yusuke1997/dblp-id-title huggingface dataset:
Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans
Formation of VEGF isoform-specific spatial distributions governing angiogenesis: computational analysis
Non-stationary 13 C metabolic flux analysis of Chinese hamster ovary cells in batch culture using extracellular labeling highlights metabolic reversibility and compartmentation
Genetic studies of complex human diseases: Characterizing SNP-disease associations using Bayesian networks
A Cys-capping motif unique to small leucine-rich repeat proteins and proteoglycans of the extracellular matrix
Inferring a transcriptional regulatory network of the cytokinesis-related genes by network component analysis
Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy
Extinction, coexistence, and localized patterns of a bacterial population with contact-dependent inhibition
Prior knowledge guided active modules identification: an integrated multi-objective approach
Is RNA-dependent RNA polymerase essential for transposon control?
Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis
Energy metabolism and glutamate-glutamine cycle in the brain: a stoichiometric modeling perspective
Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and disease genes
Gene networks associated with conditional fear in mice identified using a systems genetics approach
Comprehensive proteomic analysis of bovine spermatozoa of varying fertility rates and identification of biomarkers associated with fertility
High-dimensional omics data analysis using a variable screening protocol with prior knowledge integration (SKI)
Mathematical modeling and analysis of insulin clearance in vivo
Determining modular organization of protein interaction networks by maximizing modularity density
Boolean ErbB network reconstructions and perturbation simulations reveal individual drug response in different breast cancer cell lines
A metabolite-centric view on flux distributions in genome-scale metabolic models
Understanding system dynamics of an adaptive enzyme network from globally profiled kinetic parameters
An improved method for functional similarity analysis of genes based on Gene Ontology
A link prediction approach to cancer drug sensitivity prediction
Modeling the NF-κB mediated inflammatory response predicts cytokine waves in tissue
Interspecies gene function prediction using semantic similarity
Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation
Structured sparse CCA for brain imaging genetics via graph OSCAR
Understanding network concepts in modules
A method for determining the robustness of bio-molecular oscillator models
Compartmentation of glycogen metabolism revealed from 13 C isotopologue distributions
A mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions
Systemic remodeling of the redox regulatory network due to RNAi perturbations of glutaredoxin 1, thioredoxin 1, and glucose-6-phosphate dehydrogenase
Network-based logistic regression integration method for biomarker identification
Analysing GCN4 translational control in yeast by stochastic chemical kinetics modelling and simulation
How yeast re-programmes its transcriptional profile in response to different nutrient impulses
A protein network-guided screen for cell cycle regulators in Drosophila
Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms
Single-molecule modeling of mRNA degradation by miRNA: Lessons from data
Systems analysis of iron metabolism: the network of iron pools and fluxes
rHVDM - a fast and user-friendly R package to predict transcription factor targets from microarray time series data
The zipper mechanism in phagocytosis: energetic requirements and variability in phagocytic cup shape
BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features
Systematic quantitative characterization of cellular responses induced by multiple signals
Phenotype prediction from genome-wide association studies: application to smoking behaviors
The whole-organism heavy chain B cell repertoire from Zebrafish self-organizes into distinct network features
Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects
Characterizing dynamic regulatory programs in mouse lung development and their potential association with tumourigenesis via miRNA-TF-mRNA circuits
A bioinformatics approach reveals novel interactions of the OVOL transcription factors in the regulation of epithelial - mesenchymal cell reprogramming and cancer progression
A comprehensive map of the influenza A virus replication cycle
DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression
Inferring causal genomic alterations in breast cancer using gene expression data
GridCell: a stochastic particle-based biological system simulator
Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite
From desk to bed: Computational simulations provide indication for rheumatoid arthritis clinical trials
Arsenic biosenseor: a step further
DBAC: A simple prediction method for protein binding hot spots based on burial levels and deeply buried atomic contacts
New tools for self-organized pattern formation
Gene regulatory network underlying the immortalization of epithelial cells
Markov State Models of gene regulatory networks
Structurally robust biological networks
A Bayesian framework for integrating genomic data to aid function prediction
Predicting protein-binding regions in RNA using nucleotide profiles and compositions
Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient
A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors
Rule-based regulatory and metabolic model for Quorum sensing in P. aeruginosa
Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1
Predicting protein complex in protein interaction network - a supervised learning based method
The phenotype control kernel of a biomolecular regulatory network
An optimally evolved connective ratio of neural networks that maximizes the occurrence of synchronized bursting behavior
Modelling human protein interaction networks as metric spaces has potential in disease research and drug target discovery
A predictive computational model of the kinetic mechanism of stimulus-induced transducer methylation and feedback regulation through CheY in archaeal phototaxis and chemotaxis
Hypoxia-dependent sequestration of an oxygen sensor by a widespread structural motif can shape the hypoxic response - a predictive kinetic model
Constructing a gene semantic similarity network for the inference of disease genes
Dynamic optimization of distributed biological systems using robust and efficient numerical techniques
Metabolic network visualization eliminating node redundance and preserving metabolic pathways
BRCA-Monet: a breast cancer specific drug treatment mode-of-action network for treatment effective prediction using large scale microarray database
Counting motifs in dynamic networks
Rational design of 13 C-labeling experiments for metabolic flux analysis in mammalian cells
Construction of a large scale integrated map of macrophage pathogen recognition and effector systems
Brownian diffusion of AMPA receptors is sufficient to explain fast onset of LTP
Kinetic modelling of phospholipid synthesis in Plasmodium knowlesi unravels crucial steps and relative importance of multiple pathways
Global dynamic optimization approach to predict activation in metabolic pathways
Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance
Constraints on signaling network logic reveal functional subgraphs on Multiple Myeloma OMIC data
A simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network
Compound stress response in stomatal closure: a mathematical model of ABA and ethylene interaction in guard cells
Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation
A proof for loop-law constraints in stoichiometric metabolic networks
Optimal drug combinations and minimal hitting sets
Anti-TNF- αtreatment-related pathways and biomarkers revealed by transcriptome analysis in Chinese psoriasis patients
Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems
A method for efficient Bayesian optimization of self-assembly systems from scattering data
Designing a parallel evolutionary algorithm for inferring gene networks on the cloud computing environment
Validation of a model of the GAL regulatory system via robustness analysis of its bistability characteristics
A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle
GeneTopics - interpretation of gene sets via literature-driven topic models
Glioma cell fate decisions mediated by Dll1-Jag1-Fringe in Notch1 signaling pathway
Long-term prediction of fish growth under varying ambient temperature using a multiscale dynamic model
The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism
mRNA stability and the unfolding of gene expression in the long-period yeast metabolic cycle
A physarum-inspired prize-collecting steiner tree approach to identify subnetworks for drug repositioning
Degeneration of penicillin production in ethanol-limited chemostat cultivations of Penicillium chrysogenum: A systems biology approach
Reconstruction and analysis of a genome-scale metabolic model of the oleaginous fungus Mortierella alpina
Evolution of context dependent regulation by expansion of feast/famine regulatory proteins
A conceptual cellular interaction model of left ventricular remodelling post-MI: dynamic network with exit-entry competition strategy
A sequence-based method to predict the impact of regulatory variants using random forest
Prediction of protein interaction types based on sequence and network features
Superpixel-based segmentation of muscle fibers in multi-channel microscopy
An enzyme-centric approach for modelling non-linear biological complexity
Increased robustness of early embryogenesis through collective decision-making by key transcription factors
Multi-objective optimization framework to obtain model-based guidelines for tuning biological synthetic devices: an adaptive network case
Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico
Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network
The synthetic histone-binding regulator protein PcTF activates interferon genes in breast cancer cells
Meta-analysis of estrogen response in MCF-7 distinguishes early target genes involved in signaling and cell proliferation from later target genes involved in cell cycle and DNA repair
Automated Bayesian model development for frequency detection in biological time series
Modeling cardiac β-adrenergic signaling with normalized-Hill differential equations: comparison with a biochemical model
Characterization of aberrant pathways across human cancers
Cooperative binding mitigates the high-dose hook effect
Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling
Flux Design: In silico design of cell factories based on correlation of pathway fluxes to desired properties
Signal duration and the time scale dependence of signal integration in biochemical pathways
Metabolic modeling of a chronic wound biofilm consortium predicts spatial partitioning of bacterial species
A correction method for systematic error in 1 H-NMR time-course data validated through stochastic cell culture simulation
Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways
Data mining techniques in a CGH-based breast cancer subtype profiling: an immune perspective with comparative study
Integrating transcriptomics and metabonomics to unravel modes-of-action of 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin (TCDD) in HepG2 cells
Registry of BioBricks models using CellML
Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures
Metabolic modeling and response surface analysis of an Escherichia coli strain engineered for shikimic acid production
A data integration approach for cell cycle analysis oriented to model simulation in systems biology
Correction to: MISC: missing imputation for single-cell RNA sequencing data
Towards a mathematical model of the cAMP pathway in S. cerevisiae
SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks
Essential operating principles for tumor spheroid growth
The effects of protein interactions, gene essentiality and regulatory regions on expression variation
Gene expression profiles and signaling mechanisms in α2B-adrenoceptor-evoked proliferation of vascular smooth muscle cells
Modeling RNA interference in mammalian cells
Systematic identification of an integrative network module during senescence from time-series gene expression
Integrated Weighted Gene Co-expression Network Analysis with an Application to Chronic Fatigue Syndrome
Network signatures link hepatic effects of anti-diabetic interventions with systemic disease parameters
Quartet-based methods to reconstruct phylogenetic networks
QSurface: fast identification of surface expression markers in cancers
Mathematical modelling of multi-site protein-ligand interactions
Nuclear Factor kappa B is central to Marek's Disease herpesvirus induced neoplastic transformation of CD30 expressing lymphocytes in-vivo
Elementary signaling modes predict the essentiality of signal transduction network components
Opening up the blackbox: an interpretable deep neural network-based classifier for cell-type specific enhancer predictions
How informative is your kinetic model?: using resampling methods for model invalidation
Global insights into energetic and metabolic networks in Rhodobacter sphaeroides
Efficient, sparse biological network determination
Catabolic efficiency of aerobic glycolysis: The Warburg effect revisited
Systematic variations associated with renal disease uncovered by parallel metabolomics of urine and serum
URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries
Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory
Identification of AMP-activated protein kinase targets by a consensus sequence search of the proteome
Positive regulation of Rho GTPase activity by RhoGDIs as a result of their direct interaction with GAPs
A systems biology analysis of brain microvascular endothelial cell lipotoxicity
An integrative approach for measuring semantic similarities using gene ontology
Consensus and conflict cards for metabolic pathway databases
Genome-wide meta-analysis of genetic susceptible genes for Type 2 Diabetes
Intra-relation reconstruction from inter-relation: miRNA to gene expression
Analysis of global control of Escherichia coli carbohydrate uptake
Modelling genetic regulatory networks from specified behaviours
Mathematical modeling of the dynamic storage of iron in ferritin
Identification of reaction organization patterns that naturally cluster enzymatic transformations
Prediction of signaling cross-talks contributing to acquired drug resistance in breast cancer cells by Bayesian statistical modeling
Improving the EFMs quality by augmenting their representativeness in LP methods
An algorithm for the reduction of genome-scale metabolic network models to meaningful core models
Quantitative evaluation and reversion analysis of the attractor landscapes of an intracellular regulatory network for colorectal cancer
iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network
RMBNToolbox: random models for biochemical networks
SABIO-RK: a database for biochemical reactions and their kinetics
Mechanism of PP2A-mediated IKKβ dephosphorylation: a systems biological approach
Identifying model error in metabolic flux analysis - a generalized least squares approach
Functional pathway mapping analysis for hypoxia-inducible factors
Roles of the creatine kinase system and myoglobin in maintaining energetic state in the working heart
Modeling the dependence of respiration and photosynthesis upon light, acetate, carbon dioxide, nitrate and ammonium in Chlamydomonas reinhardtii using design of experiments and multiple regression
Systematic Comparison of C3 and C4 Plants Based on Metabolic Network Analysis
Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network
DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference
Deterministic mathematical models of the cAMP pathway in Saccharomyces cerevisiae
Transcription profiling of lung adenocarcinomas of c-myc-transgenic mice: Identification of the c-myc regulatory gene network
An agent-based model of the Notch signaling pathway elucidates three levels of complexity in the determination of developmental patterning
A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule"
Topology of molecular interaction networks
Leveraging syntactic and semantic graph kernels to extract pharmacokinetic drug drug interactions from biomedical literature
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2
TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks
Ultrasensitive Responses and Specificity in Cell Signaling
The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways
Modeling biological systems with uncertain kinetic data using fuzzy continuous Petri nets
Tav4SB: integrating tools for analysis of kinetic models of biological systems
Statistical methods on detecting differentially expressed genes for RNA-seq data
Tracing dynamic biological processes during phase transition
A flexible view of metabolic network
Impact of kinetic isotope effects in isotopic studies of metabolic systems
Spatiotemporal modeling of microbial metabolism
A transcriptional analysis of carotenoid, chlorophyll and plastidial isoprenoid biosynthesis genes during development and osmotic stress responses in Arabidopsis thaliana
Exploring molecular backgrounds of quality traits in rice by predictive models based on high-coverage metabolomics
The role of noise and positive feedback in the onset of autosomal dominant diseases
Source and regulation of flux variability in Escherichia coli
Computational analysis of the roles of ER-Golgi network in the cell cycle
Metabolic pathway alignment between species using a comprehensive and flexible similarity measure
Mathematical analysis of the regulation of competing methyltransferases
Modelling the influence of dimerisation sequence dissimilarities on the auxin signalling network
Systematic reconstruction of TRANSPATH data into Cell System Markup Language
Polytomy identification in microbial phylogenetic reconstruction
A Boolean probabilistic model of metabolic adaptation to oxygen in relation to iron homeostasis and oxidative stress
The Arabidopsis phytohormone crosstalk network involves a consecutive metabolic route and circular control units of transcription factors that regulate enzyme-encoding genes
MDD-carb: a combinatorial model for the identification of protein carbonylation sites with substrate motifs
Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks
A geometric method for contour extraction of Drosophila embryos
Correction to: Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone
A novel function prediction approach using protein overlap networks
Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae
Strong negative self regulation of Prokaryotic transcription factors increases the intrinsic noise of protein expression
Prioritization of disease microRNAs through a human phenome-microRNAome network
ANDSystem: an Associative Network Discovery System for automated literature mining in the field of biology
On cycles in the transcription network of Saccharomyces cerevisiae
SParSE++: improved event-based stochastic parameter search
Dynamic morphometric characterization of local connective tissue network structure in humans using ultrasound
Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow
Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case
Detecting cellular reprogramming determinants by differential stability analysis of gene regulatory networks
Conditional random field approach to prediction of protein-protein interactions using domain information
Modeling the effector - regulatory T cell cross-regulation reveals the intrinsic character of relapses in Multiple Sclerosis
Noise characteristics of interlocked repressilators
Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network
Nanog induced intermediate state in regulating stem cell differentiation and reprogramming
OptFlux: an open-source software platform for in silico metabolic engineering
Efficiency of complex production in changing environment
An integrative approach to inferring biologically meaningful gene modules
Erratum to: 'Conditional robustness analysis for fragility discovery and target identification in biochemical networks and in cancer systems biology'
Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits
PPSampler2: Predicting protein complexes more accurately and efficiently by sampling
Cellular automaton-based model for radiation-induced bystander effects
Bayesian parameter estimation for nonlinear modelling of biological pathways
The role of actin in capacitation-related signaling: an in silico and in vitro study
The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes
Reconstruction of gene networks using prior knowledge
Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae
The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression
Mathematical modeling of left ventricular dimensional changes in mice during aging
miRNA-regulated dynamics in circadian oscillator models
Investigation of anti-cancer mechanisms by comparative analysis of naked mole rat and rat
SEEK: a systems biology data and model management platform
Theoretical basis of the community effect in development
Improved protein-protein interactions prediction via weighted sparse representation model combining continuous wavelet descriptor and PseAA composition
Tracing regulatory routes in metabolism using generalised supply-demand analysis
Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity
A 3D multiscale model of cancer stem cell in tumor development
Detection of type 2 diabetes related modules and genes based on epigenetic networks
Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis
Short linear motifs in intrinsically disordered regions modulate HOG signaling capacity
Specialized or flexible feed-forward loop motifs: a question of topology