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1. Literature Studies‏‎ (232 revisions)
2. A comparison of methods for quantifying prediction uncertainty in systems biology‏‎ (48 revisions)
3. Hierarchical optimization for the efficient parametrization of ODE models‏‎ (22 revisions)
4. Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis‏‎ (22 revisions)
5. DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts‏‎ (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. Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16‏‎ (16 revisions)
10. Benchmarking optimization methods for parameter estimation in large kinetic models‏‎ (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. Benchmark problems for dynamic modeling of intracellular processes‏‎ (11 revisions)
17. Gene set analysis methods: a systematic comparison‏‎ (11 revisions)
18. Benchmarking Projects‏‎ (10 revisions)
19. Guidelines for Summarizing a Literature Study‏‎ (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. Benchmarking Studies in Computational Biology‏‎ (9 revisions)
23. Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics.‏‎ (9 revisions)
24. Project 20 Benchmark Problems for Modelling Intracellular Processes‏‎ (6 revisions)
25. Getting started with MediaWiki‏‎ (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. Main Page‏‎ (4 revisions - redirect page)
31. Parameter Estimation and Variable Selection for Big Systems of Linear Ordinary Differential Equations: A Matrix-Based Approach‏‎ (4 revisions)
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. A comparative study of evaluating missing value imputation methods in label-free proteomics‏‎ (3 revisions)
38. Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy‏‎ (3 revisions)
39. Chemometric methods in data processing of mass spectrometry-based metabolomics: A review‏‎ (3 revisions)
40. An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics‏‎ (2 revisions)
41. Parameter estimation with bio-inspired meta-heuristic optimization: modeling the dynamics of endocytosis‏‎ (2 revisions)
42. An improved algorithm for peak detection in mass spectra based on continuous wavelet transform‏‎ (2 revisions)
43. Comparison of peak‐picking workflows for untargeted liquid chromatography/high‐resolution mass spectrometry metabolomics data analysis‏‎ (2 revisions)
44. Efficient computation of steady states in large-scale ODE models of biochemical reaction networks‏‎ (2 revisions)
45. Testing structural identifiability by a simple scaling method‏‎ (2 revisions)
46. Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data‏‎ (2 revisions)
47. Efficient parameterization of large-scale dynamic models based on relative measurements‏‎ (2 revisions)
48. Predicting Breast Cancer Survivability Using Data Mining Techniques‏‎ (2 revisions)
49. The effects of nonignorable missing data on label-free mass spectrometry proteomics experiments‏‎ (2 revisions)
50. NOREVA: normalization and evaluation of MS-based metabolomics data‏‎ (2 revisions)

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