Hi, I’m Alon. I love data, exploring, visualising and modeling it, and using it to increase our understanding and solve major problems in biology, biomed and biotechnology.

I’m a senior researcher 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 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.

Alon Diament Carmel


These are a number of recent and selected publications. You may find a complete list here.

Sleep and respiratory disease

Detection of co-evolving gene modules in 3D in the genomes of S. cerevisiae and S. pombe

Enhanced 3D genome reconstruction


Here you will find some of my recent projects.


My second brain is the open source note-taking app Joplin. I developed Joplin extensions that have been downloaded over 10k times, from editor enhancements to an AI assistant (and contributed to other popular plugins). 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, annotate and summarise them, or compile an automatic review of the scientific literature (see also this blog post).

  • This plugin is a personal knowledge management (PKM) and task management system, based on tagging of paragraphs and tasks. It is a simple and powerful tool for organising and navigating through your notes.

tag navigator


One project that I led at Pheno.AI and is publically available, is a python package for accessing the unique datasets that we build, aimed at making them easily accessible for academic and clinical 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 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).

Position-Specific ChimeraMap: an algorithm for engineering expression-optimised genes

  • 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).


Feel free to drop me a line.

hi {at} alondmnt {dot} com