yusuke1997/dblp-id-title huggingface dataset:
Homeostatic set-points are physical and foundational to organism autonomy
Effects of light environment on the induction of chlorophyll fluorescence in leaves: A comparative study of Tradescantia species of different ecotypes
Controlling the ratchet effect through the symmetries of the systems: Application to molecular motors
An efficient method for stochastic simulation of biological populations in continuous time
Entropy, externality and human evolution
Biological computation running on quantum computation
Influence of time delay and channel blocking on multiple coherence resonance in Hodgkin-Huxley neuron networks
A hypothetical role of cortico-basal ganglia-thalamocortical loops in visual processing
Geometric analysis of pathways dynamics: Application to versatility of TGF-β receptors
A mechanistic approach to optimize combination antibiotic therapy
Efficient solutions to hard computational problems by P systems with symport/antiport rules and membrane division
Circular mixed sets
Modeling the role of ATP metabolism in articular cartilage and osteoarthritis
Dynamical behavior of two predators competing over a single prey
Extended Bayesian inference incorporating symmetry bias
Biosystem models, generated from a complex rule/reaction/influence network and from two functionality prototypes
Biomolecular computation with molecular beacons for quantitative analysis of target nucleic acids
Predicting gene expression level by the transcription factor binding signals in human embryonic stem cells
Global stability of a transport-related infection model with general incidence rate in two heterogeneous cities
A minimum principle in codon-anticodon interaction
Robustness against point mutations of genetic code extensions under consideration of wobble-like effects
Spatial waves and temporal oscillations in vertebrate limb development
The Unscented Kalman Filter estimates the plasma insulin from glucose measurement
Effect of synaptic plasticity on sensory coding and steady-state filtering properties in the electric sense
Assortative mating at loci under recent natural selection in humans
Quantitative analysis of photosynthetic carbon metabolism in protoplasts and intact leaves of barley. Determination of carbon fluxes and pool sizes of metabolites in different cellular compartments
Comparing functional responses in predator-infected eco-epidemics models
Gene-regulatory context of honey bee worker sterility
An integrated parametric model for MT self-assembly formation analysis
Estimating daytime ecosystem respiration from eddy-flux data
Exploring discrete space-time models for information transfer: Analogies from mycelial networks to the cosmic web
Reflexivity, coding and quantum biology
A general framework dedicated to computational morphogenesis Part I - Constitutive equations
Corrigendum to "An efficient approach for identifying important biomarkers for biomedical diagnosis" [Biosystems 237 (2024) 105163]
A Bayesian approach to the probability of coronary heart disease subject to the -308 tumor necrosis factor-α SNP
Formation and maintenance of tubular membrane projections: Experiments and numerical calculations
Analysis of fluctuation in protein abundance without promoter regulation based on Escherichia coli continuous culture
Negative membrane potentials potentiate multicellularity
Neuronal in vitro activity is more sensitive to valproate than intracellular ATP: Considerations on conversion problems of IC 50 in vitro data for animal replacement
Energy saving mechanisms, collective behavior and the variation range hypothesis in biological systems: A review
Positive circuits and d-dimensional spatial differentiation: Application to the formation of sense organs in Drosophila
Information reduction in a reverberatory neuronal network through convergence to complex oscillatory firing patterns
Small universal spiking neural P systems
A never-ending prediction: meta-prediction, counter-oscillatory system and traumatic affordance
Field guide to Nath's research work on ATP synthesis and hydrolysis
The direction of evolution: The rise of cooperative organization
The evolution of the Glycomic Codes of extracellular matrices
The genetic code and its p-adic ultrametric modeling
The metabolic control theory: Its development and its application to mitochondrial oxidative phosphorylation
Multiplicative noise is beneficial for the transmission of sensory signals in simple neuron models
Modeling the origin, evolution, and functioning of the genetic code
The Rücker-Markov invariants of complex Bio-Systems: Applications in Parasitology and Neuroinformatics
D'Arcy W. Thompson's On Growth and Form: A landmark for the mathematical foundations of epigenetics
Reversible and irreversible mitochondrial swelling: Effects of variable mitochondrial activity
The question of quantum communication between cancer cells
Mutation-selection dynamics and error threshold in an evolutionary model for Turing machines
On interaction of proteinoids with simulated neural networks
Objective patterns in the evolving network of non-equivalent observers
Gene regulatory network inference: Data integration in dynamic models - A review
Enrichment and ecosystem stability: Effect of toxic food
Metacode: One code to rule them all
Minimizing enzyme mass to decompose flux distribution for identifying biologically relevant elementary flux modes
The genetic code and its optimization for kinetic energy conservation in polypeptide chains
A novel bio-heuristic computing algorithm to solve the capacitated vehicle routing problem based on Adleman-Lipton model
Super-rational aspiration induced strategy updating helps resolve the tragedy of the commons in a cooperation system with exit rights
Stability analysis for HIV infection delay model with protease inhibitor
Dynamical and topological robustness of the mammalian cell cycle network: A reverse engineering approach
Prediction and analysis of prokaryotic promoters based on sequence features
Binary oppositions, algebraic holography and stochastic rules in genetic informatics
On the origin of three base periodicity in genomes
A statistical approach to the identification of diploid cellular automata based on incomplete observations
Fractional nutrient uptake model of plant roots
A dynamical system for the IGF1-AKT signaling pathway in skeletal muscle adaptation
Scaling and fractal behaviour underlying meiotic recombination
Two linearities for quantum computing in the lambda calculus
Computational models of signalling networks for non-linear control
Cooperation, involuntary defection, and Polymorphic Evolutionary Games
Crucial steps to life: From chemical reactions to code using agents
Computational analysis of IL-6/IL-22 signaling in liver disease
The common misuse of noise decomposition as applied to genetic systems
The selectivity of noise and coupling for coherence biresonance and array-enhanced coherence biresonance in coupled neural systems
Computer modeling of electron and proton transport in chloroplasts
Using activity time windows and logical representation to reduce the complexity of biological network models: G1/S checkpoint pathway with DNA damage
The calculus of codes - From entropy, complexity, and information to life
Evolution and maintenance of phenotypic plasticity
Is meaning commensurable in scientific theories? From arbitrariness to non-nomological relations in meaning-making
What if houses were powered by milk?
Evolution as a search for organizational equilibrium
Analytical tool for COVID-19 using an SIR model equivalent to the chain reaction equation of infection
Endogenous regulation of selection pressure: A minimal game-theoretical model
Human face as a biosocial marker in human evolution
Species extinction and permanence of an impulsively controlled two-prey one-predator system with seasonal effects
Genes on the circular code alphabet
Observation of optimal gecko's adhesion on nanorough surfaces
Stretching tension effects in permeability transition pores of inner mitochondrial membrane
Olfactory signal coding in an odor background
Archaeal Origins of Eukaryotic Cell and Nucleus
Morphogenetic origin of natural variation
Electromechanics of polarized cell growth
Software for evaluation of immune cell activation (Application note)
A real-time spiking cerebellum model for learning robot control
Modelling evolutionary cell behaviour using neural networks: Application to tumour growth
Early detection of glaucoma integrated with deep learning models over medical devices
Balancing the cellular budget: Lessons in metabolism from microbes to cancer
Bio-inspired self-organizing cellular systems
Chasing the tail: The emergence of autocatalytic networks
Reverse engineering genetic networks using nonlinear saturation kinetics
Integrating fuzzy DEMATEL and Constructal Law for biofouling dynamics in Marine Growth Prevention Systems
Spiking neural network model for memorizing sequences with forward and backward recall
Fast heterosynaptic learning in a robot food retrieval task inspired by the limbic system
Maize root behavior as three-inputs-three-outputs logical gates due to positive gravitropism and nutritropism
Evolutionary computation for reconstructing threshold networks of the tryptophan operon in Escherichia coli
Quaternionic representation of the genetic code
IntApop: A web service for predicting apoptotic protein interactions in humans
Competition for finite resources as coordination mechanism for morphogenesis: An evolutionary algorithm study of digital embryogeny
Lynn Margulis (1938-2011)
Effects of complementary loop composition in truncated R3C ligase ribozymes on kiss switch activation
CHTW(R)-system in Ca2+ transport modelling
Up-and-down movement of a sliding actin filament in the in vitro motility assay
The spiderweb of error-detecting codes in the genetic information
Offset response of the olfactory projection neurons in the moth antennal lobe
Flock members experience gas pressures higher than lone individuals
Toward an adequate mathematical model of mental space: Conscious/unconscious dynamics on m-adic trees
Selection advantage of metabolic over non-metabolic replicators: A kinetic analysis
Cartography of the multiple formal systems of molecular autopoiesis: from the biology of cognition and enaction to anticipation and active inference
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
Code biology and the problem of emergence
ACoM: A classification method for elementary flux modes based on motif finding
Structure of a randomly grown 2-d network
Temporal constraints of a gene regulatory network: Refining a qualitative simulation
The evolutionary influence of binding site organisation on gene regulatory networks
Rule-based modelling of conjugative plasmid transfer and incompatibility
Ecological succession as an energy dispersal process
Getting the news in milliseconds: The role of early novelty detection in active electrosensory exploration
Mean-field Boolean network model of a signal transduction network
On the length scale dependence of DNA conformational change under local perturbation
Differences in dynamics between discrete strategies and continuous strategies in a multi-player game with a linear payoff structure
Critical-like self-organization and natural selection: Two facets of a single evolutionary process?
From a coenzyme-like mechanism to homochirality
Quantum information as the scientific basis for the explanation of human consciousness and its evolution
Logical modelling of myelofibrotic microenvironment predicts dysregulated progenitor stem cell crosstalk
On chirality of slime mould
Probabilistic transition from unstable predator-prey interaction to stable coexistence of Dictyostelium discoideum and Escherichia coli
Cooperative combinatorial optimization: Evolutionary computation case study
On stochastic Gilpin-Ayala population model with Markovian switching
The reversibility of cellular determination: An evolutive pattern of epigenetic plasticity
A simple and fast ANN-based method of studying slow-wave sleep microstructure in freely moving rats
The effect of colored noise on spatiotemporal dynamics of biological invasion in a diffusive predator-prey system
Networks of polarized splicing processors as problem solvers
Optimal control applied to a temperature dependent schistosomiasis model
Morphogenesis of active shells
Editorial: Petri nets for cellular process modelling
Ensuring wholeness: Using Code Biology to overcome the autonomy-heteronomy divide
Do elementary flux modes combine linearly at the "atomic" level? Integrating tracer-based metabolomics data and elementary flux modes
Vladimir Voevodsky on mathematics and life
Pocketknife tRNA hypothesis: Anticodons in mammal mitochondrial tRNA side-arm loops translate proteins?
A model of dopamine modulated glutamatergic synapse
Phase coherent quasi-particle formation in biological systems
Fast and asymptotic computation of the fixation probability for Moran processes on graphs
Anticipation, memory, and top-down causation in living systems
PhotoMEA: An opto-electronic biosensor for monitoring in vitro neuronal network activity
Control of neural chaos by synaptic noise
An approach to the plant body: Assessing concrete and abstract aspects
Evolution of cellular automata with memory: The Density Classification Task
The need for a concept of shape homeostasis
Crosstalk pathway inference using topological information and biclustering of gene expression data
Synechism 2.0: Contours of a new theory of continuity in bioengineering
Noise generation, amplification and propagation in chemotactic signaling systems of living cells
Thermal fluctuations biased for directional motion in molecular motors
Titian's mythological paintings: A pictorial personal code
Monitoring in a predator-prey systems via a class of high order observer design
The mathematical biophysics of Nicolas Rashevsky
Cooperation in structured populations via coupled reputation and learning: A spatial evolutionary game approach
Dimerization induces bimodality in protein number distributions
Symmetry and entropy of biological patterns: Discrete Walsh functions for 2D image analysis
Statistical evidence for power law temporal correlations in exploratory behaviour of rats
Expert-guided multi-objective optimization: An efficient strategy for parameter estimation of biological systems with limited data
Metabolic Control Analysis of triacylglycerol accumulation in oilseed rape
Comparison of modelling approaches demonstrated for p16-mediated signalling pathway in higher eukaryotes
Brain and behavior share features of a critical state dynamics
First order phase transition and hysteresis in a cell's maintenance of the membrane potential - An essential role for the inward potassium rectifiers
Electrical activity of fungi: Spikes detection and complexity analysis
Robustness and evolvability: Revisited, redefined and applied
Adaptive flexibility of cells through nonequilibrium entropy production
Reinhart Heinrich: In memoriam of an exceptional scholar
Collective durotaxis along a self-generated mobile stiffness gradient in vivo
Corrigendum to "On chirality of slime mould" [BioSystems 140 (2016) 23-27]
Firing statistics of inhibitory neuron with delayed feedback. II: Non-Markovian behavior
"Ideal correlations" for biological activity of peptides
Protein-DNA target search relies on quantum walk
Nonextensive realizations in interacting ion channels: Implications for mechano-electrical transducer mechanisms
The differentiation code
The concepts of code biology
Computational modeling of epithelial-mesenchymal transformations
Modelling metapopulations with stochastic membrane systems
Errors of the ancestral translation, LUCA, and nature of its direct descendants
The linear allometric relationship between total metabolic energy per life span and body mass of mammals
Internal quantum constraints of natural computation in autopoietic systems
Functional connections between auditory cortical fields in humans revealed by Granger causality analysis of intra-cranial evoked potentials to sounds: Comparison of two methods
Information processing and energy efficiency of temperature-sensitive Morris-Lecar neuron
Evolving an ecology of mathematical expressions with grammatical evolution
Rational decision making in biological systems
Evaluating the statistical similarity of neural network activity and connectivity via eigenvector angles
Optimal control problems of mosquito-borne disease subject to changes in feeding behavior of Aedes mosquitoes
Generation of random sequences using DNA cryptography for OTP encryption
Comparison of the molecular topologies of stress-activated transcription factors HSF1, AP-1, NRF2, and NF-κB in their induction kinetics of HMOX1
Cardiac cell: a biological laser?
Surface contraction waves or cell proliferation waves in the presumptive neurectoderm during amphibian gastrulation: Mexican axolotl versus African clawed frog
cAMP-regulated dynamics of the mammalian circadian clock
An integrated approach to understand the regulatory role of miR-27 family in breast cancer metastasis
Temporal regulation of gene expression and pathways in chemotherapy-induced senescence in HeLa cervical cancer cell line
Complex dynamic behavioral transitions in auditory neurons induced by chaotic activity
Toward understanding the emergence of life: A dual function of the system of nucleotides in the metabolically closed autopoietic organization
Computational image analysis from the transverse plane of Drosophila embryos
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 life
Turing instability on multiplex simplicial epidemic networks with cross-diffusion and behavioral delay
A new method: Characterize and quantify biofilm wrinkles by UNet and Sholl Analysis
A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information
Determining parameter distribution in within-host severe P. falciparum malaria
On the semantics of ecoacoustic codes
Microtubules as mechanical force sensors
Oxygen-glucose deprivation-induced enhancement of extracellular ATP-P2Y purinoceptors signaling for the propagation of astrocytic calcium waves
Passive competition between pairs of self-ordering proto-replicators and the effect of primitive membranes
Is Darwinian selection a retrograde driving force of evolution?
Modeling hydrochory effects on the Tunisian island populations of Pancratium maritimum L. using colored Petri nets
DNA strand generation for DNA computing by using a multi-objective differential evolution algorithm
Rule-based computing system for microbial interactions and communications: Evolution in virtual bacterial populations
Generation of genetic codes with 2-adic codon algebra and adaptive dynamics
Origins of the Embryo: Self-organization through cybernetic regulation
Symbiogenesis as a driving force of evolution: The legacy of Boris Kozo-Polyansky
Invasion of cooperators in lattice populations: Linear and non-linear public good games
Combining kinetic orders for efficient S-System modelling of gene regulatory network
Modelling persistence over generations in biological and cultural evolution based on differential paces of change
Cancer cell motility: Optimizing spatial search strategies
Stochastic analysis of Chemical Reaction Networks using Linear Noise Approximation
Random effects inducing heart pathological dynamics: An approach based on mathematical models
The origins of ATP synthases, the identity of LUCA, and the progenote
Multiobjective optimization to reconstruct biological networks
Deep learning based genome analysis and NGS-RNA LL identification with a novel hybrid model
Emergence of scale-free distribution in protein-protein interaction networks based on random selection of interacting domain pairs
Spatiotemporal dynamics of the Calvin cycle: Multistationarity and symmetry breaking instabilities
Disease Probability Index (DPI, χ): A new alignment-free scoring method to evaluate the propensities of polypeptide sequences leading to disease onset
Affinity analysis of differentially expressed genes in hepatocytes expressing HCV core genotype 1b or 3a
The body of knowledge: On the role of the living body in grounding embodied cognition
HOKF: High Order Kalman Filter for Epilepsy Forecasting Modeling
The role of dynamic stimulation pattern in the analysis of bistable intracellular networks
Multiple sequence alignment using multi-objective based bacterial foraging optimization algorithm
Evolving locomotion for a 12-DOF quadruped robot in simulated environments
Mathematical analysis of a cholera model with public health interventions
The sensual cell: Feeling and affect in unicellular species
Contrasting philosophical and scientific views in the long history of studying the generation of form in development
Hypothetical novel simulations to explain the evolutionary survival of the hypo-reproductive extreme tail in the complex human diversity
The Second Special Issue on Code Biology - An overview
Evolution of cooperation in multigame with environmental space and delay
The entropic and symbolic components of information
Inferring directions of evolution from patterns of variation: The legacy of Sergei Meyen
A neural mechanism of phase-locked responses to sinusoidally amplitude-modulated signals in the inferior colliculus
A coinfection model for HIV and HCV
Towards a first implementation of the WLIMES approach in living system studies advancing the diagnostics and therapy in augmented personalized medicine
The epoch-making importance of Ervin Bauer's theoretical biology
Amoeba-based computing for traveling salesman problem: Long-term correlations between spatially separated individual cells of Physarum polycephalum
Epigenetic landscape of interacting cells: A model simulation for developmental process
Structure and behavior in Boolean monotonic model pools
Reevaluating human-microbiota symbiosis: Strain-level insights and evolutionary perspectives across animal species
Towards a general theory of the major cooperative evolutionary transitions
Computation by inverse causality: A universal principle to produce symbols for the external reality in living systems
Fixed-points in random Boolean networks: The impact of parallelism in the Barabási-Albert scale-free topology case
Modelling 18 O 2 and 16 O 2 unidirectional fluxes in plants: I. Regulation of pre-industrial atmosphere
Nuclear quantum effects explain chemiosmosis: The power of the proton
From nullomers to abundant motifs: Fractals, CpG Bias, and Chargaff's rules in genomic sequences
Intelligence: Natural, artificial, or what?
Mechano-electrical vibrations of microtubules - Link to subcellular morphology
RNA tetraplex as a primordial peptide synthesis scaffold
A new parallel DNA algorithm to solve the task scheduling problem based on inspired computational model
Easy parameter identifiability analysis with COPASI
Conceptualisation of articular cartilage as a giant reverse micelle: A hypothetical mechanism for joint biocushioning and lubrication
A first perturbome of Pseudomonas aeruginosa : Identification of core genes related to multiple perturbations by a machine learning approach
Algebraic properties of automata associated to Petri nets and applications to computation in biological systems
Why does a cell function? New arguments in favor of quantum effects
The effect of nanoparticles on plankton dynamics: A mathematical model
Assessing the potential of surface-immobilized molecular logic machines for integration with solid state technology
Neural networks from biological to artificial and vice versa
On the Cramér-Rao bound applicability and the role of Fisher information in computational neuroscience
Joint optimization of replicative rate and information storage set the letter size of primordial genetic alphabet
Intracellular viral kinetics limited by the supply of amino acids for synthesis of viral proteins
A model of optimal protein allocation during phototrophic growth
Holistic system analysis of the energetic power and efficiency of animal production
Erythrocyte: A systems model of the control of aggregation and deformability