Saber HQ
Friendly notes on what I’m building, reading, and figuring out.
Explore why autoencoders shine; this post pairs plain-language basics with demos, figures, and a walkthrough video.
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ntEmbd turns nucleotide sequences into vector embeddings; explore training setup, benchmarks, and GitHub repo links.
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Trans-NanoSim captures nanopore transcript quirks; learn how benchmarks and simulations accelerate RNA tooling workflows.
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My name is Saber. I’m a Research Scientist with 12+ years of experience in genomics, data science, and machine learning. I earned my Ph.D. in Bioinformatics at the University of British Columbia (UBC), where I was advised by Prof. Dr. Inanc Birol, working at the Bioinformatics Technology Lab. During my Ph.D., I broadly worked on developing computational tools and software solutions for next-generation sequencing technologies. My doctoral dissertation (see here) was focused on utilizing machine learning in transcriptome analysis. I am passionate about contributing to the understanding, controlling, and training of foundation models for biology. Before starting at UBC, I received my M.Sc. in Bioinformatics from METU, where I was advised by Dr. Hilal Kazan and Dr. Yesim Aydin Son. My B.Sc. was in Information Technology Engineering.