yusuke1997/dblp-id-title huggingface dataset:
A self-training semi-supervised SVM algorithm and its application in an EEG-based brain computer interface speller system
Using data dimensionality reduction for recognition of incomplete dynamic gestures
Split and merge algorithm for deep learning and its application for additional classes
Maximizing generalized mean of trace ratios for discriminative feature learning
Multi-dataset fusion for multi-task learning on face attribute recognition
Random forest clustering for discrete sequences
Superlearning and neural network magic
Multiple vocabulary coding for 3D shape retrieval using Bag of Covariances
CPredictor3.0: detecting protein complexes from PPI networks with expression data and functional annotations
Projection to latent pathways (PLP): a constrained projection to latent variables (PLS) method for elementary flux modes discrimination
Retraction Note: Predicting new molecular targets for rhein using network pharmacology
Mathematical model of uptake and metabolism of arsenic(III) in human hepatocytes - Incorporation of cellular antioxidant response and threshold-dependent behavior
Identifying cooperative transcription factors in yeast using multiple data sources
Inferring pleiotropy by network analysis: linked diseases in the human PPI network
Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles
Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome
Constructing an integrated genetic and epigenetic cellular network for whole cellular mechanism using high-throughput next-generation sequencing data
GNE: a deep learning framework for gene network inference by aggregating biological information
Removing bias against membrane proteins in interaction networks
Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti
Astrocyte - neuron lactate shuttle may boost more ATP supply to the neuron under hypoxic conditions - in silico study supported by in vitro expression data
Inferring Drosophila gap gene regulatory network: a parameter sensitivity and perturbation analysis
Abstract analysis of pathways using the BN++ software framework
Prediction of kinase inhibitor response using activity profiling, in vitro screening, and elastic net regression
Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale
A multilevel data integration resource for breast cancer study
Wnt signal transduction pathways: modules, development and evolution
A system for success: BMC Systems Biology, a new open access journal
Model checking optimal finite-horizon control for probabilistic gene regulatory networks
Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli
Computational identification of tumour suppressor protein p53 target genes
SHARKview: a tool for the visualization of systems biology data
A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations
Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior
Weighted set enrichment of gene expression data
Conditional robustness analysis for fragility discovery and target identification in biochemical networks and in cancer systems biology
PFF - an integrated database of residues and fragments critical for protein folding
Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria
Defining a Modular Signalling Network from the Fly Interactome
Revealing functionally coherent subsets using a spectral clustering and an information integration approach
Complex-based analysis of dysregulated cellular processes in cancer
Inferring domain-domain interactions from protein-protein interactions in the complex network conformation
Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscle
BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology
So what do we really mean when we say that systems biology is holistic?
An integrated machine learning approach for predicting DosR-regulated genes in Mycobacterium tuberculosis
MiR-206-mediated dynamic mechanism of the mammalian circadian clock
Simulating Quantitative Cellular Responses Using Asynchronous Threshold Boolean Network Ensembles
The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti
Modeling cellular deformations using the level set formalism
Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data
Explaining oscillations and variability in the p53-Mdm2 system
Inferring modules from human protein interactome classes
Mathematical model on Alzheimer's disease
Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling
Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size
Characterizing redescriptions using persistent homology to isolate genetic pathways contributing to pathogenesis
Systems biological approach on neurological disorders: a novel molecular connectivity to aging and psychiatric diseases
Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties
Sparse representation approaches for the classification of high-dimensional biological data
Dynamic genome-scale metabolic modeling of the yeast Pichia pastoris
Inference of gene pathways using mixture Bayesian networks
13 C metabolic flux analysis shows that resistin impairs the metabolic response to insulin in L6E9 myotubes
Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework
Influence networks based on coexpression improve drug target discovery for the development of novel cancer therapeutics
Metabolic effects of influenza virus infection in cultured animal cells: Intra- and extracellular metabolite profiling
Investigation on changes of modularity and robustness by edge-removal mutations in signaling networks
A possibilistic framework for constraint-based metabolic flux analysis
The last generation of bacterial growth in limiting nutrient
Identifying aging-related genes in mouse hippocampus using gateway nodes
Evolutionary tradeoffs, Pareto optimality and the morphology of ammonite shells
Mapping the stabilome: a novel computational method for classifying metabolic protein stability
Gene expression model (in)validation by Fourier analysis
Large scale study of anti-sense regulation by differential network analysis
RNF14 is a regulator of mitochondrial and immune function in muscle
Computational modelling and analysis of the molecular network regulating sporulation initiation in Bacillus subtilis
Validation of a constraint-based model of Pichia pastoris metabolism under data scarcity
Single-cell phenomics reveals intra-species variation of phenotypic noise in yeast
A systematic analysis of FDA-approved anticancer drugs
Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model
Identification of new progestogen-associated networks in mammalian ovulation using bioinformatics
A higher-order numerical framework for stochastic simulation of chemical reaction systems
Plasmodium vivax readiness to transmit: implication for malaria eradication
Integrated modeling and experimental approach for determining transcription factor profiles from fluorescent reporter data
Analog regulation of metabolic demand
Structural analysis of eyespots: dynamics of morphogenic signals that govern elemental positions in butterfly wings
Dynamical modeling of the cholesterol regulatory pathway with Boolean networks
STI-GMaS: an open-source environment for simulation of sexually-transmitted infections
A computational model of the hypothalamic - pituitary - gonadal axis in female fathead minnows (Pimephales promelas) exposed to 17α-ethynylestradiol and 17#946;-trenbolone
Modeling and analysis of flux distributions in the two branches of the phosphotransferase system in Pseudomonas putida
Post-translational regulation enables robust p53 regulation
Protein evolution on a human signaling network
Dynamic elementary mode modelling of non-steady state flux data
A computational framework for gene regulatory network inference that combines multiple methods and datasets
Improved functional overview of protein complexes using inferred epistatic relationships
A framework for evolutionary systems biology
Variance stabilising transformations for NMR metabolomics data
Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network
Noise characteristics of the Escherichia coli rotary motor
Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction
Inferring microbial interaction network from microbiome data using RMN algorithm
Identifying targets of multiple co-regulating transcription factors from expression time-series by Bayesian model comparison
Statistical Inference Methods for Sparse Biological Time Series Data
The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response
MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences
Protein-protein interaction prediction based on multiple kernels and partial network with linear programming
Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology
From networks of protein interactions to networks of functional dependencies
Identification of mutated core cancer modules by integrating somatic mutation, copy number variation, and gene expression data
Bio-informatics analysis of a gene co-expression module in adipose tissue containing the diet-responsive gene Nnat
A versatile mathematical work-flow to explore how Cancer Stem Cell fate influences tumor progression
Escher-FBA: a web application for interactive flux balance analysis
An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks
Hypothetical biomolecular probe based on a genetic switch with tunable symmetry and stability
A diVIsive Shuffling Approach (VIStA) for gene expression analysis to identify subtypes in Chronic Obstructive Pulmonary Disease
Inference of gene regulatory networks from time series by Tsallis entropy
Deciphering causal and statistical relations of molecular aberrations and gene expressions in NCI-60 cell lines
Fusing gene expressions and transitive protein-protein interactions for inference of gene regulatory networks
An iterative identification procedure for dynamic modeling of biochemical networks
Network and matrix analysis of the respiratory disease interactome
VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing
In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps
CoryneCenter - An online resource for the integrated analysis of corynebacterial genome and transcriptome data
SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations
An ultrasensitive sorting mechanism for EGF Receptor Endocytosis
Computational modelling of energy balance in individuals with Metabolic Syndrome
Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin
Structure, function, and behaviour of computational models in systems biology
Two additive mechanisms impair the differentiation of 'substrate-selective' p38 inhibitors from classical p38 inhibitors in vitro
Function prediction of a newly extracted protein from a newly extracted lassa virus gene
Identifying protein complexes based on density and modularity in protein-protein interaction network
Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study
A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae
Snoopy's hybrid simulator: a tool to construct and simulate hybrid biological models
A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks
Ultrafast clustering of single-cell flow cytometry data using FlowGrid
Path2Models: large-scale generation of computational models from biochemical pathway maps
Master equation simulation analysis of immunostained Bicoid morphogen gradient
A high performance profile-biomarker diagnosis for mass spectral profiles
An improved dimensionality reduction method for meta-transcriptome indexing based diseases classification
Enhanceosome transcription factors preferentially dimerize with high mobility group proteins
Metabolomics of Apc Min/+ mice genetically susceptible to intestinal cancer
Uncovering the regeneration strategies of zebrafish organs: a comprehensive systems biology study on heart, cerebellum, fin, and retina regeneration
Antibacterial mechanisms identified through structural systems pharmacology
Spatially-resolved metabolic cooperativity within dense bacterial colonies
Gene set analysis exploiting the topology of a pathway
Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus
Constructing disease-specific gene networks using pair-wise relevance metric: Application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements
Three-dimensional experiments and individual based simulations show that cell proliferation drives melanoma nest formation in human skin tissue
A fast and accurate algorithm for single individual haplotyping
New perspectives: systems medicine in cardiovascular disease
Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella
A combinatorial approach to determine the context-dependent role in transcriptional and posttranscriptional regulation in Arabidopsis thaliana
Functional analysis of microRNA and transcription factor synergistic regulatory network based on identifying regulatory motifs in non-small cell lung cancer
Phenotypic heterogeneity in mycobacterial stringent response
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling
A novel interaction perturbation analysis reveals a comprehensive regulatory principle underlying various biochemical oscillators
Absorbing phenomena and escaping time for Muller's ratchet in adaptive landscape
Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana
A U-system approach for predicting metabolic behaviors and responses based on an alleged metabolic reaction network
Accelerated parallel algorithm for gene network reverse engineering
Cluster and propensity based approximation of a network
A bioinformatics approach for the interrogation of molecular events in single cells: transforming fluorescent time-lapse microscopy images into numbers
Computational drug repositioning using meta-path-based semantic network analysis
Non-compartment model to compartment model pharmacokinetics transformation meta-analysis - a multivariate nonlinear mixed model
A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer
A web server for protein-protein interaction network querying
Construction of a computable cell proliferation network focused on non-diseased lung cells
Stochastic flux analysis of chemical reaction networks
SNP-PRAGE: SNP-based parametric robust analysis of gene set enrichment
Active enhancer positions can be accurately predicted from chromatin marks and collective sequence motif data
Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics
Dengue virus causes changes of MicroRNA-genes regulatory network revealing potential targets for antiviral drugs
Global parameter search reveals design principles of the mammalian circadian clock
Detecting complexes from edge-weighted PPI networks via genes expression analysis
An integrative analysis of DNA methylation and RNA-Seq data for human heart, kidney and liver
Non-linear dimensionality reduction of signaling networks
An evaluation of minimal cellular functions to sustain a bacterial cell
Potential role of the glyoxalase pathway as a drug target in Leishmania infantum: an exact steady-state model analysis
Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach
The common ground of genomics and systems biology
Stochastic synchronization of genetic oscillator networks
Estimation of dynamic flux profiles from metabolic time series data
Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs
Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors
Systematic synergy modeling: understanding drug synergy from a systems biology perspective
Modeling the evolution of a classic genetic switch
c-Myc and viral cofactor Kaposin B co-operate to elicit angiogenesis through modulating miRNome traits of endothelial cells
Protein interaction networks as metric spaces: a novel perspective on distribution of hubs
Robust network structure of the Sln1-Ypd1-Ssk1 three-component phospho-relay prevents unintended activation of the HOG MAPK pathway in Saccharomyces cerevisiae
OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains
A general framework for modeling growth and division of mammalian cells
Genes associated with genotype-specific DNA methylation in squamous cell carcinoma as candidate drug targets
MaGnET: a software tool for integrated visualisation of functional genomic data relating to the malaria parasite
Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana
Computational systems biology in the big data era
Information propagation within the Genetic Network of Saccharomyces cerevisiae
Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis
Ranges of control in the transcriptional regulation of Escherichia coli
Integrated analysis of mutations, miRNA and mRNA expression in glioblastoma
Inference of complex biological networks: distinguishability issues and optimization-based solutions
Trade-offs between drug toxicity and benefit in the multi-antibiotic resistance system underlie optimal growth of E. coli
New network topology approaches reveal differential correlation patterns in breast cancer
Symbolic flux analysis for genome-scale metabolic networks
An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro
Progesterone signalling in broiler skeletal muscle is associated with divergent feed efficiency
Seeded Bayesian Networks: Constructing genetic networks from microarray data
Further developments towards a genome-scale metabolic model of yeast
The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis
Analysis of a spatial gene expression database for sea anemone Nematostella vectensis during early development
On control of singleton attractors in multiple Boolean networks: integer programming-based method
SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework
Heterogeneity reduces sensitivity of cell death for TNF-Stimuli
Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer
Synchronization ability of coupled cell-cycle oscillators in changing environments
Metabolic investigation of host/pathogen interaction using MS2-infected Escherichia coli
Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates
A multi-level study of recombinant Pichia pastoris in different oxygen conditions
Dynamic Optimization with Particle Swarms (DOPS): a meta-heuristic for parameter estimation in biochemical models
Transdifferentiation of pancreatic cells by loss of contact-mediated signaling
A tree-like Bayesian structure learning algorithm for small-sample datasets from complex biological model systems
Understanding dynamics using sensitivity analysis: caveat and solution
Network-based biomarkers enhance classical approaches to prognostic gene expression signatures
Regulatory network reconstruction using an integral additive model with flexible kernel functions
Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions
Discovery of metabolite biomarkers: flux analysis and reaction-reaction network approach
Modeling heterogeneous responsiveness of intrinsic apoptosis pathway
Transcription factor and microRNA-regulated network motifs for cancer and signal transduction networks
Quantitative maps of genetic interactions in yeast - Comparative evaluation and integrative analysis
An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis
Simulating epidermal growth factor receptor interaction with ligand
Automatic validation of computational models using pseudo-3D spatio-temporal model checking
Predicting and characterizing selective multiple drug treatments for metabolic diseases and cancer
TF-Cluster: A pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM)
The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus
Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae
Inference of domain-disease associations from domain-protein, protein-disease and disease-disease relationships
A quantitative systems pharmacology (QSP) model for Pneumocystis treatment in mice
A combinatorial approach of Proteomics and Systems Biology in unravelling the mechanisms of acute kidney injury (AKI): involvement of NMDA receptor GRIN1 in murine AKI
Discovery of Boolean metabolic networks: integer linear programming based approach
Effects of downstream genes on synthetic genetic circuits
Predicting the points of interaction of small molecules in the NF-κB pathway
Optimization of personalized therapies for anticancer treatment
Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach
Identification of key player genes in gene regulatory networks
Frequency-based time-series gene expression recomposition using PRIISM
Simulation methods with extended stability for stiff biochemical Kinetics
A systems approach identifies co-signaling molecules of early growth response 1 transcription factor in immobilization stress
16S rRNA metagenome clustering and diversity estimation using locality sensitive hashing
Characterization of regulatory features of housekeeping and tissue-specific regulators within tissue regulatory networks
Autoimmunity and tumor immunology: two facets of a probabilistic immune system
Systems genetics analyses predict a transcription role for P2P-R: Molecular confirmation that P2P-R is a transcriptional co-repressor
Mining functional subgraphs from cancer protein-protein interaction networks
Analysis of Alzheimer's disease severity across brain regions by topological analysis of gene co-expression networks
Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces