Biosystems

Article	Citations
Editorial Board	33
A multi-cell model for the C4 photosynthetic pathway in developing wheat grains based upon tissue-specific transcriptome data	31
Morphological forms arising from the evolutionary process are topologies	31
The local-global relationship of nature	28
Gene as a dynamical notion: An extensive and integrative vision. Redefining the gene concept, from traditional to genic-interaction, as a new dynamical version	27
Stretching tension effects in permeability transition pores of inner mitochondrial membrane	27
Construction of a human body model for acupuncture and moxibustion treatment by colored Petri nets	24
Childhood in social learning models with changing environments: Implications for human evolution	23
Motility disorders and disintegration into separate cells of Trichoplax sp. H2 in the presence of Zn2+ ions and L-cysteine molecules: A systems approach	22
Reconfiguring SETI in the microbial context: Panspermia as a solution to Fermi's paradox	21
Temporal regulation of gene expression and pathways in chemotherapy-induced senescence in HeLa cervical cancer cell line	20
Biological computation running on quantum computation	20
Exploring the patterns of evolution: Core thoughts and focus on the saltational model	18
Editorial: Petri nets for cellular process modelling	18
Control analysis in the identification of key enzymes driving metabolic adaptations: Towards drug target discovery	16
The biological information flow: From cell theory to a new evolutionary synthesis	16
Spiking neural networks produce informational closure by stimulus avoidance	16
Fine structure of a partition in the spike glycoprotein encoded in the SARS-CoV-2 genome	16
Intrinsic growth rate and evolution of the Premnotrypes Vorax population using fuzzy information	16
Application of CRISPR Cas systems in DNA recorders and writers	15
The regulatory network that controls lymphopoiesis	15
Hypothesis of macroscopic quantum state in biological systems and discussion on the possibility of its experimental verification	15
Editorial Board	15
Modeling the interaction between donor-derived regulatory T cells and effector T cells early after allogeneic hematopoietic stem cell transplantation	15
Editorial Board	15

Information–energy equivalence and the emergence of self-replicating biological systems	15
Social satisficing: Multi-agent reinforcement learning with satisficing agents	14
Editorial: Fundamental principles of biological computation: From molecular computing to evolutionary complexity	14
Fertilization and development of Arbacia lixula eggs are affected by osmolality conditions	14
Filter feature selection based Boolean Modelling for Genetic Network Inference	14
Cholesterol plays a decisive role in tetraspanin assemblies during bilayer deformations	14
Modeling SELEX for regulatory regions using Royal Road and Royal Staircase fitness functions	13
Principles of cognitive biology and the concept of biocivilisations	13
A new mathematical model of folate homeostasis in E. coli highlights the potential importance of the folinic acid futile cycle in cell growth	13
Spatial waves and temporal oscillations in vertebrate limb development	13
Animal design advantage from the analogy between friction and body heat loss	13
Combining kinetic orders for efficient S-System modelling of gene regulatory network	13
Exploring natural anthraquinones as potential MMP2 inhibitors: A computational study	13
Aggregate Boid behavior to aid in artificial autopoietic organization	12
Rapid clade divergence and phyletic gradualism in an interacting particle model of sympatric speciation	12
The epoch-making importance of Ervin Bauer's theoretical biology	12
Karyotype as code of codes: An inheritance platform to shape the pattern and scale of evolution	12
Editorial: Systems bioinformatics for medicine	12
A mathematician’s view of the unreasonable ineffectiveness of mathematics in biology	12
Editorial Board	11
Optimizing ruminant nutrition: Insights from a comprehensive analysis of silage composition and in vitro gas production dynamics using nonlinear models	11
Impact of social reward on the evolution of cooperation in voluntary prisoner’s dilemma	11
Phase offset determines alpha modulation of gamma phase coherence and hence signal transmission	11
Information encoded in gene-frequency trajectories	11
Editorial Board	11
An integrative machine learning model for the identification of tumor T-cell antigens	11
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	11
The major evolutionary transitions and codes of life	10
Loss and fixation of strongly favoured new variants: Understanding and extending Haldane’s result via the Wright–Fisher model	10
Collective dynamics of a coupled Hindmarsh–Rose neurons with locally active memristor	10
From Empedocles to Symbiogenetics: Lynn Margulis's revolutionary influence on evolutionary biology	10
Autopoiesis: Foundations of life, cognition, and emergence of self/other	10
Memetic approach to cultural evolution	10
Dimerization induces bimodality in protein number distributions	9
Generation of genetic codes with 2-adic codon algebra and adaptive dynamics	9
The effect of avian eggshell membrane structure on microbial penetration: A simulation study	9
I-circular codes	9
Contrasting philosophical and scientific views in the long history of studying the generation of form in development	9
A multi-scale agent-based model for avascular tumour growth	9
Editorial Board	9
The modularity codes	9
Developmental noise, entropy, and biological system condition	9
Effects of predator modulation and vector preference on pathogen transmission in plant populations	9
Degradation-driven protein level oscillation in the yeast Saccharomyces cerevisiae	9
Trinucleotide k-circular codes I: Theory	8
All lockdowns are not equal: Reducing epidemic impact through evolutionary computation	8
Cartography of the multiple formal systems of molecular autopoiesis: from the biology of cognition and enaction to anticipation and active inference	8
The necessity of hierarchy for living systems	8
Editorial Board	8
Editorial Board	8

Enhanced effective codon numbers to understand codon usage bias	8
The emergence of a fractal structure of formal logic via the spatiotemporal reflexive self-identification	8
Genome-scale prediction of bacterial promoters	8
Book Review	8
On the minimal elements of the genetic code and their semiotic functions (degeneracy, complementarity, wobbling)	8
Serial Endosymbiosis Theory: From biology to astronomy and back to the origin of life	8
Unravelling the nexus: Towards a unified model of development, ageing, and cancer	7
Cell jamming-to-unjamming transitions and vice versa in development: Physical aspects	7
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	7
Thermodynamic analysis of energy coupling by determination of the Onsager phenomenological coefficients for a 3×3 system of coupled chemical reactions and transport in ATP synthesis and its mechanisti	7
Discovering ecoacoustic codes in beehives: First evidence and perspectives	7
Perception of color in primates: A conceptual color neurons hypothesis	7
Competition for finite resources as coordination mechanism for morphogenesis: An evolutionary algorithm study of digital embryogeny	7
Light sensitive Belousov–Zhabotinsky medium accommodates multiple logic gates	7
Cell and extracellular matrix growth theory and its implications for tumorigenesis	7
Natural gradient ascent in evolutionary games	7
C-Biomarker.net: A Cytoscape app for the identification of cancer biomarker genes from cores of large biomolecular networks	7
Toward an ethics of autopoietic technology: Stress, care, and intelligence	7
Size matters in metabolic scaling: Critical role of the thermodynamic efficiency of ATP synthesis and its dependence on mitochondrial 7
Editorial Board	7
The origins of the cell membrane, the progenote, and the universal ancestor (LUCA)	7
Effect of single nucleotide polymorphisms on the structure of long noncoding RNAs and their interaction with RNA binding proteins	7
Protein-DNA target search relies on quantum walk	7
Theories of the origin of the genetic code: Strong corroboration for the coevolution theory	7
VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology	7
The chromolinker hypothesis: Are eukaryotic genomes also circular?	6
Senescence, change, and competition: When the desire to pick one model harms our understanding	6
The sensual cell: Feeling and affect in unicellular species	6
RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences	6
In enzymatic reactions, the reverse reaction reduces product noise	6
Cosmos, mind, matter: Is mind in spacetime?	6
The grid-cell normative model: Unifying ‘principles’	6
Psychological origin of quantum logic: An orthomodular lattice derived from natural-born intelligence without Hilbert space	6
Nuclear Quantum Effects Explain Chemiosmosis: The Power of the Proton	6
Techno-ethical concerns related to genetic sequencing reports	6
Prediction of prokaryotic and eukaryotic promoters based on information-theoretic features	6
Evaluating the statistical similarity of neural network activity and connectivity via eigenvector angles	6
Influence analysis of network evolution on Parrondo effect	6
Intelligence: Natural, artificial, or what?	6
SetQuence & SetOmic: Deep set transformers for whole genome and exome tumour analysis	6
Endless forms of endless formation — The morphogenesis of organisms and scientific objects	6
Causal Modeling and Thermodynamics: Towards a new convergence of the two fields	6
Dynamics of two feed forward genetic motifs in the presence of molecular noise	6
Gene regulatory networks with binary weights	6
Mathematical model of coffee tree’s rust control using snails as biological agents	6
Genetic code, the problem of coding biological cycles, and cyclic Gray codes	6
Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game	6
Getting the news in milliseconds: The role of early novelty detection in active electrosensory exploration	6
A critical role of the periplasm in copper homeostasis in Gram-negative bacteria	6
Exploring the effects of high curvature section distribution and density in termite tunnels on food transport efficiency: A simulation study	5
Extracellular interplay of amyloid fibrils and neural cells	5
Book Review	5
Encoding of non-biological information for its long-term storage in DNA	5
The cell as a realization of the (M, R) system	5
Visualizing genomic data: The mixing perspective	5
A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information	5
How do soldier crabs behave when seeing vibrating robots?	5
Combination of survival movement strategies in cyclic game systems during an epidemic	5
Freezing of gait in Parkinson’s disease: Classification using computational intelligence	5
Consequences of asymmetric mutational pressure for the dynamic of linear B-cell epitopes repertoire of influenza a virus neuraminidase rearrangement	5
Artificial immune system features added to breast cancer clinical data for machine learning (ML) applications	5
Modelling ethnogenesis	5
A degenerative process underlying hierarchic transitions in evolution	5
Temperature dependence of IR exciton emission spectra in Müller cell intermediate filaments	5
Analytical solution of Nye–Tinker–Barber model by Laplace transform	5
The mitochondrial challenge: Disorders and prevention strategies	5
A computational design of a programmable biological processor	5
The promoting effect of adaptive persistence aspiration on the cooperation based on the consideration of payoff and environment in prisoner's dilemma game	5
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	5
Binary oppositions, algebraic holography and stochastic rules in genetic informatics	5
Evolution, physics, and education	5
From chaos to clock in recurrent neural net. Case study	5
Editorial: Computational approaches in cancer modelling	5
Chaos, complexity and computation in the evolution of biological systems	5
The osseous fusion patterns in an equine limb: A theoretical deconstruction of the evolutionary mechanisms	5
A quantum-like information processing model with memory noise for question order effect	5
On paradoxes between optimal growth, metabolic control analysis, and flux balance analysis	5
Causal intuition in the indefinite world: Meta-analysis and simulations	5
Editorial: 2020 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB 2020)	5
Quantum propensities in the brain cortex and free will	5

Modeling the origin, evolution, and functioning of the genetic code	4
An efficient approach for identifying important biomarkers for biomedical diagnosis	4
Effect of the electromagnetic induction in the electrical activity of the Kazantsev model of inferior Olive Neuron model	4
Editorial Board	4
A model integrating multiple processes of synchronization and coherence for information instantiation within a cortical area	4
The problem of evolutionary directionality 50 years following the works of Sergei Meyen	4
How nanoparticles can induce dimerization and aggregation of cells in blood or lymph	4
Identification of Ca	4
Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum	4
Characterisation of the fig-fig wasp holobiont	4
Whole-cell metabolic control analysis	4
Genes on the circular code alphabet	4
Editorial Board	4
The hiatus between organism and machine evolution: Contrasting mixed microbial communities with robots	4
Understanding cancer from a biophysical, developmental and systems biology perspective using the landscapes-attractor model	4
Immune cell-specific and common molecular signatures in rheumatoid arthritis through molecular network approaches	4
Editorial Board	4
High-speed parameter search of dynamic biological pathways from time-course transcriptomic profiles using high-level Petri net	4
New algorithm for the analysis of nucleotide and amino acid evolutionary relationships based on Klein four-group	4
Editorial Board	4
A dynamical system for the IGF1-AKT signaling pathway in skeletal muscle adaptation	4
Modelling energy-harvesting processes in primitive cells: Proton transport across bilayers driven by the oxidation of sulfite	4
Mitotic waves in an import-diffusion model with multiple nuclei in a shared cytoplasm	4
The time of appearance of the genetic code	4
Editorial Board	4
Cholesterol-ester prevents lipoprotein core from solidifying: Molecular dynamics simulation	4
A memory access gate controlled by dynamic contexts	4
Editorial Board	4
Sensing, feeling and sentience in unicellular organisms and living cells	4
“Assembly Theory” in life-origin models: A critical review	4
Editorial Board	4
Autopoiesis of the artificial: from systems to cognition	4
Natural intelligence and the ‘economy’ of social emotions: A connection with AI sentiment analysis	4
Reversible and irreversible mitochondrial swelling: Effects of variable mitochondrial activity	4
Editorial Board	4
Relational model of the standard genetic code	4
Structure and behavior in Boolean monotonic model pools	4
Comparing the complexity of written and molecular symbolic systems	4
The drawbridge of nature: Evolutionary complexification as a generation and novel interpretation of coding systems	4
Synthetic biological neural networks: From current implementations to future perspectives	4
A possible origin of life in nonpolar environments	4
The evolution and development of consciousness: the subject-object emergence hypothesis	3
Mixed-monolayer functionalized gold nanoparticles for cancer treatment: Atomistic molecular dynamics simulations study	3
Intrinsic structural disorder on proteins is involved in the interactome evolution	3
Novel amino acid distance matrices based on conductance measure	3
On coevolution: Asymmetry in the NKCS model	3
A biochemically-realisable relational model of the self-manufacturing cell	3
Spatial organisation plasticity reduces disease infection risk in rock–paper–scissors models	3
Viruses, immunity and evolution	3
Efim Liberman toward the comprehension of the phenomenon of life	3
The stochastic organization of genomes and the doctrine of energy-information evolution based on bio-antenna arrays	3
The evolutionary arch of bioenergetics from prebiotic mechanisms to the emergence of a cellular respiratory chain	3
Distributional features of triplet codons in genomes underlie the diversification of life	3
Evolutionary stability of developmental commitment	3
Theoretical analysis of reversible and irreversible mitochondrial swelling in vivo	3
Homeostasis and information processing: The key frames for the thermodynamics of biological systems	3
Buckling forces and the wavy folds between pleural epithelial cells	3
Single-cell classification, analysis, and its application using deep learning techniques	3
The innate story code	3
A first perturbome of Pseudomonas aeruginosa: Identification of core genes related to multiple perturbations by a machine learning approach	3
Editorial Board	3
Evolution and maintenance of phenotypic plasticity	3
Is distance from equilibrium a good indicator for a reaction’s flux control?	3
Removing quote marks from the RNA polymerase II CTD ‘code’	3
Multi-scale modeling of hippo signaling identifies homeostatic control by YAP-LATS negative feedback	3
Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples	3
Non-monotone cellular automata: Order prevails over chaos	3
An exploration of ecoacoustics and its applications in conservation ecology	3
The genetic code and its p-adic ultrametric modeling	3
Quantitative description of neuronal calcium dynamics in C. elegans’ thermoreception	3
Three levels of information processing in the brain	3
An approach to the plant body: Assessing concrete and abstract aspects	3
Adversarial deep evolutionary learning for drug design	3
The metabolic control theory: Its development and its application to mitochondrial oxidative phosphorylation	3
A novel mathematical model of AIDS-associated Kaposi's sarcoma: Analysis and optimal control	3
Coloured fuzzy Petri nets for modelling and analysing membrane systems	3
Electrical frequency discrimination by fungi Pleurotus ostreatus	3
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.	3
From the principle of sustainable non-equilibrium to sustainable development	3
Determining cellular lineage directed networks in hematopoiesis using single-cell transcriptomic data and volatility-constrained correlation	3
Quantum Brain Dynamics and Virtual Reality	3
Gaidai reliability method for high-dimensional spatio-temporal biosystems	3
Neuron quantum computers and a way to unification of science: A compendium of Efim Liberman's scientific work	3
Swelling and membrane potential dynamics of glial Müller cells	3
Super-rational aspiration induced strategy updating helps resolve the tragedy of the commons in a cooperation system with exit rights	3
Editorial Board	3
Small-sample continual learning classification method with vaccine to update memory cells based on the artificial immune system	3
AI in predicting COPD in the Canadian population	3
Eco-crossover, or environmentally regulated crossing-over, and natural selection are two irreplaceable drivers of adaptive evolution: Eco-crossover hypothesis	3
Evolution of cooperation in multigame with environmental space and delay	3
Bipolar reasoning in feedback pathways	3
Light induced spiking of proteinoids	3
From Reactions to Reflection: A Recursive Framework for the Evolution of Cognition and Complexity	3
Primal awareness, evolutionary restriction, life and the origin of quantum mechanics	3
The molecular memory code and synaptic plasticity: A synthesis	3