yusuke1997/dblp-id-title huggingface dataset:
A novel hypothesis about mechanism of thalidomide action on pattern formation
Model for a population-based microbial oscillator
The genetic code is very close to a global optimum in a model of its origin taking into account both the partition energy of amino acids and their biosynthetic relationships
Indication of quantum mechanical electron transport in human substantia nigra tissue from conductive atomic force microscopy analysis
Modular genetic regulatory networks increase organization during pattern formation
Primal awareness, evolutionary restriction, life and the origin of quantum mechanics
A biogenic principle within the constructal law: The flow of information in biological systems
Pattern recall in networks of chaotic neurons
The first lines of divergence in the Bacteria domain were the hyperthermophilic organisms, the Thermotogales and the Aquificales, and not the mesophilic Planctomycetales
Synthetic collective intelligence
Physiological changes of a green alga (Micractinium sp.) involved in an early-stage of association with Tetrahymena thermophila during 5-year microcosm culture
QSAR using evolved neural networks for the inhibition of mutant PfDHFR by pyrimethamine derivatives
Neuron quantum computers and a way to unification of science: A compendium of Efim Liberman's scientific work
A heuristic perspective on non-variational free energy modulation at the sleep-like edge
The emergence of locally adaptive institutions: Insights from traditional social structures of East African pastoralists
Amino acid activation analysis of primitive aminoacyl-tRNA synthetases encoded by both strands of a single gene using the malachite green assay
A unified pathogenic hypothesis for mental disorders based on schismogenesis
Modeling the interaction between donor-derived regulatory T cells and effector T cells early after allogeneic hematopoietic stem cell transplantation
Multi-timescale event-scheduling in multi-agent immune simulation models
A theoretical study on mathematical modelling of an infectious disease with application of optimal control
The genetic code is not universal
Multilayered neural network with structural lateral inhibition for incremental learning and conceptualization
Paint4Net: COBRA Toolbox extension for visualization of stoichiometric models of metabolism
The search image as link between sensation, perception and action
The canonical and non-canonical NF-κB pathways and their crosstalk: A comparative study based on Petri nets
First phase release coefficient of insulin in subjects with normal glucose tolerance on glucose infusion analyzed by computer simulation
The stochastic organization of genomes and the doctrine of energy-information evolution based on bio-antenna arrays
Modes and cuts in metabolic networks: Complexity and algorithms
Entropy is better related to unification than to order
Variability in resource productivity drives community dynamics in intraguild predation systems
Dynamics of HIV infection studied with cellular automata and conformon-P systems
Identification of common factors among fibrosarcoma, rhabdomyosarcoma, and osteosarcoma by network analysis
Effects of AMPARs trafficking and glutamate-receptors binding probability on stochastic variability of EPSC
Floral advertisement and the competition for pollination services
The drawbridge of nature: Evolutionary complexification as a generation and novel interpretation of coding systems
Fast and reliable prediction of domain-peptide binding affinity using coarse-grained structure models
Field-induced coherence and Fröhlich condensation in hydrated DNA
Natural born intelligence manifesto: Illustrating the dynamic perspective for consciousness
Phylogenetic tree construction using sequential stochastic approximation Monte Carlo
A simple scaling of the effectiveness of supporting mutual cooperation in donor-recipient games by various reciprocity mechanisms
Combination of survival movement strategies in cyclic game systems during an epidemic
A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models
Modelling autonomy: Simulating the essence of life and cognition
A mathematical model of the biochemical network underlying left-right asymmetry establishment in mammals
A framework for modeling information propagation of biological systems at critical states
Cholesterol plays a decisive role in tetraspanin assemblies during bilayer deformations
Reproducing bursting interspike interval statistics of the gustatory cortex
On comparing composition principles of long DNA sequences with those of random ones
INDEX: Incremental depth extension approach for protein-protein interaction networks alignment
Causal intuition in the indefinite world: Meta-analysis and simulations
Spiking neural P systems with structural plasticity and weights
Stochastic modeling of the transmission of respiratory syncytial virus (RSV) in the region of Valencia, Spain
A P system and a constructive membrane-inspired DNA algorithm for solving the Maximum Clique Problem
Logic circuits based on molecular spider systems
Code poiesis: Life's fuel
Voevodsky's unfinished project: Filling the gap between pure and applied mathematics
Putative mitochondrial polypeptides coded by expanded quadruplet codons, decoded by antisense tRNAs with unusual anticodons
Origin and diversification of a metabolic cycle in oligomer world
Exploring the complexity and chaotic behavior in plankton-fish system with mutual interference and time delay
A Data-Distribution and Successive Spline Points based discretization approach for evolving gene regulatory networks from scRNA-Seq time-series data using Cartesian Genetic Programming
Error-correcting codes and information in biology
Standard Genetic Code vs. Supersymmetry Genetic Code - Alphabetical table vs. physicochemical table
Quantum information and the problem of mechanisms of biological evolution
How to describe genes: Enlightenment from the quaternary number system
Exploring the implicit interlayer regulatory mechanism between cells and tissue: Stochastic mathematical analyses of the spontaneous ordering in beating synchronization
Inhibitor titrations reveal low control of glyceraldehyde 3-phosphate dehydrogenase and high control of hexokinase on glycolytic flux in an aggressive triple-negative breast cancer cell line
The splicing code
William Bateson, black slavery, eugenics and speciation: The relative roles of politics and science
Cell jamming-to-unjamming transitions and vice versa in development: Physical aspects
Aminoacylation of short hairpin RNAs through kissing-loop interactions indicates evolutionary trend of RNA molecules
From membranes to systems: Self-configuration and self-replication in membrane systems
An efficient approach for identifying important biomarkers for biomedical diagnosis
Kinetic analysis on the sensitivity of glucose- or glyoxal-induced LDL glycation to the inhibitory effect of Psidium guajava extract in a physiomimic system
Metabolic ecology in aquatic ecosystems: Viewed from trophic compartments and communities in food webs
Teeth between the eyes: Extra-oral dentition in chimaeras as evidence for biological codes
The scientometric approach to Code Biology: What the title tells about the field
CytoNCA: A cytoscape plugin for centrality analysis and evaluation of protein interaction networks
Morphogenetic processes as data: Quantitative structure in the Drosophila eye imaginal disc
Kinetic Monte Carlo simulation of the initial phases of chlorophyll fluorescence from photosystem II
Hierarchical coarse-graining model for photosystem II including electron and excitation-energy transfer processes
A design framework to model retinas
Computational prediction of origin of replication in bacterial genomes using correlated entropy measure (CEM)
A multi-modal algorithm based on an NSGA-II scheme for phylogenetic tree inference
Computational complexity of algorithms for sequence comparison, short-read assembly and genome alignment
Enhanced effective codon numbers to understand codon usage bias
Reproducibility and usability of chronic virus infection model using agent-based simulation; comparing with a mathematical model
SetQuence & SetOmic: Deep set transformers for whole genome and exome tumour analysis
Unravelling the nexus: Towards a unified model of development, ageing, and cancer
Thermodynamic balance of photosynthesis and transpiration at increasing CO 2 concentrations and rapid light fluctuations
Efficiency of rate and latency coding with respect to metabolic cost and time
On electrical gates on fungal colony
Entering the labyrinth: A hypothesis about the emergence of metabolism from protobiotic routes
Taking the example of computer systems engineering for the analysis of biological cell systems
Overview: Early history of crop growth and photosynthesis modeling
Computational Methods in Systems Biology
Transient and sustained elementary flux mode networks on a catalytic string-based chemical evolution model
Bisimilar Booleanization of multivalued networks
Breaking down calcium timing in heterogenous cells populations
Compositional perspectives on human brain aging
Nonlinear calcium ion waves along actin filaments control active hair-bundle motility
BIOCOMPUTATION: Some history and prospects
The comparison of biophysical properties of DB-67 and its ester DB-67-4ABTFA determined by fluorescence spectroscopy methods
Strong energy component is more important than spectral selectivity in modeling responses of midbrain auditory neurons to wide-band environmental sounds
Softness-based adaptive mesh refinement algorithm for soft tissue deformation
Spiking neural networks produce informational closure by stimulus avoidance
Prediction of replication sites in Saccharomyces cerevisiae genome using DNA segment properties: Multi-view ensemble learning (MEL) approach
Bistability in gene transcription: Interplay of messenger RNA, protein, and nonprotein coding RNA
Optimism in the face of uncertainty supported by a statistically-designed multi-armed bandit algorithm
Construction of a DNA nano-object directly demonstrates computation
Bayesian learning of sparse gene regulatory networks
Chaotic vibration of microtubules and biological information processing
GPUPeP: Parallel Enzymatic Numerical P System simulator with a Python-based interface
AI in predicting COPD in the Canadian population
Coupling oscillations and switches in genetic networks
Robustness of expression pattern formation due to dynamic equilibrium in gap gene system of an early Drosophila embryo
Cognitive control and consciousness in open biological systems
Adaptive evolution of anti-predator ability promotes the diversity of prey species: Critical function analysis
Ecological boundaries in the context of hierarchy theory
Ca 2+ dysregulation in the endoplasmic reticulum related to Alzheimer's disease: A review on experimental progress and computational modeling
"Cylindrical worlds" in biology: Does the aggregation strategy give a selective advantage?
A cultured human neural network operates a robotic actuator
Decay of connection probabilities with distance in 2D and 3D neuronal networks
Scale-invariant dissipation underlies enzyme catalytic performance
Quantum-like modeling in biology with open quantum systems and instruments
Impacts of emergent structural topologies on the stability of an adaptive plant-animal network
Two coherent definitions of the life process derived from the half-chaos theory and the (unintentional) purposeful information theory
Uncovering dual oscillatory regimes in p53-mdm2 dynamics: A data-driven modeling approach with implications for cancer suppression
Using neurons to maintain autonomy: Learning from C. elegans
Models of genetic code structure evolution with variable number of coded labels
Design of accurate predictors for DNA-binding sites in proteins using hybrid SVM-PSSM method
Dynamical properties of LFPs from mice with unilateral injection of TeNT
Homeostatic plasticity improves signal propagation in continuous-time recurrent neural networks
Supercritical and subcritical Hopf-bifurcations in a two-delayed prey-predator system with density-dependent mortality of predator and strong Allee effect in prey
Characteristics of codon usage bias in two regions downstream of the initiation codons of foot-and-mouth disease virus
Changes in the fluctuation of the contraction rhythm of spontaneously beating cardiac myocytes in cultures with and without cardiac fibroblasts
Data-driven optimizations for model checking of multi-valued regulatory networks
Bipolar reasoning in feedback pathways
To swim or not to swim: A population-level model of Xenopus tadpole decision making and locomotor behaviour
Coloured fuzzy Petri nets for modelling and analysing membrane systems
Validation and discovery from computational biology models
Psychological 'double-slit experiment' in decision making: Quantum versus classical
On the use of multi-objective evolutionary algorithms for survival analysis
A novel generalized design methodology and realization of Boolean operations using DNA
Rule-based modelling of biological systems using regulated rewriting
Simulation of behavioral profiles in the plus-maze: A Classification and Regression Tree approach
3d-SPADE: Significance evaluation of spatio-temporal patterns of various temporal extents
Effects of replicative fitness on competing HIV strains
Managing bioengineering complexity with AI techniques
Tug-of-war model for the two-bandit problem: Nonlocally-correlated parallel exploration via resource conservation
Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game
A review of the methods for neuronal response latency estimation
Identification of potential targets in biological signalling systems through network perturbation analysis
The incorporation of epigenetics in artificial gene regulatory networks
Novel recurrent neural network for modelling biological networks: Oscillatory p53 interaction dynamics
Asynchronous spatial evolutionary games
Reinterpretation of Jagendorf's classic experiment on photophosphorylation
Modelling congenital transmission of Chagas' disease
Causal Modeling and Thermodynamics: Towards a new convergence of the two fields
Molecular dynamics simulation of a myosin subfragment-1 docking with an actin filament
Structural reduction of amino acid activating ribozyme KK13
Non-linear molecular pattern classification using molecular beacons with multiple targets
Escherichia coli autoinducer-2 uptake network does not display hysteretic behavior but AI-2 synthesis rate controls transient bifurcation
A possible mechanism for determining the directionality of myosin molecular motors
Density dependent neurodynamics
Opportunities in multiscale modeling of mosquito-borne flaviviruses
Inverse Bayesian inference as a key of consciousness featuring a macroscopic quantum logical structure
Freezing of gait in Parkinson's disease: Classification using computational intelligence
Identification of Ca2+ oscillations with the 0-1 test for periodic and chaotic time-series: One- and two-parameter bifurcations
Individual-based modelling of angiogenesis inside three-dimensional porous biomaterials
Revisiting Carl Jung's archetype theory a psychobiological approach
Gamma radiation-induced in vitro hormetic apogamy in the fern Pityrogramma calomelanos (L.) link
Modelling logistic growth by a new diffusion process: Application to biological systems
Congenital programs of the behavior and nontrivial quantum effects in the neurons work
Modularity in biological thought: Sketch of a unifying theoretical framework
Organization principles of biological networks: An explorative study
Simulating the folding of HP-sequences with a minimalist model in an inhomogeneous medium
Degeneracy allows for both apparent homogeneity and diversification in populations
The evolutionary dynamics of language
Dynamical behaviors and optimal harvesting of an intraguild prey-predator fishery model with Michaelis-Menten type predator harvesting
On the role of emotion in biological and robotic autonomy
Information about a form (on the dynamic laws of morphogenesis)
Emergence of robust regulatory motifs from in silico evolution of sustained oscillation
Covalent attachment of actin filaments to Tween 80 coated polystyrene beads for cargo transportation
Flux coupling analysis of metabolic networks is sensitive to missing reactions
Complex systems biology approach to understanding coordination of JAK-STAT signaling
Mean-reverting neuronal model based on two alternating patterns
The evolutionary dynamics of expectations: Interactions among codes in inter-human communications
Characterizing ISI and sub-threshold membrane potential distributions: Ensemble of IF neurons with random squared-noise intensity
Animal and human behavior to maximize energy income and to minimize its expenditure
The key role of the elongation factors in the origin of the organization of the genetic code
Why dengue and yellow fever coexist in some areas of the world and not in others?
Unitary circular code motifs in genomes of eukaryotes
Dynamic maternal gradients and morphogenetic networks in Drosophila early embryo
Ecosystem-based reservoir computing. Hypothesis paper
Origin of the temporal stability control of living system nonequilibrium
Modeling bacterial immune systems: Strategies for expression of toxic - but useful - molecules
Biomedical implications of information processing in chemical systems: Non-classical approach to photochemistry of coordination compounds
An energy landscape-based theoretical framework for understanding the self-organization of functions in a living system under the dynamical component interaction
Anticipation: Beyond synthetic biology and cognitive robotics
Phenomic prediction of maize hybrids
The impact of additional food on plankton dynamics in the absence and presence of toxicity
Integrated constraints based analysis of an engineered violacein pathway in Escherichia coli
Synchronization transitions induced by the fluctuation of adaptive coupling strength in delayed Newman-Watts neuronal networks
A hierarchical approach to model parameter optimization for developmental systems
A new fast algorithm for solving the minimum spanning tree problem based on DNA molecules computation
On architectures of circuits implemented in simulated Belousov-Zhabotinsky droplets
Metschnikowia bicuspidata in aquaculture: Pathogenesis, characteristics, and biocontrol approaches
Quantifying noise-induced stability of a cortical fast-spiking cell model with Kv3-channel-like current
Cholesterol-ester prevents lipoprotein core from solidifying: Molecular dynamics simulation
Modular assembling process of an in-silico protocell
Using lattice SIS epidemiological model with clustered treatment to investigate epidemic control
Dissipative scaling of development and aging in multicellular organisms
On the possibility of implementing a quantum entanglement distribution in a biosystem: Microtubules
The Neurobehavioral State hypothesis
Lynn Margulis and Boris Kozo-Polyansky: How the Symbiogenesis was translated from Russian
Monte Carlo simulation from proton slip to "coupled" proton flow in ATP synthase based on the bi-site mechanism
Evolutionary constraints or opportunities?
A new integrated symmetrical table for genetic codes
Gene regulatory networks in Drosophila early embryonic development as a model for the study of the temporal identity of neuroblasts
A computational model for telomere-dependent cell-replicative aging
Metabolic limits on classical information processing by biological cells
Drug scheduling of cancer chemotherapy based on natural actor-critic approach
The interplay between DNA damage and autophagy in lung cancer: A mathematical study
Three levels of information processing in the brain
Stages and causes of the evolution of language and consciousness: A theoretical reconstruction
A cellular mechanism for multi-robot construction via evolutionary multi-objective optimization of a gene regulatory network
Entropic particle transport in periodic channels
A Unified Holographic Framework for neural computation and consciousness: From lipid membranes to the Schumann resonance
Phi in physiology, psychology and biomechanics: The golden ratio between myth and science
The biological information flow: From cell theory to a new evolutionary synthesis
DNA approach to solve clustering problem based on a mutual order
Application of dynamic point process models to cardiovascular control
The dynamics of a Lotka-Volterra predator-prey model with state dependent impulsive harvest for predator
A study of indirect reciprocity involving a reputation system or a simple tag system in a one-shot, multi-player game
Continuum modeling of mechano-dependent reactions in tissues composed of mechanically active cells
Fixed charges in the gel matrix of sensor chips and dissociation in diffusion gradients influence the detection of fast protein-protein interactions
Systems theory, thermodynamics and life: Integrated thinking across ecology, organization and biological evolution
Systemic study of a natural feedback loop in Huntington's disease at the onset of neurodegeneration
Using radial basis function on the general form of Chou's pseudo amino acid composition and PSSM to predict subcellular locations of proteins with both single and multiple sites
Implications on visual apperception: Energy, duration, structure and synchronization
The origins of photosynthetic systems: Clues from the phosphorus and sulphur chemical scenarios
A metric space for semantic containment: Towards the implementation of genetic firewalls
Quantum aspects of the brain-mind relationship: A hypothesis with supporting evidence
Engineering cellulosic bioreactors by template assisted DNA shuffling and in vitro recombination (TADSir)
A model of autowave self-organization as a hierarchy of active media in the biological evolution
Quantifying pleiotropy through directed signaling networks: A synchronous Boolean network approach and in-silico pleiotropic scoring
Analysis of the initiation of viral infection under flow conditions with applications to transmission in feed
Traffic optimization in railroad networks using an algorithm mimicking an amoeba-like organism, Physarum plasmodium
The evolutionary dynamics of social systems - Looking for a new dialog
Spatiotemporal patterns provoked by environmental variability in a predator-prey model
Collective dynamics of a coupled Hindmarsh-Rose neurons with locally active memristor
COVID-19 spatio-temporal forecast in England
Unique features of nucleotide and codon usage patterns in mycoplasmas revealed by information entropy
Morphomechanics of Development. Lev V. Beloussov, Andrei Lipchinsky. Springer International Publishing, Cham, Heidelberg, New York, Dordrecht, London, 2015, xv+195 pp., ISBN 978-3-319-13989-0 (HB), ISBN 978-3-319-13990-6 (eBook), doi: 10.1007/978-3-319-13990-6
Integrate-and-fire network model of activity propagation from thalamus to cortex
Overview of the third special issue in code biology
A self adaptive hybrid enhanced artificial bee colony algorithm for continuous optimization problems
Protein-drug interactome analysis of SSRI-mediated neurorecovery following stroke
Fundamental, Quantitative Traits of the "Sociotype"
A theoretical steady state analysis indicates that induction of Escherichia coli glnALG operon can display all-or-none behavior
Qualitative, semi-quantitative, and quantitative simulation of the osmoregulation system in yeast
Quantifying the information transmitted in a single stimulus
Living cognition and the nature of organisms
Identification of dual-tropic HIV-1 using evolved neural networks
Unraveling power-law scaling through exponential cell division dynamics
A delay model for quorum sensing of Pseudomonas putida
Identifiability and online estimation of diagnostic parameters with in the glucose insulin homeostasis
Energy efficiency of information transmission by electrically coupled neurons
Kinetic analyses and mathematical modeling of primary photochemical and photoelectrochemical processes in plant photosystems
Evolving experience-dependent robust behaviour in embodied agents
The indispensable role of time in autonomous development
A biophysical approach to cancer dynamics: Quantum chaos and energy turbulence