Biosystems

Article	Citations
Role of fear in a predator-prey system with ratio-dependent functional response in deterministic and stochastic environment	46
Reactive fungal wearable	41
On Boolean gates in fungal colony	31
The drawbridge of nature: Evolutionary complexification as a generation and novel interpretation of coding systems	27
Computational modelling and optimal control of measles epidemic in human population	26
Electrical activity of fungi: Spikes detection and complexity analysis	26
Towards proteinoid computers. Hypothesis paper	25
A novel method for segmenting brain tumor using modified watershed algorithm in MRI image with FPGA	25
Quantum-like modeling in biology with open quantum systems and instruments	24
On multistep tumor growth models of fractional variable-order	22
Deep learning based genome analysis and NGS-RNA LL identification with a novel hybrid model	20
The origin of symbiogenesis: An annotated English translation of Mereschkowsky's 1910 paper on the theory of two plasma lineages	20
Toward a formal theory of embodied cognition	19
Dynamical behaviors and optimal harvesting of an intraguild prey-predator fishery model with Michaelis-Menten type predator harvesting	18
Role of calcium oscillations in sperm physiology	17
The semantic theory of language	17
Human evolution is biological & technological evolution	17
The role of symbiosis in the first colonization of the seafloor by macrobiota: Insights from the oldest Ediacaran biota (Newfoundland, Canada)	17
Karyotype coding: The creation and maintenance of system information for complexity and biodiversity	16
Cellular sentience as the primary source of biological order and evolution	16
Fractional Mathematical Oncology: On the potential of non-integer order calculus applied to interdisciplinary models	15
Beyond planetary-scale feedback self-regulation: Gaia as an autopoietic system	15
Mathematics in biological reality: The emergence of natural computation in living systems	15
Yeast cell segmentation in microstructured environments with deep learning	15
The molecular memory code and synaptic plasticity: A synthesis	15

Fungal electronics	14
The late appearance of DNA, the nature of the LUCA and ancestors of the domains of life	14
Archaeal Origins of Eukaryotic Cell and Nucleus	13
Amino acid activation analysis of primitive aminoacyl-tRNA synthetases encoded by both strands of a single gene using the malachite green assay	13
Exploring the complexity and chaotic behavior in plankton–fish system with mutual interference and time delay	13
Multi-parameter exploration of dynamics of regulatory networks	13
Towards a general theory of the major cooperative evolutionary transitions	13
A secured cryptographic system based on DNA and a hybrid key generation approach	13
Neurons as hierarchies of quantum reference frames	12
PDE based geometry model for BCG immunotherapy of bladder cancer	12
Artificial immune system features added to breast cancer clinical data for machine learning (ML) applications	12
Revisiting the edge of chaos: Again?	12
Quantum-like model for unconscious–conscious interaction and emotional coloring of perceptions and other conscious experiences	12
The major evolutionary transitions and codes of life	12
Toward understanding the emergence of life: A dual function of the system of nucleotides in the metabolically closed autopoietic organization	12
Metabolic limits on classical information processing by biological cells	12
Relational biology and Church's thesis	11
A systems theory of biological evolution	11
Life and living beings under the perspective of organic macrocodes	11
Freedom and evolution in the dynamics of social systems	11
Probability of change in life: Amino acid changes in single nucleotide substitutions	11
Prokaryotic symbiotic consortia and the origin of nucleated cells: A critical review of Lynn Margulis hypothesis	11
The phylogenetic distribution of the glutaminyl-tRNA synthetase and Glu-tRNAGln amidotransferase in the fundamental lineages would imply that the ancestor of archaea, that of eukaryotes and LUCA were	11
A mathematician’s view of the unreasonable ineffectiveness of mathematics in biology	11
The emergence of locally adaptive institutions: Insights from traditional social structures of East African pastoralists	11
Analysis of a breast cancer mathematical model by a new method to find an optimal protocol for H	11
Non-genetic inheritance: Evolution above the organismal level	11
LUCA as well as the ancestors of archaea, bacteria and eukaryotes were progenotes: Inference from the distribution and diversity of the reading mechanism of the AUA and AUG codons in the domains of li	11
The evolutionary dynamics of social systems via reflexive transformation of external reality	11
Metacode: One code to rule them all	10
Voevodsky's unfinished project: Filling the gap between pure and applied mathematics	10
Mixed-monolayer functionalized gold nanoparticles for cancer treatment: Atomistic molecular dynamics simulations study	10
On the effects of the modularity of gene regulatory networks on phenotypic variability and its association with robustness	10
Archetypes and code biology	10
Light sensitive Belousov–Zhabotinsky medium accommodates multiple logic gates	10
Living wearables: Bacterial reactive glove	10
French flag gradients and Turing reaction-diffusion versus differentiation waves as models of morphogenesis	10
From Empedocles to Symbiogenetics: Lynn Margulis's revolutionary influence on evolutionary biology	9
Symbiogenesis as a driving force of evolution: The legacy of Boris Kozo-Polyansky	9
A simple measure for biocomplexity	9
The rise of languaging	9
Hyperbolic rules of the cooperative organization of eukaryotic and prokaryotic genomes	9
Quantum aspects of the brain-mind relationship: A hypothesis with supporting evidence	9
Optimality of circular codes versus the genetic code after frameshift errors	9
Is it possible that cells have had more than one origin?	9
Fuzzy-based self organizing aggregation method for swarm robots	9
Stability switching and hydra effect in a predator–prey metapopulation model	9
LUCA to LECA, the Lucacene: A model for the gigayear delay from the first prokaryote to eukaryogenesis	9
Morphology changes induced by intercellular gap junction blocking: A reaction-diffusion mechanism	9
Complexification of eukaryote phenotype: Adaptive immuno-cognitive systems as unique Gödelian blockchain distributed ledger	9

The information continuum model of evolution	8
A Monte Carlo method for in silico modeling and visualization of Waddington’s epigenetic landscape with intermediate details	8
Regulative development as a model for origin of life and artificial life studies	8
Nothing in evolution makes sense except in the light of code biology	8
Computing within bacteria: Programming of bacterial behavior by means of a plasmid encoding a perceptron neural network	8
Fertilization and development of Arbacia lixula eggs are affected by osmolality conditions	8
A survey of within-host and between-hosts modelling for antibiotic resistance	8
Order stability via Fröhlich condensation in bio, eco, and social systems: The quantum-like approach	8
COVID-19 spatio-temporal forecast in England	8
A short tutorial on the Janus-faced logic of differentiation waves and differentiation trees and their evolution	8
Random effects inducing heart pathological dynamics: An approach based on mathematical models	8
Standard Genetic Code vs. Supersymmetry Genetic Code – Alphabetical table vs. physicochemical table	8
Algebraic harmony and probabilities in genomes. Long-range coherence in quantum code biology	8
An organisational systems-biology view of viruses explains why they are not alive	8
Eco-crossover, or environmentally regulated crossing-over, and natural selection are two irreplaceable drivers of adaptive evolution: Eco-crossover hypothesis	8
Stability analysis and optimal control of HPV infection model with early-stage cervical cancer	8
Category theory and foundations of life science: A structuralist perspective on cognition	7
Combination of survival movement strategies in cyclic game systems during an epidemic	7
Three types of logical structure resulting from the trilemma of free will, determinism and locality	7
Overview of the third special issue in code biology	7
“How” vs. “Why” questions in symbiogenesis, and the causal role of synergy	7
Information processing and energy efficiency of temperature-sensitive Morris-Lecar neuron	7
Infinite combinatorics in mathematical biology	7
Cell and extracellular matrix growth theory and its implications for tumorigenesis	7
Harnessing adaptive novelty for automated generation of cancer treatments	7
Ervin Bauer's concept of biological thermodynamics and its different evaluations	7
The phylogenetic distribution of the cell division system would not imply a cellular LUCA but a progenotic LUCA	7
Study of the bioenergetics to identify the novel pathways as a drug target against Mycobacterium tuberculosis using Petri net	7
Virions and respiratory droplets in air: Diffusion, drift, and contact with the epithelium	7
Psychological ‘double-slit experiment’ in decision making: Quantum versus classical	7
Stochastic models coupling gene expression and partitioning in cell division in Escherichia coli	7
Transfer functions of proteinoid microspheres	7
How an information perspective helps overcome the challenge of biology to physics	6
Code biology and the problem of emergence	6
Dynamic interactive self organizing aggregation method in swarm robots	6
Sociotype and cultural evolution: The acceleration of cultural change alongside industrial revolutions	6
MRWMDA: A novel framework to infer miRNA-disease associations	6
AI in predicting COPD in the Canadian population	6
The modularity codes	6
Are we on the cusp of a new paradigm for biology? The illogic of molecular developmental biology versus Janus-faced control of embryogenesis via differentiation waves	6
The genetic code is very close to a global optimum in a model of its origin taking into account both the partition energy of amino acids and their biosynthetic relationships	6
On the context-sensitive grammar of the genetic code	6
The canonical and non-canonical NF-κB pathways and their crosstalk: A comparative study based on Petri nets	6
p-Adic mathematics and theoretical biology	6
Biosemiotics comprehension of PrP code and prion disease	6
Kinetic modelling of compartmentalised reaction networks	6
Living systems are smarter bots: Slime mold semiosis versus AI symbol manipulation	6
Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples	6
The evolutionary stages of the complexity of biological catalysts mark and clarify the phases of the origin of the genetic code: A model for the origin of the reading frame with codons from proto-mRNA	6
Competition for finite resources as coordination mechanism for morphogenesis: An evolutionary algorithm study of digital embryogeny	6
The RNase P, LUCA, the ancestors of the life domains, the progenote, and the tree of life	6
Phosphorylation and acylation transfer reactions: Clues to a dual origin of metabolism	6
The theoretical foundations of enaction: Precariousness	6
Impact of transposable elements on the evolution of complex living systems and their epigenetic control	6
Biological thermodynamics: Ervin Bauer and the unification of life sciences and physics	6
D'Arcy W. Thompson's On Growth and Form: A landmark for the mathematical foundations of epigenetics	6
A biochemically-realisable relational model of the self-manufacturing cell	6
GPUPeP: Parallel Enzymatic Numerical P System simulator with a Python-based interface	6
A dynamical system for the IGF1-AKT signaling pathway in skeletal muscle adaptation	6
The biological information flow: From cell theory to a new evolutionary synthesis	6
VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology	6
Modeling autopoiesis and cognition with reaction networks	6
Modeling inherited physiological structures based on hyperbolic numbers	6
Prediction and analysis of prokaryotic promoters based on sequence features	5
Potential role of the X circular code in the regulation of gene expression	5
Dimensionality reduction for visualizing high-dimensional biological data	5
Coloured fuzzy Petri nets for modelling and analysing membrane systems	5
Calcium ions tune the beats of cilia and flagella	5
Neuron quantum computers and a way to unification of science: A compendium of Efim Liberman's scientific work	5
Viruses, immunity and evolution	5
Spatial waves and temporal oscillations in vertebrate limb development	5
A percolation model of natural selection	5
Identification of subtype specific biomarkers of clear cell renal cell carcinoma using random forest and greedy algorithm	5
Symbiogenesis is driven through hierarchical reorganization of an ecosystem under closed or semi-closed conditions	5
Structural impact due to PPQEE deletion in multiple cancer associated protein - Integrin αV: An In silico exploration	5
Entropy, externality and human evolution	5
The role of self-maintaining resilient reaction networks in the origin and evolution of life	5
What controls carbon sequestration in plants under which conditions?	5
Removing quote marks from the RNA polymerase II CTD ‘code’	5
The stochastic organization of genomes and the doctrine of energy-information evolution based on bio-antenna arrays	5

Relational model of the standard genetic code	5
The origins of the cell membrane, the progenote, and the universal ancestor (LUCA)	5
Biological computation running on quantum computation	5
Bisimilar Booleanization of multivalued networks	5
Dive into machine learning algorithms for influenza virus host prediction with hemagglutinin sequences	5
The lower threshold as a unifying principle between Code Biology and Biosemiotics	5
Perfection is the enemy of evolution	5
Toward the biological model of the hippocampus as the successor representation agent	5
The interplay between DNA damage and autophagy in lung cancer: A mathematical study	5
From RNA to DNA: Insights about the transition of informational molecule in the biological systems based on the structural proximity between the polymerases	5
Systemic evolutionary changes in mammalian gene expression	5
Evolution, physics, and education	5
A multi-scale agent-based model for avascular tumour growth	5
Protein-DNA target search relies on quantum walk	5
Energy infrastructure of evolution for system with infinite number of links with environment	5
Shuffling type of biological evolution based on horizontal gene transfer and the biosphere gene pool hypothesis	5
A Petri nets-based framework for whole-cell modeling	5
Collective excitations at non-equilibrium phase transition in metabolically active red blood cells	4
Reversible and irreversible mitochondrial swelling: Effects of variable mitochondrial activity	4
Monte Carlo simulation of COVID-19 pandemic using Planck’s probability distribution	4
Cell-to-cell diversification in ERBB-RAS-MAPK signal transduction that produces cell-type specific growth factor responses	4
Evolution of cooperation in multigame with environmental space and delay	4
On electrical gates on fungal colony	4
Analysis of the initiation of viral infection under flow conditions with applications to transmission in feed	4
Follicular waves in ontogenesis and female fertility	4
A methodology for analyzing and forecasting sociopolitical destabilization	4
Comments on Vladimir Voevodsky's biologically motivated works	4
Temporary and permanent control of partially specified Boolean networks	4
Motility disorders and disintegration into separate cells of Trichoplax sp. H2 in the presence of Zn2+ ions and L-cysteine molecules: A systems approach	4
The maximality of circular codes in genes statistically verified	4
Spatial organisation plasticity reduces disease infection risk in rock–paper–scissors models	4
Causal and non-causal explanations in code biology	4
Decoding the double trouble: A mathematical modelling of co-infection dynamics of SARS-CoV-2 and influenza-like illness	4
Light induced spiking of proteinoids	4
Evolution and maintenance of phenotypic plasticity	4
Aminoacylation of short hairpin RNAs through kissing-loop interactions indicates evolutionary trend of RNA molecules	4
Dynamical diversity of mitochondrial BK channels located in different cell types	4
Living with the emergence of agents on physical terms	4
The role of the “Thiodendron” consortium in postulating the karyomastigont chimaera of the endosymbiosis theory by Lynn Margulis	4
Stochasticity in transcriptional, splicing and translational regulations in time and frequency domains	4
Logic gates in nanoscale based on interaction of thiolated DNA with AuNPs and strand displacement	4
Computation in biological systems as a quantum mechanical simulation	4
Quantum propensities in the brain cortex and free will	4
Macroevolution, differentiation trees, and the growth of coding systems	4
Modeling SELEX for regulatory regions using Royal Road and Royal Staircase fitness functions	4
Propagation of electrical signals by fungi	4
The impact of additional food on plankton dynamics in the absence and presence of toxicity	4
Super-rational aspiration induced strategy updating helps resolve the tragedy of the commons in a cooperation system with exit rights	4
A category theoretic approach to metaphor comprehension: Theory of indeterminate natural transformation	4
A first perturbome of Pseudomonas aeruginosa: Identification of core genes related to multiple perturbations by a machine learning approach	4
The evolution and development of consciousness: the subject-object emergence hypothesis	4
Approaching biology through the retrocausal apex in physics	4
Binary oppositions, algebraic holography and stochastic rules in genetic informatics	4
Modeling a cancerous tumor development in a virtual patient suffering from a depressed state of mind: Simulation of somatic evolution with a customized genetic algorithm	4
A paradigm shift for the Great Bifurcation	4
From autopoiesis to self-optimization: Toward an enactive model of biological regulation	4
Étienne Geoffroy Saint-Hilaire as a predecessor of the epigenetic concept of evolution	4
A protein folding robot driven by a self-taught agent	4
Serial Endosymbiosis Theory: From biology to astronomy and back to the origin of life	4
Morphogenetic systems: Models and experiments	4
Errors of the ancestral translation, LUCA, and nature of its direct descendants	4
The reversibility of cellular determination: An evolutive pattern of epigenetic plasticity	4
What we have learned about evolutionary genome change in the past 7 decades	3
An approach to the plant body: Assessing concrete and abstract aspects	3
Evolution of stability of socioeconomic system functioning: Some approaches to modeling (with an application to the case of Egypt, 2011–2013)	3
Chaos, complexity and computation in the evolution of biological systems	3
Natural pyrrolysine-biased translation of stop codons in mitochondrial peptides entirely coded by expanded codons	3
A degenerative process underlying hierarchic transitions in evolution	3
Psychological origin of quantum logic: An orthomodular lattice derived from natural-born intelligence without Hilbert space	3
Simulation of multiple microenvironments shows a pivot role of RPTPs on the control of Epithelial-to-Mesenchymal Transition	3
Filter feature selection based Boolean Modelling for Genetic Network Inference	3
Identification of breast cancer prognostic modules via differential module selection based on weighted gene Co-expression network analysis	3
Surface contraction waves or cell proliferation waves in the presumptive neurectoderm during amphibian gastrulation: Mexican axolotl versus African clawed frog	3
Chloroplast history clarified by the criterion of light-harvesting complex	3
A trampoline effect occurring in the stages of planetary reseeding	3
Arguments against the stereochemical theory of the origin of the genetic code	3
Genes on the circular code alphabet	3
Chaotic vibration of microtubules and biological information processing	3
Gaidai reliability method for high-dimensional spatio-temporal biosystems	3
Karyotype as code of codes: An inheritance platform to shape the pattern and scale of evolution	3
On the minimal elements of the genetic code and their semiotic functions (degeneracy, complementarity, wobbling)	3
Mean-reverting neuronal model based on two alternating patterns	3
A centrality based multi-objective approach to disease gene association	3
Construction of a human body model for acupuncture and moxibustion treatment by colored Petri nets	3
Small-sample continual learning classification method with vaccine to update memory cells based on the artificial immune system	3
From axiomatic systems to the Dogmatic gene and beyond	3
In pursuit of the framework behind the biosphere: S-curves, self-assembly and the genetic entropy paradox	3
Editorial: Computational approaches in cancer modelling	3
The hiatus between organism and machine evolution: Contrasting mixed microbial communities with robots	3
The cell as a realization of the (M, R) system	3
Encoding of non-biological information for its long-term storage in DNA	3
Cholesterol plays a decisive role in tetraspanin assemblies during bilayer deformations	3
Genome-scale prediction of bacterial promoters	3
An investigation into the energy transfer efficiency of a two-pigment photosynthetic system using a macroscopic quantum model	3
Cultural life: Theory and empirical testing	3