yusuke1997/dblp-id-title huggingface dataset:
Sociotype and cultural evolution the acceleration of cultural change alongside industrial revolutions
On the way towards 'basic autonomous agents': Stochastic simulations of minimal lipid-peptide cells
Data-driven dynamical modelling of a pathogen-infected plant gene regulatory network: A comparative analysis
An immune-inspired swarm aggregation algorithm for self-healing swarm robotic systems
A computational approach to validate novel drug targets of gentianine from Swertiya chirayita in Plasmodium falciparum
Mutual trust and cooperation in the evolutionary hawks-doves game
The polyphyletic origins of glycyl-tRNA synthetase and lysyl-tRNA synthetase and their implications
Corrigendum to "Dynamics of an SIR model with vaccination dependent on past prevalence with high order distributed delay" [BioSystems 129 (2015) 50-65]
Exact numerical calculation of fixation probability and time on graphs
miRNAFinder: A comprehensive web resource for plant Pre-microRNA classification
Cosmos MIND and matter: Is mind in spacetime?
Stochastic P systems and the simulation of biochemical processes with dynamic compartments
The modularity codes
MateSim: Monte Carlo simulation for the generation of mating tables
Molecular motor translocation kinetics: Application of Monte Carlo computer simulations to determine microscopic kinetic parameters
Advances in the integration of transcriptional regulatory information into genome-scale metabolic models
Morphogenetic systems: Models and experiments
Stepwise identification of potent antimicrobial peptides from human genome
The role of self-maintaining resilient reaction networks in the origin and evolution of life
Fluctuation as a tool of biological molecular machines
Using epigenetic networks for the analysis of movement associated with levodopa therapy for Parkinson's disease
Stability analysis and optimal vaccination of an SIR epidemic model
Biosemiotics comprehension of PrP code and prion disease
Inhibitory control of site-specific synaptic plasticity in a model CA1 pyramidal neuron
Total enzyme activity constraint and homeostatic constraint impact on the optimization potential of a kinetic model
Natural pyrrolysine-biased translation of stop codons in mitochondrial peptides entirely coded by expanded codons
New structural variation in evolutionary searches of RNA neutral networks
The anion recognition properties of hydrazone derivatives containing anthracene
Effects of Poisson noise in a IF model with STDP and spontaneous replay of periodic spatiotemporal patterns, in absence of cue stimulation
Corrigendum to "Paleo-phyllotaxis: Fucales, bryophytes, lycophytes and monilophytes" [BioSystems 255 (2025) 105541]
Optimal parameter settings for information processing in gene regulatory networks
Progressive plasticity of auditory cortex during appetitive operant conditioning
The enhancement of stability of p53 in MTBP induced p53-MDM2 regulatory network
Estimation of plasma insulin concentration under glycemic variability using nonlinear filtering techniques
Modelling the early steps of transduction in insect olfactory receptor neurons
In silico investigation of novel biological pathways: The role of CD200 in regulation of T cell priming in experimental autoimmune encephalomyelitis
Interspike interval densities of resonate and fire neurons
Improving the efficiency of evolutionary de novo peptide design: Strategies for probing configuration and parameter settings
Multi-parameter exploration of dynamics of regulatory networks
Generalized model of closed microecosystem «alga - micro-consumers»
On symmetries, resonances and photonic crystals in morphogenesis
Periodic patterns in distributions of peptide masses
The promoting effect of adaptive persistence aspiration on the cooperation based on the consideration of payoff and environment in prisoner's dilemma game
Fungal electronics
Insight into the binding mode and the structural features of the pyrimidine derivatives as human A 2A adenosine receptor antagonists
Establishment of screening system toward discovery of kinase inhibitors using label-free on-chip phosphorylation assays
Punctuated evolution and robustness in morphogenesis
A sequence-based analysis of the pointer distribution of stichotrichous ciliates
The first Special Issue on code biology - A bird's-eye view
Evolutionary stability of developmental commitment
The dynamics of a harvested predator-prey system with Holling type IV functional response
A minimal mathematical model of nonphotochemical quenching of chlorophyll fluorescence
Cell cycles during early steps of amphibian embryogenesis: A review
Directional hearing in a silicon cricket
Evolutionary development of tensegrity structures
Mathematical modelling for the assessment of the effect of drug application delays in metronomic chemotherapy of cancer due to physiological constraints
Exploring landscape structure effect on termite territory size using a model approach
A note on the complexity of finding and enumerating elementary modes
The theory of oxygen hemoglobin association
The origin of autonomous agents by natural selection
Dynamical diversity of mitochondrial BK channels located in different cell types
The human extended mitochondrial metabolic network: New hubs from lipids
Circular cut codes in genetic information
A novel analytical method for evolutionary graph theory problems
Modeling the emergence of HIV-1 drug resistance resulting from antiretroviral therapy: Insights from theoretical and numerical studies
Species coexistence of communities with intraguild predation: The role of refuges used by the resource and the intraguild prey
RNAdt: An online tutorial and data portal for the RNA structurome era
Effect of the electromagnetic induction in the electrical activity of the Kazantsev model of inferior Olive Neuron model
Probable relationship between partitions of the set of codons and the origin of the genetic code
Ohmic-Polarization transition in hydrated DNA
Transformation of the inherent energy in food to ATP and transformations of our knowledge about the mechanism
Karyotype as code of codes: An inheritance platform to shape the pattern and scale of evolution
Metabolism is the tie: The Bertalanffy-type cancer growth model as common denominator of various modelling approaches
Morphogenetic fields in embryogenesis, regeneration, and cancer: Non-local control of complex patterning
Slow update stochastic simulation algorithms for modeling complex biochemical networks
Caenorhabditis elegans body wall muscles are simple actuators
Dialogue and causality: Global description from local observations and vague communications
Embryoid bodies from mouse stem cells express oxytocin receptor, Oct-4 and DAZL
Chromatin remodeling in silico: A stochastic model for SWI/SNF
The necessity of hierarchy for living systems
Nirmala indices bridge molecular connectivity and genetic stability: A graph-theoretic lens on purines and pyrimidines
A test of the adaptive network explanation of functional disorders using a machine learning analysis of symptoms
Studying the capability of different cancer hallmarks to initiate tumor growth using a cellular automaton simulation. Application in a cancer stem cell context
Modeling gonorrhea and HIV co-interaction
A new hierarchical approach to multi-level model abstraction for simplifying ODE models of biological networks and a case study: The G1/S Checkpoint/DNA damage signalling pathways of mammalian cell cycle
Synthetic biological neural networks: From current implementations to future perspectives
Fractional Mathematical Oncology: On the potential of non-integer order calculus applied to interdisciplinary models
Spatial multi-omics technologies and applications in cancer
GeRNet: a gene regulatory network tool
Flowing boundaries in autopoietic systems and microniche construction
How do soldier crabs behave when seeing vibrating robots?
Natural computation and its limits: Efim Liberman at the dawn of a new science
Tools-4-Metatool (T4M): Online suite of web-tools to process stoichiometric network analysis data from Metatool
The genotype-phenotype relationship and evolutionary genetics in the light of the Metabolic Control Analysis
Computer simulation of interaction of photosystem 1 with plastocyanin and ferredoxin
The meiotic-mitotic initiation switch in budding yeast maintains its function robustly against sensitive parameter perturbations
A knowledge driven supervised learning approach to identify gene network of differentially up-regulated genes during neuronal senescence in Rattus norvegicus
Biotensegrity is the super-stability hypothesis for biology
Hybrid agent-based model for quantitative in-silico cell-free protein synthesis
Identification of subtype specific biomarkers of clear cell renal cell carcinoma using random forest and greedy algorithm
SBDyNetVis: a visualization tool of dynamic network for systems biology model
Retrieving relevant experiments: The case of microRNA microarrays
Equalizing the information amounts of protein and mRNA by information theory
Causation, constructors and codes
Two complementary perspectives on inter-individual genetic distance
Sustainability and optimal control of an exploited prey predator system through provision of alternative food to predator
Robustness and regularity of oscillations in neuronal populations
The cluster model of energy transduction in biological systems
Simulation of neurocomputing based on the photophobic reactions of Euglena with optical feedback stimulation
Reflexive structure of the conscious subject and the origin of language codes
A step into the RNA world: Conditional analysis of hydrogel formation of adenosine 5′-monophosphate induced by cyanuric acid
Bio-analog dissipative structures and principles of biological behavior
A degenerative process underlying hierarchic transitions in evolution
Linear codes and the mitochondrial genetic code
Kinesin's walk: Springy or gated head coordination?
Information coding in vasopressin neurons - The role of asynchronous bistable burst firing
Biased Brownian motion mechanism for processivity and directionality of single-headed myosin-VI
Modelling efficiency in insect olfactory information processing
Spontaneous deadlock breaking on amoeba-based neurocomputer
Biological mechanisms contradict AI consciousness: The spaces between the notes
On eukaryotic intelligence: Signaling system's guidance in the evolution of multicellular organization
Optimization of CO 2 fixation in photosynthetic cells via thermodynamic buffering
Quantum-like model of cognitive decision making and information processing
The publications of embryologist Lev V. Beloussov
A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem
Effects of reciprocal inhibitory coupling in model neurons
CM-viewer: Visualizing interaction network of co-mutated and mutually exclusively mutated cancer genes
Evolution of early development in dipterans: Reverse-engineering the gap gene network in the moth midge Clogmia albipunctata (Psychodidae)
Special issue: Integration of OMICs datasets into Metabolic Pathway Analysis
DNA based random key generation and management for OTP encryption
Climatic seasonality may affect ecological network structure: Food webs and mutualistic networks
Responses of midbrain auditory neurons to two different environmental sounds - A new approach on cross-sound modeling
Perception of color in primates: A conceptual color neurons hypothesis
Protein crystal's shape and polymorphism prediction within the limits resulting from the exploration of the Miyazawa-Jernigan matrix
Modeling acclimatization by hybrid systems: Condition changes alter biological system behavior models
A multiorganism based method for Bayesian gene network estimation
On the infodynamics of ramifications in constructal design
An account of a century of ATP research
How robust are neural network models of stimulus generalization?
Combining Metabolic Pathway Analysis with Evolutionary Game Theory. Explaining the occurrence of low-yield pathways by an analytic optimization approach
Computational modelling and optimal control of measles epidemic in human population
Mitochondrial tRNAs as light strand replication origins: Similarity between anticodon loops and the loop of the light strand replication origin predicts initiation of DNA replication
Value saturation: Architecture of subjective necessity
Exact burst-size distributions for gene-expression models with complex promoter structure
Corrigendum to: "Field programmable chemistry: Integrated chemical and electronic processing of informational molecules towards electronic chemical cells" [Biosystems, (2012) 109: 2-17]
The Kanizsa triangle illusion in foraging ants
"Life-bearing molecules" versus "life-embodying systems": Two contrasting views on the what-is-life (WIL) problem persisting from the early days of molecular biology to the post-genomic cell- and organism-level biology
BIN-CT: Urban waste collection based on predicting the container fill level
miSEA: microRNA set enrichment analysis
A case for aneural cognition: E. coli and its cognitive repertoire
Prediction and Boolean logical modelling of synergistic microRNA regulatory networks during reprogramming of male germline pluripotent stem cells
Hydra effects in stable food chain models
Loss and fixation of strongly favoured new variants: Understanding and extending Haldane's result via the Wright-Fisher model
On some models of extended mechanism in code biology
Enrichment and stability: A phenomenological coupling of energy value and carrying capacity
The complex fluctuations of probabilistic Boolean networks
Integration of thermodynamic, quantum and hierarchical theories of information in the context of Peircean semiosis - A review
Using monoids for the integration of genomic and metabolic parameters in the prediction of phenotypes in regulatory cascades
The development of code systems during eukaryogenesis and the rise of multicellularity
What controls network reciprocity in the Prisoner's Dilemma game?
Grounding information in thermodynamics and the ungroundedness of language: A missing aspect of anthropogenesis
Kinematic linkage models of muscle contraction: A mechanical engineering perspective
Quantum propensities in the brain cortex and free will
Self-organization and entropy reduction in a living cell
Optimal treatment of an SIR epidemic model with time delay
Simple example of structure versus property relationship applied to a reduced-friction biosystem, a quite personal opinion
Mathematical fundamentals for the noise immunity of the genetic code
"How" vs. "Why" questions in symbiogenesis, and the causal role of synergy
Role of cascades in converting oscillatory signals into stationary step-like responses
How evolution makes us age: Introducing the evolvable soma theory of ageing
Self-organization in dissipative structures: A thermodynamic theory for the emergence of prebiotic cells and their epigenetic evolution
Cellular non-linear network model of microbial fuel cell
The effect of developmental variation on hybridization and rarity in Stipoid grasses
Autonomy: What is it?
Origin of homochirality in peptides: The first milestone at the origin of life
A novel method for segmenting brain tumor using modified watershed algorithm in MRI image with FPGA
The HSA affinity of warfarin and flurbiprofen determined by fluorescence anisotropy measurements of camptothecin
The synchronization properties of a network of inhibitory interneurons depend on the biophysical model
Learning in human neural networks on microelectrode arrays
Dynamics of prostate cancer stem cells with diffusion and organism response
What is Quantum in probabilistic explanations of the sure-thing principle violation?
Spectral bounds for Sombor and Sombor energy indices: A graph-theoretic study of neurotransmitter molecular networks
Cultural life: Theory and empirical testing
Studying organisational closure in biological systems with process-enablement graphs
Are there grounded semantics in (model) organisms?
Modelling of syntactical processing in the cortex
On coevolution: Asymmetry in the NKCS model
A p- adic approach to the TSPO gene
Genetic algorithm to estimate the input parameters of Klatt and HLSyn formant-based speech synthesizers
A biochemically-realisable relational model of the self-manufacturing cell
Fragile X mental retardation protein modulates translation of proteins with predicted tendencies for liquid-liquid phase separation
Clust&See: A Cytoscape plugin for the identification, visualization and manipulation of network clusters
Examining multi-objective deep reinforcement learning frameworks for molecular design
Metabolic control analysis of the transsulfuration pathway and the compensatory role of the cysteine transport in Trypanosoma cruzi
Biology from a quantum
Quantum contextuality and cognitive contextuality: The significance of violations of Bell-type inequalities
Thermal diodes, transistors and logic: Review of unconventional computing methods
Learning the selectivity of V2 and V4 neurons using non-linear multi-layer wavelet networks
Evolution of small and large ribosomal RNAs from accretion of tRNA subelements
Biased Lévy-walk pattern in the exploratory behavior of the Physarum plasmodium
Quantum algorithm for de novo DNA sequence assembly based on quantum walks on graphs
The origin and evolution of life as continuing expansion of viral hosts
Degradation-driven protein level oscillation in the yeast Saccharomyces cerevisiae
Calcium signalling in astrocytes and modulation of neural activity
Linked Gauss-Diffusion processes for modeling a finite-size neuronal network
Artificial algae algorithm with multi-light source for numerical optimization and applications
Dimensionality reduction for visualizing high-dimensional biological data
The late appearance of DNA, the nature of the LUCA and ancestors of the domains of life
Stability analysis of a model for HIV infection with RTI and three intracellular delays
HIV-miR-H1 evolvability during HIV pathogenesis
The molecular memory code and synaptic plasticity: A synthesis
Gene expression cancer classification using modified K-Nearest Neighbors technique
Characterization and classification of adherent cells in monolayer culture using automated tracking and evolutionary algorithms
Automatic reconstruction of the mouse segmentation network from an experimental evidence database
DNA-based cryptographic methods for data hiding in DNA media
Locally adaptive aggregation of organisms under death risk in rock-paper-scissors models
ESVM: Evolutionary support vector machine for automatic feature selection and classification of microarray data
Evaluation of intermolecular forces in a circulating system
From reactions to reflection: A recursive framework for the evolution of cognition and complexity
Local community detection as pattern restoration by attractor dynamics of recurrent neural networks
The problem of evolutionary directionality 50 years following the works of Sergei Meyen
Monte Carlo simulation of COVID-19 pandemic using Planck's probability distribution
Optimality in the standard genetic code is robust with respect to comparison code sets
Evolutionary classification of toxin mediated interactions in microorganisms
On integrating experimental and theoretical models to determine physical mechanisms of morphogenesis
The competition of ecological resonances in the quantum metabolic model of cancer: Potential energetic interventions
Problematic issues of ATP synthesis in vivo
Optimal length distribution of termite tunnel branches for efficient food search and resource transportation
Simulation of a bounded symport/antiport P system with Brane calculi
Slowly modulating fluctuations as mesoscopic distortions occurring on an actin filament
Brownian motion, fluctuation and life
Robust patterning of gene expression based on internal coordinate system of cells
A novel approach to encode melodies in DNA
Genome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens
2022 IEEE conference on computational intelligence in bioinformatics and computational biology (IEEE CIBCB, 2022)
An algorithm for the transformation of the Petri net models of biological signaling networks into influence graphs
Complexity of automated gene annotation
From the hierarchical organization of the central nervous system to the hierarchical aspects of biocodes
Evolving fuzzy rules to model gene expression
Overview of the fourth special issue in code biology
Food codes as an AI-based framework to investigate bird foraging ecology and interspecific interactions
Predator-prey dynamics in P systems ruled by metabolic algorithm
Networks of passive competition between multiple self-ordering proto-replicators and the effect of primitive membranes
Prediction markets and their potential role in biomedical research - A review
Use of directed quasi-metric distances for quantifying the information of gene families
Pest management through continuous and impulsive control strategies
2015 Information Processing in Cells and Tissues (IPCAT 2015)
Modular organization of cancer signaling networks is associated with patient survivability
Adversarial deep evolutionary learning for drug design
Review: Methods of firing rate estimation
Stability switching and hydra effect in a predator-prey metapopulation model
Microbial mutualism promoting the coexistence of competing species: Double-layer model for two competing hosts and one microbial species
Trinucleotide k-circular codes I: Theory
Identification of multivariable Boolean patterns in microbiome and microbial gene composition data
A rate distortion approach to protein symmetry
A general resolution of intractable problems in polynomial time through DNA Computing
The role of symbiosis in the first colonization of the seafloor by macrobiota: Insights from the oldest Ediacaran biota (Newfoundland, Canada)
Spike-timing-dependent plasticity enhanced synchronization transitions induced by autapses in adaptive Newman-Watts neuronal networks
All lockdowns are not equal: Reducing epidemic impact through evolutionary computation
Modeling autopoiesis and cognition with reaction networks
Information and the living tree of life: A theory of measurement grounded in biology
EvoMS: An evolutionary tool to find de novo metabolic pathways
Nucleosome organization in sequences of alternative events in human genome
From RNA to DNA: Emergence of reverse transcriptases from an ancestral RNA-dependent RNA polymerase
Intracellular RNA delivery by lipid nanoparticles: Diffusion, degradation, and release
Non-equilibrium thermodynamical description of rhythmic motion patterns of active systems: A canonical-dissipative approach
Towards measuring the semantic capacity of a physical medium demonstrated with elementary cellular automata
Neurons as hierarchies of quantum reference frames
Turing and von Neumann machines: Completing the new mechanism
A compositional framework for Boolean networks
The emergence of a fractal structure of formal logic via the spatiotemporal reflexive self-identification
MRWMDA: A novel framework to infer miRNA-disease associations
Modeling the cell cycle: From deterministic models to hybrid systems
Mapping chemical structure-activity information of HAART-drug cocktails over complex networks of AIDS epidemiology and socioeconomic data of U.S. counties
Evolutionary framework of the human interactome: Unicellular and multicellular giant clusters
Overview of the fifth special issue in Code Biology
Macroevolution, differentiation trees, and the growth of coding systems
A neural network model of semantic memory linking feature-based object representation and words
Acoustic codes from a rural sanctuary: How ecoacoustic events operate across a landscape scale
Aging and group selection: New arguments in favor of partially directed evolution
A kinetic model structure for delayed fluorescence from plants
Slime mould: The fundamental mechanisms of biological cognition
The Molecular Basis of Differentiation Wave Activity in Embryogenesis
Computation in biological systems as a quantum mechanical simulation
Modeling of decision-making process for moving straight using inverse Bayesian inference
Neural plasticity, heterochrony, and the onto-phylogeny of consciousness