Open-source mechanistic model for ion exchange chromatography
An atlas of AAV genetic variants
A verification and grounding layer for AI-driven genome writing. Foundation models and a grounded co-scientist agent propose edits; PEN-STACK checks each against validated tools, never a language model: where a write is safe and durable, which enzyme makes it, and where it goes off-target. Calibrated, provenance-tracked, pre-registered.
I write here sometimes!
SSV-Conta quantify and characterize DNA contaminants from gene therapy vector sequenced by Illumina system.
SiRNA Seeker is a webapp built with Django in Python, which offers an intuitive interface for researchers to access and efficiently use a siRNA design algorithm.
A live pre-synthesis specificity gate for AI-designed enhancers: a frozen external measured-activity model plus a multi-agent Claude verifier. Cross-lab AUROC 0.80 on 93,435 independent designs.
A GLUE project for comparative genomic analysis of parvoviruses
O siRNA Seeker é um algoritmo que automatiza a identificação de siRNA,.
Gene editor cutting/repair kinetics curve fitting script
Compile lentiviral vector integration sites from sequencing pipeline
This model makes predictions on LNP Encapsulation Efficiency % based on training data acquired from the LNP Atlas project
GEM | Gene Edit Machine: A machine learning-enhanced platform capable of classifying and optimizing gene variants for reduced pathogenicity. Featuring multi-database integration, research-backed feature engineering, optimized DNA and Protein-level analyses, and an intelligent guided + stochastic mutation algorithm "ReGen".
Benchmark-validated chimeric read detection for AAV vectors on Oxford Nanopore. F1 0.973 with zero false positives, measured against a ground-truth read simulator.
This repository provides the source code, scripts, and usage instructions that serve as supplementary materials for the book Bioinformatics of Autoimmune Diseases by Hamid D. Ismail. It is designed to support reproducibility and hands-on learning by offering practical examples, data analysis pipelines, and tools discussed throughout the chapters.
Variational lineage inference from gene therapy assays with insertional mutagenesis and somatic mutations
Multi-axis scoring framework that ranks programmable genome editors across eight orthogonal axes into a single PenScore to guide experimental design and benchmarking.
Open computational research on STRC-related DFNB16 hearing loss and gene-therapy hypotheses.
Scientific background article on CRISPR/Cas technology and gene therapy (2026)
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