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⁦Sam Jones, PhD⁩ just published a great article about our GBE (Genome Biology and Evolution) work in The New York Times! ⁦UCI Charlie Dunlop School of Biological Sciences⁩ Hydra DNA Reveals There’s More Than One Way to Regrow a Head - The New York Times nytimes.com/2021/12/11/sci…

Ali Mortazavi, professor of developmental & cell #biology, is featured in The New York Times as he takes “a big step in understanding how a hydra regenerates its head.” So proud of the amazing research done by our faculty! Read more: nytimes.com/2021/12/11/sci…

Excited to share! combined data & biology-driven approaches to single cell transcriptomics of #stress-sensitive #CRH neurons identifies novel cell populations & shows selective impact of earlylife adversity. Kudos Annabel Short Ali Mortazavi Biological Psychiatry sciencedirect.com/science/articl….

Our work on cataloging experimentally derived TSSs is now out in Genome Research! genome.cshlp.org/content/32/2/3… A collaborative effort by Zlab@UMassMed Zhiping Weng Kaili Fan Henry Pratt Xiao-Ou Zhang Ali Mortazavi Fairlie Reese / @fairlie.bsky.social (1/5)

This is an absolute travesty driven by the worst form of privileged, elitist Berkeley NIMBYs who chose to live in a city home to America's best public university, and now want to destroy it for everyone else. berkeleyside.org/2022/02/14/uc-…

Great collaboration between Annabel in the Baram lab and my now graduated student Christina! More great work from Annabel on its way…

As a public service announcement, #severance is an amazing and incredibly addictive show and you should be watching it! Personally, the show reminds me as much about life as graduate student as my now thankfully forgotten corporate life.

Happy to present our new preprint: L-GIREMI uncovers RNA editing sites in long-read RNA-seq. Applied to ENCODE Project PacBio data. Great collaboration w/ Ali Mortazavi lab! biorxiv.org/content/10.110…

Analysis of #scRNAseq requires constant, tedious, interaction with genomics databases. To facilitate querying from Ensembl et al., Laura Luebbert, PhD developed gget: biorxiv.org/content/10.110… (code @ github.com/pachterlab/gget). gget has many uses; a 🧵on the its amazing versatility: 1/

This work was motivated by the need to obtain data for this preprint: biorxiv.org/content/10.110… and we thank Ali Mortazavi for his suggestion to include ffq querying of the ENCODE database. (7/7)

The Kvon lab is hiring! We have an opening for a fully funded postdoctoral scholar position(s). If you are interested in studying mammalian gene regulation in sunny Southern California, apply here: recruit.ap.uci.edu/JPF07799. Please RT

Just came across an 2019 eLife scRNA paper with the following section title in the results: “Components reflect known biology but also highlight sets of genes with mysterious purpose” 🧐 This paper has now been cited 69 times. We are probably going to have to cite it too. 😔

Don’t forget that Fascists predate Nazis in Italy (and France, Spain, etc…) and also survived WWII. It’s just that they are now getting popular enough to lead national governments driven by anti-immigration hatred. But of course, the very same ideas have resurged in the US too.

An absolute pleasure to be at UC Irvine today to give a lecture and meet Ali Mortazavi, JingZhang, vivek swarup and others!

Shocking that one of the senior authors of DESeq2, which has been cited >44,000 times, doesn't care if the program performs better or worse than a new Python implementation.

I am so excited to finally share the bioRxiv version of our manuscript on investigating transcript structure diversity in the ENCODE Project long-read RNA-seq dataset: biorxiv.org/content/10.110… Tweet thread coming tomorrow!

Reminder that I'm defending in a little over a week! (8/21 at 3 PM Pacific). Sign up to get details here: tinyurl.com/fairliedefense Thanks to Bryan (he/him) for the amazing poster and Narges Rezaie for coming over to take ridiculous pictures of me 🙃

If you are interested in genome regulatory systems (and who is not?) you really should apply to our department!

This is pretty striking. Take one single cell experiment, split it into random "batches", correct the batches, and look at change in nearest neighbor cell rank. Big changes (not good)!

In a new work led by Rebekah Loving, joint with Ali Mortazavi and his lab, we introduce a method based on kallisto for accurate quantification of Oxford Nanopore or PacBio long-read RNA-seq, and demonstrate its accuracy with numerous comparisons and benchmarks 1/🧵 biorxiv.org/content/10.110…