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1 | 1 | --- |
2 | | -title: "Saber HQ" |
| 2 | +title: Introduction |
| 3 | +bookHeadingAnchor: false |
| 4 | +layout: landing |
3 | 5 | --- |
4 | 6 |
|
5 | | -## Welcome! |
| 7 | +<div class="book-hero"> |
6 | 8 |
|
7 | | -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](https://www.bcgsc.ca/people/inanc-birol), working at the [Bioinformatics Technology Lab](https://www.birollab.ca/). During my Ph.D., I broadly worked on developing computational tools and software solutions for next-generation sequencing technologies. My doctoral dissertation (see [here](https://open.library.ubc.ca/soa/cIRcle/collections/ubctheses/24/items/1.0444844)) 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. |
| 9 | +# SABER HQ |
| 10 | +Friendly notes on what I'm building, reading, and figuring out. |
8 | 11 |
|
9 | | -Before starting at UBC, I received my M.Sc. in Bioinformatics from [METU](https://ii.metu.edu.tr/), where I was advised by Dr. Hilal Kazan and Dr. Yesim Aydin Son. My B.Sc. was in Information Technology Engineering. |
| 12 | +{{< badge style="info" title="Version" value="0.1.0" >}} {{< badge style="default" title="Year" value="2025" >}} |
10 | 13 |
|
11 | | -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](https://newsletter.saberhq.com/) to join a growing community of friendly readers. ❤️ |
| 14 | +{{<button href="/resume">}}Resume{{</button>}} |
12 | 15 |
|
13 | | -## Recent news |
| 16 | +</div> |
14 | 17 |
|
15 | | -September 2025: Created this website. I am starting to embrace simplicity in my life and decided to create a minimalistic statis website to share my work and thoughts. If you like the style and theme, look into Hugo's [book theme](https://themes.gohugo.io/themes/book/). |
| 18 | +{{% columns %}} |
| 19 | +- ## <a href="/podcast/" class="title-link">Podcast</a> |
| 20 | + I talk through new research papers in **AI and biology**, the ones shaping how we think about future. This is where I unpack the science I’m reading — new papers, big breakthroughs, and the occasional headline worth a second look. It’s half lab notebook, half **conversation with an AI sidekick.** |
16 | 21 |
|
17 | | -July 2025: I got an offer for my first post-PhD position as Computational Scientist at [Genentech](https://www.gene.com/), where I will be working on the development of foundation models for virtual cells. |
| 22 | +- ## <a href="/newsletter/" class="title-link">Newsletter</a> |
| 23 | + Like _Morning Brew_, but for people who read **preprints for fun!** Each week I break down the biggest AI × Bio ideas into quick, snackable updates you can read over coffee. It’s the stuff I’d be sending friends and labmates anyway — just wrapped up in one weekly note. |
| 24 | +{{% /columns %}} |
18 | 25 |
|
19 | | -July 2025: Attended [ICML 2025](https://icml.cc/) in Vancouver, Canada. Had a wonderful time connecting with people in AI x Bio community and learned a lot during amazing workshops on [Multi-modal Foundation Models and Large Language Models for Life Sciences](https://icml.cc/virtual/2025/workshop/39959) as well as [Generative AI for Biology](https://icml.cc/virtual/2025/workshop/39968). |
20 | 26 |
|
21 | | -December 2024: Attended [NeurIPS 2024](https://neurips.cc/) in Vancouver, Canada. |
| 27 | +{{% columns %}} |
| 28 | +- {{< card title="Card" image="" >}} |
| 29 | + ### <a href="/blog/autoencoders" class="title-link">Why Autoencoders are so Effective?</a> |
| 30 | + Nullam feugiat urna massa, et fringilla metus consectetur molestie. Suspendisse sed congue orci, eu congue metus. |
| 31 | + {{< /card >}} |
22 | 32 |
|
23 | | -July 2024: Defended my Ph.D. dissertation and graduated from the University of British Columbia. |
| 33 | +- {{< card title="Card" image="" >}} |
| 34 | + ### <a href="/blog/ntEmbd" class="title-link">ntEmbd for RNA embeddings</a> |
| 35 | + Suspendisse sed congue orci, eu congue metus. Nullam feugiat urna massa, et fringilla metus consectetur molestie. |
| 36 | + {{< /card >}} |
24 | 37 |
|
25 | | -June 2024: The LRGASP research is published in Nature Methods. |
26 | | - |
27 | | -May 2024: ntEmbd is available on BioRxiv. |
28 | | - |
29 | | -June 2023: Presented ntEmbd at the ISMB/ECCB conference in Lyon, France. |
30 | | - |
31 | | -May 2023: RNA-Bloom2 is published in Nature Communications. |
32 | | - |
33 | | -March 2023: Meta-NanoSim is published in GigaScience. |
34 | | - |
35 | | -## Research |
36 | | -For the most updated and full list of publications, please visit my [Google Scholar](https://scholar.google.com/citations?user=q2fsO2IAAAAJ&hl=en). |
37 | | - |
38 | | -ntEmbd: deep learning embedding for nucleotide sequences |
39 | | -Hafezqorani et al. BioRxiv, 2024 |
40 | | -https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11092672/ |
41 | | - |
42 | | -Systematic assessment of long-read RNA-seq methods for transcript identification and quantification |
43 | | -LRGASP Consortium, et al. Nature Methods, 2024 |
44 | | -https://doi.org/10.1038/s41592-024-02298-3 |
45 | | - |
46 | | -Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2 |
47 | | -Nip, Hafezqorani et al. Nature Communications, 2023 |
48 | | -https://doi.org/10.1038/s41467-023-38553-y |
49 | | - |
50 | | -Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim |
51 | | -Yang, Lo, Nip, Hafezqorani et al. GigaScience, 2023 |
52 | | -https://doi.org/10.1093/gigascience/giad013 |
53 | | - |
54 | | -RNA-Scoop: interactive visualization of transcripts in single-cell transcriptomes. |
55 | | -Stephenson, Nip, Hafezqorani et al. NAR Genomics and Bioinformatics, 2021 |
56 | | -https://doi.org/10.1093/nargab/lqab105 |
57 | | - |
58 | | -Trans-NanoSim characterizes and simulates nanopore RNA-seq data |
59 | | -Hafezqorani et al. GigaScience, 2020 |
60 | | -https://doi.org/10.1093/gigascience/giaa061 |
61 | | - |
62 | | -RBPSponge: genome-wide identification of lncRNAs that sponge RBPs |
63 | | -Hafezqorani et al. Bioinformatics, 2019 |
64 | | -https://doi.org/10.1093/bioinformatics/btz448 |
65 | | - |
66 | | -Predicting clinical outcomes in neuroblastoma with genomic data integration |
67 | | -Baali, Acar, Aderinwale, Hafezqorani et al. Biology Direct, 2018 |
68 | | -https://doi.org/10.1186/s13062-018-0223-8 |
69 | | - |
70 | | -Modeling the combined effect of RNA-binding proteins and microRNAs in post-transcriptional regulation |
71 | | -Hafezqorani et al. Nucleic Acids Research, 2016 |
72 | | -https://doi.org/10.1093/nar/gkw048 |
73 | | - |
74 | | -## Selected Talks & Presentations |
75 | | -ISMB / ECCB (MLCSB COSI) - Lyon, France - 2023 | ntEmbd (first author) |
76 | | - |
77 | | -Genome Informatics - Virtual - 2021 | ntEmbd (first author) |
78 | | - |
79 | | -ISMB (Microbiome COSI) - Virtual - 2020 | Meta-NanoSim (co-author) |
80 | | - |
81 | | -ISMB (BioVis COSI) - Virtual - 2020 | RNA-Scoop (co-author) |
82 | | - |
83 | | -ISMB / ECCB (HiTSeq COSI) - Basel, Switzerland - 2019 | Trans-NanoSim (first author) |
84 | | - |
85 | | -ISMB / ECCB (RNA COSI) - Basel, Switzerland - 2019 | RNA-Bloom (co-author) |
86 | | - |
87 | | -Genome Informatics - Cambridge, United Kingdom - 2018 | Trans-NanoSim (first author) |
88 | | - |
89 | | -HIBIT - Antalya, Turkey - 2018 | Trans-NanoSim (first author) |
90 | | - |
91 | | -ISMB / ECCB (RNA COSI) - Prague, Czech Republic - 2017 | RBPSponge (first author) |
92 | | - |
93 | | -ISMB / ECCB (CAMDA COSI) - Prague, Czech Republic - 2017 | Neuroblastoma (first author) |
94 | | - |
95 | | -FEBS - Kusadasi, Turkey - 2016 | APA in lung squamous cell carcinoma (first author) |
96 | | - |
97 | | -ISMB / ECCB (RNA COSI) - Dublin, Ireland - 2015 | RBP-mediated regulation in cancer (first author) |
| 38 | +- {{< card title="Card" image="" >}} |
| 39 | + ### <a href="/blog/NanoSim" class="title-link">NanoSim simulates ONT sequencing data</a> |
| 40 | + Suspendisse sed congue orci, eu congue metus. Nullam feugiat urna massa, et fringilla metus consectetur molestie. |
| 41 | + {{< /card >}} |
| 42 | +{{% /columns %}} |
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