yusuke1997/dblp-id-title huggingface dataset:
Nervous system-related gene regulatory networks and functional evolution of ETS proteins across species
Theoretical justification of computing the 3-base periodicity using nucleotide distribution variance
Stress-induced failure of embodied cognition: A general model
Continuous computation in engineered gene circuits
Event-driven simulation of cerebellar granule cells
Coding of distributed, topographic and non-specific representations within the brain
A cortical network model of cognitive and emotional influences in human decision making
Shear-stress-induced swirling flow in biological systems
Deamination gradients within codons after 12 position swap predict amino acid hydrophobicity and parallel β-sheet conformational preference
Lisa Sattenspiel with contributions from Alun Lloyd. The Geographic Spread of Infectious Diseases, Models and Applications, Princeton Press (2009). ISBN-13: 978-0-691-12132-1
A novel algorithm to calculate elementary modes: Analysis of Campylobacter jejuni metabolism
The threat of asymptomatic carriers and the benefits of testing
Prolegomenon to patterns in evolution
Robustness analysis of EGFR signaling network with a multi-objective evolutionary algorithm
Coding the presence of visual objects in a recurrent neural network of visual cortex
regEfmtool: Speeding up elementary flux mode calculation using transcriptional regulatory rules in the form of three-state logic
Solving dynamical inverse problems by means of Metabolic P systems
Influence factors on the correlations between expression levels of neighboring pattern genes
Toward bridging the gap between life and physics
Construction of bacteria-eukaryote synthetic mutualism
Elucidation of the molecular mechanism of heat shock proteins and its correlation with K722Q mutations in Lon protease
Unsolved morphogenesis problems and the hidden order
Information encoded in gene-frequency trajectories
Oscillation and coding in a formal neural network considered as a guide for plausible simulations of the insect olfactory system
PTEN expression can be used as a switch between senescence and apoptosis in breast cancer cells according to a logical model of the G2/M checkpoint
Elastic, dipole-dipole interaction and viscosity impact on vibrational properties of anisotropic hexagonal microtubule lattice
Category theory and foundations of life science: A structuralist perspective on cognition
Symmetry based mechanism for hand-over-hand molecular motors
A biochemically semi-detailed model of auxin-mediated vein formation in plant leaves
The Nath-Luxuriæ principles: Unified thermodynamic framework for molecular assembly and non-ergodicity via ATP synthesis/hydrolysis example
Clarifying tetrapod embryogenesis by a dorso-ventral analysis of the tissue flows during early stages of chicken development
Asynchronous time-space model for evolutionary market
Exploring the spatial effects influencing the EGFR/ERK pathway dynamics with machine learning surrogate models
Color image encryption scheme using CML and DNA sequence operations
Swinger RNAs with sharp switches between regular transcription and transcription systematically exchanging ribonucleotides: Case studies
Predicting the physiological response of Tivela stultorum hearts with digoxin from cardiac parameters using artificial neural networks
A quantitative measure for discriminating between self and non-self antigens in immune response
Analysis of a Schnute postulate-based unified growth model for model selection in evolutionary computations
Spacial models of malfunctioned protein complexes help to elucidate signal transduction critical for insulin release
Possibility of high performance quantum computation by superluminal evanescent photons in living systems
Mitochondrial swinger replication: DNA replication systematically exchanging nucleotides and short 16S ribosomal DNA swinger inserts
Three types of logical structure resulting from the trilemma of free will, determinism and locality
Mathematical modeling of cell cycle regulation in response to DNA damage: Exploring mechanisms of cell-fate determination
Stochastic simulations on a model of circadian rhythm generation
Nonlinearities in mating sounds of American crocodiles
Stochasticity in transcriptional, splicing and translational regulations in time and frequency domains
Inferring population statistics of receptor neurons sensitivities and firing-rates from general functional requirements
Comments on Musha's theorem that an evanescent photon in the microtubule is a superluminal particle
Genome-wide characterization and prediction of Arabidopsis thaliana replication origins
Evolution of cooperation on dynamical graphs
Representational fluidity in embodied (artificial) cognition
Mathematical models in cancer therapy
A cell pattern generation model based on an extended artificial regulatory network
Selecting a minimal number of relevant genes from microarray data to design accurate tissue classifiers
A systems theory of biological evolution
Coloured noise induces phenotypic diversity with energy dissipation
Encoding of non-biological information for its long-term storage in DNA
On multistep tumor growth models of fractional variable-order
Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals
Boolean network identification from perturbation time series data combining dynamics abstraction and logic programming
Global sensitivity analysis and model-based reactive scheduling of targeted cancer immunotherapy
Proposal of an apposite strategy-updating rule for the vaccination game where hubs refer to hubs and lower-degree agents refer to lower-degree agents
Evaluation of dynamic behavior forecasting parameters in the process of transition rule induction of unidimensional cellular automata
Integrated simulation with experimentation is a powerful tool for understanding diatom valve morphogenesis
Richness of emotion in people with dementia
Stochastic resonance in two simple compare-and-fire models
Incorporating gene ontology into fuzzy relational clustering of microarray gene expression data
A modeled dynamic regulatory network of NF-κB and IL-6 mediated by miRNA
Tellurium: An extensible python-based modeling environment for systems and synthetic biology
Global warming description using Daisyworld model with greenhouse gases
Spiking neural P systems with multiple channels and anti-spikes
Scale-free dynamics of somatic adaptability in immune system
A workflow for the hybrid modelling and simulation of multi-timescale biological systems
The local-global relationship of nature
A complex vector space model of single neuronal coding and experience
A three-dimensional multi-agent-based model for the evolution of Chagas' disease
Mathematical modelling of fluid transport and its regulation at multiple scales
The theoretical foundations of enaction: Precariousness
Generation model of positional values as cell operation during the development of multicellular organisms
Quantum cognition based on an ambiguous representation derived from a rough set approximation
Defining and finding lifelike entities with a lazy filter
Determining cellular lineage directed networks in hematopoiesis using single-cell transcriptomic data and volatility-constrained correlation
Constructal thermodynamics and its semantic ontology in autopoietic, digital, and computational architectural and urban space open systems
A network cell with molecular agents that divides from centrosome signals
Improving noise resistance of intrinsic rhythms in a square-wave burster model
Adaptive moment closure for parameter inference of biochemical reaction networks
Finding minimal generating set for metabolic network with reversible pathways
Chaos, complexity and computation in the evolution of biological systems
Energy infrastructure of evolution for system with infinite number of links with environment
Prokaryotic symbiotic consortia and the origin of nucleated cells: A critical review of Lynn Margulis hypothesis
Harnessing adaptive novelty for automated generation of cancer treatments
Effect of disease-selective predation on prey infected by contact and external sources
Model of two noise source dependent Ornstein-Uhlenbeck processes applied to postural sway
Quantifying protein modularity and evolvability: A comparison of different techniques
Emergence of cooperative linkages by random intensity of selection on a network
Editorial: Selected papers from the 14th international neural coding workshop, Seattle, Washington
Generalized population dynamics model of aphids in wheat based on catastrophe theory
Interactions between species and environments from incomplete information
Coupling and biological free-energy transduction processes as a bridge between physics and life: Molecular-level instantiation of Ervin Bauer's pioneering concepts in biological thermodynamics
Do motifs reflect evolved function? - No convergent evolution of genetic regulatory network subgraph topologies
Time-delayed intermittent oscillations and chaos in a transcriptional and post-transcriptional gene regulatory network for long-term memory
Characteristic comparison between two types of miRNA precursors in metazoan species
A model of molecular vector machine of proteins
Corrigendum to "What if houses were powered by milk?" [Biosystems 153 (2017) 1-5]
On the spherical prototype of a complex dissipative late-stage formation seen in terms of least action Vojta-Natanson principle
Thermodynamic analysis of energy coupling by determination of the Onsager phenomenological coefficients for a 3×3 system of coupled chemical reactions and transport in ATP synthesis and its mechanistic implications
Ferritin and neuromelanin "quantum dot" array structures in dopamine neurons of the substantia nigra pars compacta and norepinephrine neurons of the locus coeruleus
Optimizing ruminant nutrition: Insights from a comprehensive analysis of silage composition and in vitro gas production dynamics using nonlinear models
Intrinsic growth rate and evolution of the Premnotrypes Vorax population using fuzzy information
An improved hybrid of particle swarm optimization and the gravitational search algorithm to produce a kinetic parameter estimation of aspartate biochemical pathways
From correlation to causation: Unraveling the impact of closure on open-ended evolution within the Kauffman model
Evolution of Henrik Kacser's thought: Early publications on the organization of the whole system
Cellular "bauplans": Evolving unicellular forms by means of Julia sets and Pickover biomorphs
Discovering ecoacoustic codes in beehives: First evidence and perspectives
Cell and extracellular matrix growth theory and its implications for tumorigenesis
Synchronous firing by specific pairs of cercal giant interneurons in crickets encodes wind direction
Thermodynamic understanding of flower pigmentation
Evaluating the effectiveness of several synchronization control methods applying to the electrically and the chemically coupled hindmarsh-rose neurons
Phenotypic plasticity of Escherichia coli at initial stage of symbiosis with Dictyostelium discoideum
Intelligence as high-dimensional coherence: The observable dimensionality bound and computational tractability
The existence of the two domains of life, Bacteria and Archaea, would in itself imply that LUCA and the ancestors of these domains were progenotes
Modeling of the entangled states transfer processes in microtubule tryptophan system
On universal coding events in protein biogenesis
Quantum information theoretic approach to the hard problem of consciousness
Mixed-monolayer functionalized gold nanoparticles for cancer treatment: Atomistic molecular dynamics simulations study
On the transitional character and regularity of planetary abiogenesis
Phosphene phenomenon: A new concept
Reframing neural decussation: A vision-based theory for contralateral control
Analysis of synonymous codon usage in 11 Human Bocavirus isolates
PDE based geometry model for BCG immunotherapy of bladder cancer
Natural chymotrypsin-like-cleaved human mitochondrial peptides confirm tetra-, pentacodon, non-canonical RNA translations
Genetic coding algorithm for sense and antisense peptide interactions
Self-identities and durability of biosystems via their abstracting capacity
A Petri nets-based framework for whole-cell modeling
Applying DNA computation to intractable problems in social network analysis
Algebraic harmony and probabilities in genomes. Long-range coherence in quantum code biology
Role of 10-11 bp periodicities of eukaryotic DNA sequence in nucleosome positioning
Random models of Menzerath-Altmann law in genomes
A satisficing and bricoleur approach to sensorimotor cognition
A mathematical model on the effect of M. denticulata weed on different winter crops
A review of evolutionary graph theory with applications to game theory
Probing the early phase of rapid instructed rule encoding
A guide to gene regulatory network inference for obtaining predictive solutions: Underlying assumptions and fundamental biological and data constraints
Arguments against the stereochemical theory of the origin of the genetic code
Classification of antituberculosis herbs for remedial purposes by using fuzzy sets
Solving the SAT problem using a DNA computing algorithm based on ligase chain reaction
Paleo-phyllotaxis: Fucales, bryophytes, lycophytes and monilophytes
Bacterial foraging algorithm with varying population
Thermodynamics of Nath's 2-ion model for ATP synthesis
Information-energy equivalence and the emergence of self-replicating biological systems
Mining Dense Overlapping Subgraphs in weighted protein-protein interaction networks
Biosociological ethodiversity in the social system
Reconfiguring SETI in the microbial context: Panspermia as a solution to Fermi's paradox
A simulation model of the conventional kinesin based on the Driven-by-Detachment mechanism
A Bayesian approach to investigating presumed retinal micro(nano)plastics
Are we on the cusp of a new paradigm for biology? The illogic of molecular developmental biology versus Janus-faced control of embryogenesis via differentiation waves
Bifurcation analysis and effects of changing ionic conductances on pacemaker rhythm in a sinoatrial node cell model
Is HIV infection associated with an increased risk for cholera? Insights from a mathematical model
A critical role of the periplasm in copper homeostasis in Gram-negative bacteria
Coevolutionary games - A mini review
Structural simplification of chemical reaction networks in partial steady states
Human-driven evolution of cultivated plants and the origin of early civilizations: The concept of Neolithic revolution in the works of Nikolai Vavilov
Using matrix of thresholding partial correlation coefficients to infer regulatory network
Shuffling type of biological evolution based on horizontal gene transfer and the biosphere gene pool hypothesis
What initially brought about communications?
Theoretical formulation and analysis of the deterministic dendritic cell algorithm
Modelling foraging ants in a dynamic and confined environment
On the minimal elements of the genetic code and their semiotic functions (degeneracy, complementarity, wobbling)
Prigoginian informational dissipation (PID) as the cause of the emergence of a proto-self
Randomness in self-organized phenomena. A case study: Retinal angiogenesis
Reactive fungal wearable
Investigating the properties of bio-chemical networks of artificial organisms with opposing behaviours
Mathematical definition of human language, and modeling of will and consciousness based on the human language
Quantum formalism to describe binocular rivalry
Robust chemical circuits
How signals of calcium ions initiate the beats of cilia and flagella
From autopoiesis to self-optimization: Toward an enactive model of biological regulation
A general framework dedicated to computational morphogenesis Part II - Knowledge representation and architecture
Optimizing metabolic pathways by screening for feasible synthetic reactions
Corrigendum to "Cosmos, mind, matter: Is mind in spacetime?" [Biosyst. (2024) 105262]
Removing quote marks from the RNA polymerase II CTD 'code'
Design of interacting multi-stable nucleic acids for molecular information processing
A study of dependency features of spike trains through copulas
Editorial introduction to the special issue on bio(nano)materials with structure-property relationship
Embodied essentialism in the reconstruction of the animal sign in robot animal design
Dive into machine learning algorithms for influenza virus host prediction with hemagglutinin sequences
Implementing conventional logic unconventionally: Photochromic molecular populations as registers and logic gates
Gallstone formation as an example of the two-step space confined aggregation process
Local and global dynamics in collective movements of embryonic cells
Comparison of codon usage and tRNAs in mitochondrial genomes of Candida species
Unexpected extra exon skipping in the DYSF gene during restoring the reading frame by CRISPR/Cas9
Outbreaks of the measles in the Dutch Bible Belt and in other places - New prospects for a 1000 year old virus
Towards the Big History of information. Approaching the origins of information behaviour
Light induced spiking of proteinoids
From code to archetype: Toward a unified theory of biological, neural, and artificial artifacts
Propagation of electrical signals by fungi
Combining evolution and self-organization to find natural Boolean representations in unconventional computational media
A hybrid phase-synchronization framework for rotary motors: Discrete dynamics in ATP synthase and continuous dynamics in the bacterial flagellar motor
Visualizing genomic data: The mixing perspective
Navigation-specific neural coding in the visual system of Drosophila
Lamellar lubrication in vivo and vitro: Friction testing of hexagonal boron nitride
Novel mathematical models for cell-mediated cytotoxicity assays without applying enzyme kinetics but with combinations and probability: Bystanders in bulk effector cells influence results of cell-mediated cytotoxicity assays
Dynamic regulation of growing domains for elongating and branching morphogenesis in plants
Ecological drivers for the absence of task shifting in termite-tunneling activity: A simulation study
Perfect anomalous transport of subdiffusive cargos by molecular motors in viscoelastic cytosol
Evidence for transmitter operated electrical synapses (TOES) in ampullary electroreceptor organs
The stochastic model of non-equilibrium mutagen-induced alterations of DNA: Implication to genetic instability in cancer
A ball microscope for viewing the entire surface of amphibian embryos
The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis
The living organism: Strengthening the basis
Kinetic modelling of compartmentalised reaction networks
The Canonical Table of the Genetic Code as a periodic system of triplets
On the thermodynamics of multilevel evolution
Unidirectional movement of an actin filament taking advantage of temperature gradients
H-CORE: Enabling genome-scale Bayesian analysis of biological systems without prior knowledge
Logic gates in nanoscale based on interaction of thiolated DNA with AuNPs and strand displacement
Corrigendum to "The concepts of code biology" [Biosyst. 248 (2025) 105400 1-6]
In silico study of kinetochore control, amplification, and inhibition effects in MCC assembly
The bioelectric code: An ancient computational medium for dynamic control of growth and form
Avian influenza A H5N1 hemagglutinin protein models have distinct structural patterns re-occurring across the 1959-2023 strains
LUCA to LECA, the Lucacene: A model for the gigayear delay from the first prokaryote to eukaryogenesis
Topological singularities and symmetry breaking in development
A system of recurrent neural networks for modularising, parameterising and dynamic analysis of cell signalling networks
Construction of amino acids reduced alphabets from molecular descriptors for interpretation of N-carbamylase, luciferase and PI3K mutations
Rebuilding Iberian motorways with slime mould
Spin torque oscillator neuroanalog of von Neumann's microwave computer
The induction and maintenance of in vitro plant morphogenesis as viewed from a new perspective, with theoretical and constructive implications
Quantum mechanical model for information transfer from DNA to protein
Ecoacoustic codes and ecological complexity
Protein folding and the robustness of cells
Analytical description of coincidence detection synaptic mechanisms in the auditory pathway
A modified estimation distribution algorithm based on extreme elitism
From a homeostatic to a homeodynamic self
Rule-based simulation of temperate bacteriophage infection: Restriction-modification as a limiter to infection in bacterial populations
TMTCPT: The Tree Method based on the Taxonomic Categorization and the Phylogenetic Tree for fine-grained categorization
A graph-based approach to analyze flux-balanced pathways in metabolic networks
Reality and imagination intertwined: A sensorimotor paradox interpretation
Genome-wide characterization of the SiDof gene family in foxtail millet (Setaria italica)
The pseudoentropy of allele frequency trajectories, the persistence of variation, and the effective population size
Childhood in social learning models with changing environments: Implications for human evolution
How nanoparticles can induce dimerization and aggregation of cells in blood or lymph
Domains of laws yet domains of No Law: Energy and work, responsible free will choice, and doing
Modeling the C. elegans germline stem cell genetic network using automated reasoning
Origins of learned reciprocity in solitary ciliates searching grouped 'courting' assurances at quantum efficiencies
Genetic code, the problem of coding biological cycles, and cyclic Gray codes
Disentangling a complex response in cell reprogramming and probing the Waddington landscape by automatic construction of Petri nets
Low-density lipoprotein accumulation within the right coronary artery walls for physiological and hypertension conditions
Spike frequency adaptation facilitates the encoding of input gradient in insect olfactory projection neurons
The cell as a semiotic system that realizes closure to efficient causation: The semiotic (M, R) system
What do stimulated beta cells have in common with cancer cells?
From memory disorders to the development of depression: A system approach
Normal diffusion in a medium connected to a subdiffusive medium with absorption
Approaching biology through the retrocausal apex in physics
The RNase P, LUCA, the ancestors of the life domains, the progenote, and the tree of life
Effects of confinement and crowding on folding of model proteins
Quantum Brain Dynamics and Virtual Reality
The impact of interspecific competition on lineage evolution and a rapid peak shift by interdemic genetic mixing in experimental bacterial populations
Hidden pattern discovery on event related potential EEG signals
Cell differentiation processes as spatial networks: Identifying four-dimensional structure in embryogenesis
Anti-wetting wing surface characteristics of a water bug, Diplonychus annulatus
Theory of interface: Category theory, directed networks and evolution of biological networks
Multi-scale modeling of hippo signaling identifies homeostatic control by YAP-LATS negative feedback
Synchrony of spatial populations induced by colored environmental noise and dispersal
A category theoretic approach to metaphor comprehension: Theory of indeterminate natural transformation
Selection and flexible optimization of binding modes from conformation ensembles
Diffusion-convection effects on drug distribution at the cell membrane level in a patch-clamp setup
A dynamical model of the regulatory network controlling lymphopoiesis
Communication and complexity in a GRN-based multicellular system for graph colouring
libsbmljs - Enabling web-based SBML tools
Why the power of diversity does not always produce better groups and societies
Computer simulation and experimental self-assembly of irradiated glycine amino acid under magnetic fields: Its possible significance in prebiotic chemistry
Effects of Mg 2+ on in vivo transcriptional dynamics of the lar promoter
Gradistics: An underappreciated dimension in evolutionary space
A mathematical model of P53 gene regulatory networks under radiotherapy