yusuke1997/dblp-id-title huggingface dataset:
Using potential master regulator sites and paralogous expansion to construct tissue-specific transcriptional networks
Gene autoregulation via intronic microRNAs and its functions
Resource constrained flux balance analysis predicts selective pressure on the global structure of metabolic networks
International Conference on Genome Informatics (GIW 2013) in Singapore: introduction to the systems biology contributions
Sensitivity analysis of biological Boolean networks using information fusion based on nonadditive set functions
Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production
Kinetic modeling and exploratory numerical simulation of chloroplastic starch degradation
Systems approach to investigating host-pathogen interactions in infections with the biothreat agent Francisella. Constraints-based model of Francisella tularensis
Multiway modeling and analysis in stem cell systems biology
The evolution of metabolic networks of E. coli
Molecular mechanistic associations of human diseases
Improvement of experimental testing and network training conditions with genome-wide microarrays for more accurate predictions of drug gene targets
Protein-protein interaction as a predictor of subcellular location
Identification of functional modules using network topology and high-throughput data
Tip cell overtaking occurs as a side effect of sprouting in computational models of angiogenesis
Transcriptome meta-analysis reveals a central role for sex steroids in the degeneration of hippocampal neurons in Alzheimer's disease
cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila
An efficient graph theory based method to identify every minimal reaction set in a metabolic network
Models of sequestration and receptor cross-talk for explaining multiple mutants in plant stem cell regulation
Coordinated modular functionality and prognostic potential of a heart failure biomarker-driven interaction network
Analysis of metabolome data by a maximum likelihood approach
ENNET: inferring large gene regulatory networks from expression data using gradient boosting
Annual acknowledgement of reviewers
Membrane related dynamics and the formation of actin in cells growing on micro-topographies: a spatial computational model
Modularity-based credible prediction of disease genes and detection of disease subtypes on the phenotype-gene heterogeneous network
Cliques for the identification of gene signatures for colorectal cancer across population
Using genetic markers to orient the edges in quantitative trait networks: The NEO software
Clustering and evolutionary analysis of small RNAs identify regulatory siRNA clusters induced under drought stress in rice
Of text and gene - using text mining methods to uncover hidden knowledge in toxicogenomics
Phenotype prediction in regulated metabolic networks
Impaired coupling of local and global functional feedbacks underlies abnormal synchronization and negative symptoms of schizophrenia
Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production
Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks
Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach
Receptor-guided 3D-QSAR studies, molecular dynamics simulation and free energy calculations of Btk kinase inhibitors
The coupling of pathways and processes through shared components
Structural similarity of genetically interacting proteins
Predicting outcomes of steady-state 13 C isotope tracing experiments using Monte Carlo sampling
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms
Identifying cancer biomarkers by network-constrained support vector machines
An in silico model of the ubiquitin-proteasome system that incorporates normal homeostasis and age-related decline
Gene regulatory network of human adipocyte differentiation
Identification of yeast cell cycle regulated genes based on genomic features
A computational model of invasive aspergillosis in the lung and the role of iron
Probability distributed time delays: integrating spatial effects into temporal models
How to formalise the meaning of a bio-model: a case study
In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae
Modelling the cAMP pathway using BioNessie, and the use of BVP techniques for solving ODEs
Convergence of Logic of Cellular Regulation in Different Premalignant Cells by an Information Theoretic Approach
A renewal model for the emergence of anomalous solute crowding in liposomes
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats
STATegra EMS: an Experiment Management System for complex next-generation omics experiments
Dynamics of receptor and protein transducer homodimerisation
The protein-protein interaction network of eyestalk, Y-organ and hepatopancreas in Chinese mitten crab Eriocheir sinensis
Clustered microRNAs' coordination in regulating protein-protein interaction network
A scalable method for discovering significant subnetworks
Adaptive information processing of network modules to dynamic and spatial stimuli
Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster
The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force?
The extraction of drug-disease correlations based on module distance in incomplete human interactome
An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules
Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models
Regulation of leukotriene and 5oxoETE synthesis and the effect of 5-lipoxygenase inhibitors: a mathematical modeling approach
Visualising the immune repertoire
Qualitative dynamics semantics for SBGN process description
Modeling de novo granulation of anaerobic sludge
Inferring ancient metabolism using ancestral core metabolic models of enterobacteria
Systems analysis of non-parenchymal cell modulation of liver repair across multiple regeneration modes
Optimality and evolution of transcriptionally regulated gene expression
Deciphering the signaling mechanisms of the plant cell wall degradation machinery in Aspergillus oryzae
Use of prior knowledge for the analysis of high-throughput transcriptomics and metabolomics data
ALC: automated reduction of rule-based models
Predicting target-ligand interactions using protein ligand-binding site and ligand substructures
LSM-W2: laser scanning microscopy worker for wheat leaf surface morphology
Multi-component gene network design as a survival strategy in diverse environments
Dynamical modeling of microRNA action on the protein translation process
Knowledge-based compact disease models identify new molecular players contributing to early-stage Alzheimer's disease
A graph kernel method for DNA-binding site prediction
DASMiner: discovering and integrating data from DAS sources
Individual vs. combinatorial effect of elevated CO 2 conditions and salinity stress on Arabidopsis thaliana liquid cultures: Comparing the early molecular response using time-series transcriptomic and metabolomic analyses
The genotype-phenotype relationship in multicellular pattern-generating models - the neglected role of pattern descriptors
Set-base dynamical parameter estimation and model invalidation for biochemical reaction networks
Transformation of metabolism with age and lifestyle in Antarctic seals: a case study of systems biology approach to cross-species microarray experiment
iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states
Stochastic modelling of biochemical systems of multi-step reactions using a simplified two-variable model
A scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD+/NADH+ imbalance
Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway
Latent phenotypes pervade gene regulatory circuits
An approach to evaluate the topological significance of motifs and other patterns in regulatory networks
Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis
A novel two-layer SVM model in miRNA Drosha processing site detection
Detection of driver metabolites in the human liver metabolic network using structural controllability analysis
Correction to: A quantitative systems pharmacology (QSP) model for Pneumocystis treatment in mice
Accurate, precise modeling of cell proliferation kinetics from time-lapse imaging and automated image analysis of agar yeast culture arrays
Sampling-based Bayesian approaches reveal the importance of quasi-bistable behavior in cellular decision processes on the example of the MAPK signaling pathway in PC-12 cell lines
Computational developments in microRNA-regulated protein-protein interactions
How to prevent viremia rebound? Evidence from a PRRSv data-supported model of immune response
Computational design of proteins with new functions
Learning stochastic process-based models of dynamical systems from knowledge and data
Interlinked nonlinear subnetworks underlie the formation of robust cellular patterns in Arabidopsis epidermis: a dynamic spatial model
Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data
Discovery of substrate cycles in large scale metabolic networks using hierarchical modularity
Network-based characterization of drug-protein interaction signatures with a space-efficient approach
A specialized ODE integrator for the efficient computation of parameter sensitivities
A novel mathematical model of ATM/p53/NF- κ B pathways points to the importance of the DDR switch-off mechanisms
Statistical model comparison applied to common network motifs
Integration of enzyme activities into metabolic flux distributions by elementary mode analysis
A rule-based model of insulin signalling pathway
Time delay induced transition of gene switch and stochastic resonance in a genetic transcriptional regulatory model
Fungal volatile fingerprints and machine learning: potential of discriminating and classifying dermatophyte species
NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis
Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials
Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data
Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92
An objective function exploiting suboptimal solutions in metabolic networks
Regulation of the yeast metabolic cycle by transcription factors with periodic activities
Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions
Joint estimation of causal effects from observational and intervention gene expression data
Network methods for describing sample relationships in genomic datasets: application to Huntington's disease
Mining significant high utility gene regulation sequential patterns
Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast
Integrating multiple types of data to predict novel cell cycle-related genes
Manatee invariants reveal functional pathways in signaling networks
Likelihood based observability analysis and confidence intervals for predictions of dynamic models
A methodology for multivariate phenotype-based genome-wide association studies to mine pleiotropic genes
Avoiding transcription factor competition at promoter level increases the chances of obtaining oscillation
Context sensitivity in individual-based modeling
Systems biology analysis of mitogen activated protein kinase inhibitor resistance in malignant melanoma
Embracing noise to improve cross-batch prediction accuracy
Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks
In silico identification of a multi-functional regulatory protein involved in Holliday junction resolution in bacteria
Discovery of small protein complexes from PPI networks with size-specific supervised weighting
Computational modeling of the EGFR network elucidates control mechanisms regulating signal dynamics
A network perspective on metabolic inconsistency
Correction: Tracing dynamic biological processes during phase transition
PPI network analyses of human WD40 protein family systematically reveal their tendency to assemble complexes and facilitate the complex predictions
Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data
Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression
Fast Bayesian inference for gene regulatory networks using ScanBMA
Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs
Mathematical model of TGF-βsignalling: feedback coupling is consistent with signal switching
Feedback regulation in a stem cell model with acute myeloid leukaemia
A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities
Communicating oscillatory networks: frequency domain analysis
From genes to networks: in systematic points of view
Hot spot prediction in protein-protein interactions by an ensemble system
Kernel-PCA data integration with enhanced interpretability
iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data
The mathematics of tanning
Mining for novel candidate clock genes in the circadian regulatory network
A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue
Correction to: dengue virus causes changes of MicroRNA-genes regulatory network revealing potential targets for antiviral drugs
Exploring metabolic pathway disruption in the subchronic phencyclidine model of schizophrenia with the Generalized Singular Value Decomposition
Fathead minnow steroidogenesis: in silico analyses reveals tradeoffs between nominal target efficacy and robustness to cross-talk
Predicting new molecular targets for rhein using network pharmacology
Computational modelling of chemotaxis in cooperative phenomena in bacterial populations
Highly sensitive inference of time-delayed gene regulation by network deconvolution
MicrobesFlux: a web platform for drafting metabolic models from the KEGG database
Integrative analysis of large scale expression profiles reveals core transcriptional response and coordination between multiple cellular processes in a cyanobacterium
Stochastic modeling suggests that noise reduces differentiation efficiency by inducing a heterogeneous drug response in glioma differentiation therapy
Membrane potential independent transport of NH3 in the absence of ammonium permeases in Saccharomyces cerevisiae
Selecting high-quality negative samples for effectively predicting protein-RNA interactions
MetaNET - a web-accessible interactive platform for biological metabolic network analysis
A method for zooming of nonlinear models of biochemical systems
Modeling mutant phenotypes and oscillatory dynamics in the Saccharomyces cerevisiae cAMP-PKA pathway
Robustness analysis on interspecies interaction network for iron and glucose competition between Candida albicans and zebrafish during infection
An integrated proteomics analysis of bone tissues in response to mechanical stimulation
Identification of novel microRNA regulatory pathways associated with heterogeneous prostate cancer
One hub-one process: a tool based view on regulatory network topology
Stochastic simulations of the tetracycline operon
MP-Align: alignment of metabolic pathways
The internal state of medium spiny neurons varies in response to different input signals
Exploiting the pathway structure of metabolism to reveal high-order epistasis
Gene regulation is governed by a core network in hepatocellular carcinoma
Time-resolved metabolomics reveals metabolic modulation in rice foliage
A yeast's eye view of mammalian reproduction: cross-species gene co-expression in meiotic prophase
Huntington's disease: from experimental results to interaction networks, patho-pathway construction and disease hypothesis
Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle
Prediction of disease genes using tissue-specified gene-gene network
FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data
Insight into model mechanisms through automatic parameter fitting: a new methodological framework for model development
Multicriteria global optimization for biocircuit design
Dynamical pathway analysis
A dynamic time order network for time-series gene expression data analysis
A model of HIV drug resistance driven by heterogeneities in host immunity and adherence patterns
JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations
MC 3 : a steady-state model and constraint consistency checker for biochemical networks
OMACC: an Optical-Map-Assisted Contig Connector for improving de novo genome assembly
A deterministic map of Waddington's epigenetic landscape for cell fate specification
Monotonicity, frustration, and ordered response: an analysis of the energy landscape of perturbed large-scale biological networks
Leveraging social networks for understanding the evolution of epidemics
Improving protein function prediction using domain and protein complexes in PPI networks
Disentangling function from topology to infer the network properties of disease genes
Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels
Integrated cellular network of transcription regulations and protein-protein interactions
Roles of alternative splicing in modulating transcriptional regulation
Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge
Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli
Dynamic estimation of specific fluxes in metabolic networks using non-linear dynamic optimization
Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data
Hybrid method to solve HP model on 3D lattice and to probe protein stability upon amino acid mutations
Fluxomers: a new approach for 13 C metabolic flux analysis
A Boolean-based systems biology approach to predict novel genes associated with cancer: Application to colorectal cancer
Systems biology as an emerging paradigm in transfusion medicine
A simple theoretical framework for understanding heterogeneous differentiation of CD4 + T cells
BCM: toolkit for Bayesian analysis of Computational Models using samplers
Understanding disease mechanisms with models of signaling pathway activities
Corbi: a new R package for biological network alignment and querying
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks
A computational approach to resolve cell level contributions to early glandular epithelial cancer progression
Prediction and evolution of transcription factors and their evolutionary families in prokaryotes
iAK692: A genome-scale metabolic model of Spirulina platensis C1
Metabolism as means for hypoxia adaptation: metabolic profiling and flux balance analysis
Gene network analysis shows immune-signaling and ERK1/2 as novel genetic markers for multiple addiction phenotypes: alcohol, smoking and opioid addiction
Evolution of metabolic network organization
mAPC-GibbsOS: an integrated approach for robust identification of gene regulatory networks
Integrative network analysis reveals active microRNAs and their functions in gastric cancer
In silico feasibility of novel biodegradation pathways for 1, 2, 4-trichlorobenzene
COBRApy: COnstraints-Based Reconstruction and Analysis for Python
Complex receptor-ligand dynamics control the response of the VEGF system to protease injury
A network-based approach for predicting key enzymes explaining metabolite abundance alterations in a disease phenotype
A system based network approach to ethanol tolerance in Saccharomyces cerevisiae
Rosen's (M, R) system in process algebra
FCMDAP: using miRNA family and cluster information to improve the prediction accuracy of disease related miRNAs
Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network
Connecting extracellular metabolomic measurements to intracellular flux states in yeast
Initial characterization of the human central proteome
Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants
Analysis of a dynamic model of guard cell signaling reveals the stability of signal propagation
Optimal enumeration of state space of finitely buffered stochastic molecular networks and exact computation of steady state landscape probability
In vitro gene regulatory networks predict in vivo function of liver
Extracting expression modules from perturbational gene expression compendia
Knowledge management for systems biology a general and visually driven framework applied to translational medicine
Parameter estimation of qualitative biological regulatory networks on high performance computing hardware
Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy
Comparative multi-goal tradeoffs in systems engineering of microbial metabolism
Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation
Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming
MicroRNAs coordinately regulate protein complexes
NetworkViewer: visualizing biochemical reaction networks with embedded rendering of molecular interaction rules
Nested sampling for parameter inference in systems biology: application to an exemplar circadian model
Forecasting influenza A pandemic outbreak using protein dynamical network biomarkers
Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks
A variational approach to parameter estimation in ordinary differential equations
Systems biology surveillance decrypts pathological transcriptome remodeling
Landscape reveals critical network structures for sharpening gene expression boundaries
A vertex similarity-based framework to discover and rank orphan disease-related genes
JunD/AP1 regulatory network analysis during macrophage activation in a rat model of crescentic glomerulonephritis
Estrategic aspects by technology transfer from the academic and business development of the bioinformatics in Costa Rica and the central American region
Finding directionality and gene-disease predictions in disease associations
Bayesian model selection validates a biokinetic model for zirconium processing in humans
A computational method for predicting regulation of human microRNAs on the influenza virus genome
EnRICH: Extraction and Ranking using Integration and Criteria Heuristics
Computational analysis of calcium signaling and membrane electrophysiology in cerebellar Purkinje neurons associated with ataxia
Stochastic parameter search for events
Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice