Hi, I’m Alon. I love diving into data—exploring, visualising, and modelling it—to address major challenges in biology, biomedicine, and biotechnology. I enjoy building tools and sharing them with the community. Tinkering with others’ tools, collaborating, and taking them to the next level is something I find truly rewarding.
I’m a principal data scientist at Pheno.AI. I completed a Ph.D. under the supervision of Prof. Tamir Tuller at the Computational Systems and Synthetic Biology Lab in Tel Aviv University. I’m an Azrieli Fellowship and Edmond J. Safra Center for Bioinformatics alumni. Previously I graduated from the Technion, and earned a M.Sc. in Electrical Engineering, and a B.Sc. in Electrical Engineering and Physics.
Publications
These are a number of recent and selected publications. You may find a complete list here.
My second brain is the open source note-taking app Joplin. I developed Joplin extensions that have been downloaded over 25k times, from editor enhancements to an AI assistant (andcontributedto otherpopularplugins). Here are two highlights:
Jarvis is an AI note-taking assistant. You can chat with it, ask questions about your notes (RAG), autocomplete text, run semantic search over notes, tag and summarise them, or compile an automatic review of the scientific literature (see also this blog post).
The Inline Tag Navigator plugin is a personal knowledge management (PKM) and task system, based on tagging of paragraphs and tasks. It is a simple and powerful tool for organising and navigating through your notes. The following example demonstrates how to build a music database using the plugin:
Work
One project that I led at Pheno.AI and is publically available, is a python package for accessing and analysing the unique datasets that we build, aimed at making them easily accessible for academic and clinical research.
Research
During my PhD I worked on diverse projects, some of which resulted in software tools:
I studied DNA sequences of genes, looking for patterns that may affect their level of expression. For example, the following Python (>10k downloads) and MATLAB packages provide both novel and traditional tools for analysing codon usage bias (CUB) (see also our paper).
I worked on algorithms to engineer genes (computational synthetic biology). For example, ChimeraUGEM was developed for adapting / optimising the coding sequence of a target gene to a host organism, and for predicting its expression (see also our paper).
I analysed the way DNA is spatially organised in the cell. For example, SCOM is a method that compares how genes are organised in 3D in different organisms via a network clustering approach (see also our paper).
