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- 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
- Getting started with MediaWiki
- Guidelines for Summarizing a Literature Study
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- Hierarchical optimization for the efficient parametrization of ODE models
- Hybrid optimization method with general switching strategy for parameter estimation
- 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
- Literature Studies
- 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