Biosystems

Article	Citations
Role of fear in a predator-prey system with ratio-dependent functional response in deterministic and stochastic environment	48
Reactive fungal wearable	44
Electrical activity of fungi: Spikes detection and complexity analysis	31
Quantum-like modeling in biology with open quantum systems and instruments	31
Towards proteinoid computers. Hypothesis paper	30
A novel method for segmenting brain tumor using modified watershed algorithm in MRI image with FPGA	28
The drawbridge of nature: Evolutionary complexification as a generation and novel interpretation of coding systems	28
Cellular sentience as the primary source of biological order and evolution	26
The molecular memory code and synaptic plasticity: A synthesis	26
The origin of symbiogenesis: An annotated English translation of Mereschkowsky's 1910 paper on the theory of two plasma lineages	25
Karyotype coding: The creation and maintenance of system information for complexity and biodiversity	24
On multistep tumor growth models of fractional variable-order	23
Dynamical behaviors and optimal harvesting of an intraguild prey-predator fishery model with Michaelis-Menten type predator harvesting	22
Toward a formal theory of embodied cognition	20
Role of calcium oscillations in sperm physiology	20
Deep learning based genome analysis and NGS-RNA LL identification with a novel hybrid model	20
The role of symbiosis in the first colonization of the seafloor by macrobiota: Insights from the oldest Ediacaran biota (Newfoundland, Canada)	20
COVID-19 spatio-temporal forecast in England	18
Fungal electronics	18
PDE based geometry model for BCG immunotherapy of bladder cancer	16
Fractional Mathematical Oncology: On the potential of non-integer order calculus applied to interdisciplinary models	16
Yeast cell segmentation in microstructured environments with deep learning	16
Exploring the complexity and chaotic behavior in plankton–fish system with mutual interference and time delay	16
Toward understanding the emergence of life: A dual function of the system of nucleotides in the metabolically closed autopoietic organization	16
Amino acid activation analysis of primitive aminoacyl-tRNA synthetases encoded by both strands of a single gene using the malachite green assay	16

Revisiting the edge of chaos: Again?	15
Quantum-like model for unconscious–conscious interaction and emotional coloring of perceptions and other conscious experiences	15
Metabolic limits on classical information processing by biological cells	15
A secured cryptographic system based on DNA and a hybrid key generation approach	15
Towards a general theory of the major cooperative evolutionary transitions	15
Mathematics in biological reality: The emergence of natural computation in living systems	15
Beyond planetary-scale feedback self-regulation: Gaia as an autopoietic system	15
Biological thermodynamics: Ervin Bauer and the unification of life sciences and physics	15
The late appearance of DNA, the nature of the LUCA and ancestors of the domains of life	15
A mathematician’s view of the unreasonable ineffectiveness of mathematics in biology	15
Archetypes and code biology	14
The rise of languaging	14
Ervin Bauer's concept of biological thermodynamics and its different evaluations	14
Artificial immune system features added to breast cancer clinical data for machine learning (ML) applications	14
A short tutorial on the Janus-faced logic of differentiation waves and differentiation trees and their evolution	13
On the effects of the modularity of gene regulatory networks on phenotypic variability and its association with robustness	13
Quantum aspects of the brain-mind relationship: A hypothesis with supporting evidence	13
Transfer functions of proteinoid microspheres	13
The major evolutionary transitions and codes of life	13
Neurons as hierarchies of quantum reference frames	13
Analysis of a breast cancer mathematical model by a new method to find an optimal protocol for H	13
Life and living beings under the perspective of organic macrocodes	13
A systems theory of biological evolution	13
Archaeal Origins of Eukaryotic Cell and Nucleus	13
The emergence of locally adaptive institutions: Insights from traditional social structures of East African pastoralists	12
The phylogenetic distribution of the cell division system would not imply a cellular LUCA but a progenotic LUCA	12
Stability analysis and optimal control of HPV infection model with early-stage cervical cancer	12
The theoretical foundations of enaction: Precariousness	12
Regulative development as a model for origin of life and artificial life studies	12
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	12
Living wearables: Bacterial reactive glove	12
LUCA to LECA, the Lucacene: A model for the gigayear delay from the first prokaryote to eukaryogenesis	12
Is it possible that cells have had more than one origin?	12
Gaidai reliability method for high-dimensional spatio-temporal biosystems	12
Relational biology and Church's thesis	11
Morphology changes induced by intercellular gap junction blocking: A reaction-diffusion mechanism	11
From Empedocles to Symbiogenetics: Lynn Margulis's revolutionary influence on evolutionary biology	11
Voevodsky's unfinished project: Filling the gap between pure and applied mathematics	11
Non-genetic inheritance: Evolution above the organismal level	11
The evolutionary dynamics of social systems via reflexive transformation of external reality	11
Metacode: One code to rule them all	11
Prokaryotic symbiotic consortia and the origin of nucleated cells: A critical review of Lynn Margulis hypothesis	11
Mixed-monolayer functionalized gold nanoparticles for cancer treatment: Atomistic molecular dynamics simulations study	11
Perfection is the enemy of evolution	10
Light sensitive Belousov–Zhabotinsky medium accommodates multiple logic gates	10
p-Adic mathematics and theoretical biology	10
Complexification of eukaryote phenotype: Adaptive immuno-cognitive systems as unique Gödelian blockchain distributed ledger	10
Hyperbolic rules of the cooperative organization of eukaryotic and prokaryotic genomes	10
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	10
A simple measure for biocomplexity	10

Computing within bacteria: Programming of bacterial behavior by means of a plasmid encoding a perceptron neural network	10
A Monte Carlo method for in silico modeling and visualization of Waddington’s epigenetic landscape with intermediate details	10
Symbiogenesis as a driving force of evolution: The legacy of Boris Kozo-Polyansky	9
Standard Genetic Code vs. Supersymmetry Genetic Code – Alphabetical table vs. physicochemical table	9
A biochemically-realisable relational model of the self-manufacturing cell	9
Competition for finite resources as coordination mechanism for morphogenesis: An evolutionary algorithm study of digital embryogeny	9
Fertilization and development of Arbacia lixula eggs are affected by osmolality conditions	9
Nothing in evolution makes sense except in the light of code biology	9
Order stability via Fröhlich condensation in bio, eco, and social systems: The quantum-like approach	9
Eco-crossover, or environmentally regulated crossing-over, and natural selection are two irreplaceable drivers of adaptive evolution: Eco-crossover hypothesis	9
Karyotype as code of codes: An inheritance platform to shape the pattern and scale of evolution	9
Algebraic harmony and probabilities in genomes. Long-range coherence in quantum code biology	9
An organisational systems-biology view of viruses explains why they are not alive	9
Dive into machine learning algorithms for influenza virus host prediction with hemagglutinin sequences	9
Category theory and foundations of life science: A structuralist perspective on cognition	9
Stability switching and hydra effect in a predator–prey metapopulation model	9
Overview of the third special issue in code biology	8
A Petri nets-based framework for whole-cell modeling	8
D'Arcy W. Thompson's On Growth and Form: A landmark for the mathematical foundations of epigenetics	8
AI in predicting COPD in the Canadian population	8
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	8
Decoding the double trouble: A mathematical modelling of co-infection dynamics of SARS-CoV-2 and influenza-like illness	8
The information continuum model of evolution	8
Study of the bioenergetics to identify the novel pathways as a drug target against Mycobacterium tuberculosis using Petri net	8
Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples	8
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	8
The canonical and non-canonical NF-κB pathways and their crosstalk: A comparative study based on Petri nets	8
“How” vs. “Why” questions in symbiogenesis, and the causal role of synergy	8
Virions and respiratory droplets in air: Diffusion, drift, and contact with the epithelium	8
Combination of survival movement strategies in cyclic game systems during an epidemic	8
Harnessing adaptive novelty for automated generation of cancer treatments	8
The modularity codes	7
Temporal cohesion as a candidate for negentropy in biological thermodynamics	7
Macroevolution, differentiation trees, and the growth of coding systems	7
Removing quote marks from the RNA polymerase II CTD ‘code’	7
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	7
Relational model of the standard genetic code	7
The origins of the cell membrane, the progenote, and the universal ancestor (LUCA)	7
A multi-scale agent-based model for avascular tumour growth	7
Phosphorylation and acylation transfer reactions: Clues to a dual origin of metabolism	7
Information processing and energy efficiency of temperature-sensitive Morris-Lecar neuron	7
Infinite combinatorics in mathematical biology	7
Quantum propensities in the brain cortex and free will	7
Protein-DNA target search relies on quantum walk	7
Cell and extracellular matrix growth theory and its implications for tumorigenesis	7
Spatial waves and temporal oscillations in vertebrate limb development	7
The RNase P, LUCA, the ancestors of the life domains, the progenote, and the tree of life	7
Impact of transposable elements on the evolution of complex living systems and their epigenetic control	7
Kinetic modelling of compartmentalised reaction networks	7
Viruses, immunity and evolution	7
Evolution of cooperation in multigame with environmental space and delay	7
VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology	7
The maximality of circular codes in genes statistically verified	6
Coloured fuzzy Petri nets for modelling and analysing membrane systems	6
The reversibility of cellular determination: An evolutive pattern of epigenetic plasticity	6
Neuron quantum computers and a way to unification of science: A compendium of Efim Liberman's scientific work	6
Cholesterol plays a decisive role in tetraspanin assemblies during bilayer deformations	6
Identification of subtype specific biomarkers of clear cell renal cell carcinoma using random forest and greedy algorithm	6
How an information perspective helps overcome the challenge of biology to physics	6
Dimensionality reduction for visualizing high-dimensional biological data	6
Origin of the temporal stability control of living system nonequilibrium	6
Systems theory, thermodynamics and life: Integrated thinking across ecology, organization and biological evolution.	6
MRWMDA: A novel framework to infer miRNA-disease associations	6
Propagation of electrical signals by fungi	6
Light induced spiking of proteinoids	6
The biological information flow: From cell theory to a new evolutionary synthesis	6
Modeling inherited physiological structures based on hyperbolic numbers	6
Modeling autopoiesis and cognition with reaction networks	6
Code biology and the problem of emergence	6
The role of self-maintaining resilient reaction networks in the origin and evolution of life	6
Biosemiotics comprehension of PrP code and prion disease	6
Arguments against the stereochemical theory of the origin of the genetic code	6
Living systems are smarter bots: Slime mold semiosis versus AI symbol manipulation	6
Adversarial deep evolutionary learning for drug design	6
A dynamical system for the IGF1-AKT signaling pathway in skeletal muscle adaptation	6
On the context-sensitive grammar of the genetic code	6
Modeling tumor growth using fractal calculus: Insights into tumor dynamics	6
Maize root behavior as three-inputs-three-outputs logical gates due to positive gravitropism and nutritropism	6
Dynamic interactive self organizing aggregation method in swarm robots	6
Errors of the ancestral translation, LUCA, and nature of its direct descendants	5

Bisimilar Booleanization of multivalued networks	5
What controls carbon sequestration in plants under which conditions?	5
Entering the labyrinth: A hypothesis about the emergence of metabolism from protobiotic routes	5
Systemic evolutionary changes in mammalian gene expression	5
Étienne Geoffroy Saint-Hilaire as a predecessor of the epigenetic concept of evolution	5
Cell-to-cell diversification in ERBB-RAS-MAPK signal transduction that produces cell-type specific growth factor responses	5
Prediction and analysis of prokaryotic promoters based on sequence features	5
A first perturbome of Pseudomonas aeruginosa: Identification of core genes related to multiple perturbations by a machine learning approach	5
Structural impact due to PPQEE deletion in multiple cancer associated protein - Integrin αV: An In silico exploration	5
RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences	5
Motility disorders and disintegration into separate cells of Trichoplax sp. H2 in the presence of Zn2+ ions and L-cysteine molecules: A systems approach	5
Potential role of the X circular code in the regulation of gene expression	5
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	5
The impact of additional food on plankton dynamics in the absence and presence of toxicity	5
Energy infrastructure of evolution for system with infinite number of links with environment	5
The interplay between DNA damage and autophagy in lung cancer: A mathematical study	5
Symbiogenesis is driven through hierarchical reorganization of an ecosystem under closed or semi-closed conditions	5
Evolution, physics, and education	5
Life, its definition, origin, evolution, and four-dimensional hierarchical structure	5
Dynamical diversity of mitochondrial BK channels located in different cell types	5
The lower threshold as a unifying principle between Code Biology and Biosemiotics	5
Evolution and maintenance of phenotypic plasticity	5
Computation in biological systems as a quantum mechanical simulation	5
Modeling SELEX for regulatory regions using Royal Road and Royal Staircase fitness functions	5
Monte Carlo simulation of COVID-19 pandemic using Planck’s probability distribution	5
Proposal of an apposite strategy-updating rule for the vaccination game where hubs refer to hubs and lower-degree agents refer to lower-degree agents.	5
A category theoretic approach to metaphor comprehension: Theory of indeterminate natural transformation	5
The stochastic organization of genomes and the doctrine of energy-information evolution based on bio-antenna arrays	5
Control analysis of collagen synthesis by glycine, proline and lysine in bovine chondrocytes in vitro – Its relevance for medicine and nutrition	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
Aminoacylation of short hairpin RNAs through kissing-loop interactions indicates evolutionary trend of RNA molecules	5
Spike frequency adaptation facilitates the encoding of input gradient in insect olfactory projection neurons	5
From autopoiesis to self-optimization: Toward an enactive model of biological regulation	5
Super-rational aspiration induced strategy updating helps resolve the tragedy of the commons in a cooperation system with exit rights	5
Follicular waves in ontogenesis and female fertility	5
Cultural life: Theory and empirical testing	5
Toward the biological model of the hippocampus as the successor representation agent	5
Biological computation running on quantum computation	5
The absence of the evolutionary state of the Prokaryote would imply a polyphyletic origin of proteins and that LUCA, the ancestor of bacteria and that of archaea were progenotes	5
A protein folding robot driven by a self-taught agent	5