Alon Diament Carmel

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

• MyHeritage Launches Genetic Groups [video]

• New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the coding region (2020)
  S Bergman, A Diament, T Tuller
  Bioinformatics

• ChimeraUGEM: unsupervised gene expression modeling in any given organism (2019) [website]
  A Diament&, I Weiner&, N Shahar&, …, T Tuller
  Bioinformatics

• The extent of ribosome queuing in budding yeast (2018)
  A Diament&, A Feldman&, E Schochet, M Kupiec, Y Arava, T Tuller
  PLoS computational biology 14 (1), e1005951

• Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence (2017) [website]
  A Diament, T Tuller
  Nucleic acids research 45 (8), 4330-4343

• Estimation of ribosome profiling performance and reproducibility at various levels of resolution (2016)
  A Diament, T Tuller
  Biology Direct 11 (1), 24

• Improving 3D genome reconstructions using orthologous and functional constraints (2015)
  A Diament, T Tuller
  PLoS computational biology 11 (5), e1004298

• Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function (2014) [code]
  A Diament, RY Pinter, T Tuller
  Nature Communications 5, 5876

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).

• 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.

• 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.

These are a few of my favorite things:

• The Technicalities is my Indie-Yiddish duo with Shira Z. Carmel, my wife.
• I practice SHODO (Japanese calligraphy).
• I take notes.
• I like running.
• My favorite childhood (and adulthood) toy.
• I opened a blog for the Tuller Lab students, where we share our tips and advice.