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

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