Hi, I’m Alon. I love data, exploring, visualizing 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 alumni and an alumni of the Edmond J. Safra Center for Bioinformatics. 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.

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:

  • Jarvis is an AI note-taking assistant for Joplin based on NLP models (such as OpenAI/GPT, Hugging Face, Google PaLM, Universal Sentence Encoder). You can chat with it (including prompt templates), use your personal notes as additional context in the chat, automatically annotate notes, perform semantic search, or compile an automatic review of the scientific literature. The latter feature is also available as a Visual Studio Code extension. Read more about it in this blog post.


  • I developed a Python package and a MATLAB package of analysis tools for genomic sequences, focusing on codon usage bias (CUB). These include, among others, the CUFS model that we developed to measure the distance between pairs of genes in terms of their codon usage.

  • ChimeraUGEM is an algorithm and a software tool that I developed for predicting gene expression as well as optimizing the coding sequence of a target gene to any host organism (see our paper).

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

  • Thought Trails are a visualization of a user’s history of read documents. Trails aim to highlight your stream of thoughts by linking documents that cite one another (similarly to academic papers, wiki articles, and the like). Consecutive linked documents create a straight trail, while jumps back to previous topics generate curved branches. This is available as a plugin for the Joplin note taking app.

Thought Trails

  • SCOM is a method for inter-species clustering and comparison of 3D gene organization.

  • PARASCHUT is a set of parallel job scheduling utils, for easier management of large projects on computer clusters.


Feel free to drop me a line.

alon {at} alondmnt {dot} com