yusuke1997/dblp-id-title huggingface dataset:
Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations
PMAMCA: prediction of microRNA-disease association utilizing a matrix completion approach
Insights from systems pharmacology into cardiovascular drug discovery and therapy
Stat and interferon genes identified by network analysis differentially regulate primitive and definitive erythropoiesis
Core modular blood and brain biomarkers in social defeat mouse model for post traumatic stress disorder
Decoding complex biological networks - tracing essential and modulatory parameters in complex and simplified models of the cell cycle
Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso
microRNAs' differential regulations mediate the progress of Human Papillomavirus (HPV)-induced Cervical Intraepithelial Neoplasia (CIN)
Modelling non-Markovian dynamics in biochemical reactions
A condition-specific codon optimization approach for improved heterologous gene expression in Saccharomyces cerevisiae
Validation of an FBA model for Pichia pastoris in chemostat cultures
Identification of putative drug targets for human sperm-egg interaction defect using protein network approach
Discriminating between rival biochemical network models: three approaches to optimal experiment design
Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction
A two-step framework for inferring direct protein-protein interaction network from AP-MS data
Differential networking meta-analysis of gastric cancer across Asian and American racial groups
A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data
From ERα66 to ERα36: a generic method for validating a prognosis marker of breast tumor progression
Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram
Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs
An Integrative multi-lineage model of variation in leukopoiesis and acute myelogenous leukemia
Predicting and understanding comprehensive drug-drug interactions via semi-nonnegative matrix factorization
Reaction-contingency based bipartite Boolean modelling
A systematic design method for robust synthetic biology to satisfy design specifications
Can single knockouts accurately single out gene functions?
mRNA translation and protein synthesis: an analysis of different modelling methodologies and a new PBN based approach
Mining breast cancer genes with a network based noise-tolerant approach
Improvement of phylogenetic method to analyze compositional heterogeneity
Stress-specific response of the p53-Mdm2 feedback loop
Parameter estimation and inference for stochastic reaction-diffusion systems: application to morphogenesis in D. melanogaster
Quantifying the roles of random motility and directed motility using advection-diffusion theory for a 3T3 fibroblast cell migration assay stimulated with an electric field
Engineering a synthetic molecular oscillator based on the Lotka-Volterra dynamic
Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast
The long journey to a Systems Biology of neuronal function
The decrease of consistence probability: at the crossroad of catastrophic transition of a biological system
3D Protein structure prediction with genetic tabu search algorithm
Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction
Finding low-conductance sets with dense interactions (FLCD) for better protein complex prediction
Challenges in horizontal model integration
Noise regulation by quorum sensing in low mRNA copy number systems
The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks
Integrating systems biology models and biomedical ontologies
Mimvec: a deep learning approach for analyzing the human phenome
Identification of upstream regulators for prognostic expression signature genes in colorectal cancer
Efficient parametric analysis of the chemical master equation through model order reduction
Identifying the topology of signaling networks from partial RNAi data
Meta-analysis of sex differences in gene expression in schizophrenia
Towards a quantitative understanding of the MITF-PIAS3-STAT3 connection
sybil - Efficient constraint-based modelling in R
Biomarker robustness reveals the PDGF network as driving disease outcome in ovarian cancer patients in multiple studies
Regulatory coordination of clustered microRNAs based on microRNA-transcription factor regulatory network
Small RNA profiles in soybean primary root tips under water deficit
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach
In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae
Integration of transcriptional inputs at promoters of the arabinose catabolic pathway
Robust dynamical pattern formation from a multifunctional minimal genetic circuit
Modelling chemotherapy effects on granulopoiesis
From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli
Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway
Stochastic adaptation and fold-change detection: from single-cell to population behavior
Construction of the influenza A virus infection-induced cell-specific inflammatory regulatory network based on mutual information and optimization
STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies
Analyzing fixed points of intracellular regulation networks with interrelated feedback topology
In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer
Annotating activation/inhibition relationships to protein-protein interactions using gene ontology relations
Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion
Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks
Identifying essential genes in bacterial metabolic networks with machine learning methods
HGPEC: a Cytoscape app for prediction of novel disease-gene and disease-disease associations and evidence collection based on a random walk on heterogeneous network
A transfer function approach to measuring cell inheritance
Identification of parameter correlations for parameter estimation in dynamic biological models
Robust Control of PEP Formation Rate in the Carbon Fixation Pathway of C 4 Plants by a Bi-functional Enzyme
Identification of control targets in Boolean molecular network models via computational algebra
SSER: Species specific essential reactions database
Tetramer formation in Arabidopsis MADS domain proteins: analysis of a protein-protein interaction network
Detangling PPI networks to uncover functionally meaningful clusters
Accurate multiple network alignment through context-sensitive random walk
Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum
A graphical model approach for inferring large-scale networks integrating gene expression and genetic polymorphism
Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms
A dynamical systems model of progesterone receptor interactions with inflammation in human parturition
Reframing gene essentiality in terms of adaptive flexibility
Hierarchical combinatorial deep learning architecture for pancreas segmentation of medical computed tomography cancer images
The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene
Identification of neutral biochemical network models from time series data
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps
Snazer: the simulations and networks analyzer
Supervised maximum-likelihood weighting of composite protein networks for complex prediction
FluxMap: A VANTED add-on for the visual exploration of flux distributions in biological networks
Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis
Designing optimal cell factories: integer programming couples elementary mode analysis with regulation
A multi-omic analysis of human naïve CD4+ T cells
Molecular and cellular factors control signal transduction via switchable allosteric modulator proteins (SAMPs)
Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum
DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts
Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks
Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets
Combinatorial network of transcriptional regulation and microRNA regulation in human cancer
FiloDetect: automatic detection of filopodia from fluorescence microscopy images
A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis
Integrative genomics identifies candidate microRNAs for pathogenesis of experimental biliary atresia
Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design
Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints
Robustness from flexibility in the fungal circadian clock
Modeling protein network evolution under genome duplication and domain shuffling
Microarrays expression measurement
Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data
CD8 + T cell response to adenovirusvaccination and subsequent suppression of tumor growth: modeling, simulation and analysis
A Drosophila systems model of pentylenetetrazole induced locomotor plasticity responsive to antiepileptic drugs
Functional network of glycan-related molecules: Glyco-Net in Glycoconjugate Data Bank
How to identify essential genes from molecular networks?
DNetDB: The human disease network database based on dysfunctional regulation mechanism
Dynamics of p53 and NF-κ
The integration of weighted human gene association networks based on link prediction
Mechanisms of gap gene expression canalization in the Drosophila blastoderm
Identifying MicroRNA-mRNA regulatory network in colorectal cancer by a combination of expression profile and bioinformatics analysis
Inferring context-sensitive Probabilistic Boolean Networks from gene expression data under multi-biological conditions
A new model of time scheme for progression of colorectal cancer
A computational tool for directing Taxus spp. cell culture metabolism from growth to Taxol ® , a diterpene alkaloid, production
Interactomics profiling of the negative regulatory function of carbon monoxide on RANKL-treated RAW 264.7 cells during osteoclastogenesis
Computational systems biology: integration of sequence, structure, network, and dynamics
Protein complex forming ability is favored over the features of interacting partners in determining the evolutionary rates of proteins in the yeast protein-protein interaction networks
Metabolic host responses to malarial infection during the intraerythrocytic developmental cycle
New insights about host response to smallpox using microarray data
A method for automated pathogenic content estimation with application to rheumatoid arthritis
A framework for biomedical figure segmentation towards image-based document retrieval
Machine learning based analyses on metabolic networks supports high-throughput knockout screens
Structural and functional analysis of cellular networks with CellNetAnalyzer
Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences
Modelling the evolution of transcriptional control networks using stochastic simulations and evolutionary computational methods
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
Kinase inhibitors can produce off-target effects and activate linked pathways by retroactivity
Employing conservation of co-expression to improve functional inference
Bayesian inference of the kinetic parameters of a realistic MAPK/ERK pathway
Comparisons of gene coexpression network modules in breast cancer and ovarian cancer
The biological context of HIV-1 host interactions reveals subtle insights into a system hijack
Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare
Modeling and analysis of the dynamic behavior of the XlnR regulon in Aspergillus niger
A kinetic model for RNA-interference of focal adhesions
A combined model reduction algorithm for controlled biochemical systems
On the architecture of cell regulation networks
Support vector machine prediction of enzyme function with conjoint triad feature and hierarchical context
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations
Revealing metabolite biomarkers for acupuncture treatment by linear programming based feature selection
Stochastic Modeling of B Lymphocyte Terminal Differentiation and Its Suppression by Dioxin
Different designs of kinase-phosphatase interactions and phosphatase sequestration shapes the robustness and signal flow in the MAPK cascade
Exploring pathway interactions in insulin resistant mouse liver
Genome-scale resources for Thermoanaerobacterium saccharolyticum
(Im)Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-expression regulation: marrying control engineering with metabolic control analysis
Crosstalk between transcription factors and microRNAs in human protein interaction network
An improved kinetic model for the acetone-butanol-ethanol pathway of Clostridium acetobutylicum and model-based perturbation analysis
Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data
Similarity in expression accounts for correlated evolution of interacting proteins
Summarizing cellular responses as biological process networks
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language
Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase
The drug cocktail network
Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca
Design of novel semisynethetic metalloenzyme from thermolysin
Molecules for memory: modelling CaMKII
Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks
Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy