Adaptive sequence alignment for metagenomic data analysis.

ECCB2024: The 23rd European Conference on Computational Biology.

Cell-connectivity-guided trajectory inference from single-cell data.

VarSCAT: A computational tool for sequence context annotations of genomic variants.

Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data.

scShaper: an ensemble method for fast and accurate linear trajectory inference from single-cell RNA-seq data.

Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data.

Estimating cell type-specific differential expression using deconvolution.

Correction to: PhosPiR: an automated phosphoproteomic pipeline in R.

PhosPiR: an automated phosphoproteomic pipeline in R.

Crowdsourcing digital health measures to predict Parkinson's disease severity: the Parkinson's Disease Digital Biomarker DREAM Challenge.

ILoReg: a tool for high-resolution cell population identification from single-cell RNA-seq data.

Stable Iterative Variable Selection.

Systematic evaluation of differential splicing tools for RNA-seq studies.

SimPhospho: a software tool enabling confident phosphosite assignment.

Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics.

A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation.

A systematic evaluation of normalization methods in quantitative label-free proteomics.

ROTS: An R package for reproducibility-optimized statistical testing.

Comparison of methods to detect differentially expressed genes between single-cell populations.

A predictive model of overall survival in patients with metastatic castration-resistant prostate cancer.

Empirical comparison of structure-based pathway methods.

Comparison of software packages for detecting differential expression in RNA-seq studies.

Mining proteomic data for biomedical research.

Fully scalable online-preprocessing algorithm for short oligonucleotide microarray atlases

Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays.

Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets.

Reproducibility-Optimized Test Statistic for Ranking Genes in Microarray Studies.

Missing value imputation improves clustering and interpretation of gene expression microarray data.

Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process.

Inference of Gene Coexpression Networks by Integrative Analysis across Microarray Experiments.

Improving missing value estimation in microarray data with gene ontology.