yusuke1997/dblp-id-title huggingface dataset:
Testing amino acid-codon affinity hypothesis using molecular docking
The limits of falsifiability: Dimensionality, measurement thresholds, and the sub-Landauer domain in biological systems
E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes
An organisational systems-biology view of viruses explains why they are not alive
The ambiguity of the basic terms related to eukaryotes and the more consistent etymology based on eukaryotic signatures in Asgard archaea
Identification of SPAM messages using an approach inspired on the immune system
On the legacy of W.S. McCulloch
Cyclic Concatenated Genetic Encoder: A mathematical proposal for biological inferences
Locus dependence in epigenetic chromatin silencing
Filter feature selection based Boolean Modelling for Genetic Network Inference
Effect of weight-added regulatory networks on constraint-based metabolic models of Escherichia coli
The emergence of theoretical biology: Two fundamental works of Ervin Bauer (1890-1938) in English translation
Gene grouping strategy for network modeling from a small time-series dataset: An illustrative analysis of human organogenesis
Identification of regulatory variables for state transition of biological networks
Mathematical modeling of laser based potato cutting and peeling
Ambush strategy enhances organisms' performance in rock-paper-scissors games
Inference of intrinsic spiking irregularity based on the Kullback-Leibler information
Rich dynamics in a predator-prey model with both noise and periodic force
NIK and IKKbeta interdependence in NF-kappaB signalling - Flux analysis of regulation through metabolites
Life, its definition, origin, evolution, and four-dimensional hierarchical structure
Erratum to "Random models of Menzerath-Altmann law in genomes" (BioSystems 107(3) (2012) 167-173)
Gradients of seed photosynthesis and its role for oxygen balancing
Spiking neural P systems with multiple channels and polarizations
Analytical solution of Nye-Tinker-Barber model by Laplace transform
On (sub)mesoscopic scale peculiarities of diffusion driven growth in an active matter confined space, and related (bio)material realizations
Machine-learning-based structural analysis of interactions between antibodies and antigens
Hindmarsh-Rose neuron model with memristors
Multiple roles of Adenomatous Polyposis Coli gene in Wnt Signalling - a Computational Model
A stochastic model for interacting neurons in the olfactory bulb
Algorithmic and complexity results for decompositions of biological networks into monotone subsystems
Evolutionary games on networks and payoff invariance under replicator dynamics
Scaling laws in bacterial genomes: A side-effect of selection of mutational robustness?
The system-resonance approach in modeling genetic structures
Modelling the effects of contaminated environments on HFMD infections in mainland China
Habitat variability does not generally promote metabolic network modularity in flies and mammals
Intracellular miRNA or siRNA delivery and function
Modeling the effects of insecticides resistance on malaria vector control in endemic regions of Kenya
Peter Sterling's What is Health? Allostasis and the Evolution of Human Design, MIT Press, Cambridge, Massachusetts (2020), 225 pp., hardcover
Network induction for epidemic profiles with a novel representation
A global optimization algorithm inspired in the behavior of selfish herds
In silico minimalist approach to study 2D HP protein folding into an inhomogeneous space mimicking osmolyte effect: First trial in the search of foldameric backbones
The error minimization of the genetic code would have been determined by natural selection and not by a neutral evolution
scSAGRN: Inferring gene regulatory networks from single-cell multi-omics using spatial association
Model-based investigation of the circadian clock and cell cycle coupling in mouse embryonic fibroblasts: Prediction of RevErb-α up-regulation during mitosis
The significance of sex
Life and living beings under the perspective of organic macrocodes
A Markovian approach to the control of genetic regulatory networks
Corrigendum to "Classification of antituberculosis herbs for remedial purposes by using fuzzy sets" [Biosystems 94 (2008) 285-289]
Differentiation of a free-living alga into forms with ecto- and endosymbiotic associations with heterotrophic organisms in a 5-year microcosm culture
The major evolutionary transitions and codes of life
Use of evolved artificial regulatory networks to simulate 3D cell differentiation
Invasion dynamics of epidemic with the Allee effect
Active centrum hypothesis: The origin of chiral homogeneity and the RNA-world
Information processing in cells and tissues
STIM1 regulates pancreatic β-cell behaviour: A modelling study
Editorial: The foundations of mathematics and theoretical biology
Whole-cell metabolic control analysis
EMI model: A scale free biophysical framework for human consciousness, cognition and behaviour
On evaluation of infection probabilities for different age groups
Real time computation: Zooming in on population codes
Hierarchical pattern formation during amphibian limb regeneration
Chaos control via feeding switching in an omnivory system
Patterns of nucleotide asymmetries in plant and animal genomes
The time of appearance of the genetic code
Non-genetic inheritance: Evolution above the organismal level
Prevalence of prime mass residues in single point mutations and their importance to protein stability, function and evolution
Study of biocomplexity in an aquatic ecosystem through ascendency
Food encounter rate of simulated termite tunnels in heterogeneous landscapes
The tri-flow adaptiveness of codes in major evolutionary transitions
Balancing maximum sustainable yield and ecological resilience in an exploited two-predator one-prey system
Robustness of metabolic networks: A review of existing definitions
Immune response precision customized to tumor adaptive kinetics
On the impulsive controllability and bifurcation of a predator-pest model of IPM
Optimal control of a two-strain tuberculosis-HIV/AIDS co-infection model
The Metacontinuum: Bridging cellular composition to cognitive functions in brain organization
Input-output relations in binding neuron
Inner privacy of conscious experiences and quantum information
Local conditions for global stability in the space of codons of the genetic code
Relationship between dilemma occurrence and the existence of a weakly dominant strategy in a two-player symmetric game
Computational experiments reveal the efficacy of targeting CDK2 and CKIs for significantly lowering cellular senescence bar for potential cancer treatment
Sensitivity of the quorum sensing system is achieved by low pass filtering
Quantum logic automata generate class IV-like patterns and 1/f noise
Efim Liberman toward the comprehension of the phenomenon of life
Translation initiation modeling and mutational analysis based on the 3 ' -end of the Escherichia coli 16S rRNA sequence
The bacterial roots of the new autocracies: An essay on "Biopolitics"
A solution to the problem of proper segment positioning in the course of digit formation
Variation in base composition, structure-function relationships, and origins of structural repetition in bacterial rpsA gene
Approaching mathematical model of the immune network based DNA Strand Displacement system
A possible origin of life in nonpolar environments
What we have learned about evolutionary genome change in the past 7 decades
Bose-Einstein condensates form in heuristics learned by ciliates deciding to signal 'social' commitments
A DNA assembly model of sentence generation
Phase-locking patterns in a resonate and fire neural model with periodic drive
Reevaluation of McCulloch-Pitts-von Neumann's clock
Ecological systems as computer networks: Long distance sea dispersal as a communication medium between island plant populations
A Monte Carlo method for in silico modeling and visualization of Waddington's epigenetic landscape with intermediate details
Articular cartilage. Strong adsorption and cohesion of phospholipids with the quaternary ammonium cations providing satisfactory lubrication of natural joints
How occasional backstepping can speed up a processive motor protein
Benchmark for quantitative characterization of circadian clock cycles
Modelling gene expression control using P systems: The Lac Operon, a case study
Non-monotone cellular automata: Order prevails over chaos
Profile comparison revealed deviation from structural constraint at the positively selected sites
Techno-ethical concerns related to genetic sequencing reports
A model integrating multiple processes of synchronization and coherence for information instantiation within a cortical area
From Darwin to teleonomy: A categorical final-cause calculus for evolution
Implementation of a Hebbian chemoreceptor model for diffusive source localization
How organisms decrease their entropy
Influence of oxidative stress on women's fertility: A model with a generational age Caputo's fractional derivative
Robustness of circadian rhythms in the presence of molecular fluctuations: An investigation based on a mechanistic, statistical theory and a simulation algorithm
Biological networks in metabolic P systems
Laws of taxation for multicellular organisms: The economics of sleep
A New Solution for Maximal Clique Problem based Sticker Model
Revisiting the edge of chaos: Again?
Biological thermodynamics: Bridging the gap between physics and life
A quantum walks assisted algorithm for peptide and protein folding prediction
Effective identification and differential analysis of anticancer peptides
Chemical oscillatory reactions with proteinoids
Memory versus spatial disorder in the support of cooperation
Freedom and evolution in the dynamics of social systems
Using topographic networks to build a representation of consciousness
Phase offset determines alpha modulation of gamma phase coherence and hence signal transmission
Towards plant wires
Molecular mechanisms of encoding and decoding information in cell computing
A two-agent model applied to the biological control of the sugarcane borer (Diatraea saccharalis) by the egg parasitoid Trichogramma galloi and the larvae parasitoid Cotesia flavipes
Integrated signaling pathway and gene expression regulatory model to dissect dynamics of Escherichia coli challenged mammary epithelial cells
Global architecture of metabolite distributions across species and its formation mechanisms
Modelling the optimal timing in metabolic pathway activation - Use of Pontryagin's Maximum Principle and role of the Golden section
"Assembly Theory" in life-origin models: A critical review
A personal retrospective on the second half of the 20th century
Size matters in metabolic scaling: Critical role of the thermodynamic efficiency of ATP synthesis and its dependence on mitochondrial H+ leak across mammalian species
A word of appreciation to our publisher Anthony Newman
When Maxwell's Demon leaves the room
Follow up estimation of Aedes aegypti entomological parameters and mathematical modellings
Identifying DNA splice sites using hypernetworks with artificial molecular evolution
Evolutionary modelling of feed forward loops in gene regulatory networks
Programmatic access to logical models in the Cell Collective modeling environment via a REST API
DNA-based random number generation in security circuitry
Glycols modulate terminator stem stability and ligand-dependency of a glycine riboswitch
The stepping motor protein as a feedback control ratchet
Determination of the fraction of active inputs required by a neuron to fire
Single-cell classification, analysis, and its application using deep learning techniques
Synchronization Studies of Hindmarsh-Rose Neuron Networks: Unraveling the Influence of connection induced memristive synapse
The Double Homunculus model of self-reflective systems
A deterministic mechanism producing the loose coupling phenomenon observed in an actomyosin system
Visualizing multi-omics data in metabolic networks with the software Omix - A case study
Evolution of form and function in a model of differentiated multicellular organisms with gene regulatory networks
Mathematical model of coffee tree's rust control using snails as biological agents
Event-driven simulation of neural population synchronization facilitated by electrical coupling
A categorical and entropic framework for Bayesian networks and consciousness
Adult attachment style and lateral preferences in physical proximity
A protein folding robot driven by a self-taught agent
An individual-based model applied to the study of different fishing strategies of Pintado Pseudoplatystoma corruscans (Agassiz, 1829)
The role of crossover operator in evolutionary-based approach to the problem of genetic code optimization
On paradoxes between optimal growth, metabolic control analysis, and flux balance analysis
On allosteric control model of bone turnover cycle containing osteocyte regulation loop
Word games and molecular recognition - The creative control of endothelial cell function
GATA TF Class Classifier: AI-based functional prediction and taxonomic profiling in angiosperm GATA transcription factors
Experimental solutions to problems defining the origin of codon-directed protein synthesis
Modelling the dynamic structure of biological state-based systems
A trade-off relationship between energetic cost and entropic cost for in vitro evolution
Genomic comparison using data mining techniques based on a possibilistic fuzzy sets model
Modeling force-velocity relation in skeletal muscle isotonic contraction using an artificial neural network
On the relationship between membranes and ambients
Hybrid, randomized and high capacity conservative mutations DNA-based steganography for large sized data
Sociality of an agent during morphogenetic canalization: Asynchronous updating with potential resonance
On the origin of mental representations
Special issue: Computational models in photosynthesis
Special edition of BioSystems: Information processing in cells and tissues
Systems-level characterization of the kernel mechanism of the cyanobacterial circadian oscillator
Mitotic waves in an import-diffusion model with multiple nuclei in a shared cytoplasm
Perspectives on the Neuroscience of Cognition and Consciousness
Cancer memory as a mechanism to establish malignancy
A mathematical framework for the statistical interpretation of biological growth models
Altered intensity coding in the salicylate-overdose animal model of tinnitus
Dynamics and mechanisms of oscillatory photosynthesis
Unitary structure of palindromes in DNA
Computer simulations of in vitro morphogenesis
Gaidai reliability method for high-dimensional spatio-temporal biosystems
Spatial organisation plasticity reduces disease infection risk in rock-paper-scissors models
Elucidating the adaptation and temporal coordination of metabolic pathways using in-silico evolution
Temporary and permanent control of partially specified Boolean networks
Steady state approach to model gene regulatory networks - Simulation of microarray experiments
Sequential spiking neural P systems with exhaustive use of rules
Codes of praxis: How recursivity constitutes human social practices
Bayesian consolidation of retinal micro(nano)plastic hypothesis: From existential confirmation to spatial-phenotypic inference
A neural circuit model for changing the amount of information maintained in short-term memory depending on stimuli relationships
A mathematical investigation on the active substance pulsatory release from a solution-charged liposome
Sensory fusion in Physarum polycephalum and implementing multi-sensory functional computation
Is there a relationship between embryonic bioelectric currents and differentiation waves?
Tetracoding increases with body temperature in Lepidosauria
Living systems are smarter bots: Slime mold semiosis versus AI symbol manipulation
The role of pectin in plant morphogenesis
Effect of monochromatic light on the behavior of the ctenophore Mnemiopsis leidyi (A. Agassiz, 1865)
Topology and thermodynamics of gaseous ligands diffusion paths in human neuroglobin
p -Adic hierarchical properties of the genetic code
Principles of cognitive biology and the concept of biocivilisations
Charting the dynamics of translation
Aggregate Boid behavior to aid in artificial autopoietic organization
The repertoire of candidate archaeal noncoding RNAs and their association with temperature adaptation
On the significance of sodium ionic channels in analysis of the breast cancer metastaticity
Neural coding of numerousness
Stoichiometric network reconstruction and analysis of yeast sphingolipid metabolism incorporating different states of hydroxylation
Diving into cancer OXPHOS - The application of metabolic control analysis to cell and tissue research
Memory boosts turn taking in evolutionary dilemma games
Remarks on neurocybernetics and its links to computing science. To the memory of Prof. Luigi M. Ricciardi
An in silico platform for the study of epithelial pre-invasive neoplastic development
Regulative development as a model for origin of life and artificial life studies
Interaction between the immune system and acute myeloid leukemia: A model incorporating promotion of regulatory T cell expansion by leukemic cells
Knee joint injury and repair modeled by membrane systems
Complex adaptation and system structure
Coacervates meet the RNP-world: liquid-liquid phase separation and the emergence of biological compartmentalization
Contribution of AMPA and NMDA receptors in the spontaneous firing patterns of single neurons in autaptic culture
On Boolean gates in fungal colony
Semi-synthetic minimal cells as a tool for biochemical ICT
The role of internal duplication in the evolution of multi-domain proteins
Homeostasis and information processing: The key frames for the thermodynamics of biological systems
Estimating a drug's elimination rate-constant or half-life from a single blood sample: a practical approach with particular benefits for critically ill/vulnerable patients
mRNA function after intracellular delivery and release
Calcium messages in flagella are faster than messenger particles
Transfer function of protoplasmic tubes of Physarum polycephalum
What is code biology?
Evolution of hierarchy in bacterial metabolic networks
Toward a hierarchical virtual screening and toxicity risk analysis for identifying novel CA XII inhibitors
Virions and respiratory droplets in air: Diffusion, drift, and contact with the epithelium
Perfection is the enemy of evolution
Robustness and aging - A systems-level perspective
Beyond the genome: A multi-scale, agent-based taxonomy of biological codes and energetic constraints
Designing convergent cellular automata
Decoding the double trouble: A mathematical modelling of co-infection dynamics of SARS-CoV-2 and influenza-like illness
Synaptic imbalances in endogenous psychoses
Evolving Boolean regulatory networks with epigenetic control
Molecular orbitals of delocalized electron clouds in neuronal domains
Assessing the effect of zooprophylaxis on zoonotic cutaneous leishmaniasis transmission: A system dynamics approach
Triadic conceptual structure of the maximum entropy approach to evolution
Comparing the complexity of written and molecular symbolic systems
Integration of intracellular signaling: Biological analogues of wires, processors and memories organized by a centrosome 3D reference system
A Markovian engine for a biological energy transducer: The catalytic wheel
Stochastic Chemical Kinetics. Theory and (Mostly) Systems Biological Applications, P. Erdi, G. Lente. Springer (2014)
Symmetrizing object and meta levels organizes thinking
Relational model of all genetic codes
Non-Gaussian noise-optimized intracellular cytosolic calcium oscillations
Role of signal-dependent noise during maintenance of isometric force
A novel bio-inspired optimization model based on Yellow Saddle Goatfish behavior
Temporal sub units in dendritic trees
Simulating autonomous anticipation: The importance of Dubois' conjecture
An evolutionary system using development and artificial Genetic Regulatory Networks for electronic circuit design
Automatic analysis of computation in biochemical reactions
Generic oscillation patterns of the developing systems and their role in the origin and evolution of ontogeny
The evolution of senescence in multi-component systems
Editorial: Systems bioinformatics for medicine
Bézier curve parametrisation and echo state network methods for solving optimal control problems of SIR model
Lacunarity as a novel measure of cancer cells behavior
Analysis of gene regulatory network models with graded and binary transcriptional responses
Quantum biology and human carcinogenesis
Corrigendum to "Mathematical analysis of a cholera model with public health interventions" [Biosystems, 105 (3) (2011), 190-200]
Properties of network structures, structure coefficients, and benefit-to-cost ratios
Impulse pattern in bi-directionally coupled model neurons of different dynamics
Self-organized perturbations enhance class IV behavior and 1/f power spectrum in elementary cellular automata
A rationale for the symmetries by base substitutions of degeneracy in the genetic code
Hierarchy of codon usage frequencies from codon-anticodon interaction in the crystal basis model
Mathematical folding of node chains in a molecular network
Spontaneous activity of living cells
Cell-to-cell diversification in ERBB-RAS-MAPK signal transduction that produces cell-type specific growth factor responses
Thermodynamic for biological development: A hypothesis
p-Adic mathematics and theoretical biology
DNA biosensors that reason
A discriminative test among the different theories proposed to explain the origin of the genetic code: The coevolution theory finds additional support
Modeling inherited physiological structures based on hyperbolic numbers
Gray code representation of the universal genetic code: Generation of never born protein sequences using Toeplitz matrix approach
The cell as a realization of the (M, R) system
On the time to reach a critical number of infections in epidemic models with infective and susceptible immigrants
Exploring natural anthraquinones as potential MMP2 inhibitors: A computational study
Structural evidence for electromagnetic resonance in plant morphogenesis
The information continuum model of evolution
An irreversible thermodynamic model of prebiological dissipative molecular structures inside vacuoles at the surface of the Archean Ocean
Adaptive evolution of body size subject to indirect effect in trophic cascade system
m-CALP - Yet another way of generating handwritten data through evolution for pattern recognition
Fast Bayesian parameter estimation for stochastic logistic growth models
Fundamentals of evolutionary transformations in biological systems
Searching the principal genes for neural differentiation of mouse ES cells by factorizing eigengenes of clusters
Sequence classification with side effect machines evolved via ring optimization
Image correction method for the colour contrast effect using inverse processes of the brain
New insights into the human body iron metabolism analyzed by a Petri net based approach
Construction and elementary mode analysis of a metabolic model for Shewanella oneidensis MR-1
An interplay between compositional constraint and natural selection dictates the codon usage pattern among select Galliformes
In silico prediction of the cell proliferation in porous scaffold using model of effective pore
Reconstruction and analysis of a genome-scale metabolic model of Methylovorus sp. MP688, a high-level pyrroloquinolone quinone producer
Amino acid content of beta strands and alpha helices depends on their flanking secondary structure elements
Codon-anticodon interaction and the genetic code evolution
Artificial immune system features added to breast cancer clinical data for machine learning (ML) applications
Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum
Social satisficing: Multi-agent reinforcement learning with satisficing agents
Immune cell-specific and common molecular signatures in rheumatoid arthritis through molecular network approaches
The lamin code
Viruses, immunity and evolution
A CLIQUE algorithm using DNA computing techniques based on closed-circle DNA sequences