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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

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