yusuke1997/dblp-id-title huggingface dataset:
Feedforward non-Michaelis-Menten mechanism for CO 2 uptake by Rubisco: Contribution of carbonic anhydrases and photorespiration to optimization of photosynthetic carbon assimilation
A multi-scale agent-based model for avascular tumour growth
An integrative explanation of action
Inversion and crossover recombination contributions to the spacing between two functionally linked genes
Kinetic aspects of enzyme-mediated repair of DNA single-strand breaks
In silico identification of gene amplification targets based on analysis of production and growth coupling
Logic of two antagonizing intra-species quorum sensing systems in bacteria
The principle "like begets like" in algebra-matrix genetics and code biology
A mean field Ising model for cortical rotation in amphibian one-cell stage embryos
Computational simulation of a gene regulatory network implementing an extendable synchronous single-input delay flip-flop
A multi-objective differential evolutionary approach toward more stable gene regulatory networks
Codon bias from minimization of codon-anticodon interaction
Optimality of circular codes versus the genetic code after frameshift errors
Representing life: A natural philosophical project,
The chromolinker hypothesis: Are eukaryotic genomes also circular?
Toward the biological model of the hippocampus as the successor representation agent
Dreams as a code language
A new mathematical model of folate homeostasis in E. coli highlights the potential importance of the folinic acid futile cycle in cell growth
On prokaryotic intelligence: Strategies for sensing the environment
Dynamic modelling and tristability analysis of misfolded α-synuclein degraded via autophagy in Parkinson's disease
Stochastic model of template-directed elongation processes in biology
Phase-locking of bursting neuronal firing to dominant LFP frequency components
The mitochondrial challenge: Disorders and prevention strategies
Stochasticity and functionality of neural systems: Mathematical modelling of axon growth in the spinal cord of tadpole
Stability analysis and optimal control of HPV infection model with early-stage cervical cancer
A short tutorial on the Janus-faced logic of differentiation waves and differentiation trees and their evolution
Quantitative description of neuronal calcium dynamics in C. elegans' thermoreception
Molecular dynamics simulation for the reversed power stroke motion of a myosin subfragment-1
Towards the development of robot immune system: A combined approach involving innate immune cells and T-lymphocytes
Can biophysics tell us something about the weak equivalence principle vis a vis the thought experiment of Einstein involving human subjects?
Étienne Geoffroy Saint-Hilaire as a predecessor of the epigenetic concept of evolution
A model of stepping kinetics for rotary enzymes. Application to the F1-ATPase
On the importance of modelling the internal spatial dynamics of biological cells
Computational analysis of the oscillatory dynamics in the processes of CO 2 assimilation and photorespiration
C-DEVA: Detection, evaluation, visualization and annotation of clusters from biological networks
The processes generating quantum entanglement in DNA
Structural and information-theoretic complexity measures of brain networks: Evolutionary aspects and implications
An evolutionary approach for gene selection and classification of microarray data based on SVM error-bound theories
Editorial: Waves in fertilization, cell division and embryogenesis
Is information the other face of causation in biological systems?
Using network context as a filter for miRNA target prediction
The role of regulation in the origin and synthetic modelling of minimal cognition
CAMND: Comparative analysis of metabolic network decomposition based on previous and two new criteria, a web based application
Probability of change in life: Amino acid changes in single nucleotide substitutions
Genome evolution by transformation, expansion and contraction (GETEC)
Gaia again
The semantic theory of language
Rhodobase, a meta-analytical tool for reconstructing gene regulatory networks in a model photosynthetic bacterium
Evolution of the RNA world: From signals to codes
Computational modeling and analysis of the impacts of sleep deprivation on glucose stimulated insulin secretion
RPPApipe: A pipeline for the analysis of reverse-phase protein array data
A robust correlation estimator and nonlinear recurrent model to infer genetic interactions in Saccharomyces cerevisiae and pathways of pulmonary disease in Homo sapiens
Collective computational intelligence in biology - Emergence of memory in somatic tissues
Spatio-temporal dynamics of glycolysis in cell layers. A mathematical model
Simulating cooperative behavior in human collective search pattern
Role of calcium oscillations in sperm physiology
Biomechanical properties of 3D-printed bone models
Variable context Markov chains for HIV protease cleavage site prediction
Stochastic noncooperative and cooperative evolutionary game strategies of a population of biological networks under natural selection
Morphological forms arising from the evolutionary process are topologies
Construction of pan-cancer regulatory networks based on causal inference
Computational modeling of neural plasticity for self-organization of neural networks
Liquid state machines and cultured cortical networks: The separation property
An Information Framework of Intelligence
Modeling of glycolytic wave propagation in an open spatial reactor with inhomogeneous substrate influx
Toward an improved discrimination of outer membrane proteins using a sequence-based approach
R-Models: A mathematical framework for capturing notions of abstraction and assistance in reproductive systems
Resource exploitation strategies in the presence of traffic between food sources
On the synthesis of DNA error correcting codes
Herbivore-induced pollinator limitation increases community stability of mutualism-antagonism continuum
A neural circuit model of emotional learning using two pathways with different granularity and speed of information processing
A modified approach to the measurement problem: Objective reduction in the retinal molecule prior to conformational change
A parallel algorithm for solving the n-queens problem based on inspired computational model
Semiotic realms: Codes, language, mind. A psychoanalytic perspective
Information transfer through a signaling module with feedback: A perturbative approach
Detailed analysis of the quantum relaxation features in the cell microtubules: Markovian and non-Markovian dynamics
Predator-prey population dynamics may induce the evolutionary dynamics of behavioral unpredictability
Metastability, criticality and phase transitions in brain and its models
A neural mechanism of dynamic gating of task-relevant information by top-down influence in primary visual cortex
Threshold dynamics of the Transmission of Antibiotic-Resistant Infections
Propagating wave based on transition of interaction within animal group
Global/temporal gene expression analysis of Escherichia coli in the early stages of symbiotic relationship development with the cellular slime mold Dictyostelium discoideum
Simulation of multiple microenvironments shows a pivot role of RPTPs on the control of Epithelial-to-Mesenchymal Transition
The evolutionary arch of bioenergetics from prebiotic mechanisms to the emergence of a cellular respiratory chain
Energy propagation along polypeptide α-helix: Experimental data and ab initio zone structure
A new approach to the automatic identification of organism evolution using neural networks
A thermal ratchet model of tRNA-mRNA translocation by the ribosome
On anti-occurrence of subsets of transitions in Petri net-based models of complex biological systems
KatzDriver: A network based method to cancer causal genes discovery in gene regulatory network
Stability of an underactuated bipedal gait
A multi-objective optimisation approach for the linear modelling of cerebral autoregulation system
A mathematical consideration of the word-composition vector method in comparison of biological sequences
Fitting dynamic growth models of biological phenomena from sample observations through Gaussian diffusion processes
Evolutionary epistemology: Reviewing and reviving with new data the research programme for distributed biological intelligence
Dynamic analysis on the calcium oscillation model considering the influences of mitochondria
Biostructural theory of the living systems
An optimal control problem for carrier dependent diseases
Visual perception and imagery: A new molecular hypothesis
The physics of the urge to have freedom
Observation and control in a model of a cell population affected by radiation
A termination criterion for parameter estimation in stochastic models in systems biology
Exploring the effects of high curvature section distribution and density in termite tunnels on food transport efficiency: A simulation study
Design of state estimator for genetic regulatory networks with time-varying delays and randomly occurring uncertainties
CSML2SBML: A novel tool for converting quantitative biological pathway models from CSML into SBML
Karyotype coding: The creation and maintenance of system information for complexity and biodiversity
From the principle of sustainable non-equilibrium to sustainable development
Discriminating coding, non-coding and regulatory regions using rescaled range and detrended fluctuation analysis
Softsatisficing: Risk-sensitive softmax action selection
Phylogenetic analyses of penicillia based on partial calmodulin gene sequences
Biosupersymmetry
Extracellular interplay of amyloid fibrils and neural cells
Influence analysis of network evolution on Parrondo effect
Quantum-like environment adaptive model for creation of phenotype
A discriminative method for remote homology detection based on n-peptide compositions with reduced amino acid alphabets
Boredom begets creativity: A solution to the exploitation-exploration trade-off in predictive coding
Viral thresholds and semiotic resonance: Rethinking the continuum between life and non-life
Reflections on 'plant neurobiology'
Mechanics and resonance of the cyanobacterial circadian oscillator
A simple model of the electrosensory electromotor loop in Gymnotus omarorum
Modelling energy-harvesting processes in primitive cells: Proton transport across bilayers driven by the oxidation of sulfite
Short non-coded peptides interacting with cofactors facilitated the integration of early chemical networks
Effect of stimulus-driven pruning on the detection of spatiotemporal patterns of activity in large neural networks
Spatiotemporal patterning of uterine excitation patterns in human labour
Evolution of robustness to damage in artificial 3-dimensional development
Efficiency of neural transmission as a function of synaptic noise, threshold, and source characteristics
Localized activation of proteins in a free intracellular space: Dependence of cellular morphologies and reaction schemes
Capsule formation induced by flow
Towards a Possible Definition of Consciousness
In enzymatic reactions, the reverse reaction reduces product noise
Prey detection mechanism of elasmobranchs
A paradigm shift for the Great Bifurcation
Analysis of an evolutionary algorithm for complex fuzzy cognitive map learning based on graph theory metrics and output concepts
Modeling 3-D diffusion using queueing networks
Patterns of evolution
A new simplex approach to highlight multi-scale feeding behaviors in forager species from stomach contents: Application to insectivore lizard population
An efficient estimation of distribution algorithm with rank-one modification and population reduction
Characterization of tradeoffs in biomolecular signaling
Analysis of Shannon's entropy to contrast between the Embodied and Neurocentrist hypothesis of conscious experience
Archetypes and code biology
I-circular codes
Heterogeneity of cells may explain allometric scaling of metabolic rate
On the way to a new science
Memory induced-mechanism of noise attenuator of myosin V molecular motors
Modeling and simulation of the initial phases of chlorophyll fluorescence from Photosystem II
On the emergence of eukaryotes and other enigmas
Timing inaccessibility and the projection bound: Resolving Maxwell's demon for continuous biological substrates
A mathematical model of the Gac/Rsm quorum sensing network in Pseudomonas fluorescens
Evidence for transcriptase quantum processing implies entanglement and decoherence of superposition proton states
Discrete Svelteness: Evaluating flow structures in generative constructal design
Impact of Chemo-therapy on Optimal Control of Malaria Disease with Infected Immigrants
Emergence of the scale-invariant proportion in a flock from the metric-topological interaction
The concerted nature between three catalytic subunits driving the F 1 rotary motor
A simulation study of mutations in the genetic regulatory hierarchy for butterfly eyespot focus determination
Humans and microbes: A systems theory perspective on coevolution
A semiotic framework for evolutionary and developmental biology
Corrigendum to "The single-process biochemical reaction of Rubisco: A unified theory and model with the effects of irradiance, CO 2 and rate-limiting step on the kinetics of C 3 and C 4 photosynthesis from gas exchange" [Bio Systems 103 (2) (2011) 265-284]
Cultural accumulation or stasis? The impact of imitation and early teaching on hominin cultural evolution
Phosphorylation and acylation transfer reactions: Clues to a dual origin of metabolism
Modeling of the quantum entangled state transfer protocol in the cell microtubules
A percolation model of natural selection
Computational intelligence and machine learning in bioinformatics and computational biology
From reaction to reflection: A recursive framework for the evolution and structure of intelligence
Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes
Comments on Vladimir Voevodsky's biologically motivated works
Ribonucleic acid genome mutations induced by the Casimir effect
Robot control with biological cells
Analysis of stochasticity in promoter activation by using a dual-fluorescence reporter system
Dynamical modeling of viral spread in spatially distributed populations: stochastic origins of oscillations and density dependence
Dynamics of asynchronous random Boolean networks with asynchrony generated by stochastic processes
The role of transients in auditory processing
Monitoring in a Lotka-Volterra model
Transient bifurcations in neural error correction
Transforming bottom-up topographic representations with top-down signals in the brain
Dynamic properties of a delayed protein cross talk model
Inhibition of quorum sensing in a computational biofilm simulation
Monte Carlo simulation of early molecular evolution in the RNA World
Optimal control analysis of a malaria disease transmission model that includes treatment and vaccination with waning immunity
Statistical evidence for ancestral correlation patterns
Animal design advantage from the analogy between friction and body heat loss
A neural model of feature attention in motion perception
Toward a formal theory of embodied cognition
Firing statistics of inhibitory neuron with delayed feedback. I. Output ISI probability density
Mathematical analysis-based feasibility study of pre-emptive medicine for Staphylococcus aureus infectious disease: Early detection and antibiotic-free maintenance therapy
Life and fate of Ervin Bauer (1890-1938), the eminent scholar and foundational theoretical biologist
Modelling the fitness landscapes of a SCRaMbLEd yeast genome
A possible mechanism of processive nucleotide and repeat additions by the telomerase
In search for evolutionary roots of a mindful cognition: A Darwinian view on sustained intentional awareness
Coevolution of honest signaling and cooperative norms by cultural group selection
Theory and practice of natural computing: Sixth edition
Using intersection information to map stimulus information transfer within neural networks
Modes of evolution in a parasite-host interaction: Dis-entangling factors determining the evolution of regulated fimbriation in E. coli
Keyword extraction, ranking, and organization for the neuroinformatics platform
The role of pure mathematics in resolving complex biological problems: Applications to F1-ATPase, achievements, and future directions
Diversity of temporal correlations between genes in models of noisy and noiseless gene networks
Physical limits of natural computation as the biological constraints of morphogenesis, evolution, and consciousness: On the 100th anniversary of Efim Liberman (1925-2011)
Formation flight design via Constructal Law
Predicting link directionality in gene regulation from gene expression profiles using volatility-constrained correlation
Hypothesis of macroscopic quantum state in biological systems and discussion on the possibility of its experimental verification
Corrigendum to "A CLIQUE algorithm using DNA computing techniques based on closed-circle DNA sequences*" [Biosystems 105 (2011) 73-82]
Equilibrium control of nonlinear verticum-type systems, applied to integrated pest control
Is there a bias in the codon frequency corresponding to homo-repeats found in human proteins?
A limit in the dynamic increase in the accuracy of group migration
Guaranteed satisficing and finite regret: Analysis of a cognitive satisficing value function
Polymerization of non-complementary RNA: Systematic symmetric nucleotide exchanges mainly involving uracil produce mitochondrial RNA transcripts coding for cryptic overlapping genes
On the evolution of scale-free topologies with a gene regulatory network model
Ion channel density and threshold dynamics of repetitive firing in a cortical neuron model
From reinforcement learning to agency: Frameworks for understanding basal cognition
Boolean networks with biologically relevant rules show ordered behavior
Optimization of the standard genetic code in terms of two mutation types: Point mutations and frameshifts
Statistical algorithms for the analysis of deleterious genetic mutations
Applying a multiobjective metaheuristic inspired by honey bees to phylogenetic inference
Constructing a bridge between functioning of oscillatory neuronal networks and quantum-like cognition along with quantum-inspired computation and AI
Nucleotide correlation based measure for identifying origin of replication in genomic sequences
Toward an ethics of autopoietic technology: Stress, care, and intelligence
Effects of the transmissibility and virulence of pathogens on intraguild predation in fragmented landscapes
Evaluating clustering methods within the Artificial Ecosystem Algorithm and their application to bike redistribution in London
Multi-ENPS simulator support tool with automatic file inter-conversion and multi-membrane execution
How (not) to model autonomous behaviour
Automating the search of molecular motor templates by evolutionary methods
A quantum mechanical approach towards the calculation of transition probabilities between DNA codons
Prediction of prokaryotic and eukaryotic promoters based on information-theoretic features
Automatic recognition and measurement of butterfly eyespot patterns
Intra-specific competition in predator can promote the coexistence of an eco-epidemiological model with strong Allee effects in prey
miRNAfe: A comprehensive tool for feature extraction in microRNA prediction
ModuleMaster: A new tool to decipher transcriptional regulatory networks
Is distance from equilibrium a good indicator for a reaction's flux control?
How prokaryotes 'encode' their environment: Systemic tools for organizing the information flow
Code biology and aesthetics
Modelling 18 O 2 and 16 O 2 unidirectional fluxes in plants: II. Analysis of Rubisco evolution
Hodgkin-Huxley type modelling and parameter estimation of GnRH neurons
Modeling tumor growth using fractal calculus: Insights into tumor dynamics
Structure and dynamics of the 'protein folding code' inferred using Tlusty's topological rate distortion approach
Information transmission and processing in G-protein-coupled-receptor complexes
Imperfect identity of autonomous living system
Quantitative transformation for implementation of adder circuits in physical systems
Evolution of eukaryotes as a story of survival and growth of mitochondrial DNA over two billion years
Trinucleotide k-circular codes II: Biology
Reprint of: Analysis of an evolutionary algorithm for complex fuzzy cognitive map learning based on graph theory metrics and output concepts
A general model on the origin of biological codes
A Condition-Enumeration Tree method for mining biclusters from DNA microarray data sets
Analysis of codon usage in type 1 and the new genotypes of duck hepatitis virus
Formal derivation of qualitative dynamical models from biochemical networks
Do phytoplankton communities evolve through a self-regulatory abundance-diversity relationship?
Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations
Effect of single nucleotide polymorphisms on the structure of long noncoding RNAs and their interaction with RNA binding proteins
Neural membrane microdomains as computational systems: Toward molecular modeling in the study of neural disease
Mathematical modeling of immune modulation by glucocorticoids
A neural circuit model forming semantic network with exception using spike-timing-dependent plasticity of inhibitory synapses
A multi-cell model for the C4 photosynthetic pathway in developing wheat grains based upon tissue-specific transcriptome data
A diffusive model of the ball and chain inactivation
Temperature effects on neuronal firing rates and tonic-to-bursting transitions
Effects of predator modulation and vector preference on pathogen transmission in plant populations
Fine structure of a partition in the spike glycoprotein encoded in the SARS-CoV-2 genome
Modulation of calcium signals by fluorescent dyes in the presence of tubular endoplasmic reticulum: A modelling approach
Cognitively inspired reinforcement learning architecture and its application to giant-swing motion control
On models of the genetic code generated by binary dichotomic algorithms
The energetics, chemistry, and mechanics of a processive motor protein
Who benefits from cellular immune response during the Chagas disease?
Neural networks through the lens of evolutionary dynamics
Advanced technologies and mathematical metacognition: The present and future orientation
Auto-/heterotrophic endosymbiosis evolves in a mature stage of ecosystem development in a microcosm composed of an alga, a bacterium and a ciliate
Collective excitations at non-equilibrium phase transition in metabolically active red blood cells
Predict prokaryotic proteins through detecting N-formylmethionine residues in protein sequences using support vector machine
Potential role of the X circular code in the regulation of gene expression
Proton-polarized states in DNA
Cell response in mixtures of surfactant-culture medium - Towards a systemic approach to cell-based treatments for focal osteoarthritis
Internal logic viewed from observation space: Theory and a case study
The history of Ervin Bauer's publications on the theory of life
An application programming interface for CellNetAnalyzer
The role of Fenton reaction in ROS-induced toxicity underlying atherosclerosis - modeled and analyzed using a Petri net-based approach
Self-organizing proto-replicators and the origin of life
A survey of within-host and between-hosts modelling for antibiotic resistance
Steady state and (bi-) stability evaluation of simple protease signalling networks
On the Gompertzian growth in the fractal space-time
PhDSeeker: Pheromone-Directed Seeker for metabolic pathways
Fault detection and therapeutic intervention in gene regulatory networks using SAT solvers
Using steady-state formula to estimate time-dependent parameters of stochastic gene transcription models
Revealing the properties of the radical-pair magnetoreceptor using pulsed photo-excitation timed with pulsed rf
A memory access gate controlled by dynamic contexts
Effect of diseases on symbiotic systems
I. Soltesz and K. Staley, Editors, Computational Neuroscience in Epilepsy, Academic Press (2008) ISBN-10: 0123736498, ISBN-13: 978-0123736499