Latest

• Gut Microbial Disruption in Critically Ill Patients with COVID-19-Associated Pulmonary Aspergillosis
• On the limits of graph neural networks for the early diagnosis of Alzheimer’s disease
• TF-Prioritizer: a java pipeline to prioritize condition-specific transcription factors
• 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
• SimBu: Bias-aware simulation of bulk RNA-seq data with variable cell type composition
• DysRegNet: Patient-specific and confounder-aware dysregulated network inference
• Systematic analysis of alternative splicing in time course data using Spycone
• Multi-Omics Regulatory Network Inference in the Presence of Missing Data
• 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
• 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
• Network pharmacology: curing causal mechanisms instead of treating symptoms
• 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
• Network tools for de novo endophenotyping and detecting disease mechanisms
• Looking at protein-protein interaction networks from the perspective of alternative splicing
• Tissue heterogeneity is prevalent in gene expression studies
• 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
• Big data for Systems Medicine
• BALSAM—An Interactive Online Platform for Breath Analysis, Visualization and Classification
• DIGGER: exploring the functional role of alternative splicing in protein interactions
• Individualized predictions of changes in knee pain, quality of life and walking speed following patient education and exercise therapy in patients with knee osteoarthritis – a prognostic model study
• Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes
• PTPN2 Deficiency Enhances Programmed T Cell Expansion and Survival Capacity of Activated T Cells
• Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing
• Multi-Omics Analysis in a Network Context (in "Reference Module in Biomedical Sciences")
• EpiRegio: analysis and retrieval of regulatory elements linked to genes
• Mechanistic Modeling and Multiscale Applications for Precision Medicine: Theory and Practice
• Mass-spectrometry-based draft of the Arabidopsis proteome
• De Novo Pathway Enrichment with KeyPathwayMiner
• De Novo Pathway-Based Classification of Breast Cancer Subtypes
• EpiGEN: an epistasis simulation pipeline
• Immunedeconv: An R Package for Unified Access to Computational Methods for Estimating Immune Cell Fractions from Bulk RNA-Sequencing Data
• In Silico Cell-Type Deconvolution Methods in Cancer Immunotherapy
• Quantitative comparison of within-sample heterogeneity scores for DNA methylation data
• The mRNA-binding Protein TTP/ZFP36 in Hepatocarcinogenesis and Hepatocellular Carcinoma
• BioAtlas verbindet Mikrobiomsequenzdaten und GEO-Informationen
• CFP suppresses breast cancer cell growth by TES-mediated upregulation of the transcription factor DDIT3
• Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology
• Hepatocellular Carcinoma and Nuclear Paraspeckles: Induction in Chemoresistance and Prediction for Poor Survival
• Large-scale inference of competing endogenous RNA networks with sparse partial correlation
• MiRNA-181d expression significantly affects treatment responses to carmustine wafer implantation
• THU-470-The mRNA-binding protein tristetraprolin promotes hepatocarcinogenesis but inhibits tumour progression in liver cancer
• An ontology-based method for assessing batch effect adjustmentapproaches in heterogeneous datasets
• MiRNA-181d Expression Significantly Affects Treatment Responsesto Carmustine Wafer Implantation
• JAMI - Fast computation of Conditional Mutual Information for ceRNA network analysis
• Nuclear Paraspeckles in Chemoresistance and Poor Survival in HCC
• De novo pathway-based biomarker identification
• Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform
• Systematic screening of isogenic cancer cells identifies DUSP6 as context-specific synthetic lethal target in melanoma
• DeepBlueR: large-scale epigenomic analysis in R
• On the performance of de novo pathway enrichment
• Protein-based nanotoxicology assessment strategy
• Ten Simple Rules for Developing Usable Software in Computational Biology
• The long non-coding RNA H19 suppresses carcinogenesis and chemoresistance in hepatocellular carcinoma
• Efficient Management of High-Throughput Screening Libraries with SAVANAH
• Comprehensive analysis of high-throughput screens with HiTSeekR
• DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets
• KeyPathwayMinerWeb: online multi-omics network enrichment
• Robust de novo pathway enrichment with KeyPathwayMiner 5
• Development of Bioinformatics Tools for Biomedical High-Throughput Analyses
• OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework
• Reverse Phase Protein Arrays for High-throughput Toxicity Screening
• 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
• Integrated Automation of High-Throughput Screening and Reverse Phase Protein Array Sample Preparation
• Reverse Phase Protein Arrays for High-Throughput Protein Measurements in Mammospheres