Open-source mechanistic model for ion exchange chromatography
An atlas of AAV genetic variants
I write here sometimes!
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.
SSV-Conta quantify and characterize DNA contaminants from gene therapy vector sequenced by Illumina system.
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.
A GLUE project for comparative genomic analysis of parvoviruses
O siRNA Seeker é um algoritmo que automatiza a identificação de siRNA,.
This model makes predictions on LNP Encapsulation Efficiency % based on training data acquired from the LNP Atlas project
Compile lentiviral vector integration sites from sequencing pipeline
Gene editor cutting/repair kinetics curve fitting script
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.
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".
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.
Variational lineage inference from gene therapy assays with insertional mutagenesis and somatic mutations
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.
Dyno Therapeutics is an AI and biotechnology company building high-performance gene delivery technologies to unlock the potential of next-generation genetic medicine. Using its CapsidMap platform, which combines machine learning with high-throughput in vivo measurement, Dyno designs novel adeno-associated virus (AAV) capsids with improved tissue…
Asimov is a synthetic biology company building an integrated platform for the intelligent design of living systems. Its Edge Systems (CHO for biologics, LV for cell therapies, AAV for gene therapies, and RNA for RNA medicines) combine engineered mammalian host cells, a library of more than 1,000 validated genetic parts, and cloud-based genetic…
Fractyl Health, Inc. (Nasdaq: GUTS) is a clinical-stage metabolic therapeutics company developing treatments that target the root causes of type 2 diabetes and obesity rather than managing symptoms.
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