yusuke1997/dblp-id-title huggingface dataset:
Relational biology and Church's thesis
Predicting changes of reaction networks with partial kinetic information
The idea of constancy in development and evolution - Scientific and philosophical perspectives
Cooperative actions between myosin heads bring effective functions
A portable structural analysis library for reaction networks
Quantum-like model for unconscious-conscious interaction and emotional coloring of perceptions and other conscious experiences
Simple scaling of cooperation in donor-recipient games
Modelling 18 O 2 and 16 O 2 unidirectional fluxes in plants. III: Fitting of experimental data by a simple model
The autonomy of biological individuals and artificial models
Codes across (life)sciences
Patchy spread patterns in three-species bistable systems with facultative mutualism
Construction of a human body model for acupuncture and moxibustion treatment by colored Petri nets
Dynamics of tRNA dissociation in early and later cycles of translation elongation by the ribosome
Temporal coding: The relevance of classical activity, its relation to pattern frequency bands, and a remark on recoding of excitatory drive into phase shifts
Sensing, feeling and sentience in unicellular organisms and living cells
Electric field generated by axial longitudinal vibration modes of microtubule
Converting differential-equation models of biological systems to membrane computing
Hidden in plain view: degeneracy in complex systems
Editorial: Symbiogenesis and progressive evolution
Statistical methods for identification of golden ratio
Cross-scale sensitivity analysis of a non-small cell lung cancer model: Linking molecular signaling properties to cellular behavior
Transverse interaction in DNA molecule
PRIdictor: Protein-RNA Interaction predictor
Mathematical modeling on bacterial resistance to multiple antibiotics caused by spontaneous mutations
Understanding how replication processes can maintain systems away from equilibrium using Algorithmic Information Theory
Maintenance and characterization of spontaneous contraction rhythm in cultured cardiac myocytes fused with cardiac fibroblasts
ProLoc: Prediction of protein subnuclear localization using SVM with automatic selection from physicochemical composition features
Preservation of dynamic properties in qualitative modeling frameworks for gene regulatory networks
Optimal control strategies and cost-effectiveness analysis of a malaria model
Continuity and discontinuity in evolutionary processes with emphasis on plants
Evolutionary origin of B family DNA-dependent DNA polymerases from retrotranscriptases
Multi-objective shadow prices point at principles of metabolic regulation
Simulation of the effects of microtubules in the cortical rotation of amphibian embryos in normal and zero gravity
Influence of the temporal distribution of electric pulses on transcallosal single unit responses
Mechanisms of developmental robustness
Modeling the fitness of plant morphologies across three levels of complexity
Modelling 18 O 2 and 16 O 2 unidirectional fluxes in plants. IV: Role of conductance and laws of its regulation in C 3 plants
A binary representation of the genetic code
Computational, theoretical, and experimental approaches to morphogenesis
A simple neuronal model with intrinsic saturation of the firing frequency
Toward a system-level understanding of microRNA pathway via mathematical modeling
Major transitions in the physiological machinery of cognition
Morphogenesis as a macroscopic self-organizing process
Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach
Retrocausal regulation for the onset of a reaction cycle
Genome-scale reconstruction of a metabolic network for Gluconobacter oxydans 621H
Effective decoders for DNA codes
Robustness of G1/S checkpoint pathways in cell cycle regulation based on probability of DNA-damaged cells passing as healthy cells
Quantum formalism as an optimisation procedure of information flows for physical and biological systems
Metazoa: Animal Life and the Birth of the Mind, Peter Godfrey-Smith. Farrar, Straus and Giroux, New York, NY (2020), 352, $28, ISBN: 9780374207946
Anthropogenesis and the origin of human consciousness
A pattern to regenerate through turnover
Autonomy: An information theoretic perspective
A global solution to a hyperbolic problem for blood flow modelling
Cyclic decomposition explains a photosynthetic down regulation for Chlamydomonas reinhardtii
Influence of aluminum oxide on the prebiotic thermal synthesis of Gly-Glu-(Gly-Glu) n polymer
Dynamics, synchronization and traveling wave patterns of flux coupled network of Chay neurons
Operator model for evolutionary dynamics
An integrative machine learning model for the identification of tumor T-cell antigens
Living with the emergence of agents on physical terms
Fungal skin for robots
Coenzyme world model of the origin of life
Embryogenesis Explained, Natalie K. Gordon, Richard Gordon. World Scientific, 2016, 784 pp., ISBN: 978-981-4350-48-8 (hardcover), ISBN: 978-981-4740-69-2 (ebook)
Classification of riboswitch sequences using k -mer frequencies
When is altruistic punishment useful in social dilemmas?
In vitro molecular pattern classification via DNA-based weighted-sum operation
Metabolic control analysis as a strategy to identify therapeutic targets, the case of cancer glycolysis
On the effects of the modularity of gene regulatory networks on phenotypic variability and its association with robustness
Effect of dispersal in two-patch prey-predator system with positive density dependence growth of preys
Temperature dependence of IR exciton emission spectra in Müller cell intermediate filaments
Automated Synthesis and Analysis of Switching Gene Regulatory Networks
Information capacity and its approximations under metabolic cost in a simple homogeneous population of neurons
Yeast cell segmentation in microstructured environments with deep learning
Physical limits of computation and emergence of life
Global dynamics of an SIRS epidemic model with saturation incidence
A proposed Information-Based modality for the treatment of cancer
A quantum mechanical analysis of the light-harvesting complex 2 (LH2) from purple photosynthetic bacteria: Insights into the electrostatic effects of transmembrane helices
Decoding spike timing: The differential reverse-correlation method
The acoustic communities: Definition, description and ecological role
Punctuated equilibrium based on a locally ambiguous niche
Intrinsic structural disorder on proteins is involved in the interactome evolution
Development of antibiotic regimens using graph based evolutionary algorithms
An investigation of the plausibility of stochastic resonance in tubulin dimers
Computational irreducibility as the foundation of agency: A formal model connecting undecidability to autonomous behavior in complex systems
How tumor growth can be influenced by delayed interactions between cancer cells and the microenvironment?
Evolutionary dynamics of cooperation coupled with ecological feedback compensation
Dynamic polymorphism of actin as activation mechanism for cell motility
The effectiveness of mutation operation in the case of Estimation of Distribution Algorithms
Living wearables: Bacterial reactive glove
Pharmacophore mapping-based virtual screening followed by molecular docking studies in search of potential acetylcholinesterase inhibitors as anti-Alzheimer's agents
Sensitivity and stability: A signal propagation sweet spot in a sheet of recurrent centre crossing neurons
Control analysis in the identification of key enzymes driving metabolic adaptations: Towards drug target discovery
Population-reaction model and microbial experimental ecosystems for understanding hierarchical dynamics of ecosystems
Rumer's transformation: A symmetry puzzle standing for half a century
How simple autonomous decisions evolve into robust behaviours?: A review from neurorobotics, cognitive, self-organized and artificial immune systems fields
Learning and memory in soldier crabs: Evidence from escape task trials
How an information perspective helps overcome the challenge of biology to physics
Effects of store-operated and receptor-operated calcium channels on synchronization of calcium oscillations in astrocytes
Genome-wide analysis of H3K36me3 and its regulations to cancer-related genes expression in human cell lines
An investigation into the energy transfer efficiency of a two-pigment photosynthetic system using a macroscopic quantum model
Network-based identification of diagnosis-specific trans-omic biomarkers via integration of multiple omics data
An emergence of formal logic induced by an internal agent
Positive feedback and temperature mediated molecular switch controls differential gene regulation in Bordetella pertussis
Morphomechanical reactions and mechanically stressed structures in amphibian embryos, as related to gastrulation and axial organs formation
Effect of filaments within the synaptic cleft on the response of excitatory synapses simulated by computer experiments
Why metabolic systems are rarely chaotic
GNC-app: A new Cytoscape app to rate gene networks biological coherence using gene-gene indirect relationships
A computational design of a programmable biological processor
The innate story code
Eutherians intrinsically run a higher risk of replication deficiency
The origin of symbiogenesis: An annotated English translation of Mereschkowsky's 1910 paper on the theory of two plasma lineages
Insuperable problems of the genetic code initially emerging in an RNA world
Stochastic models for inferring genetic regulation from microarray gene expression data
Evolutionary conservation and functional implications of circular code motifs in eukaryotic genomes
Chirality in a quaternionic representation of the genetic code
Buckling forces and the wavy folds between pleural epithelial cells
Delay-induced model for tumor-immune interaction and control of malignant tumor growth
Biophysical properties and computational modeling of calcium spikes in serotonergic neurons of the dorsal raphe nucleus
Death wins against life in a spatially extended model of the caspase-3/8 feedback loop
Two hybrid compaction algorithms for the layout optimization problem
How is the equilibrium of continuous strategy game different from that of discrete strategy game?
Dynamic interactive self organizing aggregation method in swarm robots
Least ranked human individuals exhibit scale free behavioral responses in hierarchical social systems
A reason for intermittent fasting to suppress the awakening of dormant breast tumors
Derivation of rigorous conditions for high cell-type diversity by algebraic approach
Characterising neurological time series data using biologically motivated networks of coupled discrete maps
Entropy and the arrow of time in population dynamics
A formal approach to evolution as self-referential language
Two genetic codes, one genome: Frameshifted primate mitochondrial genes code for additional proteins in presence of antisense antitermination tRNAs
Computing within bacteria: Programming of bacterial behavior by means of a plasmid encoding a perceptron neural network
DNA strand displacement system running logic programs
Relative stability of network states in Boolean network models of gene regulation in development
An exploration of ecoacoustics and its applications in conservation ecology
Understanding nature's selection of genetic languages
The Cipher of the Genetic Code
Nonlinear electronic circuit with neuron like bursting and spiking dynamics
Artificial intelligence and synthetic biology: A tri-temporal contribution
A simple measure for biocomplexity
A neurobiological model of the recovery strategies from perturbed walking
Endless forms of endless formation - The morphogenesis of organisms and scientific objects
Editorial: 2020 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB 2020)
Impact of transposable elements on the evolution of complex living systems and their epigenetic control
Modeling a cancerous tumor development in a virtual patient suffering from a depressed state of mind: Simulation of somatic evolution with a customized genetic algorithm
Information processing mechanisms in microtubules at physiological temperature: Model predictions for experimental tests
Disproportional fraction of inactive components leads to the variation in metabolic scaling
The hiatus between organism and machine evolution: Contrasting mixed microbial communities with robots
Accurate prediction of enzyme subfamily class using an adaptive fuzzy k-nearest neighbor method
Universal dynamical function behind all genetic codes: P-adic attractor dynamical model
Genetic coding and united-hypercomplex systems in the models of algebraic biology
Control analysis of collagen synthesis by glycine, proline and lysine in bovine chondrocytes in vitro - Its relevance for medicine and nutrition
Pandemic preparedness and new model developments for airborne diseases transmitting via aerosols
Dynamics of an SIR model with vaccination dependent on past prevalence with high-order distributed delay
Applying attractor dynamics to infer gene regulatory interactions involved in cellular differentiation
LatinPSO: An algorithm for simultaneously inferring structure and parameters of ordinary differential equations models
Modelling ethnogenesis
Extending Tlusty's rate distortion index theorem method to the glycome: Do even 'low level' biochemical phenomena require sophisticated cognitive paradigms?
Memory retrieval dynamics and storage capacity of a modular network model of association cortex with featural decomposition
Dynamics of two feed forward genetic motifs in the presence of molecular noise
Neuropharmacology beyond reductionism - A likely prospect
How biological codes break causal chains to enable autonomy for organisms
Towards proteinoid computers. Hypothesis paper
Evolution of the mental model: From archaic myths to modern myths
The regulatory network that controls the differentiation of T lymphocytes
Reviewing evidence for systematic transcriptional deletions, nucleotide exchanges, and expanded codons, and peptide clusters in human mitochondria
Mathematics in biological reality: The emergence of natural computation in living systems
Kinetics of cancer metastasis
A quantum-like information processing model with memory noise for question order effect
First report on exploring structural requirements of alpha and beta thymidine analogs for PfTMPK inhibitory activity using in silico studies
Effect of directional migration on Lotka-Volterra system with desert
Single molecule FRET for the study on structural dynamics of biomolecules
The role of the " Thiodendron " consortium in postulating the karyomastigont chimaera of the endosymbiosis theory by Lynn Margulis
From network-to-antibody robustness in a bio-inspired immune system
A Wiener-type neuronal model in the presence of exponential refractoriness
Computational power and generative capacity of genetic systems
Systems biology of synaptic plasticity: A review on N-methyl-d-aspartate receptor mediated biochemical pathways and related mathematical models
Petri net modelling of gene regulation of the Duchenne muscular dystrophy
Multi-scale lines and edges in V1 and beyond: Brightness, object categorization and recognition, and consciousness
Circular code identified by the codon usage
Entropy decrease associated to solute compartmentalization in the cell
Viscous DNA and RNA: Quantum damped dynamical random systems
Morphology changes induced by intercellular gap junction blocking: A reaction-diffusion mechanism
Prebiotic thermal polymerization of crystals of amino acids via the diketopiperazine reaction
The Fokker-Planck approach for the cooperative molecular motor model with finite number of motors
Getting into shape: Optimal ligand gradients for axonal guidance
Modelling of phytoplankton allelopathy with Monod-Haldane-type functional response - A mathematical study
Light-induced ATP production and proton translocation, two independent phenomena in Halobacterium salinarum archaea cells
Human cognitive limitations and emotions: The emergence of social complexity
From chaos to clock in recurrent neural net. Case study
Folding small proteins via annealing stochastic approximation Monte Carlo
Eco-crossover, or environmentally regulated crossing-over, and natural selection are two irreplaceable drivers of adaptive evolution: Eco-crossover hypothesis
Corrigendum to "A biophysical approach to cancer dynamics: Quantum chaos and energy turbulence" [BioSystems 156-157 (June-July) (2017) 1-22]
Overtaking method based on sand-sifter mechanism: Why do optimistic value functions find optimal solutions in multi-armed bandit problems?
The distribution of information for sEMG signals in the rectal cancer treatment process
A comprehensive study of multiple mapping and feature selection for correction strategy in the analysis of small RNAs from SOLiD sequencing
Modeling Chagas disease in Chile: From vector to congenital transmission
Time rescaling and pattern formation in biological evolution
Impact of social reward on the evolution of cooperation in voluntary prisoner's dilemma
Order stability via Fröhlich condensation in bio, eco, and social systems: The quantum-like approach
The quantum Zeno effect immunizes the avian compass against the deleterious effects of exchange and dipolar interactions
Comparative protein analysis of the chitin metabolic pathway in extant organisms: A complex network approach
Fractal calculus in tumor growth simulations: The proof is in the pudding
Mathematical constraints on a family of biodiversity measures via connections with Rényi entropy
Structural analyzes suggest that MiSSP13 and MiSSP16.5 may act as proteases inhibitors during ectomycorrhiza establishment in Laccaria bicolor
Benchmarking a memetic algorithm for ordering microarray data
Chlorophyll fluorescence in the leaves of Tradescantia species of different ecological groups: Induction events at different intensities of actinic light
Circadian transcription in liver
An ancient frame-shifting event in the highly conserved KPNA gene family has undergone extensive compensation by natural selection in vertebrates
Plant leaf computing
Follicular waves in ontogenesis and female fertility
Analysis of metabolic network based on conservation of molecular structure
Incorporating antagonistic pleiotropy into models for molecular replicators
Games network and application to PAs system
Exploring cooperation evolution in biological and social systems through donation and moral sentiment
Biological complexity, quantum coherent states and the problem of efficient transmission of information inside a cell
Natural hierarchy emerges from energy dispersal
Therapeutic rewiring by means of desynchronizing brain stimulation
High-speed parameter search of dynamic biological pathways from time-course transcriptomic profiles using high-level Petri net
Particle sorting by Paramecium cilia arrays
150 Years since the birth of Lev Berg: Nomogenesis is more relevant today than ever
Spatiotemporal models in biology and the health sciences
Proteins as fuzzy controllers: Auto tuning a biological fuzzy inference system to predict protein dynamics in complex biological networks
Substantial changes in synaptic firing frequencies induced by glial ATP hysteresis
Epithelial folding in the morphogenesis of the colonial marine hydrozoan, Dynamena pumila
A control measure for epidemic spread based on the susceptible-infectious-susceptible (SIS) model
A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information
From axiomatic systems to the Dogmatic gene and beyond
Mechanisms of directed evolution of morphological structures and the problems of morphogenesis
Inhomogeneous retino-cortical mapping is supported and stabilized with correlation-learning during self-motion
Study of the bioenergetics to identify the novel pathways as a drug target against Mycobacterium tuberculosis using Petri net
Quantum biology at the cellular level - Elements of the research program
Comparison of metabolite profiles in U87 glioma cells and mesenchymal stem cells
Computational morphogenesis - Embryogenesis, cancer research and digital pathology
The evolution of proteome: From the primeval to the very dawn of LUCA
Temporal cohesion as a candidate for negentropy in biological thermodynamics
Within-host influenza dynamics: A small-scale mathematical modeling approach
A computational model of chemotaxis-based cell aggregation
A declarative constraint-based method for analyzing discrete genetic regulatory networks
Conductance versus current noise in a neuronal model for noisy subthreshold oscillations and related spike generation
Ervin Bauer's concept of biological thermodynamics and its different evaluations
On a phase diagram for random neural networks with embedded spike timing dependent plasticity
New algorithm for the analysis of nucleotide and amino acid evolutionary relationships based on Klein four-group
Simple mechanisms of early life - simulation model on the origin of semi-cells
The genotypic complexity of evolved fault-tolerant and noise-robust circuits
SBcoyote: An extensible Python-based reaction editor and viewer
Proto-object categorisation and local gist vision using low-level spatial features
Senescence, change, and competition: When the desire to pick one model harms our understanding
Filtering noise for synchronised activity in multi-trial electrophysiology data using Wiener and Kalman filters
French flag gradients and Turing reaction-diffusion versus differentiation waves as models of morphogenesis
The regulatory network that controls lymphopoiesis
Nonlinear transient computation as a potential "kernel trick" in cortical processing
Obesity, body heat loss, and efficiency in movement
Demographics of genetic admixture and expansion
Light-addressed single-neuron stimulation in dissociated neuronal cultures with sparse expression of ChR2
P systems applications to systems biology
Firing and intrinsic properties of antennal lobe neurons in the Noctuid moth Agrotis ipsilon
Identification of breast cancer prognostic modules via differential module selection based on weighted gene Co-expression network analysis
Dual selection of a genetic switch by a single selection marker
Neurons and neural networks to model proteins and protein networks
Multi-factor vaccination game and optimal control of a SVIS epidemic model
Physarum polycephalum: Towards a biological controller
Slime mould logic gates based on frequency changes of electrical potential oscillation
Dynamic landscape models of coevolutionary games
Exploring the patterns of evolution: Core thoughts and focus on the saltational model
Periodicity in the embryo: Emergence of order in space, diffusion of order in time
An immune network inspired evolutionary algorithm for the diagnosis of Parkinson's disease
Towards Physarum binary adders
The Net of Life, a short story: Intricate patterns of gene flows across hundreds of extant genomes, all the way to LUCA
Structural analysis of in silico mutant experiments of human inner-kinetochore structure
From life to evolution: the differentiation between storage and interface in natural and cultural systems
Parametric inference of neuronal response latency in presence of a background signal
Elucidation of productive alanine recognition mechanism by Escherichia coli alanyl-tRNA synthetase
Morphomechanical rules of embryonic development
Accurate phenotypic self-replication as a necessary cause for biological evolution
On the origin of biological teleonomy
Two-wave model of the muscle contraction
Photochromic molecular implementations of universal computation
Hopf bifurcation in the shadow of extinction: Collaborating with epidemic dynamics through lethal mutations and declining ancestor infections
PS II model based analysis of transient fluorescence yield measured on whole leaves of Arabidopsis thaliana after excitation with light flashes of different energies
Decoding viruses: An alternative perspective on their history, origins and role in nature
Mathematical modeling and sensitivity analysis of G1/S phase in the cell cycle including the DNA-damage signal transduction pathway