Instructor at @StanfordMed, interested in statistical & ML methods for scRNA-Seq and RNA splicing @StanfordDBDS @StanfordBiochem
Stanford, CA
Joined July 2012
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Excited to share our latest paper out in @NatureBiotech with @marekkoki and @sdeorowicz, introducing sc-SPLASH: a reference-free statistical method for variation detection beyond gene expression in barcoded scRNA-seq (10x) and spatial transcriptomics. nature.com/articles/s41587-0…
sc-SPLASH is integerated into SPLASH2 pipeline and is available at: github.com/refresh-bio/splas…. Also, our BKC tool is available as a standalone tool at: github.com/refresh-bio/bkc (check them out!)
Roozbeh Dehghannasiri retweeted
Reference-free discovery with barcoded single-cell sequencing - @SalzmanLab @sdeorowicz go.nature.com/4cqxwLp
Iran will rise 💚🤍❤️
#DigitalBlackoutIran
#FreeIran
What’s unfolding in Iran may be the most consequential and underreported story in the world. Free elections there won’t just be a human rights victory. The fall of the Ayatollahs will release tens of millions of people, who come from one of the most creative civilizations in history. Iranian culture has shaped art, science and innovation for centuries. Suppressing it hurts not just Iranians, but humanity as a whole.
Honored to have been part of this multi-year effort, published in two @Nature papers, to map cell types in mouse lemur, an emerging genetic model organism.
Double paper alert in @Nature! A team of 150+ scientists, led by @StephenQuake, Mark Krasnow/@Stanford & #CZBiohubSF Genomics, published on Tabula Microcebus, a cell atlas of gene expression data from 226K single cells from mouse lemur organs & tissues.
czbiohub.org/life-science/ne…
Roozbeh Dehghannasiri retweeted
Mouse lemurs are the smallest and fastest-reproducing primates, and now there's an impressive mouse lemur molecular cell atlas
go.nature.com/3H8vaE2
Roozbeh Dehghannasiri retweeted
Nature research paper: Mouse lemur cell atlas informs primate genes, physiology and disease
go.nature.com/3Hd7fDj
Happy to share our latest paper with @marekkoki on SPLASH2 for ultra-efficient reference-free discovery directly on raw sequencing reads out in @NatureBiotech, supervised by @SalzmanLab and @sdeorowicz, and with great contributions from @TBaharav.
nature.com/articles/s41587-0…
Analyzing the entire Cancer Cell Line Encyclopedia (CCLE) with a single-line command, we rediscovered BCR-ABL1 fusion and identified substantial unannotated AS, including cancer-type-specific cryptic exons in cancer genes (eg RAB36 and PTEN) and insertions missed by STAR in HOOK3
Check out SPLASH2 at: github.com/refresh-bio/SPLAS…
along with detailed documentation for running and biological interpretation of results, plus a notebook for alternative splicing analysis
Roozbeh Dehghannasiri retweeted
BREAKING NEWS
The Norwegian Nobel Committee has decided to award the 2023 #NobelPeacePrize to Narges Mohammadi for her fight against the oppression of women in Iran and her fight to promote human rights and freedom for all.
#NobelPrize
Roozbeh Dehghannasiri retweeted
Our August issue is live! 🎉
nature.com/nmeth/volumes/20/…
On the cover, a benchmarking study assessed 16 bioinformatics tools for their abilities to capture true-positive and false-positive circular RNAs.
Cover by @DrawImpacts.
Roozbeh Dehghannasiri retweeted
A large-scale study from @jvdesomp and colleagues benchmarks computational tools for circRNA detection, as well as provides a resource of 315,000 unique putative circRNAs detected in 3 human cell types.
nature.com/articles/s41592-0…