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- Benchmark problems for dynamic modeling of intracellular processes (11 revisions)
- Gene set analysis methods: a systematic comparison (11 revisions)
- MethCP: Differentially Methylated Region Detection with Change Point Models (bioRxiv) (12 revisions)
- Performance of objective functions and optimization procedures for parameter estimation in system biology models (13 revisions)
- Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks (14 revisions)
- Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus (15 revisions)
- A general modular framework for gene set enrichment analysis (15 revisions)
- Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 (16 revisions)
- Benchmarking optimization methods for parameter estimation in large kinetic models (16 revisions)
- Fast derivatives of likelihood functionals for ODE based models using adjoint-state method (17 revisions)
- Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies (19 revisions)
- Lessons Learned from Quantitative Dynamical Modeling in Systems Biology (20 revisions)
- Hierarchical optimization for the efficient parametrization of ODE models (22 revisions)
- Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis (22 revisions)
- DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts (22 revisions)
- A comparison of methods for quantifying prediction uncertainty in systems biology (48 revisions)
- Literature Studies (232 revisions)