Jan Baumbach

Latest

• circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging
• Systematic analysis of alternative splicing in time course data using Spycone
• Network-based approaches for modeling disease regulation and progression
• TF-Prioritizer: a java pipeline to prioritize condition-specific transcription factors
• Inference of differential gene regulatory networks from gene expression data using boosted differential trees
• Namco: A microbiome explorer
• Un-biased housekeeping gene panel selection for high-validity gene expression analysis
• Cancer driver drug interaction explorer
• The Limits of Molecular Signatures for Pancreatic Ductal Adenocarcinoma Subtyping
• DysRegNet: Patient-specific and confounder-aware dysregulated network inference
• spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape
• KeyPathwayMineR: de novo pathway enrichment in the R ecosystem
• sPLINK: A Federated, Privacy-Preserving Tool as a Robust Alternative to Meta-Analysis in Genome-Wide Association Studies
• Alternative splicing analysis benchmark with DICAST
• Robust disease module mining via enumeration of diverse prize-collecting Steiner trees
• Mass cytometry of platelet-rich plasma: a new approach to analyze platelet surface expression and reactivity
• Flimma: a federated and privacy-preserving tool for differential gene expression analysis
• Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases
• A Systematic Comparison of Novel and Existing Differential Analysis Methods for CyTOF Data
• The AIMe registry for artificial intelligence in biomedical research
• Platelet Surface Protein Expression and Reactivity upon TRAP Stimulation after BNT162b2 Vaccination
• The FeatureCloud AI Store for Federated Learning in Biomedicine and Beyond
• Network analysis methods for studying microbial communities: A mini review
• Clinical epigenetics settings for cancer and cardiovascular diseases: real-life applications of network medicine at the bedside
• On the limits of active module identification
• Machine learning for deciphering cell heterogeneity and gene regulation
• On the Consistency between Gene Expression and the Gene Regulatory Network of Corynebacterium glutamicum
• ASimulatoR: splice-aware RNA-Seq data simulation
• Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing
• SPONGEdb: a pan-cancer resource for competing endogenous RNA interactions
• SARS-CoV-2 infection is associated with a pro-thrombotic platelet phenotype
• BiCoN: Network-constrained biclustering of patients and omics data
• A framework for modeling epistatic interaction
• Federated Multi-Mini-Batch: An Efficient Training Approach to Federated Learning in Non-IID Environments
• Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research
• BALSAM—An Interactive Online Platform for Breath Analysis, Visualization and Classification
• DIGGER: exploring the functional role of alternative splicing in protein interactions
• PTPN2 Deficiency Enhances Programmed T Cell Expansion and Survival Capacity of Activated T Cells
• Multi-Omics Analysis in a Network Context (in "Reference Module in Biomedical Sciences")
• Mechanistic Modeling and Multiscale Applications for Precision Medicine: Theory and Practice
• EpiGEN: an epistasis simulation pipeline
• BioAtlas verbindet Mikrobiomsequenzdaten und GEO-Informationen
• Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology
• De novo pathway-based biomarker identification
• On the performance of de novo pathway enrichment
• Efficient Management of High-Throughput Screening Libraries with SAVANAH
• Comprehensive analysis of high-throughput screens with HiTSeekR
• KeyPathwayMinerWeb: online multi-omics network enrichment
• Robust de novo pathway enrichment with KeyPathwayMiner 5
• OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework
• Microarray R-based analysis of complex lysate experiments with MIRACLE
• Efficient Sample Tracking With OpenLabFramework
• Classification of Breast Cancer Subtypes by combining GeneExpression and DNA Methylation Data