
The origins of the cell membrane, the progenote, and the universal ancestor (LUCA)	6
Fractional nutrient uptake model of plant roots	5
Evolution and maintenance of phenotypic plasticity	5
Combination of survival movement strategies in cyclic game systems during an epidemic	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
Effect of the electromagnetic induction in the electrical activity of the Kazantsev model of inferior Olive Neuron model	5

Construction of amino acids reduced alphabets from molecular descriptors for interpretation of N-carbamylase, luciferase and PI3K mutations	5
The cell as a semiotic system that realizes closure to efficient causation: The semiotic (M, R) system	5
Evolutionary origin of B family DNA-dependent DNA polymerases from retrotranscriptases	5
Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach	5
Psychological origin of quantum logic: An orthomodular lattice derived from natural-born intelligence without Hilbert space	5
Electrical frequency discrimination by fungi Pleurotus ostreatus	5
Causal intuition in the indefinite world: Meta-analysis and simulations	5
Thermal diodes, transistors and logic: Review of unconventional computing methods	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
Editorial Board	5
Estimation of discrepancy of color qualia using Kullback-Leibler divergence	5
Synchronization Studies of Hindmarsh–Rose Neuron Networks: Unraveling the Influence of connection induced memristive synapse	5
Benchmark for quantitative characterization of circadian clock cycles	5
The problem of evolutionary directionality 50 years following the works of Sergei Meyen	5
A computational design of a programmable biological processor	5
Identification of Ca	5
Influence of oxidative stress on women’s fertility: A model with a generational age Caputo’s fractional derivative	5
A new method: Characterize and quantify biofilm wrinkles by UNet and Sholl Analysis	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
Robustness and evolvability: Revisited, redefined and applied	5
Viscous DNA and RNA: Quantum damped dynamical random systems	4
The repertoire of candidate archaeal noncoding RNAs and their association with temperature adaptation	4
Corrigendum to “Paleo-phyllotaxis: Fucales, bryophytes, lycophytes and monilophytes” [BioSystems 255 (2025) 105541]	4
Is Darwinian selection a retrograde driving force of evolution?	4
Memory induced-mechanism of noise attenuator of myosin V molecular motors	4
Code Biology and abduction in the creative process	4
Prigoginian informational dissipation (PID) as the cause of the emergence of a proto-self	4
Is meaning commensurable in scientific theories? From arbitrariness to non-nomological relations in meaning-making	4
Using monoids for the integration of genomic and metabolic parameters in the prediction of phenotypes in regulatory cascades	4
Corrigendum to “Role of calcium oscillations in sperm physiology” [BioSystems 209 (2021) 104524]	4
Impact of transposable elements on the evolution of complex living systems and their epigenetic control	4
Codes across (life)sciences	4
Food codes as an AI-based framework to investigate bird foraging ecology and interspecific interactions	4
The theory of oxygen hemoglobin association	4
Two theories of action - Edelman's Neuronal group Selection and the Poetics of Paul Valéry	4
Using neurons to maintain autonomy: Learning from C. elegans	4
Toward understanding the emergence of life: A dual function of the system of nucleotides in the metabolically closed autopoietic organization	4
The phylogenetic distribution of the cell division system would not imply a cellular LUCA but a progenotic LUCA	4
Towards a Possible Definition of Consciousness	4
Biological thermodynamics: Ervin Bauer and the unification of life sciences and physics	4
Corrigendum to “The concepts of code biology” [Biosyst. 248 (2025) 105400 1–6]	4
Overview of the third special issue in code biology	4
Cosmos MIND and matter: Is mind in spacetime?	4
The limits of falsifiability: Dimensionality, measurement thresholds, and the sub-Landauer domain in biological systems	4
Perfection is the enemy of evolution	4
Identification of multivariable Boolean patterns in microbiome and microbial gene composition data	4
Editorial Board	4
Statistical algorithms for the analysis of deleterious genetic mutations	4
Formal autopoiesis: Solutions of the classical and extended functional closure equations	4
Brain and behavior share features of a critical state dynamics	4
Accurate phenotypic self-replication as a necessary cause for biological evolution.	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
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
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
A control measure for epidemic spread based on the susceptible–infectious–susceptible (SIS) model	4
Modeling of will and consciousness based on the human language: Interpretation of qualia and psychological 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
Life, its definition, origin, evolution, and four-dimensional hierarchical structure	4
Origin of the temporal stability control of living system nonequilibrium	4
miRNAFinder: A comprehensive web resource for plant Pre-microRNA classification	4
On the infodynamics of ramifications in constructal design	4
Code biology and aesthetics	4
The polyphyletic origins of glycyl-tRNA synthetase and lysyl-tRNA synthetase and their implications	4
A multi-modal algorithm based on an NSGA-II scheme for phylogenetic tree inference	4
An energy landscape-based theoretical framework for understanding the self-organization of functions in a living system under the dynamical component interaction	4
Neurons as hierarchies of quantum reference frames	4