yusuke1997/dblp-id-title huggingface dataset:
System modeling reveals the molecular mechanisms of HSC cell cycle alteration mediated by Maff and Egr3 under leukemia
Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium
Comparisons of Shewanella strains based on genome annotations, modeling, and experiments
Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer
Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures
Impact of receptor clustering on ligand binding
Systematic identifiability testing for unambiguous mechanistic modeling - application to JAK-STAT, MAP kinase, and NF-κB signaling pathway models
Drug combinatorics and side effect estimation on the signed human drug-target network
An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer
Molecular signatures for obesity and associated disorders identified through partial least square regression models
High-fidelity discrete modeling of the HPA axis: a study of regulatory plasticity in biology
The CD4+ T cell regulatory network mediates inflammatory responses during acute hyperinsulinemia: a simulation study
Stochastic modeling and simulation of reaction-diffusion system with Hill function dynamics
An Integrated Mathematical Model of Thrombin-, Histamine-and VEGF-Mediated Signalling in Endothelial Permeability
The logic of kinetic regulation in the thioredoxin system
Combinatorial motif analysis of regulatory gene expression in Mafb deficient macrophages
Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells
SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells
Identifying disease associated genes by network propagation
Identifying disease-specific genes based on their topological significance in protein networks
Simulating heterogeneous populations using Boolean models
Multitype Bellman-Harris branching model provides biological predictors of early stages of adult hippocampal neurogenesis
Comparing Alzheimer's and Parkinson's diseases networks using graph communities structure
Computational modelling elucidates the mechanism of ciliary regulation in health and disease
In silico metabolic network analysis of Arabidopsis leaves
Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators
Modelling phagosomal lipid networks that regulate actin assembly
Modeling miRNA-mRNA interactions: fitting chemical kinetics equations to microarray data
Topological effects of data incompleteness of gene regulatory networks
MICRAT: a novel algorithm for inferring gene regulatory networks using time series gene expression data
Agent-based simulation of reactions in the crowded and structured intracellular environment: Influence of mobility and location of the reactants
Searching for functional gene modules with interaction component models
Possible linkages between the inner and outer cellular states of human induced pluripotent stem cells
Spectral affinity in protein networks
Understanding key features of bacterial restriction-modification systems through quantitative modeling
13 C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose
Reconstructing cancer drug response networks using multitask learning
Genotype networks, innovation, and robustness in sulfur metabolism
Ordered structure of the transcription network inherited from the yeast whole-genome duplication
Inferring transcription factor collaborations in gene regulatory networks
Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria
Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae
Systems biology combining human- and animal-data miRNA and mRNA data identifies new targets in ureteropelvic junction obstruction
Uncovering distinct protein-network topologies in heterogeneous cell populations
Gene regulatory network analysis supports inflammation as a key neurodegeneration process in prion disease
Kinetic constraints on the sensitivity of large metabolic responses
Evidence of probabilistic behaviour in protein interaction networks
Flux balance analysis and its applications
Biological interaction networks are conserved at the module level
Towards quantitative metabolome analysis
Detection of protein complexes from affinity purification/mass spectrometry data
Systems biology approach reveals that overflow metabolism of acetate in Escherichia coli is triggered by carbon catabolite repression of acetyl-CoA synthetase
A circuit model of the temporal pattern generator of Caenorhabditis egg-laying behavior
Comparing biological networks via graph compression
On an ensemble algorithm for clustering cancer patient data
Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimization
SCNS: a graphical tool for reconstructing executable regulatory networks from single-cell genomic data
Bell-shaped and ultrasensitive dose-response in phosphorylation-dephosphorylation cycles: the role of kinase-phosphatase complex formation
Merging concepts - coupling an agent-based model of hematopoietic stem cells with an ODE model of granulopoiesis
A hierarchical approach employing metabolic and gene expression profiles to identify the pathways that confer cytotoxicity in HepG2 cells
Prediction of drugs having opposite effects on disease genes in a directed network
Dynamic simulations on the mitochondrial fatty acid Beta-oxidation network
SEQUOIA: significance enhanced network querying through context-sensitive random walk and minimization of network conductance
Bifurcation analysis informs Bayesian inference in the Hes1 feedback loop
The organization of domains in proteins obeys Menzerath-Altmann's law of language
Modelling biological systems from molecules to dynamical networks
Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases
Identifying Tmem59 related gene regulatory network of mouse neural stem cell from a compendium of expression profiles
SAVI: a statistical algorithm for variant frequency identification
Spatio-temporal modeling of signaling protein recruitment to EGFR
Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection
Predicting functional associations from metabolism using bi-partite network algorithms
Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions
Individualized therapy of HHT driven by network analysis of metabolomic profiles
Robust dynamic balance of AP-1 transcription factors in a neuronal gene regulatory network
Origin of structural difference in metabolic networks with respect to temperature
A new model to simulate and analyze proliferating cell populations in BrdU labeling experiments
Insights into the pathogenesis of axial spondyloarthropathy from network and pathway analysis
Noisy-threshold control of cell death
Biomolecular network querying: a promising approach in systems biology
Protein complex prediction based on k-connected subgraphs in protein interaction network
Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa
Pathway network inference from gene expression data
Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism
Inferring branching pathways in genome-scale metabolic networks
Modeling the ascorbate-glutathione cycle in chloroplasts under light/dark conditions
Erratum to: A novel mathematical model of ATM/p53/NF-κB pathways points to the importance of the DDR switch-off mechanisms
SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks
Efficient characterization of high-dimensional parameter spaces for systems biology
Combinatorial regulation of transcription factors and microRNAs
Modelling biochemical networks with intrinsic time delays: a hybrid semi-parametric approach
Weighted Interaction SNP Hub (WISH) network method for building genetic networks for complex diseases and traits using whole genome genotype data
Genomic distance entrained clustering and regression modelling highlights interacting genomic regions contributing to proliferation in breast cancer
Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
Genetic and environmental pathways to complex diseases
MORO: a Cytoscape app for relationship analysis between modularity and robustness in large-scale biological networks
Sets2Networks: network inference from repeated observations of sets
Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data
Integrating external biological knowledge in the construction of regulatory networks from time-series expression data
A method for inverse bifurcation of biochemical switches: inferring parameters from dose response curves
Cellular network modeling and single cell gene expression analysis reveals novel hepatic stellate cell phenotypes controlling liver regeneration dynamics
Hybrid optimization for 13 C metabolic flux analysis using systems parametrized by compactification
SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences
Statistical aspects of omics data analysis using the random compound covariate
Environmental versatility promotes modularity in genome-scale metabolic networks
Boolean network modeling of β-cell apoptosis and insulin resistance in type 2 diabetes mellitus
Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE
Bridging the gap between gene expression and metabolic phenotype via kinetic models
Coordinated regulation of acid resistance in Escherichia coli
A simple work flow for biologically inspired model reduction - application to early JAK-STAT signaling
Evolutionary conservation and over-representation of functionally enriched network patterns in the yeast regulatory network
Structural identifiability of cyclic graphical models of biological networks with latent variables
Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms
Generalized method of moments for estimating parameters of stochastic reaction networks
Navigational control of bacteria: the design of a synthetic chemotactic biological system
Network topology of NaV1.7 mutations in sodium channel-related painful disorders
Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate
RACIPE: a computational tool for modeling gene regulatory circuits using randomization
Using the protein interaction network to predict protein folds without homology
Three factors underlying incorrect in silico predictions of essential metabolic genes
Facile: a command-line network compiler for systems biology
Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics
Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis
Microbial community pattern detection in human body habitats via ensemble clustering framework
Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network
Knowledge based identification of essential signaling from genome-scale siRNA experiments
A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases
Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3
Efficient mining gapped sequential patterns for motifs in biological sequences
Extracting proteins involved in disease progression using temporally connected networks
BBH-LS: an algorithm for computing positional homologs using sequence and gene context similarity
Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum
Multiple types of data are required to identify the mechanisms influencing the spatial expansion of melanoma cell colonies
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1
Blood flow controls coagulation onset via the positive feedback of factor VII activation by factor Xa
Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi
The NetBuilder' project: development of a tool for constructing, simulating, evolving, and analysing complex regulatory networks
A comprehensive network and pathway analysis of candidate genes in major depressive disorder
Modelling gradient perception and polarization in chemotaxing Dictyostelium cells
Evaluating diabetes and hypertension disease causality using mouse phenotypes
The systems biology simulation core algorithm
NUP155 insufficiency recalibrates a pluripotent transcriptome with network remodeling of a cardiogenic signaling module
Gene Ontology Function prediction in Mollicutes using Protein-Protein Association Networks
Integration of SABIO-RK in workbenches for kinetic model design
Composite mathematical modeling of calcium signaling behind neuronal cell death in Alzheimer's disease
Arena3D: visualization of biological networks in 3D
Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche
A hotspots analysis-relation discovery representation model for revealing diabetes mellitus and obesity
Mimoza: web-based semantic zooming and navigation in metabolic networks
How neurons migrate: a dynamic in-silico model of neuronal migration in the developing cortex
Informed walks: whispering hints to gene hunters inside networks' jungle
Binding site locations and interaction of the isolated middle loop of snake neurotoxin I with muscle type nicotinic acetylcholine receptor: molecular dynamics and docking simulation study
Regulation of ERK-MAPK signaling in human epidermis
cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks
ppiPre: predicting protein-protein interactions by combining heterogeneous features
Integrating many co-splicing networks to reconstruct splicing regulatory modules
FGsub: Fusarium graminearum protein subcellular localizations predicted from primary structures
The Cell Collective: Toward an open and collaborative approach to systems biology
Deducing corticotropin-releasing hormone receptor type 1 signaling networks from gene expression data by usage of genetic algorithms and graphical Gaussian models
Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT
A novel index of protein-protein interface propensity improves interface residue recognition
Bioinformatic analysis of proteomics data
Similar temperature dependencies of glycolytic enzymes: an evolutionary adaptation to temperature dynamics?
Exploring the genetic control of glycolytic oscillations in Saccharomyces Cerevisiae
IntPath-an integrated pathway gene relationship database for model organisms and important pathogens
Unearthing the transition rates between photoreceptor conformers
Stabilization of perturbed Boolean network attractors through compensatory interactions
Characterization the regulation of herpesvirus miRNAs from the view of human protein interaction network
RaTrav: a tool for calculating mean first-passage times on biochemical networks
Quantifying uncertainty, variability and likelihood for ordinary differential equation models
Predictive integration of gene functional similarity and co-expression defines treatment response of endothelial progenitor cells
Bacterial social interactions drive the emergence of differential spatial colony structures
Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics and instationary 13 C flux analysis
Invariance and plasticity in the Drosophila melanogaster metabolomic network in response to temperature
Sex differences in hepatic one-carbon metabolism
Complex regulation of Hsf1-Skn7 activities by the catalytic subunits of PKA in Saccharomyces cerevisiae: experimental and computational evidences
Models for synthetic biology
Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study
Promoter activity dynamics in the lag phase of Escherichia coli
Joint clustering of protein interaction networks through Markov random walk
Determining and interpreting correlations in lipidomic networks found in glioblastoma cells
A quantitative model for the GCN4 translational control in Saccharomyces cerevisiae
A networks method for ranking microRNA dysregulation in cancer
Toward modular biological models: defining analog modules based on referent physiological mechanisms
Computational prediction of the human-microbial oral interactome
Confidence from uncertainty - A multi-target drug screening method from robust control theory
A quantitative estimation of the global translational activity in logarithmically growing yeast cells
targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis
The potential for non-adaptive origins of evolutionary innovations in central carbon metabolism
The hierarchical organization of natural protein interaction networks confers self-organization properties on pseudocells
Towards metabolic networks phylogeny using Petri Net-based expansional analysis
Towards understanding brain-gut-microbiome connections in Alzheimer's disease
Distinct metabolic responses of an ovarian cancer stem cell line
Noise and crosstalk in two quorum-sensing inputs of Vibrio fischeri
Computational cell model based on autonomous cell movement regulated by cell-cell signalling successfully recapitulates the "inside and outside" pattern of cell sorting
Analyzing negative feedback using a synthetic gene network expressed in the Drosophila melanogaster embryo
Set theoretical and algebraic model for redundancies in the genetic code
Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii
Molecular association of pathogenetic contributors to pre-eclampsia (pre-eclampsia associome)
A model of estrogen-related gene expression reveals non-linear effects in transcriptional response to tamoxifen
Metabolic flux analysis to study the production of a non-ribosomal lipopeptide, CDA, by Streptomyces coelicolor
A retrosynthetic biology approach to metabolic pathway design for therapeutic production
Morphogengineering roots: comparing mechanisms of morphogen gradient formation
Computational modeling of the cell-autonomous mammalian circadian oscillator
Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls
In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems
Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO
Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma
Molecular dynamics simulations studies of aurein 1.2 analogs in water and TFE/water
Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling
Global analysis of phase locking in gene expression during cell cycle: the potential in network modeling
A strategy to study pathway cross-talks of cells under repetitive exposure to stimuli
A systems biology approach to identify effective cocktail drugs
Parameter estimation of dynamic biological network models using integrated fluxes
Hematopoietic differentiation: a coordinated dynamical process towards attractor stable states
Dynamic modelling of microRNA regulation during mesenchymal stem cell differentiation
Shrunken methodology to genome-wide SNPs selection and construction of SNPs networks
petal: Co-expression network modelling in R
Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes
Stress induced telomere shortening: longer life with less mutations?
Quantitative modeling and analytic assessment of the transcription dynamics of the XlnR regulon in Aspergillus niger
KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems
Quantitative analysis of intracellular communication and signaling errors in signaling networks
Incorporating genomic, transcriptomic and clinical data: a prognostic and stem cell-like MYC and PRC imbalance in high-risk neuroblastoma
Development of an in silico method for the identification of subcomplexes involved in the biogenesis of multiprotein complexes in Saccharomyces cerevisiae
Understanding and predicting synthetic lethal genetic interactions in Saccharomyces cerevisiae using domain genetic interactions
Identifying novel glioma associated pathways based on systems biology level meta-analysis
Functional clustering of time series gene expression data by Granger causality
Metabolic modeling predicts metabolite changes in Mycobacterium tuberculosis
DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems
Unraveling functional networks: does gene clustering have a meaning?
Progression of oral carcinomas revealed by spectral reordering of a bipartite graph
Quantitative analysis of insulin-like growth factor 2 receptor and insulin-like growth factor binding proteins to identify control mechanisms for insulin-like growth factor 1 receptor phosphorylation
Dynamics and Control of the Central Carbon Metabolism in Hepatoma Cells
Hybrid modeling of biological networks: mixing temporal and qualitative biological properties
Thermodynamically consistent model calibration in chemical kinetics
Pharmacokinetics and pharmacodynamics of VEGF-neutralizing antibodies
Network evaluation from the consistency of the graph structure with the measured data
Evolvability of feed-forward loop architecture biases its abundance in transcription networks
System size reduction in stochastic simulations of the facilitated diffusion mechanism
From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data
Systems biology of the structural proteome
Analytical approximations for the amplitude and period of a relaxation oscillator
Systems biology applied to vaccine and immunotherapy development
Sig2GRN: a software tool linking signaling pathway with gene regulatory network for dynamic simulation
A unified frame of predicting side effects of drugs by using linear neighborhood similarity
Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces Cerevisiae
The plasticity of TGF-β signaling
Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052
The relationship between stochastic and deterministic quasi-steady state approximations
Docking study on mammalian CTR1 copper importer motifs
Inhibition of the interactions between eosinophil cationic protein and airway epithelial cells by traditional Chinese herbs
Dysregulation of the vascular endothelial growth factor and semaphorin ligand-receptor families in prostate cancer metastasis
Decrease of energy spilling in Escherichia coli continuous cultures with rising specific growth rate and carbon wasting
Putative human sperm Interactome: a networks study
Cloud computing and validation of expandable in silico livers
Incorporating prior knowledge improves detection of differences in bacterial growth rate
Stringent DDI-based Prediction of H. sapiens-M. tuberculosis H37Rv Protein-Protein Interactions
Estimation of diffusion constants from single molecular measurement without explicit tracking
A computational procedure for identifying master regulator candidates: a case study on diabetes progression in Goto-Kakizaki rats