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- A Comprehensive Survey of Statistical Approaches for Differential Expression Analysis in Single-Cell RNA Sequencing Studies
- 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
- 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 Quantitative Performance in Label-Free Proteomics
- 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
- Catalyst: Fast and flexible modeling of reaction networks
- 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
- Fast derivatives of likelihood functionals for ODE based models using adjoint-state method
- Funding
- Gene set analysis methods: a systematic comparison
- Guidelines for Summarizing a Literature Study
- Identification and Correction of Additive and Multiplicative Spatial Biases in Experimental High-Throughput Screening
- Identifying and quantifying metabolites by scoring peaks of GC-MS data
- Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes
- Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching
- LEMMI: a continuous benchmarking platform for metagenomics classifiers
- Lessons Learned from Quantitative Dynamical Modeling in Systems Biology
- MS‐Analyzer: preprocessing and data mining services for proteomics applications on the Grid
- Machine learning methods for predictive proteomics
- MeltDB: a software platform for the analysis and integration of metabolomics experiment data
- MetaboAnalyst: a web server for metabolomic data analysis and interpretation
- MethCP: Differentially Methylated Region Detection with Change Point Models (bioRxiv)
- Microbiome differential abundance methods produce different results across 38 datasets
- Mini-batch optimization enables training of ODE models on large-scale datasets
- Missing value estimation methods for DNA microarrays
- Missing values in mass spectrometry based metabolomics: an undervalued step in the data processing pipeline
- Mockrobiota: a public resource for microbiome bioinformatics benchmarking
- NOREVA: normalization and evaluation of MS-based metabolomics data
- Normalization regarding non-random missing values in high-throughput mass spectrometry data
- NormalyzerDE: Online Tool for Improved Normalization of Omics Expression Data and High-Sensitivity Differential Expression Analysis
- OpenMS: a flexible open-source software platform for mass spectrometry data analysis
- Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis
- Optimization and uncertainty analysis of ODE models using second order adjoint sensitivity analysis
- Optimization of miRNA-seq data preprocessing
- Parameter Estimation and Variable Selection for Big Systems of Linear Ordinary Differential Equations: A Matrix-Based Approach
- Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy
- Parameter estimation in models of biological oscillators: an automated regularised estimation approach
- Parameter estimation with bio-inspired meta-heuristic optimization: modeling the dynamics of endocytosis
- Peak alignment using wavelet pattern matching and differential evolution
- Peakbin selection in mass spectrometry data using a consensus approach with estimation of distribution algorithms
- Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis
- Predicting Breast Cancer Survivability Using Data Mining Techniques
- Preprocessing of tandem mass spectrometric data to support automatic protein identification
- Prevention, diagnosis and treatment of high-throughput sequencing data pathologies
- Project 20 Benchmark Problems for Modelling Intracellular Processes
- Project Imputation in Proteomics
- Recursive partitioning for missing data imputation in the presence of interaction effects
- Recursive partitioning for missing data imputation in the presence of interaction effects.
- Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics
- Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics.
- Robust calibration of hierarchical population models for heterogeneous cell populations
- Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
- Simultaneous Improvement in the Precision, Accuracy and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains
- Software platform for high-throughput glycomics
- TEMPLATE
- Test title
- Testing structural identifiability by a simple scaling method
- The effects of nonignorable missing data on label-free mass spectrometry proteomics experiments
- The impact of sample imbalance on identifying differentially expressed genes
- Toward a gold standard for benchmarking gene set enrichment analysis
- Tracking for parameter and state estimation in possibly misspecified partially observed linear Ordinary Differential Equations
- Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes
