Aziz Al'Khafaji

I’m looking for a PhD student to work on an exciting new collaboration with @azizalkhafaji.bsky.social at the @broadinstitute.org. Together we are using single cell long-read sequencing to understand tumour evolution and microenvironments. Hybrid computational and molecular role. 🧬

#isoforms, #illumina, #SBX

We are thrilled to have these new foundations to develop from and to deploy these transformational tools for discovery - exciting year ahead!

Single-cell RNA isoform sequencing with SBX
We demonstrate the SBX platform's ability to generate high quality RT based single-cell RNA seq data with sufficient read lengths able to resolve known and novel isoforms.

While it is still early days in the analysis – patterns are emerging and we are keen to validate our findings and demonstrate a systematic approach to biomarker identification and drug development.

.. to clinically promising RAS inhibitors. Through both transcriptomic (10x Flex) and proteomic profiling (ProteinTech, Discovery Panel), we observe differential responses across cancer subtypes and genetic backgrounds.

High-Scale Multiomic Drug Response Profiling in Multiplexed PRISM Cell Lines
In work lead by my group (MDL) and in partnership with PRISM, and CDS teams, we demonstrate the use of highly multiplexed cancer cell lines in scaled multiomic single-cell assays to derive mechanisms of drug tolerance..

3) Broad/BCL & Roche SBX sequencing technology
My group has had the privilege of working with Mark Kokoris and team on their landmark SBX sequencing technology. At AGBT, I presented some of our early efforts:

Unlocking the secrets of biology to transform health by Jacob Thaysen, CEO of Illumina, and Niall J Lennon, CSO and Chair, Broad Clinical Labs What an incredible week for Illumina, for Broad Clinical Labs, for the entire sequencing industry at this year...

..collaborative flagship efforts in single-cell atlasing of 5 billion cells and high resolution spatial atlasing.
www.linkedin.com/pulse/unlock...

Broad and Illumina have a shared experience of driving systematic discovery through development and deployment of high performance technologies at scale. I am excited to contribute to this continued tradition with..

2) Beyond the genome - Broad/BCL & Illumina flagship collaborations.
Through a flurry of internally developed methods, acquisitions, and partnerships; Illumina is making an impressive push into the multiomics space - single-cell, spatial, proteomics, methylation, and beyond.

This interdisciplinary work brought together molecular and computational expertise across my group and Victoria Popic’s lab. Special shout out to James Webber, who led the analysis. This work was supported by PacBio and Broad Clinical Labs.

Through comprehensive characterization of 10x 3’, 10x 5’, and PIPseq single-cell platforms, we demonstrate differences in isoform seq performance and develop molecular & computational approaches to minimize the impact of artifacts on analysis - a clear challenge for this next gen of transcriptomics

Multi-platform evaluation and optimization of single-cell RNA isoform sequencing Long-read transcriptomics enables isoform identification and quantification at single-cell resolution, but analysis is complicated by artifacts introduced during library preparation. We characterize t...

Fitting first post to BlueSky
Recapping a whirlwind week.. 1) isoforms, 2)illumina, 3)SBX

1) Check out our new preprint: Multi-platform evaluation and optimization of single-cell RNA isoform sequencing.

Ever wonder if/how different single-cell platforms impact RNA isoform sequencing performance?