Alaa Aldeen
Lead AI Engineer & Computational Systems Biology Architect
Multi-award-winning Life Sciences Innovator, AI Engineer, and Biotechnology Founder with a cross-disciplinary medical background spanning clinical sciences, deep neural networks, and medical device invention. Architect of Nilus Lab's Human Cardiac Ageing & Heart Failure Target Discovery Engine (12 public datasets) integrating 6 single-cell cardiac atlases, 3 bulk RNA-seq cohorts, 3 mass-spectrometry cardiac proteomes, and Open Targets v4 human genetics, as well as the 20-dimensional cardiac specialist scVI Variational Autoencoder (trained on 99,993 donor-stratified cells from the 486,134-cell Human Heart Atlas, Litviňuková et al. 2020).
Silver Medalist at the 50th International Exhibition of Inventions Geneva for inventing the Real-Time Antigen-Antibody Detection (RTAAD) diagnostic device. Granted patent holder, UK IPO design rights holder, and winner of multiple international research medals. Certified in Good Clinical Practice (GCP/NIHR), combining clinical precision with rigorous multi-omics statistical auditing.
Multi-Cohort Target Discovery & Single-Cell AI
- • 12-Dataset Cardiac Target Discovery: Built the multi-cohort discovery and audit pipeline across 6 single-cell atlases, 3 bulk cohorts, and 3 cardiac proteomes. It recovered the clinical benchmark ATP2A2 (SERCA2a) blind (rank 76 of 5,677; 3rd of 11 after filters) and produced three computational candidates: PPP1R12C/MBS85 (protein higher with age, $p = 1.1\times10^{-4}$), TMEM65 (DCM $Z = -8.008$) and SYPL2/MG29 (lower in DCM cardiomyocytes). None has been tested in the lab.
- • Deep Neural Network Model Training: Trained the 5,009-HVG, 20-dimensional latent space cardiac specialist scVI Variational Autoencoder (3,268,462 trainable parameters) on 99,993 donor-stratified cells from the 486,134-cell Human Heart Atlas (Litviňuková et al. 2020).
- • Causal Direction & Knockout Auditing: Automated HAGR GenAge/CellAge, EuropePMC, and IMPC mouse knockout directionality verification to eliminate compensatory protective brakes (ARHGAP1, NOL3, CIRBP).
- • Multi-Agent AI Systems & Workflow Engines: Architected Promatly.com, an enterprise multi-agent task orchestration platform running parallel API jobs, webhooks, and RESTful microservices.