Welcome!
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 in July 2024 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 also trained and mentored graduate students and co-authored 10 research papers. At the moment, I am passionate about contributing to the understanding, control, and training of foundation models for biology.
Before starting at UBC, I received my M.Sc. in Medical Informatics from METU, where I was advised by Dr. Hilal Kazan and Dr. Yesim Aydin Son. My B.Sc. was in Information Technology Engineering.
I share updates on my research work as blog posts on this site. And over at The Attention - my frequentish-ly newsletter 😃 - I share the latest news on research and development in the machine learning and AI field and insights from across the web on creative entrepreneurship and productivity. Sign up here to join a growing community of friendly readers. ❤️
Recent news
July 2024: Defended my Ph.D. dissertation and graduated from the University of British Columbia.
June 2024: The LRGASP research is published in Nature Methods.
May 2024: ntEmbd is available on BioRxiv.
June 2023: Presented ntEmbd at the ISMB/ECCB conference in Lyon, France.
May 2023: RNA-Bloom2 is published in Nature Communications.
March 2023: Meta-NanoSim is published in GigaScience.
Research
For the most updated and full list of publications, please visit my Google Scholar.
ntEmbd: deep learning embedding for nucleotide sequences
Hafezqorani et al. BioRxiv, 2024
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11092672/
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
LRGASP Consortium, et al. Nature Methods, 2024
https://doi.org/10.1038/s41592-024-02298-3
Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2
Nip, Hafezqorani et al. Nature Communications, 2023
https://doi.org/10.1038/s41467-023-38553-y
Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim
Yang, Lo, Nip, Hafezqorani et al. GigaScience, 2023
https://doi.org/10.1093/gigascience/giad013
RNA-Scoop: interactive visualization of transcripts in single-cell transcriptomes.
Stephenson, Nip, Hafezqorani et al. NAR Genomics and Bioinformatics, 2021
https://doi.org/10.1093/nargab/lqab105
Trans-NanoSim characterizes and simulates nanopore RNA-seq data
Hafezqorani et al. GigaScience, 2020
https://doi.org/10.1093/gigascience/giaa061
RBPSponge: genome-wide identification of lncRNAs that sponge RBPs
Hafezqorani et al. Bioinformatics, 2019
https://doi.org/10.1093/bioinformatics/btz448
Predicting clinical outcomes in neuroblastoma with genomic data integration
Baali, Acar, Aderinwale, Hafezqorani et al. Biology Direct, 2018
https://doi.org/10.1186/s13062-018-0223-8
Modeling the combined effect of RNA-binding proteins and microRNAs in post-transcriptional regulation
Hafezqorani et al. Nucleic Acids Research, 2016
https://doi.org/10.1093/nar/gkw048
Selected Talks & Presentations
ISMB / ECCB (MLCSB COSI) - Lyon, France - 2023 | ntEmbd (first author)
Genome Informatics - Virtual - 2021 | ntEmbd (first author)
ISMB (Microbiome COSI) - Virtual - 2020 | Meta-NanoSim (co-author)
ISMB (BioVis COSI) - Virtual - 2020 | RNA-Scoop (co-author)
ISMB / ECCB (HiTSeq COSI) - Basel, Switzerland - 2019 | Trans-NanoSim (first author)
ISMB / ECCB (RNA COSI) - Basel, Switzerland - 2019 | RNA-Bloom (co-author)
Genome Informatics - Cambridge, United Kingdom - 2018 | Trans-NanoSim (first author)
HIBIT - Antalya, Turkey - 2018 | Trans-NanoSim (first author)
ISMB / ECCB (RNA COSI) - Prague, Czech Republic - 2017 | RBPSponge (first author)
ISMB / ECCB (CAMDA COSI) - Prague, Czech Republic - 2017 | Neuroblastoma (first author)
FEBS - Kusadasi, Turkey - 2016 | APA in lung squamous cell carcinoma (first author)
ISMB / ECCB (RNA COSI) - Dublin, Ireland - 2015 | RBP-mediated regulation in cancer (first author)
