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Showing below up to 93 results in range #1 to #93.

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  1. A comparative study of evaluating missing value imputation methods in label-free proteomics
  2. A comparison of methods for quantifying prediction uncertainty in systems biology
  3. A general modular framework for gene set enrichment analysis
  4. A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data
  5. Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies
  6. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ
  7. An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics
  8. An improved algorithm for peak detection in mass spectra based on continuous wavelet transform
  9. Benchmark problems for dynamic modeling of intracellular processes
  10. Benchmarking Projects
  11. Benchmarking Quantitative Performance in Label-Free Proteomics
  12. Benchmarking Studies in Computational Biology
  13. Benchmarking optimization methods for parameter estimation in large kinetic models
  14. Bioinformatics and Statistics: LC‐MS (/MS) Data Preprocessing for Biomarker Discovery
  15. Chemometric methods in data processing of mass spectrometry-based metabolomics: A review
  16. Comparative evaluation of preprocessing freeware on chromatography/mass spectrometry data for signature discovery
  17. Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16
  18. Comparison of metaheuristic strategies for peakbin selection in proteomic mass spectrometry data
  19. Comparison of peak‐picking workflows for untargeted liquid chromatography/high‐resolution mass spectrometry metabolomics data analysis
  20. Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data
  21. Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems
  22. Comprehensive evaluation of untargeted metabolomics data processing software in feature detection, quantification and discriminating marker selection
  23. Concepts for Bechmarking Studies:
  24. DMR Calling from BSSEQ:
  25. DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts
  26. DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data
  27. Data-driven normalization strategies for high-throughput quantitative RT-PCR
  28. Data-driven reverse engineering of signaling pathways using ensembles of dynamic models
  29. Data processing has major impact on the outcome of quantitative label-free LC-MS analysis
  30. Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus
  31. Detecting and overcoming systematic bias in high-throughput screening technologies: a comprehensive review of practical issues and methodological solutions
  32. Efficient computation of steady states in large-scale ODE models of biochemical reaction networks
  33. Efficient parameterization of large-scale dynamic models based on relative measurements
  34. Evaluation of Derivative-Free Optimizers for Parameter Estimation in Systems Biology
  35. Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data
  36. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data
  37. Fast derivatives of likelihood functionals for ODE based models using adjoint-state method
  38. Funding
  39. Gene set analysis methods: a systematic comparison
  40. Getting started with MediaWiki
  41. Guidelines for Summarizing a Literature Study
  42. Help
  43. Hierarchical optimization for the efficient parametrization of ODE models
  44. Hybrid optimization method with general switching strategy for parameter estimation
  45. Identification and Correction of Additive and Multiplicative Spatial Biases in Experimental High-Throughput Screening
  46. Identifying and quantifying metabolites by scoring peaks of GC-MS data
  47. Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes
  48. Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching
  49. Lessons Learned from Quantitative Dynamical Modeling in Systems Biology
  50. Literature Studies
  51. MS‐Analyzer: preprocessing and data mining services for proteomics applications on the Grid
  52. Machine learning methods for predictive proteomics
  53. MeltDB: a software platform for the analysis and integration of metabolomics experiment data
  54. MetaboAnalyst: a web server for metabolomic data analysis and interpretation
  55. MethCP: Differentially Methylated Region Detection with Change Point Models (bioRxiv)
  56. Mini-batch optimization enables training of ODE models on large-scale datasets
  57. Missing value estimation methods for DNA microarrays
  58. Missing values in mass spectrometry based metabolomics: an undervalued step in the data processing pipeline
  59. NOREVA: normalization and evaluation of MS-based metabolomics data
  60. Normalization regarding non-random missing values in high-throughput mass spectrometry data
  61. NormalyzerDE: Online Tool for Improved Normalization of Omics Expression Data and High-Sensitivity Differential Expression Analysis
  62. OpenMS: a flexible open-source software platform for mass spectrometry data analysis
  63. Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis
  64. Optimization and uncertainty analysis of ODE models using second order adjoint sensitivity analysis
  65. Optimization of miRNA-seq data preprocessing
  66. Parameter Estimation and Variable Selection for Big Systems of Linear Ordinary Differential Equations: A Matrix-Based Approach
  67. Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy
  68. Parameter estimation in models of biological oscillators: an automated regularised estimation approach
  69. Parameter estimation with bio-inspired meta-heuristic optimization: modeling the dynamics of endocytosis
  70. Peak alignment using wavelet pattern matching and differential evolution
  71. Peakbin selection in mass spectrometry data using a consensus approach with estimation of distribution algorithms
  72. Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis
  73. Performance of objective functions and optimization procedures for parameter estimation in system biology models
  74. Predicting Breast Cancer Survivability Using Data Mining Techniques
  75. Preprocessing of tandem mass spectrometric data to support automatic protein identification
  76. Prevention, diagnosis and treatment of high-throughput sequencing data pathologies
  77. Project 20 Benchmark Problems for Modelling Intracellular Processes
  78. Project Imputation in Proteomics
  79. Recursive partitioning for missing data imputation in the presence of interaction effects
  80. Recursive partitioning for missing data imputation in the presence of interaction effects.
  81. Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics
  82. Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics.
  83. Robust calibration of hierarchical population models for heterogeneous cell populations
  84. Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
  85. Simultaneous Improvement in the Precision, Accuracy and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains
  86. Software platform for high-throughput glycomics
  87. TEMPLATE
  88. Testing structural identifiability by a simple scaling method
  89. The effects of nonignorable missing data on label-free mass spectrometry proteomics experiments
  90. The impact of sample imbalance on identifying differentially expressed genes
  91. Toward a gold standard for benchmarking gene set enrichment analysis
  92. Tracking for parameter and state estimation in possibly misspecified partially observed linear Ordinary Differential Equations
  93. Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes

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