yusuke1997/dblp-id-title huggingface dataset:
The emergence of ribozymes synthesizing membrane components in RNA-based protocells
The effect of predation on the prevalence and aggregation of pathogens in prey
When perceptual time stands still: Long percept-memory in binocular rivalry
Towards molecular computing: Co-development of microfluidic devices and chemical reaction media
Morphospace engineering: Morphological computation in scaffold design
Avoidance of antisense, antiterminator tRNA anticodons in vertebrate mitochondria
Theoretical approach to modelling and analysis of the bioprocess with product inhibition and impulse effect
Reflexive neural circuits and the origin of language and music codes
Implementing logical inference based on DNA assembly
Oncogenetic pedigrees: Relation between design and ability to predict mutation
Life as a self-referential deep learning system: A quantum-like Boltzmann machine model
Transport characteristics of molecular motors
On hybridising lettuce seedlings with nanoparticles and the resultant effects on the organisms' electrical characteristics
In pursuit of the framework behind the biosphere: S-curves, self-assembly and the genetic entropy paradox
Structural impact due to PPQEE deletion in multiple cancer associated protein - Integrin αV: An In silico exploration
Hyper-restorative non-equilibrium state as a driving force of biological morphogenesis
Motility disorders and disintegration into separate cells of Trichoplax sp. H2 in the presence of Zn 2+ ions and L-cysteine molecules: A systems approach
A secured cryptographic system based on DNA and a hybrid key generation approach
A call for research on the basis for polygonal pleomorphism in archaea
Conservation of key members in the course of the evolution of the insulin signaling pathway
Memetic approach to cultural evolution
Duality between decomposition and gluing: A theoretical biology via adjoint functors
A systemic approach for modeling biological evolution using Parallel DEVS
Optimal isolation control strategies and cost-effectiveness analysis of a two-strain avian influenza model
Complexification of eukaryote phenotype: Adaptive immuno-cognitive systems as unique Gödelian blockchain distributed ledger
Formal autopoiesis: Solutions of the classical and extended functional closure equations
Measurement system for simultaneous observation of myosin V chemical and mechanical events
A graph-based reflexive artificial chemistry
Natural gradient ascent in evolutionary games
Networks and games for precision medicine
Methodologies for the modeling and simulation of biochemical networks, illustrated for signal transduction pathways: A primer
An efficient method of exploring simulation models by assimilating literature and biological observational data
Statistical models of critical phenomena in fuzzy biocognition
Biomechanical and coherent phenomena in morphogenetic relaxation processes
Modelling simultaneous echo waveform reconstruction and localization in bats
Is envy one of the possible evolutionary roots of charity?
Effective Boolean dynamics analysis to identify functionally important genes in large-scale signaling networks
Language: A fresh concept to integrate syntactic and semantic information in life sciences
Editorial: Fundamental principles of biological computation: From molecular computing to evolutionary complexity
Stability analysis and optimal control of an SIR epidemic model with vaccination
Toward a Bio-Organon: A model of interdependence between energy, information and knowledge in living systems
Abnormal synchronization patterns in the electrical stimulation-contractile response coupling decrease with noise
Thermodynamic model for memory
A survey of the methodological process of modeling, inference, and evaluation of gene regulatory networks using scRNA-Seq data
The flower of the desert and a migrant experience: Two examples of personal codes
Solving satisfiability problems using a novel microarray-based DNA computer
Evolutionary acquisition of complex traits in artificial epigenetic networks
New way for cell differentiation: Reaction, diffusion and chaotic waves
Surface code model for Fibonacci helical pathways of the Orch OR microtubule
Fuzzy-based self organizing aggregation method for swarm robots
DNA computing of solutions to knapsack problems
A simple measure of the coding efficiency of a neuronal population
A hypothesis on the role of transposons
Names, classification, structure and function and their inter-relationship to the Q cycle, photosynthesis and ATP synthesis
Effects along the epithelial-mesenchymal biointerface in direct cell self-organisation: Multiscale theoretical analysis
Symbols are not uniquely human
Deciphering the dynamic binding of spicy odorants to human olfactory receptors
A mathematical model predicting host mitochondrial pyruvate transporter activity to be a critical regulator of Mycobacterium tuberculosis pathogenicity
Characterization of the norepinephrine-activation of adenylate cyclase suggests a role in memory affirmation pathways: Overexposure to epinephrine inactivates adenylate cyclase, a causal pathway for stress-pathologies
The phylogenetic distribution of the cell division system would not imply a cellular LUCA but a progenotic LUCA
Hydrophobic condensation and modular assembly model of protein folding
Professor Lev Beloussov and the birth of morphomechanics
Impacts of a high-glucose diet or starvation on microRNA-transcription factor networks in Caenorhabditis elegans through Boolean mathematical modeling
Single molecule thermodynamics in biological motors
Translation of mitochondrial swinger RNAs according to tri-, tetra- and pentacodons
Infinite combinatorics in mathematical biology
VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology
Is it possible that cells have had more than one origin?
Optimal control of drug therapy: Melding pharmacokinetics with viral dynamics
Rosen's (M, R) system in Unified Modelling Language
Unravelling intrinsically disordered and compositionally biased proteins in the cereal proteomes
Carrying pieces of information in organocatalytic bytes: Semiopoiesis - A new theory of life and its origins
Metastable states, phase transitions, and persistent neural activity
Mathematical model for plant-insect interaction with dynamic response to PAD4-BIK1 interaction and effect of BIK1 inhibition
Detecting biological associations between genes based on the theory of phase synchronization
A novel mathematical model of AIDS-associated Kaposi's sarcoma: Analysis and optimal control
Evidence for the implication of the histone code in building the genome structure
Hyperbolic rules of the cooperative organization of eukaryotic and prokaryotic genomes
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
A model of network formation by Physarum plasmodium: Interplay between cell mobility and morphogenesis
Concordant dynamic changes of global network properties in the frontoparietal and limbic compartments: An EEG study
Effects of CikA and SasA co-regulation on cyanobacterial circadian clock
Di-codon usage for classification of genes
Homeostatically regulated synchronized oscillations induced by short-term tetrodotoxin treatment in cultured neuronal network
Reciprocity phase in various 2 × 2 games by agents equipped with two-memory length strategy encouraged by grouping for interaction and adaptation
Cellular sentience as the primary source of biological order and evolution
The osseous fusion patterns in an equine limb: A theoretical deconstruction of the evolutionary mechanisms
Avian model to mitigate gut-derived immune response and oxidative stress during heat
On learning time delays between the spikes from different input neurons in a biophysical model of a pyramidal neuron
A single spike deteriorates synaptic conductance estimation
Alignment-based and alignment-free methods converge with experimental data on amino acids coded by stop codons at split between nuclear and mitochondrial genetic codes
Logical modelling of regulatory networks with GINsim 2.3
Decoding life: A detailed examination of program collection
Systemic evolutionary changes in mammalian gene expression
A hybrid DNN model using novel integrated interface features for predicting protein-protein complexes binding affinity
A comparison of the Moran Process and replicator equations for evolving social dilemma game strategies
A bio-inspired visual collision detection mechanism for cars: Combining insect inspired neurons to create a robust system
On the robustness of update schedules in Boolean networks
Quantum concepts in Psychology: Exploring the interplay of physics and the human psyche
Corrigendum to "Role of calcium oscillations in sperm physiology" [BioSystems 209 (2021) 104524]
Cosmos, mind, matter: Is mind in spacetime?
Serial Endosymbiosis Theory: From biology to astronomy and back to the origin of life
A study on emergence of alternating reciprocity in a 2 × 2 game with 2-length memory strategy
How many and which types of primary cells (domains of life) emerged from LUCA, identified employing different genetic codes
Mathematical principles and methods of biological surface lubrication with phospholipids bilayers
The enzyme-substrate complex as a cat state: A toy quantum analog
Picture representation during REM dreams: A redox molecular hypothesis
Phylogeny of genetic codes and punctuation codes within genetic codes
Similar bowtie structures and distinct largest strong components are identified in the transcriptional regulatory networks of Arabidopsis thaliana during photomorphogenesis and heat shock
An application of higher order multivariate cumulants in modelling of myoelectrical activity of porcine uterus during early pregnancy
Transcription and noise in negative feedback loops
On the nature and origin of biological information: The curious case of RNA
BaSAR - A tool in R for frequency detection
Gene regulatory networks with binary weights
Light sensitive Belousov-Zhabotinsky medium accommodates multiple logic gates
Possible involvement of ATP-purinoceptor signalling in the intercellular synchronization of intracellular Ca 2+ oscillation in cultured cardiac myocytes
Self-organization in aggregating robot swarms: A DW-KNN topological approach
Where and how could intentional programs be generated in the brain?: A hypothetical model based on glial-neuronal interactions
Building exploration with leeches Hirudo verbana
Micro-electrode array recording of extracellular electrical potentials of liquid static surface fermented Hericium erinaceus
On plant roots logical gates
Quantum effects in ion transport: A thermodynamic resource theory approach
The evolution and biophysical economics of energy currencies: from prebiotic electrochemistry to modern digital money
Biological computation and the foundations of biological organization: The legacy of the journal BioSystems
Tropomyosin as a regulator of the sliding movement of actin filaments
Viewing brain processes as Critical State Transitions across levels of organization: Neural events in Cognition and Consciousness, and general principles
Stability analysis and optimal control of an epidemic model with awareness programs by media
Analysis of network motifs in cellular regulation: Structural similarities, input-output relations and signal integration
What can synthetic biology offer to artificial intelligence (and vice versa)?
Sustainable cooperation based on reputation and habituation in the public goods game
Prediction of antimicrobial activity of large pool of peptides using quasi-SMILES
Network-wide integration of stem cell-derived neurons and mouse cortical neurons using microfabricated co-culture devices
Can the Stark-Einstein law resolve the measurement problem from an animate perspective?
BINK: Biological binary keypoint descriptor
Evolutionary algorithm for metabolic pathways synthesis
Understanding cancer from a biophysical, developmental and systems biology perspective using the landscapes-attractor model
How ambiguity codes specify molecular descriptors and information flow in Code Biology
Gene as a dynamical notion: An extensive and integrative vision. Redefining the gene concept, from traditional to genic-interaction , as a new dynamical version
Two ways for interpreting Driesch's law: "Positional information" and morphogenetic fields
The relevance of neck linker docking in the motility of kinesin
The emergence of synchronization behavior in Physarum polycephalum and its particle approximation
On the context-sensitive grammar of the genetic code
RaaMLab: A MATLAB toolbox that generates amino acid groups and reduced amino acid modes
Quantum formalism for indeterminate preferences in decision theory
Calcium ions tune the beats of cilia and flagella
Heterarchy in biological systems: A logic-based dynamical model of abstract biological network derived from time-state-scale re-entrant form
Exploitation or cooperation? Evolution of a host (ciliate)-benefiting alga in a long-term experimental microcosm culture
Evolution of stability of socioeconomic system functioning: Some approaches to modeling (with an application to the case of Egypt, 2011-2013)
Feedback enrichment analysis for transcription factor-target genes in signaling pathways
Phenotypic complexity and local variations in neutral degree
HIV-associated neuropathogenesis: A systems biology perspective for modeling and therapy
A tuneable attractor underlies yeast respiratory dynamics
Stress-generating tissue deformations in Xenopus embryos: Long-range gradients and local cell displacements
Estimation of discrepancy of color qualia using Kullback-Leibler divergence
Harvesting on a stage-structured single population model with mature individuals in a polluted environment and pulse input of environmental toxin
Simulating the maintenance of a rare fish morph experiencing negative frequency dependent selection
Evolution, physics, and education
Swelling and membrane potential dynamics of glial Müller cells
Simulation peptide toxicity using the fragments of local symmetry in amino acid sequences
C-Biomarker.net: A Cytoscape app for the identification of cancer biomarker genes from cores of large biomolecular networks
Modeling the regulation of the competence-evoking quorum sensing network in Streptococcus pneumoniae
A cell state splitter and differentiation wave working-model for embryonic stem cell development and somatic cell epigenetic reprogramming
Comparison of metabolite production capability indices generated by network analysis methods
A dynamic model for transcription elongation and sequence-dependent short pauses by RNA polymerase
Novel amino acid distance matrices based on conductance measure
Input-output relationship in galvanotactic response of Dictyostelium cells
The origins of the cell membrane, the progenote, and the universal ancestor (LUCA)
Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples
Thinking as a quantum phenomenon
Information processing in cells and tissues (IPCAT'2009): From small scale dynamics to understanding systems behavior
Thinking, holograms, and the quantum brain
A transition to a new Editor-in-Chief
Beyond planetary-scale feedback self-regulation: Gaia as an autopoietic system
Human evolution is biological & technological evolution
Mechanism and biological significance of erythrocyte homoaggregation (rouleaux formation): temperature-dependent entropic liberation of water from cells and macromolecules
Embryogenic remodeling of global chromatin and its role on structure of corresponding lattice representation
Erratum to "A discriminative method for remote homology detection based on n-peptide compositions with reduced amino acid alphabets" [BioSystems 87 (2007) 75-81]
Evolving gene regulatory networks
Dynamic-module redundancy confers robustness to the gene regulatory network involved in hair patterning of Arabidopsis epidermis
Synchrony measure for a neuron driven by excitatory and inhibitory inputs and its adaptation to experimentally-recorded data
From Empedocles to Symbiogenetics: Lynn Margulis's revolutionary influence on evolutionary biology
Coordination of top-down influence on V1 responses by interneurons and brain rhythms
Automated classification of atherosclerotic plaque from magnetic resonance images using predictive models
Optimal signal in sensory neurons under an extended rate coding concept
Theoretical analysis of reversible and irreversible mitochondrial swelling in vivo
The rise of languaging
Analysis of a competitive prey-predator system with a prey refuge
Effects of size refuge specificity on a predator-prey model
Biological wires, communication systems, and implications for disease
Complex dynamics in a fractional order nephron pressure and flow regulation model
Extraction of the molecular level biomedical event trigger based on gene ontology using radial belief neural network techniques
Monitoring environmental change in an ecosystem
The evolutionary stages of the complexity of biological catalysts mark and clarify the phases of the origin of the genetic code: A model for the origin of the reading frame with codons from proto-mRNAs with different frames
Cesium: A public database of evolved oscillatory reaction networks
In vitro molecular machine learning algorithm via symmetric internal loops of DNA
On exploration of geometrically constrained space by medicinal leeches Hirudo verbana
Elucidating effects of reaction rates on dynamics of the lac circuit in Escherichia coli
Exploring the concept of interaction computing through the discrete algebraic analysis of the Belousov-Zhabotinsky reaction
Systematically frameshifting by deletion of every 4th or 4th and 5th nucleotides during mitochondrial transcription: RNA self-hybridization regulates delRNA expression
Phantom reflexes: Muscle contractions at a frequency not physically present in the input stimuli
Small-sample continual learning classification method with vaccine to update memory cells based on the artificial immune system
On interplay between excitability and geometry
A software tool for modeling and simulation of numerical P systems
The linearity of emergent spectro-temporal receptive fields in a model of auditory cortex
Alternative splicing of mutually exclusive exons - A review
Phylogenomic proximity and metabolic discrepancy of Methanosarcina mazei Go1 across methanosarcinal genomes
DNMHMM: An approach to identify the differential nucleosome regions in multiple cell types based on a Hidden Markov Model
The effect of avian eggshell membrane structure on microbial penetration: A simulation study
Behavioural robustness: A link between distributed mechanisms and coupled transient dynamics
Toward a unified theory of ATP synthesis/hydrolysis: Integrating physics, chemistry, and biology
Generalization power of threshold Boolean networks
Progressive evolution of plants: A critical review
An efficient finite-difference strategy for sensitivity analysis of stochastic models of biochemical systems
Cortical activity pattern computation
Inferring rules of Escherichia coli translational efficiency using an artificial neural network
An economic approach to energy budgets: HOW many resources should living organisms spare?
Evolution of the genetic code: The ambiguity-reduction theory
Simulating natural selection as a culling mechanism on finite populations with the hawk-dove game
An impulsively controlled pest management model with n predator species and a common prey
Network of evolutionary processors with splicing rules and permitting context
A methodology for analyzing and forecasting sociopolitical destabilization
The evolution of the genetic code: Impasses and challenges
ConvAn: A convergence analyzing tool for optimization of biochemical networks
Reconstruction of DNA sequences using genetic algorithms and cellular automata: Towards mutation prediction?
Causal and non-causal explanations in code biology
Semiotic Agency. Science beyond Mechanism, Alexei Sharov, Morten Tønnessen. Springer, Cham (2022), 372, https: //doi.org/10.1007/978-3-030-89484-9, ISBN 978-3-030-89484-9 (eBook), Biosemiotics Springer Series, Volume 25 (Series Editors Kalevi Kull, Alexei Sharov, Claus Emmeche, Donald F. Favareau), ISBN: 978-3-030-89483-2
Cheating is evolutionarily assimilated with cooperation in the continuous snowdrift game
Automatic reconstruction of molecular and genetic networks from discrete time series data
Stabilizing patterning in the Drosophila segment polarity network by selecting models in silico
The evolutionary dynamics of social systems via reflexive transformation of external reality
Global redox cycle of biospheric carbon: Interaction of photosynthesis and earth crust processes
Analyzing resilience properties in oscillatory biological systems using parametric model checking
Symbiogenesis is driven through hierarchical reorganization of an ecosystem under closed or semi-closed conditions
Restarting and recentering genetic algorithm variations for DNA fragment assembly: The necessity of a multi-strategy approach
Modeling of will and consciousness based on the human language: Interpretation of qualia and psychological consciousness
DNA based computing for understanding complex shapes
Identifiability and identification of switched linear biological models
A centrality based multi-objective approach to disease gene association
Nothing in evolution makes sense except in the light of code biology
Increasing complexity: Mechanical guidance and feedback loops as a basis for self-organization in morphogenesis
The cAMP response element binding protein (CREB) as an integrative HUB selector in metazoans: Clues from the hydra model system
Ghost resonance in a pool of heterogeneous neurons
A fuzzy-genetic model for estimating forces from electromyographical activity of antagonistic muscles due to planar lower arm movements: The effect of nonlinear muscle properties
Molecular learning with DNA kernel machines
The basic reproduction number obtained from Jacobian and next generation matrices - A case study of dengue transmission modelling
Optimal decoding and information transmission in Hodgkin-Huxley neurons under metabolic cost constraints
Automaton models of computational genetic regulatory networks with combinatorial gene-protein interactions
Autopoiesis: Foundations of life, cognition, and emergence of self/other
2-adic morphogenesis as a metaphorical model of biological growth
Field programmable chemistry: Integrated chemical and electronic processing of informational molecules towards electronic chemical cells
Editorial: Computational approaches in cancer modelling
Determination of scoring functions for protein damage susceptibility
Centrosome as a micro-electronic generator in live cell
A phase-based stereo vision system-on-a-chip
Variability and randomness in stationary neuronal activity
Pathway-based gene-gene interaction network modelling to predict potential biomarkers of essential hypertension
Functional modeling of neural-glial interaction
Groel crystal growth and characterization
Langmuir-Blodgett based lipase nanofilms of unique structure-function relationship
The analysis of bi-level evolutionary graphs
Transfer functions of proteinoid microspheres
An explanation of biphasic characters of mRNA translocation in the ribosome
Semiosis in action: A biomolecular perspective
Electrodynamic eigenmodes in cellular morphology
The fourfold way of the genetic code
Bioinformatics and meta-analysis of expression data to investigate transcriptomic response of wheat root to abiotic stresses
Periodic coupling strength-dependent multiple coherence resonance by time delay in Newman-Watts neuronal networks
Bipedalism, childhood, and ritualisation of human sexual behaviour: A hominin model scenario of ontogenetic selection
Computational analysis of fluorescence induction curves in intact spinach leaves treated at different pH
Genetic algorithm with alternating selection pressure for protein side-chain packing and pK(a) prediction
Stationary periodic patterns in a model of growing population of motile bacteria
Rapid clade divergence and phyletic gradualism in an interacting particle model of sympatric speciation