yusuke1997/dblp-id-title huggingface dataset:
Analysis of l-glutamic acid fermentation by using a dynamic metabolic simulation model of Escherichia coli
Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model
A reconfigurable NAND/NOR genetic logic gate
Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs
The spermatozoa caught in the net: the biological networks to study the male gametes post-ejaculatory life
PINTnet: construction of condition-specific pathway interaction network by computing shortest paths on weighted PPI
cytoHubba: identifying hub objects and sub-networks from complex interactome
The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions
An online model composition tool for system biology models
Mathematical modeling of movement on fitness landscapes
An efficient algorithm for identifying primary phenotype attractors of a large-scale Boolean network
BioGraph: a web application and a graph database for querying and analyzing bioinformatics resources
Identification of key regulators in glycogen utilization in E. coli based on the simulations from a hybrid functional Petri net model
Intervention in gene regulatory networks via greedy control policies based on long-run behavior
Evaluation of rate law approximations in bottom-up kinetic models of metabolism
GraTeLPy: graph-theoretic linear stability analysis
Reconstruction of the experimentally supported human protein interactome: what can we learn?
Prediction of novel synthetic pathways for the production of desired chemicals
Balancing speed and accuracy of polyclonal T cell activation: a role for extracellular feedback
Designing a chemical program using chemical organization theory
BowTieBuilder: modeling signal transduction pathways
An in silico method for detecting overlapping functional modules from composite biological networks
Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae
Time-dependent variation of pathways and networks in a 24-hour window after cerebral ischemia-reperfusion injury
Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns
Stochastic simulations of a synthetic bacteria-yeast ecosystem
Discovering protein complexes in protein interaction networks via exploring the weak ties effect
Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines
Statistical inference of the time-varying structure of gene-regulation networks
Multivariate generalized multifactor dimensionality reduction to detect gene-gene interactions
A novel untargeted metabolomics correlation-based network analysis incorporating human metabolic reconstructions
Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer
Quantifying differences in cell line population dynamics using CellPD
Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test
Identification of Hürthle cell cancers: solving a clinical challenge with genomic sequencing and a trio of machine learning algorithms
Advances in systems biology: computational algorithms and applications
Model-based clustering reveals vitamin D dependent multi-centrality hubs in a network of vitamin-related proteins
Multi-way metamodelling facilitates insight into the complex input-output maps of nonlinear dynamic models
Parameter estimation in systems biology models using spline approximation
BacGrid: simulations of bacteria using the grid
Inferring the effective TOR-dependent network: a computational study in yeast
Network analysis of microRNAs and their regulation in human ovarian cancer
The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms
Dynamic proteomics reveals bimodal protein dynamics of cancer cells in response to HSP90 inhibitor
Computational estimation of tricarboxylic acid cycle fluxes using noisy NMR data from cardiac biopsies
Integrative analysis of differential miRNA and functional study of miR-21 by seed-targeting inhibition in multiple myeloma cells in response to berberine
Modelling the effects of cell-to-cell variability on the output of interconnected gene networks in bacterial populations
Statistical ensemble analysis for simulating extrinsic noise-driven response in NF-κ
Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis
Multi-target drug repositioning by bipartite block-wise sparse multi-task learning
Image analysis driven single-cell analytics for systems microbiology
Gene perturbation and intervention in context-sensitive stochastic Boolean networks
Increased entropy of signal transduction in the cancer metastasis phenotype
Systems biology approach to identify transcriptome reprogramming and candidate microRNA targets during the progression of polycystic kidney disease
CytoASP: a Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks
A compartment model of VEGF distribution in blood, healthy and diseased tissues
A systems approach to model natural variation in reactive properties of bacterial ribosomes
The innate immune response to ischemic injury: a multiscale modeling perspective
Multi-compartmental modeling of SORLA's influence on amyloidogenic processing in Alzheimer's disease
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets
Systems analysis of the transcriptional response of human ileocecal epithelial cells to Clostridium difficile toxins and effects on cell cycle control
Dynamic cross-regulation of antigen-specific effector and regulatory T cell subpopulations and microglia in brain autoimmunity
Optimization of lipid production with a genome-scale model of Yarrowia lipolytica
Predicting the connectivity of primate cortical networks from topological and spatial node properties
Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data
Solution of the chemical master equation by radial basis functions approximation with interface tracking
Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease
A General Life History Theory for Effects of Caloric Restriction on Health Maintenance
The capacity for multistability in small gene regulatory networks
Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0
A systems biology approach to dynamic modeling and inter-subject variability of statin pharmacokinetics in human hepatocytes
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology
Genetic and systems level analysis of Drosophila sticky/citron kinase and dFmr1 mutants reveals common regulation of genetic networks
Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation
Role of genomic architecture in the expression dynamics of long noncoding RNAs during differentiation of human neuroblastoma cells
Optimization meets systems biology
Iron acquisition and oxidative stress response in aspergillus fumigatus
Identification of transcription factor's targets using tissue-specific transcriptomic data in Arabidopsis thaliana
Reshaping the epigenetic landscape during early flower development: induction of attractor transitions by relative differences in gene decay rates
Hybrid stochastic simplifications for multiscale gene networks
Predicting network modules of cell cycle regulators using relative protein abundance statistics
Parallel-META: efficient metagenomic data analysis based on high-performance computation
Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies
SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks
Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks
XMRF: an R package to fit Markov Networks to high-throughput genetics data
An ensemble of mathematical models showing diauxic growth behaviour
Morphisms of reaction networks that couple structure to function
A parallel algorithm for de novo peptide sequencing
Patterns of human gene expression variance show strong associations with signaling network hierarchy
A search engine to identify pathway genes from expression data on multiple organisms
Continuous-time modeling of cell fate determination in Arabidopsis flowers
Systems biology modeling of omics data: effect of cyclosporine a on the Nrf2 pathway in human renal cells
Predicting implicit associated cancer genes from OMIM and MEDLINE by a new probabilistic model
Nuclear pores enable sustained perinuclear calcium oscillations
Effects of multimerization on the temporal variability of protein complex abundance
Optimization in computational systems biology
Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction
Optimisation of an exemplar oculomotor model using multi-objective genetic algorithms executed on a GPU-CPU combination
InCoB2014: Systems Biology update from the Asia-Pacific
MD-Miner: a network-based approach for personalized drug repositioning
MEMOSys: Bioinformatics platform for genome-scale metabolic models
SNP by SNP by environment interaction network of alcoholism
Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates
Regulation of dual specificity phosphatases in breast cancer during initial treatment with Herceptin: a Boolean model analysis
Computational simulations of interactions of the κ-hefutoxin1 with the voltage-gated potassium ion channels
Differential variability and correlation of gene expression identifies key genes involved in neuronal differentiation
Integrating mutation and gene expression cross-sectional data to infer cancer progression
Large-scale analysis of expression signatures reveals hidden links among diverse cellular processes
CardioNet: A human metabolic network suited for the study of cardiomyocyte metabolism
Interactive analysis of systems biology molecular expression data
An approach for dynamical network reconstruction of simple network motifs
Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent
ECOLITASTER: cellular biosensor
Codon usage variability determines the correlation between proteome and transcriptome fold changes
A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation
A checkpoints capturing timing-robust Boolean model of the budding yeast cell cycle regulatory network
OptCircuit: An optimization based method for computational design of genetic circuits
Information theoretic approach to complex biological network reconstruction: application to cytokine release in RAW 264.7 macrophages
Simulating in vitro transcriptional response of zinc homeostasis system in Escherichia coli
Engineering a synthetic anaerobic respiration for reduction of xylose to xylitol using NADH output of glucose catabolism by Escherichia coli AI21
Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z
Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway
On the correlation between drug-resistant pattern of HIV-1 protease inhibitors and binding free energy and structural changes
A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms
Classification of breast cancer patients using somatic mutation profiles and machine learning approaches
Minimally perturbing a gene regulatory network to avoid a disease phenotype: the glioma network as a test case
Global organization of protein complexome in the yeast Saccharomyces cerevisiae
Network screening of Goto-Kakizaki rat liver microarray data during diabetic progression
Estimating confidence intervals in predicted responses for oscillatory biological models
Understanding protein evolutionary rate by integrating gene co-expression with protein interactions
A novel gene network inference algorithm using predictive minimum description length approach
Logical-continuous modelling of post-translationally regulated bistability of curli fiber expression in Escherichia coli
KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics
Pathobiochemical signatures of cholestatic liver disease in bile duct ligated mice
Interactions among oscillatory pathways in NF-kappa B signaling
A Dominated Coupling From The Past algorithm for the stochastic simulation of networks of biochemical reactions
Mathematical modeling of GATA-switching for regulating the differentiation of hematopoietic stem cell
Hadamard Kernel SVM with applications for breast cancer outcome predictions
The wright stuff: reimagining path analysis reveals novel components of the sex determination hierarchy in drosophila melanogaster
Low-complexity regions within protein sequences have position-dependent roles
High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization
Simultaneous learning of instantaneous and time-delayed genetic interactions using novel information theoretic scoring technique
Properties of Boolean dynamics by node classification using feedback loops in a network
Genome-scale reconstruction of metabolic network for a halophilic extremophile, Chromohalobacter salexigens DSM 3043
3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data
Erratum to: ppiPre: predicting protein-protein interactions by combining heterogeneous features
Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition
Integration of lipidomics and transcriptomics data towards a systems biology model of sphingolipid metabolism
Construction and analysis of gene-gene dynamics influence networks based on a Boolean model
Functional approach to high-throughput plant growth analysis
Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora
Simple molecular networks that respond optimally to time-periodic stimulation
KF-finder: identification of key factors from host-microbial networks in cervical cancer
Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains
Statistical relationship between metabolic decomposition and chemical uptake predicts bioconcentration factor data for diverse chemical exposures
Characterizing criticality of proteins by systems dynamics: Escherichia coli central carbon metabolism as a working example
Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems
Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network
From bit to it: How a complex metabolic network transforms information into living matter
Automated design of bacterial genome sequences
An improved sparse representation model with structural information for Multicolour Fluorescence In-Situ Hybridization (M-FISH) image classification
Zooming of states and parameters using a lumping approach including back-translation
Redox balance is key to explaining full vs. partial switching to low-yield metabolism
The anticancer mechanism investigation of Tanshinone IIA by pharmacological clustering in protein network
Integration of metabolic databases for the reconstruction of genome-scale metabolic networks
A global statistical test for improved detection of gene activity
Constructing higher-order miRNA-mRNA interaction networks in prostate cancer via hypergraph-based learning
Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes
Untargeted metabolomics unravels functionalities of phosphorylation sites in Saccharomyces cerevisiae
Regulatory link mapping between organisms
Integration and analysis of heterogeneous microarray data sources for supporting drug target identification in atherosclerosis
METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks
Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration
A depth-first search algorithm to compute elementary flux modes by linear programming
Mathematical modelling and a systems science approach to describe the role of cytokines in the evolution of severe dengue
Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets
Discovering conditional co-regulated protein complexes by integrating diverse data sources
Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma
Network motif comparison rationalizes Sec1/Munc18-SNARE regulation mechanism in exocytosis
Identifying co-targets to fight drug resistance based on a random walk model
A cell size- and cell cycle-aware stochastic model for predicting time-dynamic gene network activity in individual cells
Discrimination of proteins using graph theoretic properties
Identification of direction in gene networks from expression and methylation
Systems analysis reveals a transcriptional reversal of the mesenchymal phenotype induced by SNAIL-inhibitor GN-25
A Bayesian active learning strategy for sequential experimental design in systems biology
A Novel microRNA and transcription factor mediated regulatory network in schizophrenia
Cross-species Conservation of context-specific networks
Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery
Retraction Note: detangling PPI networks to uncover functionally meaningful clusters
Combining laboratory and mathematical models to infer mechanisms underlying kinetic changes in macrophage susceptibility to an RNA virus
DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results
On the origin of distribution patterns of motifs in biological networks
A stochastic automaton shows how enzyme assemblies may contribute to metabolic efficiency
Quantitative reproducibility analysis for identifying reproducible targets from high-throughput experiments
How accurate is automated gap filling of metabolic models?
A semi-supervised boosting SVM for predicting hot spots at protein-protein Interfaces
The crosstalk between EGF, IGF, and Insulin cell signaling pathways - computational and experimental analysis
Dissecting the logical types of network control in gene expression profiles
Model-based virtual patient analysis of human liver regeneration predicts critical perioperative factors controlling the dynamic mode of response to resection
A dynamic network of transcription in LPS-treated human subjects
SNAVI: Desktop application for analysis and visualization of large-scale signaling networks
A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis
Computational codon optimization of synthetic gene for protein expression
Nonlinear mixed-effects modelling for single cell estimation: when, why, and how to use it
Probing the role of stochasticity in a model of the embryonic stem cell - heterogeneous gene expression and reprogramming efficiency
A formal model for analyzing drug combination effects and its application in TNF-α-induced NFκB pathway
Attractor landscape analysis of colorectal tumorigenesis and its reversion
In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study
Small molecule activators of SIRT1 replicate signaling pathways triggered by calorie restriction in vivo
Time-resolved in silico modeling of fine-tuned cAMP signaling in platelets: feedback loops, titrated phosphorylations and pharmacological modulation
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data
HSA: A Heuristic Splice Alignment Tool
On the spontaneous stochastic dynamics of a single gene: complexity of the molecular interplay at the promoter
Incorporation of enzyme concentrations into FBA and identification of optimal metabolic pathways
Pathway-gene identification for pancreatic cancer survival via doubly regularized Cox regression
CGPredictor: a systematic integrated analytic tool for mining and examining genome-scale cancer independent prognostic epigenetic marker panels
DNA interaction with sperm cells: ODE model
Improving metabolic flux predictions using absolute gene expression data
Integrative modeling of multi-omics data to identify cancer drivers and infer patient-specific gene activity
Efficient simulation of stochastic chemical kinetics with the Stochastic Bulirsch-Stoer extrapolation method
Time series gene expression profiling and temporal regulatory pathway analysis of BMP6 induced osteoblast differentiation and mineralization
Modelling with ANIMO: between fuzzy logic and differential equations
Cascading signaling pathways improve the fidelity of a stochastically and deterministically simulated molecular RS latch
A logic-based diagram of signalling pathways central to macrophage activation
BioModels linked dataset
Pride Wizard: generation of standards compliant quantitative proteomics data
Modelling overflow metabolism in Escherichia coli with flux balance analysis incorporating differential proteomic efficiencies of energy pathways
A reaction-diffusion mechanism influences cell lineage progression as a basis for formation, regeneration, and stability of intestinal crypts
A semantic proteomics dashboard (SemPoD) for data management in translational research
Prediction and ranking of human protein-protein interactions within a Bayesian framework
Constraint-based modeling analysis of the metabolism of two Pelobacter species
Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome
A model invalidation-based approach for elucidating biological signalling pathways, applied to the chemotaxis pathway in R. sphaeroides
RNA silencing can explain chlorotic infection patterns on plant leaves
Mechanistic insight into activation of MAPK signaling by pro-angiogenic factors
Advanced integration of fluid dynamics and photosynthetic reaction kinetics for microalgae culture systems
Difference in the distribution pattern of substrate enzymes in the metabolic network of Escherichia coli, according to chaperonin requirement
DGCA: A comprehensive R package for Differential Gene Correlation Analysis
Functional enrichment analysis based on long noncoding RNA associations
A multiscale approximation in a heat shock response model of E. coli
Qualitative modelling of the interplay of inflammatory status and butyrate in the human gut: a hypotheses about robust bi-stability
Computational modeling of sphingolipid metabolism
Short time-series microarray analysis: Methods and challenges
A systematic investigation of Escherichia coli central carbon metabolism in response to superoxide stress
A model comparison study of the flowering time regulatory network in Arabidopsis
Clustering reveals limits of parameter identifiability in multi-parameter models of biochemical dynamics
Effect of microarray data heterogeneity on regulatory gene module discovery
SigCS base: an integrated genetic information resource for human cerebral stroke
Petri net-based prediction of therapeutic targets that recover abnormally phosphorylated proteins in muscle atrophy