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- A benchmark of genetic variant calling pipelines using metagenomic short-read sequencing
- A comparative study of evaluating missing value imputation methods in label-free proteomics
- A comparison of methods for quantifying prediction uncertainty in systems biology
- A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling
- A general modular framework for gene set enrichment analysis
- A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data
- Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies
- Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ
- An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics
- An improved algorithm for peak detection in mass spectra based on continuous wavelet transform
- Analysing microbiome intervention design studies: Comparison of alternative multivariate statistical methods
- Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
- Benchmark of data processing methods and machine learning models for gut microbiome-based diagnosis of inflammatory bowel disease
- Benchmark problems for dynamic modeling of intracellular processes
- Benchmarking Metagenomics Tools for Taxonomic Classification
- Benchmarking Projects
- Benchmarking Quantitative Performance in Label-Free Proteomics
- Benchmarking Studies in Computational Biology
- Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases
- Benchmarking of 16S rRNA gene databases using known strain sequences
- Benchmarking optimization methods for parameter estimation in large kinetic models
- Bioinformatics and Statistics: LC‐MS (/MS) Data Preprocessing for Biomarker Discovery
- Chemometric methods in data processing of mass spectrometry-based metabolomics: A review
- Comparative evaluation of preprocessing freeware on chromatography/mass spectrometry data for signature discovery
- Comparative study of classifiers for human microbiome data
- Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16
- Comparison of metaheuristic strategies for peakbin selection in proteomic mass spectrometry data
- Comparison of peak‐picking workflows for untargeted liquid chromatography/high‐resolution mass spectrometry metabolomics data analysis
- Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data
- Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
- Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems
- Comprehensive evaluation of untargeted metabolomics data processing software in feature detection, quantification and discriminating marker selection
- Concepts for Bechmarking Studies:
- DMR Calling from BSSEQ:
- DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts
- DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data
- Data-driven normalization strategies for high-throughput quantitative RT-PCR
- Data-driven reverse engineering of signaling pathways using ensembles of dynamic models
- Data processing has major impact on the outcome of quantitative label-free LC-MS analysis
- Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus
- Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches
- Detecting and overcoming systematic bias in high-throughput screening technologies: a comprehensive review of practical issues and methodological solutions
- Distribution-based comprehensive evaluation of methods for differential expression analysis in metatranscriptomics
- Efficient computation of steady states in large-scale ODE models of biochemical reaction networks
- Efficient parameterization of large-scale dynamic models based on relative measurements
- Evaluating supervised and unsupervised background noise correction in human gut microbiome data
- Evaluation of Derivative-Free Optimizers for Parameter Estimation in Systems Biology
- Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data
- Evaluation of the microba community profiler for taxonomic profiling of metagenomic datasets from the human gut microbiome
- Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data
