yusuke1997/dblp-id-title huggingface dataset:
Detecting causality from short time-series data based on prediction of topologically equivalent attractors
Synthesizing genetic sequential logic circuit with clock pulse generator
Parameter optimization in S-system models
A trigger model of apoptosis induced by tumor necrosis factor signaling
Systematic design methodology for robust genetic transistors based on I/O specifications via promoter-RBS libraries
Nonlinear regulation enhances the phenotypic expression of trans-acting genetic polymorphisms
Extending rule-based methods to model molecular geometry and 3D model resolution
Optimal projection method determination by Logdet Divergence and perturbed von-Neumann Divergence
Information flow during gene activation by signaling molecules: ethylene transduction in Arabidopsis cells as a study system
Thermodynamically constrained steady state solution space of the E. coli metabolic network
Computational modeling of apoptotic signaling pathways induced by cisplatin
Classification of transient behaviours in a time-dependent toggle switch model
A novel approach to minimize false discovery rate in genome-wide data analysis
An effective method for refining predicted protein complexes based on protein activity and the mechanism of protein complex formation
Towards embedding Caco-2 model of gut interface in a microfluidic device to enable multi-organ models for systems biology
FlexFlux: combining metabolic flux and regulatory network analyses
Edelfosine-induced metabolic changes in cancer cells that precede the overproduction of reactive oxygen species and apoptosis
Receptor downregulation and desensitization enhance the information processing ability of signalling receptors
Computational drug repositioning through heterogeneous network clustering
A systematic survey of centrality measures for protein-protein interaction networks
70ProPred: a predictor for discovering sigma70 promoters based on combining multiple features
Dynamic optimization of biological networks under parametric uncertainty
Protein functional properties prediction in sparsely-label PPI networks through regularized non-negative matrix factorization
Drug-drug relationship based on target information: application to drug target identification
Coordinations between gene modules control the operation of plant amino acid metabolic networks
Solving the chemical master equation using sliding windows
Incremental parameter estimation of kinetic metabolic network models
Modeling of human factor Va inactivation by activated protein C
Analysis of Wnt signaling β-catenin spatial dynamics in HEK293T cells
Estimation of feasible solution space using Cluster Newton Method: application to pharmacokinetic analysis of irinotecan with physiologically-based pharmacokinetic models
Proteomic patterns of cervical cancer cell lines, a network perspective
GraphAlignment: Bayesian pairwise alignment of biological networks
Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments
Targeted protein depletion in Saccharomyces cerevisiae by activation of a bidirectional degron
Simulations of pattern dynamics for reaction-diffusion systems via SIMULINK
Translation of SBGN maps: Process Description to Activity Flow
Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach
Parameter estimation and determinability analysis applied to Drosophila gap gene circuits
Information theoretical quantification of cooperativity in signalling complexes
Stochastic simulation and analysis of biomolecular reaction networks
A global sensitivity analysis approach for morphogenesis models
A simple method for identifying parameter correlations in partially observed linear dynamic models
A plausible mechanism for auxin patterning along the developing root
Multi-omics integration reveals molecular networks and regulators of psoriasis
Screening lifespan-extending drugs in Caenorhabditis elegans via label propagation on drug-protein networks
Noise propagation through extracellular signaling leads to fluctuations in gene expression
Signaling dynamics of palmitate-induced ER stress responses mediated by ATF4 in HepG2 cells
Identification of estrogen responsive genes using esophageal squamous cell carcinoma (ESCC) as a model
Hybrid metabolic flux analysis: combining stoichiometric and statistical constraints to model the formation of complex recombinant products
How to schedule VEGF and PD-1 inhibitors in combination cancer therapy?
Integration of breast cancer gene signatures based on graph centrality
Domain-specific model selection for structural identification of the Rab5-Rab7 dynamics in endocytosis
Inferring protein domains associated with drug side effects based on drug-target interaction network
Sexually-dimorphic targeting of functionally-related genes in COPD
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions
The genetic control of growth rate: a systems biology study in yeast
Computational modelling of the regulation of Insulin signalling by oxidative stress
A module-based analytical strategy to identify novel disease-associated genes shows an inhibitory role for interleukin 7 Receptor in allergic inflammation
Towards a genome-scale kinetic model of cellular metabolism
Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs
Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network
Network-dosage compensation topologies as recurrent network motifs in natural gene networks
Global transcription regulation of RK2 plasmids: a case study in the combined use of dynamical mathematical models and statistical inference for integration of experimental data and hypothesis exploration
Visualizing post genomics data-sets on customized pathway maps by ProMeTra - aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example
The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles
An integer optimization algorithm for robust identification of non-linear gene regulatory networks
Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes
Gene regulatory networks in lactation: identification of global principles using bioinformatics
A continuous-time adaptive particle filter for estimations under measurement time uncertainties with an application to a plasma-leucine mixed effects model
Modeling the Calvin-Benson cycle
In silico modeling for tumor growth visualization
An editor for pathway drawing and data visualization in the Biopathways Workbench
Topology analysis and visualization of Potyvirus protein-protein interaction network
Potential metabolic mechanism of girls' central precocious puberty: a network analysis on urine metabonomics data
ExprEssence - Revealing the essence of differential experimental data in the context of an interaction/regulation net-work
AMBIENT: Active Modules for Bipartite Networks - using high-throughput transcriptomic data to dissect metabolic response
A computational model of PKD and CERT interactions at the trans-Golgi network of mammalian cells
ncRNA-disease association prediction based on sequence information and tripartite network
Exploring molecular links between lymph node invasion and cancer prognosis in human breast cancer
Exploring causal networks underlying fat deposition and muscularity in pigs through the integration of phenotypic, genotypic and transcriptomic data
Spice: discovery of phenotype-determining component interplays
Elucidating the mechanisms of cooperative calcium-calmodulin interactions: a structural systems biology approach
Comparison on extreme pathways reveals nature of different biological processes
A simple principle concerning the robustness of protein complex activity to changes in gene expression
Gene co-citation networks associated with worker sterility in honey bees
Anti-inflammatory effects of reactive oxygen species - a multi-valued logical model validated by formal concept analysis
Multi-level reproducibility of signature hubs in human interactome for breast cancer metastasis
Multistate Model Builder (MSMB): a flexible editor for compact biochemical models
Inferring extrinsic noise from single-cell gene expression data using approximate Bayesian computation
A computational framework for complex disease stratification from multiple large-scale datasets
BTNET : boosted tree based gene regulatory network inference algorithm using time-course measurement data
Combined logical and data-driven models for linking signalling pathways to cellular response
A mathematical model to estimate cholesterylester transfer protein (CETP) triglycerides flux in human plasma
Individual fates of mesenchymal stem cells in vitro
Genome-scale analysis of the high-efficient protein secretion system of Aspergillus oryzae
Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study
Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension
PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from H-Invitational protein-protein interactions integrative dataset
Fixation probability of a beneficial mutation conferring decreased generation time in changing environments
Information processing in the transcriptional regulatory network of yeast: Functional robustness
Network target for screening synergistic drug combinations with application to traditional Chinese medicine
Predicting internal cell fluxes at sub-optimal growth
DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases
Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth
Network features suggest new hepatocellular carcinoma treatment strategies
Noise-induced switches in network systems of the genetic toggle switch
Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions
Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds
Bioprocess data mining using regularized regression and random forests
A quantitative approach to study indirect effects among disease proteins in the human protein interaction network
Function and design of the Nox1 system in vascular smooth muscle cells
Cell functional enviromics: Unravelling the function of environmental factors
An information-flow-based model with dissipation, saturation and direction for active pathway inference
Good practice guidelines for biomarker discovery from array data: a case study for breast cancer prognosis
Gene and isoform expression signatures associated with tumor stage in kidney renal clear cell carcinoma
Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters
Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production
Biochemical fluctuations, optimisation and the linear noise approximation
Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone
cGRNB: a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets
Model composition through model reduction: a combined model of CD95 and NF-κ
Modeling of leishmaniasis infection dynamics: novel application to the design of effective therapies
Construction and analysis of the protein-protein interaction network related to essential hypertension
Identification of gene interactions associated with disease from gene expression data using synergy networks
Computational inference and analysis of genetic regulatory networks via a supervised combinatorial-optimization pattern
Differential enrichment of regulatory motifs in the composite network of protein-protein and gene regulatory interactions
In-silico comparison of two induction regimens (7 + 3 vs 7 + 3 plus additional bone marrow evaluation) in acute myeloid leukemia treatment
Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer
Effects of unpaired 1 gene overexpression on the lifespan of Drosophila melanogaster
Genome-wide analysis of regions similar to promoters of histone genes
Eigengene networks for studying the relationships between co-expression modules
Single-cell study links metabolism with nutrient signaling and reveals sources of variability
A novel neural response algorithm for protein function prediction
The function of communities in protein interaction networks at multiple scales
More than just a metabolic regulator - elucidation and validation of new targets of PdhR in Escherichia coli
UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines
Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential
A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway
Evolution of computational models in BioModels Database and the Physiome Model Repository
A novel integrated gene coexpression analysis approach reveals a prognostic three-transcription-factor signature for glioma molecular subtypes
Understanding biological systems through the lens of data
Transient oscillatory dynamics of interferon beta signaling in macrophages
DMirNet: Inferring direct microRNA-mRNA association networks
Computational gene network analysis reveals TNF-induced angiogenesis
SPSNet: subpopulation-sensitive network-based analysis of heterogeneous gene expression data
The correlation between architecture and mRNA abundance in the genetic regulatory network of Escherichia coli
Bayesian network model for identification of pathways by integrating protein interaction with genetic interaction data
Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans
A simple gene set-based method accurately predicts the synergy of drug pairs
Progress toward the construction of a tri-stable genetic toggle switch in E. coli
Determining novel functions of Arabidopsis 14-3-3 proteins in central metabolic processes
Age-correlated stress resistance improves fitness of yeast: support from agent-based simulations
Kinetic stability analysis of protein assembly on the center manifold around the critical point
Correction to: miRNAs and target genes in the blood as biomarkers for the early diagnosis of Parkinson's disease
Theoretical model of mitotic spindle microtubule growth for FRAP curve interpretation
Annotating novel genes by integrating synthetic lethals and genomic information
An integrative modeling framework reveals plasticity of TGF-β signaling
Delineating functional principles of the bow tie structure of a kinase-phosphatase network in the budding yeast
A knowledge base for Vitis vinifera functional analysis
Comparative toxicogenomics of three insensitive munitions constituents 2, 4-dinitroanisole, nitroguanidine and nitrotriazolone in the soil nematode Caenorhabditis elegans
A model reduction method for biochemical reaction networks
Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems
Transcriptional override: a regulatory network model of indirect responses to modulations in microRNA expression
Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle
Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks
TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles
Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015
A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture
Ultraviolet (IUV) and mass spectrometry (IMS) imaging for the deconvolution of microbial interactions
Hierarchy of non-glucose sugars in Escherichia coli
From pathway to population - a multiscale model of juxtacrine EGFR-MAPK signalling
Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks
Computational analysis reveals the coupling between bistability and the sign of a feedback loop in a TGF-β1 activation model
JuPOETs: a constrained multiobjective optimization approach to estimate biochemical model ensembles in the Julia programming language
A transcriptional dynamic network during Arabidopsis thaliana pollen development
The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature
InCoB2013 introduces Systems Biology as a major conference theme
Autocrine FGF feedback can establish distinct states of Nanog expression in pluripotent stem cells: a computational analysis
Reconstructing evolutionary trees in parallel for massive sequences
State feedback control design for Boolean networks
Stochastic Boolean networks: An efficient approach to modeling gene regulatory networks
LeishCyc: a biochemical pathways database for Leishmania major
Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism
Computational cell fate modelling for discovery of rewiring in apoptotic network for enhanced cancer drug sensitivity
Kinetic regulation of multi-ligand binding proteins
In silico evaluation and exploration of antibiotic tuberculosis treatment regimens
Modeling gene expression regulatory networks with the sparse vector autoregressive model
Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks
Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network
Feedback control in planarian stem cell systems
Comparative analysis of cis-regulation following stroke and seizures in subspaces of conserved eigensystems
Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana
The smallest chemical reaction system with bistability
Comparison between elementary flux modes analysis and 13C-metabolic fluxes measured in bacterial and plant cells
Clarifying off-target effects for torcetrapib using network pharmacology and reverse docking approach
A Systems Biology Strategy for Predicting Similarities and Differences of Drug Effects: Evidence for Drug-specific Modulation of Inflammation in Atherosclerosis
Multi-equilibrium property of metabolic networks: SSI module
A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database
Microarray test results should not be compensated for multiplicity of gene contents
Evaluating model reduction under parameter uncertainty
Integrating data- and model-driven strategies in systems biology
Information theoretic approaches for inference of biological networks from continuous-valued data
Network reconstruction of the mouse secretory pathway applied on CHO cell transcriptome data
Analysis of the quantitative balance between insulin-like growth factor (IGF)-1 ligand, receptor, and binding protein levels to predict cell sensitivity and therapeutic efficacy
Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma
Identifying drug-pathway association pairs based on L2, 1-integrative penalized matrix decomposition
BiologicalNetworks - tools enabling the integration of multi-scale data for the host-pathogen studies
Flux variability scanning based on enforced objective flux for identifying gene amplification targets
Palindromic sequence impedes sequencing-by-ligation mechanism
Principal process analysis of biological models
Low potency toxins reveal dense interaction networks in metabolism
Metabolic Flux-Based Modularity using Shortest Retroactive distances
Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes
The game theory of Candida albicans colonization dynamics reveals host status-responsive gene expression
The relationship between domain-domain interaction orientation and sequence similarity
Improved flower pollination algorithm for identifying essential proteins
Diffusion is capable of translating anisotropic apoptosis initiation into a homogeneous execution of cell death
Linking evolution of protein structures through fragments
A computational platform to maintain and migrate manual functional annotations for BioCyc databases
Equilibrium model selection: dTTP induced R1 dimerization
Human synthetic lethal inference as potential anti-cancer target gene detection
A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica
Kernelized partial least squares for feature reduction and classification of gene microarray data
Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis
VANTED v2: a framework for systems biology applications
Biological network motif detection and evaluation
Constructing network topologies for multiple signal-encoding functions
Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways
Detection of statistically significant network changes in complex biological networks
Co-expression of long non-coding RNAs and autism risk genes in the developing human brain
An agent-based model of triple-negative breast cancer: the interplay between chemokine receptor CCR5 expression, cancer stem cells, and hypoxia
HINT: High-quality protein interactomes and their applications in understanding human disease
Network-based scoring system for genome-scale metabolic reconstructions
Network based elucidation of drug response: from modulators to targets
Digitalization of a non-irradiated acute myeloid leukemia model
Interspecies protein-protein interaction network construction for characterization of host-pathogen interactions: a Candida albicans-zebrafish interaction study
How time delay and network design shape response patterns in biochemical negative feedback systems
Recursive regularization for inferring gene networks from time-course gene expression profiles
A systems biology investigation of neurodegenerative dementia reveals a pivotal role of autophagy
Regulation of cytoplasmic polyadenylation can generate a bistable switch
Gene, pathway and network frameworks to identify epistatic interactions of single nucleotide polymorphisms derived from GWAS data
Flux-sum analysis identifies metabolite targets for strain improvement
Defining the antigen receptor-dependent regulatory network that induces arrest of cycling immature B-lymphocytes
SPIC: A novel similarity metric for comparing transcription factor binding site motifs based on information contents
Network analysis of the transcriptional pattern of young and old cells of Escherichia coli during lag phase
DENSE: efficient and prior knowledge-driven discovery of phenotype-associated protein functional modules
Robust and efficient parameter estimation in dynamic models of biological systems
Novel alternative splicing isoform biomarkers identification from high-throughput plasma proteomics profiling of breast cancer
A new efficient approach to fit stochastic models on the basis of high-throughput experimental data using a model of IRF7 gene expression as case study
Genome-scale model-driven strain design for dicarboxylic acid production in Yarrowia lipolytica