Ali Mortazavi retweeted
In a new work led by @bound_to_love, joint with @calizavi and his lab, we introduce a method based on kallisto for accurate quantification of @nanopore or @PacBio long-read RNA-seq, and demonstrate its accuracy with numerous comparisons and benchmarks 1/🧵 biorxiv.org/content/10.110…
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Ali Mortazavi retweeted
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 this preprint biorxiv.org/content/10.110… with @Sindri_e we compared seven widely used methods for batch correction of single cell RNA-seq data. We found that all but one of the methods introduce batch effects when there are none. 1/N
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If you are interested in genome regulatory systems (and who is not?) you really should apply to our department!
A reminder that our department @UCIBioSci is conducting a search for two tenure-track assistant professor positions. The deadline is 12/15. Please reach out to me if you have any questions.
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Ali Mortazavi retweeted
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 @Bry_sci_guy for the amazing poster and @NargesRezaie10 for coming over to take ridiculous pictures of me 🙃
Thanks to @Bry_sci_guy for the amazing poster and @NargesRezaie10 for coming over to take ridiculous pictures of me 🙃
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Ali Mortazavi retweeted
I am so excited to finally share the bioRxiv version of our manuscript on investigating transcript structure diversity in the @ENCODE_NIH long-read RNA-seq dataset: biorxiv.org/content/10.110…
Tweet thread coming tomorrow!
Tweet thread coming tomorrow!
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Ali Mortazavi retweeted
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.
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Ali Mortazavi retweeted
An absolute pleasure to be at UC Irvine today to give a lecture and meet @calizavi, @JingZhang_bio, @vivekenigma and others!
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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.
Nazis are taking over Europe, again. Were they ever really gone?
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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. 😔
“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. 😔
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Ali Mortazavi retweeted
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
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Ali Mortazavi retweeted
This work was motivated by the need to obtain data for this preprint: biorxiv.org/content/10.110…
and we thank @calizavi for his suggestion to include ffq querying of the ENCODE database.
(7/7)
and we thank @calizavi for his suggestion to include ffq querying of the ENCODE database.
(7/7)
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Ali Mortazavi retweeted
Analysis of #scRNAseq requires constant, tedious, interaction with genomics databases. To facilitate querying from @ensembl et al., @NeuroLuebbert developed gget:
biorxiv.org/content/10.110… (code @ github.com/pachterlab/gget).
gget has many uses; a 🧵on the its amazing versatility: 1/
biorxiv.org/content/10.110… (code @ github.com/pachterlab/gget).
gget has many uses; a 🧵on the its amazing versatility: 1/
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Ali Mortazavi retweeted
Happy to present our new preprint: L-GIREMI uncovers RNA editing sites in long-read RNA-seq. Applied to @ENCODE_NIH @PacBio data. Great collaboration w/ @calizavi lab! biorxiv.org/content/10.110…
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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.
Personally, the show reminds me as much about life as graduate student as my now thankfully forgotten corporate life.
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Great collaboration between Annabel in the Baram lab and my now graduated student Christina! More great work from Annabel on its way…
Postdoc work with @z_baram @calizavi @JessicaLBolton @mtbirnie is in press!🎉
doi.org/10.1016/j.bpsg…
Check out our work using single cell transcriptomics of stress-sensitive CRH neurons to identify populations impacted by early-life adversity in open access @BiologicalPsyc1
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Ali Mortazavi retweeted
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-…
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Ali Mortazavi retweeted
Our work on cataloging experimentally derived TSSs is now out in @genomeresearch! genome.cshlp.org/content/32/2/3… A collaborative effort by @umassmed_zlab @ZhipingWeng @Kaili_Fan @hpratt111 @kepbod @calizavi @FairlieReese (1/5)
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Ali Mortazavi retweeted
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 @drbelshort @calizavi @BiologicalPsyc1 sciencedirect.com/science/articl….
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Ali Mortazavi retweeted
Ali Mortazavi, professor of developmental & cell #biology, is featured in @nytimes 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…
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@samjscience just published a great article about our @GenomeBiolEvol work in The New York Times! @UCIBioSci
Hydra DNA Reveals There’s More Than One Way to Regrow a Head - The New York Times nytimes.com/2021/12/11/sci…
Hydra DNA Reveals There’s More Than One Way to Regrow a Head - The New York Times nytimes.com/2021/12/11/sci…
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