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  1. A comparison of methods for quantifying prediction uncertainty in systems biology
  2. A general modular framework for gene set enrichment analysis
  3. A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data
  4. Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies
  5. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ
  6. An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics
  7. An improved algorithm for peak detection in mass spectra based on continuous wavelet transform
  8. Benchmark problems for dynamic modeling of intracellular processes
  9. Benchmarking Projects
  10. Benchmarking Studies in Computational Biology
  11. Benchmarking optimization methods for parameter estimation in large kinetic models
  12. Bioinformatics and Statistics: LC‐MS (/MS) Data Preprocessing for Biomarker Discovery
  13. Chemometric methods in data processing of mass spectrometry-based metabolomics: A review
  14. Comparative evaluation of preprocessing freeware on chromatography/mass spectrometry data for signature discovery
  15. Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16
  16. Comparison of metaheuristic strategies for peakbin selection in proteomic mass spectrometry data
  17. Comparison of peak‐picking workflows for untargeted liquid chromatography/high‐resolution mass spectrometry metabolomics data analysis
  18. Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data
  19. Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems
  20. Comprehensive evaluation of untargeted metabolomics data processing software in feature detection, quantification and discriminating marker selection
  21. Concepts for Bechmarking Studies:
  22. DMR Calling from BSSEQ:
  23. DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts
  24. DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data
  25. Data-driven normalization strategies for high-throughput quantitative RT-PCR
  26. Data-driven reverse engineering of signaling pathways using ensembles of dynamic models
  27. Data processing has major impact on the outcome of quantitative label-free LC-MS analysis
  28. Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus
  29. Detecting and overcoming systematic bias in high-throughput screening technologies: a comprehensive review of practical issues and methodological solutions
  30. Efficient computation of steady states in large-scale ODE models of biochemical reaction networks
  31. Efficient parameterization of large-scale dynamic models based on relative measurements
  32. Evaluation of Derivative-Free Optimizers for Parameter Estimation in Systems Biology
  33. Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data
  34. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data
  35. Fast derivatives of likelihood functionals for ODE based models using adjoint-state method
  36. Funding
  37. Gene set analysis methods: a systematic comparison
  38. Getting started with MediaWiki
  39. Guidelines for Summarizing a Literature Study
  40. Help
  41. Hierarchical optimization for the efficient parametrization of ODE models
  42. Hybrid optimization method with general switching strategy for parameter estimation
  43. Identification and Correction of Additive and Multiplicative Spatial Biases in Experimental High-Throughput Screening
  44. Identifying and quantifying metabolites by scoring peaks of GC-MS data
  45. Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes
  46. Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching
  47. Lessons Learned from Quantitative Dynamical Modeling in Systems Biology
  48. Literature Studies
  49. MS‐Analyzer: preprocessing and data mining services for proteomics applications on the Grid
  50. Machine learning methods for predictive proteomics

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