yusuke1997/dblp-id-title huggingface dataset:
Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs
Probabilistic strain optimization under constraint uncertainty
KDiamend: a package for detecting key drivers in a molecular ecological network of disease
Stochastic analysis of the GAL genetic switch in Saccharomyces cerevisiae: Modeling and experiments reveal hierarchy in glucose repression
Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis
Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems
Combining experimental and mathematical modeling to reveal mechanisms of macrophage-dependent left ventricular remodeling
MicroRNA 3' end nucleotide modification patterns and arm selection preference in liver tissues
Genome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach
Mass segmentation using a combined method for cancer detection
Multi-objective optimization of enzyme manipulations in metabolic networks considering resilience effects
Distinguishing the rates of gene activation from phenotypic variations
Integrated network analysis of transcriptomic and proteomic data in psoriasis
KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape
Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions
A new computational method to split large biochemical networks into coherent subnets
PFA toolbox: a MATLAB tool for Metabolic Flux Analysis
Threshold-dominated regulation hides genetic variation in gene expression networks
A computational analysis of protein-protein interaction networks in neurodegenerative diseases
The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work
Model-based extension of high-throughput to high-content data
Scope and limitations of yeast as a model organism for studying human tissue-specific pathways
From gene expression to gene regulatory networks in Arabidopsis thaliana
Finding the positive feedback loops underlying multi-stationarity
Relative impact of multi-layered genomic data on gene expression phenotypes in serous ovarian tumors
miRNAs and target genes in the blood as biomarkers for the early diagnosis of Parkinson's disease
Set membership experimental design for biological systems
A network based covariance test for detecting multivariate eQTL in saccharomyces cerevisiae
Making life difficult for Clostridium difficile: augmenting the pathogen's metabolic model with transcriptomic and codon usage data for better therapeutic target characterization
The role of TGF-β signaling and apoptosis in innate and adaptive immunity in zebrafish: a systems biology approach
In silico drug combination discovery for personalized cancer therapy
Systems biology research at BGRS-2018
Continuous time boolean modeling for biological signaling: application of Gillespie algorithm
Rule-based multi-level modeling of cell biological systems
KPP: KEGG Pathway Painter
Systematic approach to Escherichia coli cell population control using a genetic lysis circuit
MISC: missing imputation for single-cell RNA sequencing data
Inferring the conservative causal core of gene regulatory networks
PathNER: a tool for systematic identification of biological pathway mentions in the literature
Mathematical modelling of interacting mechanisms for hypoxia mediated cell cycle commitment for mesenchymal stromal cells
Annual Acknowledgement of Reviewers
Natural selection drives rapid evolution of mouse embryonic heart enhancers
Urine proteome changes associated with autonomic regulation of heart rate in cosmonauts
Optimized submerged batch fermentation strategy for systems scale studies of metabolic switching in Streptomyces coelicolor A3(2)
Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes
Computational disease modeling - fact or fiction?
Transcriptional robustness and protein interactions are associated in yeast
A systems biology approach to modelling tea (Camellia sinensis)
Parameter inference for stochastic single-cell dynamics from lineage tree data
Combining test statistics and models in bootstrapped model rejection: it is a balancing act
Critical assessment of human metabolic pathway databases: a stepping stone for future integration
IL-2 sensitivity and exogenous IL-2 concentration gradient tune the productive contact duration of CD8 + T cell-APC: a multiscale modeling study
microRNA evolution in a human transcription factor and microRNA regulatory network
Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss
EndoNet: an information resource about the intercellular signaling network
A cooperative strategy for parameter estimation in large scale systems biology models
Automated characterization of cell shape changes during amoeboid motility by skeletonization
The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize
Elongation, proliferation & migration differentiate endothelial cell phenotypes and determine capillary sprouting
Validation and selection of ODE based systems biology models: how to arrive at more reliable decisions
Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol
Parameter optimization by using differential elimination: a general approach for introducing constraints into objective functions
Applications of sensitivity analysis for drug discovery and development in the ErbB receptor network
Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes
A general co-expression network-based approach to gene expression analysis: comparison and applications
Visualising protein interaction networks with power graphs
Effects of promoter leakage on dynamics of gene expression
A genetic network model of cellular responses to lithium treatment and cocaine abuse in bipolar disorder
Epidermal growth factor receptor mutation in combination with expression of MIG6 alters gefitinib sensitivity
Combination therapy for melanoma with BRAF/MEK inhibitor and immune checkpoint inhibitor: a mathematical model
Robust sparse canonical correlation analysis
Modeling of celiac disease immune response and the therapeutic effect of potential drugs
Identification of genetic markers with synergistic survival effect in cancer
Genetic noise control via protein oligomerization
Analysis of intercellular signal transduction in the tumor microenvironment
Cancer core modules identification through genomic and transcriptomic changes correlation detection at network level
Dynamics of the discovery process of protein-protein interactions from low content studies
Bridging time scales in cellular decision making with a stochastic bistable switch
Rate control analysis of the translation initiation pathway in S. cerevisiae
MicroRNA sequence and expression database
Exploring virus relationships based on virus-host protein-protein interaction network
Evaluation of the lower protein limit in the budding yeast Saccharomyces cerevisiae using TIPI-gTOW
Gene-microRNA network module analysis for ovarian cancer
Regulation patterns in signaling networks of cancer
Constraint-based perturbation analysis with cluster Newton method: a case study of personalized parameter estimations with irinotecan whole-body physiologically based pharmacokinetic model
Robust synchronization control scheme of a population of nonlinear stochastic synthetic genetic oscillators under intrinsic and extrinsic molecular noise via quorum sensing
Data integration in the era of omics: current and future challenges
Fluxome study of Pseudomonas fluorescens reveals major reorganisation of carbon flux through central metabolic pathways in response to inactivation of the anti-sigma factor MucA
Qualitative networks: a symbolic approach to analyze biological signaling networks
Constructing stochastic models from deterministic process equations by propensity adjustment
Two-stage flux balance analysis of metabolic networks for drug target identification
A systematic molecular circuit design method for gene networks under biochemical time delays and molecular noises
Vascular endothelial growth factor A as predictive marker for mTOR inhibition in relapsing high-grade serous ovarian cancer
Reconstruction of metabolic pathways for the cattle genome
On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella
Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae
Modeling suggests that gene circuit architecture controls phenotypic variability in a bacterial persistence network
Identification of novel drug targets for diamond-blackfan anemia based on RPS19 gene mutation using protein-protein interaction network
miR2Gene: pattern discovery of single gene, multiple genes, and pathways by enrichment analysis of their microRNA regulators
Genotype networks in metabolic reaction spaces
Physiological fidelity or model parsimony? The relative performance of reverse-toxicokinetic modeling approaches
Missing value imputation for microarray data: a comprehensive comparison study and a web tool
Primary sex determination of placental mammals: a modelling study uncovers dynamical developmental constraints in the formation of Sertoli and granulosa cells
Dynamics of the quorum sensing switch: stochastic and non-stationary effects
Genomic phenotyping of the essential and non-essential yeast genome detects novel pathways for alkylation resistance
A review of imaging techniques for systems biology
Is the transcript from the overlapping region of two converging genes part of either gene?
Single molecules can operate as primitive biological sensors, switches and oscillators
On finite-horizon control of genetic regulatory networks with multiple hard-constraints
In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks
Parameter adaptations during phenotype transitions in progressive diseases
A probabilistic context-free grammar for the detection of binding sites from a protein sequence
Using the ratio of means as the effect size measure in combining results of microarray experiments
Remodeling adipose tissue through in silico modulation of fat storage for the prevention of type 2 diabetes
Dynamics of in silico leukocyte rolling, activation, and adhesion
A stem cell niche dominance theorem
Extraction of elementary rate constants from global network analysis of E. coli central metabolism
Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae
Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation
Exhaustive identification of steady state cycles in large stoichiometric networks
Signaling cascades transmit information downstream and upstream but unlikely simultaneously
Towards in vivo estimation of reaction kinetics using high-throughput metabolomics data: a maximum likelihood approach
Modelling the comet assay
Analysis of complex metabolic behavior through pathway decomposition
When the human viral infectome and diseasome networks collide: towards a systems biology platform for the aetiology of human diseases
Preeclampsia: a bioinformatics approach through protein-protein interaction networks analysis
Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress
Transcriptomic and metabolic flux analyses reveal shift of metabolic patterns during rice grain development
Visualizing regulatory interactions in metabolic networks
An novel frequent probability pattern mining algorithm based on circuit simulation method in uncertain biological networks
Identification of core T cell network based on immunome interactome
A fast and efficient count-based matrix factorization method for detecting cell types from single-cell RNAseq data
TGF-beta stimulation in human and murine cells reveals commonly affected biological processes and pathways at transcription level
Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism
Version control of pathway models using XML patches
Metabolic flux analysis for directing metabolism of Streptomyces olindensis from growth to anti-tumor drug (cosmomycin) production
Revisiting the variation of clustering coefficient of biological networks suggests new modular structure
Chemoattraction of macrophages by secretory molecules derived from cells expressing the signal peptide of eosinophil cationic protein
The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models
Increased AURKA promotes cell proliferation and predicts poor prognosis in bladder cancer
FAME, the Flux Analysis and Modeling Environment
The emerging role of microRNA-4487/6845-3p in Alzheimer's disease pathologies is induced by Aβ25-35 triggered in SH-SY5Y cell
PREAL: prediction of allergenic protein by maximum Relevance Minimum Redundancy (mRMR) feature selection
Diffusive coupling can discriminate between similar reaction mechanisms in an allosteric enzyme system
Correction to: circular RNA expression profiles during the differentiation of mouse neural stem cells
A linear programming computational framework integrates phosphor-proteomics and prior knowledge to predict drug efficacy
Bayesian inference based modelling for gene transcriptional dynamics by integrating multiple source of knowledge
Prediction of protein self-interactions using stacked long short-term memory from protein sequences information
A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count test
Exact model reduction of combinatorial reaction networks
Identification of phenotypes in patient microarrays
Systems analysis of quantitative shRNA-library screens identifies regulators of cell adhesion
Investigating the utility of clinical outcome-guided mutual information network in network-based Cox regression
Robust simplifications of multiscale biochemical networks
A regulatory network modeled from wild-type gene expression data guides functional predictions in Caenorhabditis elegans development
Pipeline design to identify key features and classify the chemotherapy response on lung cancer patients using large-scale genetic data
A polynomial based model for cell fate prediction in human diseases
Identification of regulatory structure and kinetic parameters of biochemical networks via mixed-integer dynamic optimization
Impact of the solvent capacity constraint on E. coli metabolism
Site-specific recombinatorics: in situ cellular barcoding with the Cre Lox system
Paracrine and autocrine regulation of gene expression by Wnt-inhibitor Dickkopf in wild-type and mutant hepatocytes
Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network
Bayesian modeling suggests that IL-12 (p40), IL-13 and MCP-1 drive murine cytokine networks in vivo
An Algebra-Based Method for Inferring Gene Regulatory Networks
Precise generation of systems biology models from KEGG pathways
TIGRESS: Trustful Inference of Gene REgulation using Stability Selection
Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates
PROXIMAL: a method for Prediction of Xenobiotic Metabolism
Archaic chaos: intrinsically disordered proteins in Archaea
ChIPMonk: software for viewing and analysing ChIP-on-chip data
Two accurate sequence, structure, and phylogenetic template-based RNA alignment systems
Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells
In silico prediction system of CYP450-mediated metabolism profile
Dynamic modeling of yeast meiotic initiation
Curating the innate immunity interactome
Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus
Study of gene function based on spatial co-expression in a high-resolution mouse brain atlas
Modularity and evolutionary constraints in a baculovirus gene regulatory network
Scalable prediction of compound-protein interactions using minwise hashing
PathCase-SB: integrating data sources and providing tools for systems biology research
Network properties of human disease genes with pleiotropic effects
Natural selection governs local, but not global, evolutionary gene coexpression networks in Caenorhabditis elegans
Genome-scale constraint-based modeling of Geobacter metallireducens
Computational modelling of bovine ovarian follicle development
Systems biology analysis reveals new insights into invasive lung cancer
An in silico approach combined with in vivo experiments enables the identification of a new protein whose overexpression can compensate for specific respiratory defects in Saccharomyces cerevisiae
AlzPathway: a comprehensive map of signaling pathways of Alzheimer's disease
Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains
A synthetic mammalian network to compute population borders based on engineered reciprocal cell-cell communication
Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis
Differentially co-expressed interacting protein pairs discriminate samples under distinct stages of HIV type 1 infection
Prioritizing protein complexes implicated in human diseases by network optimization
Building and analyzing protein interactome networks by cross-species comparisons
Inferring the physical connectivity of complex networks from their functional dynamics
Computer aided multi-parameter gene design: impact of synthetic dnas on protein expression enhancement
An investigation of spatial signal transduction in cellular networks
Epstein-Barr virus latency switch in human B-cells: a physico-chemical model
Photo-sensitive degron variants for tuning protein stability by light
State Space Model with hidden variables for reconstruction of gene regulatory networks
Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes
Spatial localization of the first and last enzymes effectively connects active metabolic pathways in bacteria
A cross-species analysis method to analyze animal models' similarity to human's disease state
Integrating multiple networks for protein function prediction
A chemokine gene expression signature derived from meta-analysis predicts the pathogenicity of viral respiratory infections
A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola
Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models
The dynamics and efficacy of antiviral RNA silencing: A model study
MetaDBSite: a meta approach to improve protein DNA-binding sites prediction
In silico modeling of the effects of alpha-synuclein oligomerization on dopaminergic neuronal homeostasis
Differentiation resistance through altered retinoblastoma protein function in acute lymphoblastic leukemia: in silico modeling of the deregulations in the G1/S restriction point pathway
Meta-analysis of human gene expression in response to Mycobacterium tuberculosis infection reveals potential therapeutic targets
Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise
Identifying reaction modules in metabolic pathways: bioinformatic deduction and experimental validation of a new putative route in purine catabolism
BLASSO: integration of biological knowledge into a regularized linear model
Integrated single cell data analysis reveals cell specific networks and novel coactivation markers
Elementary flux modes - state-of-the-art implementation and scope of application
On the functional diversity of dynamical behaviour in genetic and metabolic feedback systems
Role of plant MicroRNA in cross-species regulatory networks of humans
Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas
Shrinkage regression-based methods for microarray missing value imputation
Learning accurate and interpretable models based on regularized random forests regression
Inferring genetic interactions via a nonlinear model and an optimization algorithm
Adapted Boolean network models for extracellular matrix formation
Where next for the reproducibility agenda in computational biology?
Analyzing networks of phenotypes in complex diseases: methodology and applications in COPD
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks
Parameter estimation with bio-inspired meta-heuristic optimization: modeling the dynamics of endocytosis
MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology
Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell
Condor-COPASI: high-throughput computing for biochemical networks
Estimating cell diffusivity and cell proliferation rate by interpreting IncuCyte ZOOM™ assay data using the Fisher-Kolmogorov model
Quantifying differential gene connectivity between disease states for objective identification of disease-relevant genes
Noise filtering tradeoffs in spatial gradient sensing and cell polarization response
Partially observed bipartite network analysis to identify predictive connections in transcriptional regulatory networks
ARN: analysis and prediction by adipogenic professional database
A group LASSO-based method for robustly inferring gene regulatory networks from multiple time-course datasets
From protein interactions to functional annotation: graph alignment in Herpes
Predicting gene co-expression from CIS-regulatory regions
On gene dosage balance in protein complexes: a comment on Semple JI, Vavouri T, Lehner B. A simple principle concerning the robustness of protein complex activity to changes in gene expression
Expanding a dynamic flux balance model of yeast fermentation to genome-scale
Integrative network analysis of TCGA data for ovarian cancer
Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast
A mathematical model of iron import and trafficking in wild-type and Mrs3/4ΔΔ yeast cells
On optimal control policy for probabilistic Boolean network: a state reduction approach
Parameter identifiability-based optimal observation remedy for biological networks
Two-layer modular analysis of gene and protein networks in breast cancer
A quantitative model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations
Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry
Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data
Linking the ovarian cancer transcriptome and immunome
Identifying the missing proteins in human proteome by biological language model
Integrative analysis of methylation and transcriptional profiles to predict aging and construct aging specific cross-tissue networks
ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists
Modeling and analysis of the Delta-Notch dependent boundary formation in the Drosophila large intestine
The protein kinase Mζ network as a bistable switch to store neuronal memory
A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network
A mathematical model of the unfolded protein stress response reveals the decision mechanism for recovery, adaptation and apoptosis