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- Literature Studies (232 revisions)
- A comparison of methods for quantifying prediction uncertainty in systems biology (48 revisions)
- DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts (22 revisions)
- Hierarchical optimization for the efficient parametrization of ODE models (22 revisions)
- Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis (22 revisions)
- Lessons Learned from Quantitative Dynamical Modeling in Systems Biology (20 revisions)
- Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies (19 revisions)
- Fast derivatives of likelihood functionals for ODE based models using adjoint-state method (17 revisions)
- Benchmarking optimization methods for parameter estimation in large kinetic models (16 revisions)
- Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 (16 revisions)
- A general modular framework for gene set enrichment analysis (15 revisions)
- Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus (15 revisions)
- Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks (14 revisions)
- Performance of objective functions and optimization procedures for parameter estimation in system biology models (13 revisions)
- MethCP: Differentially Methylated Region Detection with Change Point Models (bioRxiv) (12 revisions)
- Gene set analysis methods: a systematic comparison (11 revisions)
- Benchmark problems for dynamic modeling of intracellular processes (11 revisions)
- Guidelines for Summarizing a Literature Study (10 revisions)
- Benchmarking Projects (10 revisions)
- Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics. (9 revisions)
- Hybrid optimization method with general switching strategy for parameter estimation (9 revisions)
- Evaluation of Derivative-Free Optimizers for Parameter Estimation in Systems Biology (9 revisions)
- Benchmarking Studies in Computational Biology (9 revisions)
- Getting started with MediaWiki (6 revisions)
- Project 20 Benchmark Problems for Modelling Intracellular Processes (6 revisions)
- Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems (5 revisions)
- Main Page (4 revisions - redirect page)
- Parameter Estimation and Variable Selection for Big Systems of Linear Ordinary Differential Equations: A Matrix-Based Approach (4 revisions)
- Parameter estimation in models of biological oscillators: an automated regularised estimation approach (4 revisions)
- Mini-batch optimization enables training of ODE models on large-scale datasets (4 revisions)
- Missing value estimation methods for DNA microarrays (4 revisions)
- Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data (4 revisions)
- Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy (3 revisions)
- Chemometric methods in data processing of mass spectrometry-based metabolomics: A review (3 revisions)
- Help (3 revisions)
- Missing values in mass spectrometry based metabolomics: an undervalued step in the data processing pipeline (3 revisions)
- Toward a gold standard for benchmarking gene set enrichment analysis (3 revisions)
- Tracking for parameter and state estimation in possibly misspecified partially observed linear Ordinary Differential Equations (3 revisions)
- A comparative study of evaluating missing value imputation methods in label-free proteomics (3 revisions)
- MS‐Analyzer: preprocessing and data mining services for proteomics applications on the Grid (2 revisions)
- Recursive partitioning for missing data imputation in the presence of interaction effects (2 revisions)
- DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data (2 revisions)
- Machine learning methods for predictive proteomics (2 revisions)
- Recursive partitioning for missing data imputation in the presence of interaction effects. (2 revisions)
- Data-driven normalization strategies for high-throughput quantitative RT-PCR (2 revisions)
- Catalyst: Fast and flexible modeling of reaction networks (2 revisions)
- Data-driven reverse engineering of signaling pathways using ensembles of dynamic models (2 revisions)
- Robust calibration of hierarchical population models for heterogeneous cell populations (2 revisions)
- An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics (2 revisions)
- Parameter estimation with bio-inspired meta-heuristic optimization: modeling the dynamics of endocytosis (2 revisions)
- An improved algorithm for peak detection in mass spectra based on continuous wavelet transform (2 revisions)
- Comparison of peak‐picking workflows for untargeted liquid chromatography/high‐resolution mass spectrometry metabolomics data analysis (2 revisions)
- Efficient computation of steady states in large-scale ODE models of biochemical reaction networks (2 revisions)
- Testing structural identifiability by a simple scaling method (2 revisions)
- Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data (2 revisions)
- Efficient parameterization of large-scale dynamic models based on relative measurements (2 revisions)
- Predicting Breast Cancer Survivability Using Data Mining Techniques (2 revisions)
- The effects of nonignorable missing data on label-free mass spectrometry proteomics experiments (2 revisions)
- NOREVA: normalization and evaluation of MS-based metabolomics data (2 revisions)
- Normalization regarding non-random missing values in high-throughput mass spectrometry data (2 revisions)
- NormalyzerDE: Online Tool for Improved Normalization of Omics Expression Data and High-Sensitivity Differential Expression Analysis (2 revisions)
- OpenMS: a flexible open-source software platform for mass spectrometry data analysis (2 revisions)
- Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes (2 revisions)
- Project Imputation in Proteomics (2 revisions)
- A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling (1 revision)
- Benchmarking of 16S rRNA gene databases using known strain sequences (1 revision)
- Optimization and uncertainty analysis of ODE models using second order adjoint sensitivity analysis (1 revision)
- Funding (1 revision)
- Optimization of miRNA-seq data preprocessing (1 revision)
- A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data (1 revision)
- Bioinformatics and Statistics: LC‐MS (/MS) Data Preprocessing for Biomarker Discovery (1 revision)
- Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics (1 revision)
- MeltDB: a software platform for the analysis and integration of metabolomics experiment data (1 revision)
- Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ (1 revision)
- Data processing has major impact on the outcome of quantitative label-free LC-MS analysis (1 revision)
- MetaboAnalyst: a web server for metabolomic data analysis and interpretation (1 revision)
- Comparative evaluation of preprocessing freeware on chromatography/mass spectrometry data for signature discovery (1 revision)
- Comparative study of classifiers for human microbiome data (1 revision)
- Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches (1 revision)
- Microbiome differential abundance methods produce different results across 38 datasets (1 revision)
- Peak alignment using wavelet pattern matching and differential evolution (1 revision)
- Simultaneous Improvement in the Precision, Accuracy and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains (1 revision)
- Analysing microbiome intervention design studies: Comparison of alternative multivariate statistical methods (1 revision)
- Detecting and overcoming systematic bias in high-throughput screening technologies: a comprehensive review of practical issues and methodological solutions (1 revision)
- Peakbin selection in mass spectrometry data using a consensus approach with estimation of distribution algorithms (1 revision)
- Software platform for high-throughput glycomics (1 revision)
- Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data (1 revision)
- Comparison of metaheuristic strategies for peakbin selection in proteomic mass spectrometry data (1 revision)
- Distribution-based comprehensive evaluation of methods for differential expression analysis in metatranscriptomics (1 revision)
- Identification and Correction of Additive and Multiplicative Spatial Biases in Experimental High-Throughput Screening (1 revision)
- Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis (1 revision)
- Test title (1 revision)
- Benchmark of data processing methods and machine learning models for gut microbiome-based diagnosis of inflammatory bowel disease (1 revision)
- Identifying and quantifying metabolites by scoring peaks of GC-MS data (1 revision)
- 20 Benchmark Models: (1 revision - redirect page)
- Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes (1 revision)
- Mockrobiota: a public resource for microbiome bioinformatics benchmarking (1 revision)
- 20 Benchmark Problem for Modelling Intracellular Processes (1 revision - redirect page)
- Benchmarking Metagenomics Tools for Taxonomic Classification (1 revision)
- Comprehensive benchmarking and ensemble approaches for metagenomic classifiers (1 revision)
