- NIAPU: Network-Informed Adaptive Positive-Unlabeled learning for disease gene identification
- WMDS.net: a network control framework for identifying key players in transcriptome programs
- NMRtist: an online platform for automated biomolecular NMR spectra analysis
- PyGenePlexus: A Python package for gene discovery using network-based machine learning
- Benchmarking tools for a priori identifiability analysis
- Efficient Penalized Generalized Linear Mixed Models for Variable Selection and Genetic Risk Prediction in High-Dimensional Data
- The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data
- GMWI-webtool: a user-friendly browser application for assessing health through metagenomic gut microbiome profiling
- TIVAN-indel: A computational framework for annotating and predicting noncoding regulatory small insertions and deletions
- Potent Antibiotic Design via Guided Search from Antibacterial Activity Evaluations
- MFR-DTA: A Multi-Functional and Robust Model for Predicting Drug-Target Binding Affinity and Region
- MS1Connect: a mass spectrometry run similarity measure
- How to optimally sample a sequence for rapid analysis
- BLTSA: pseudotime prediction for single cells by branched local tangent space alignment
- Binding Peptide Generation for MHC Class I Proteins with Deep Reinforcement Learning
- AFTGAN: Prediction of multi-type PPI based on attention free transformer and graph attention network
- NetProphet 3: A Machine-learning framework for transcription factor network mapping and multi-omics integration
- CONTRABASS: Exploiting flux constraints in genome-scale models for the detection of vulnerabilities
- Phosformer: An explainable Transformer model for protein kinase-specific phosphorylation predictions
- Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer