Alon Diament

As a computational biologist and data scientist, I’m seeking to apply my knowledge in large-scale data analysis to the development of biomedical and biotechnological solutions.

I’m a bioinformatician scientist at MyHeritage. Recently 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.

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

• The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana (2018)
  T Tuller*, A Diament*, A Yahalom, A Zemach, S Atar, DA Chamovitz
  Bioinformatics
• Modeling three-dimensional genomic organization in evolution and pathogenesis (2018)
  A Diament, T Tuller
  Seminars in Cell & Developmental Biology
• Overcoming the expression barrier of the ferredoxin‑hydrogenase chimera in Chlamydomonas reinhardtii supports a linear increment in photosynthetic hydrogen output (2018)
  I Weiner, N Shahar, Y Feldman, …, A Diament, T Tuller, I Yacoby
  Algal Research 33, 310-315
• 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
• Evidence of translation efficiency adaptation of the coding regions of the bacteriophage lambda (2017)
  E Goz, O Mioduser, A Diament, T Tuller
  DNA Research 24 (4), 333-342
• Estimation of ribosome profiling performance and reproducibility at various levels of resolution (2016)
  A Diament, T Tuller
  Biology direct 11 (1), 24
• Three-dimensional genomic organization of genes’ function in eukaryotes (2016)
  A Diament, T Tuller
  Evolutionary Biology, 233-252.
  
• Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants (2015)
  T Ben-Yehezkel, S Atar, H Zur, A Diament, E Goz, T Marx, R Cohen, …
  RNA biology 12 (9), 972-984

• 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:

• ChimeraUGEM: 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.

• SCOM: a method for inter-species clustering and comparison of 3D gene organization.
• A number of useful functions and models for gene sequence analysis, focusing on codon usage. These include, among others, the CUFS model that we developed to measure the distance between pairs of genes in terms of their codon usage.
• A toolbox for managing parallel jobs on a PBS cluster.

These are a few of my favorite things:

• The Technicalities is my Indie-Yiddish duo with Shira Z. Carmel, my wife.
• My favorite childhood (and adulthood) toy.
• I opened a blog for the Tuller Lab students, where we share our tips and advice.
• I volunteer at MESILA, an aid and information center for refugees and migrant workers.

Feel free to contact me, I’d be happy to hear from you.

alon {at} alondmnt {dot} com