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  1. Literature Studies‏‎ (203 revisions)
  2. A comparison of methods for quantifying prediction uncertainty in systems biology‏‎ (48 revisions)
  3. DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts‏‎ (22 revisions)
  4. Hierarchical optimization for the efficient parametrization of ODE models‏‎ (22 revisions)
  5. Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis‏‎ (22 revisions)
  6. Lessons Learned from Quantitative Dynamical Modeling in Systems Biology‏‎ (20 revisions)
  7. Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies‏‎ (19 revisions)
  8. Fast derivatives of likelihood functionals for ODE based models using adjoint-state method‏‎ (17 revisions)
  9. Benchmarking optimization methods for parameter estimation in large kinetic models‏‎ (16 revisions)
  10. Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16‏‎ (16 revisions)
  11. Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus‏‎ (15 revisions)
  12. A general modular framework for gene set enrichment analysis‏‎ (15 revisions)
  13. Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks‏‎ (14 revisions)
  14. Performance of objective functions and optimization procedures for parameter estimation in system biology models‏‎ (13 revisions)
  15. MethCP: Differentially Methylated Region Detection with Change Point Models (bioRxiv)‏‎ (12 revisions)
  16. Gene set analysis methods: a systematic comparison‏‎ (11 revisions)
  17. Benchmark problems for dynamic modeling of intracellular processes‏‎ (11 revisions)
  18. Guidelines for Summarizing a Literature Study‏‎ (10 revisions)
  19. Benchmarking Projects‏‎ (10 revisions)
  20. Hybrid optimization method with general switching strategy for parameter estimation‏‎ (9 revisions)
  21. Evaluation of Derivative-Free Optimizers for Parameter Estimation in Systems Biology‏‎ (9 revisions)
  22. Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics.‏‎ (9 revisions)
  23. Benchmarking Studies in Computational Biology‏‎ (8 revisions)
  24. Getting started with MediaWiki‏‎ (6 revisions)
  25. Project 20 Benchmark Problems for Modelling Intracellular Processes‏‎ (6 revisions)
  26. Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems‏‎ (5 revisions)
  27. Mini-batch optimization enables training of ODE models on large-scale datasets‏‎ (4 revisions)
  28. Missing value estimation methods for DNA microarrays‏‎ (4 revisions)
  29. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data‏‎ (4 revisions)
  30. Parameter Estimation and Variable Selection for Big Systems of Linear Ordinary Differential Equations: A Matrix-Based Approach‏‎ (4 revisions)
  31. Main Page‏‎ (4 revisions - redirect page)
  32. Parameter estimation in models of biological oscillators: an automated regularised estimation approach‏‎ (4 revisions)
  33. Help‏‎ (3 revisions)
  34. Missing values in mass spectrometry based metabolomics: an undervalued step in the data processing pipeline‏‎ (3 revisions)
  35. Toward a gold standard for benchmarking gene set enrichment analysis‏‎ (3 revisions)
  36. Tracking for parameter and state estimation in possibly misspecified partially observed linear Ordinary Differential Equations‏‎ (3 revisions)
  37. Chemometric methods in data processing of mass spectrometry-based metabolomics: A review‏‎ (3 revisions)
  38. Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy‏‎ (3 revisions)
  39. Parameter estimation with bio-inspired meta-heuristic optimization: modeling the dynamics of endocytosis‏‎ (2 revisions)
  40. An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics‏‎ (2 revisions)
  41. An improved algorithm for peak detection in mass spectra based on continuous wavelet transform‏‎ (2 revisions)
  42. Testing structural identifiability by a simple scaling method‏‎ (2 revisions)
  43. DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data‏‎ (2 revisions)
  44. Data-driven normalization strategies for high-throughput quantitative RT-PCR‏‎ (2 revisions)
  45. Data-driven reverse engineering of signaling pathways using ensembles of dynamic models‏‎ (2 revisions)
  46. Predicting Breast Cancer Survivability Using Data Mining Techniques‏‎ (2 revisions)
  47. NOREVA: normalization and evaluation of MS-based metabolomics data‏‎ (2 revisions)
  48. Normalization regarding non-random missing values in high-throughput mass spectrometry data‏‎ (2 revisions)
  49. Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes‏‎ (2 revisions)
  50. Efficient computation of steady states in large-scale ODE models of biochemical reaction networks‏‎ (2 revisions)

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