Barmada Lab

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Barmada Lab

Barmada Lab

@BarmadaLab

Barmada lab @UMich. We study cellular mechanisms underlying ALS/FTD & RNA biology with focus on neurodegeneration. (group-run account)

Ann Arbor, MI شامل ہوئے Mayıs 2020
45 فالونگ379 فالوورز
Barmada Lab
Barmada Lab@BarmadaLab·
We have an opening for a postdoc! Come work with us on ALS/FTD ⬇️
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Oscar Wilkins
Oscar Wilkins@OscarWilkins16·
@BarmadaLab I appreciate the material is v. rare so difficult to get large N! If you want to get the most from your data there are clustered analysis approaches that can sometimes improve power (versus just taking means) without raising type I error, eg Datta & Satten ncbi.nlm.nih.gov/pmc/articles/P…
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Barmada Lab
Barmada Lab@BarmadaLab·
@OscarWilkins16 An additional issue is the scarcity of the material — we try to make the most out of available tissue, which as you mentioned may bias towards false positives (or negatives). The solution would be to measure from fewer cells/sample but more samples. Harder in practice.
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Oscar Wilkins
Oscar Wilkins@OscarWilkins16·
@BarmadaLab Independence of observations is a critical assumption for the validity of the tests. But if numerous observations are drawn from a small number of replicates, then they are not independent. Accidental I'm sure. But you have overstated the significance by many orders of magnitude
Oscar Wilkins tweet media
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Barmada Lab
Barmada Lab@BarmadaLab·
@OscarWilkins16 Not quite the same. Better would be hair length in City A vs. B (but only from a sparsely populated neighborhood). We measure 100+ hairs from 3 people in City A vs. B. This way we don't throw out error estimates and variability among hairs.
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Oscar Wilkins
Oscar Wilkins@OscarWilkins16·
@BarmadaLab But your test is using N=100+ not N=3, which will hugely inflate significance. An analogy: I am interested in whether people from City A are taller than from City B. I select 3 people from each city. I then measure each of their heights 100 times. Do I have N=3, or N=300?
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Barmada Lab
Barmada Lab@BarmadaLab·
@NonselfMutation @BoeynaemsSteven The excess m6A we noted in patient tissues could very well be due to neuroinflammation. Similar changes were noted by Jiang et al. (10.1016/j.molcel.2021.07.038) in Alzheimer's brain, which also shows significant inflammation.
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Barmada Lab
Barmada Lab@BarmadaLab·
@OscarWilkins16 Thanks Oscar. The 3 biological replicates are indicated by shading while N refers to individual neurons. While the effect is not large it is statistically significant. We suspect YTHDF2 deposits only in a subset of the neurons, but definitely need to look in more patient samples!
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Oscar Wilkins
Oscar Wilkins@OscarWilkins16·
@BarmadaLab @BarmadaLab could you please correct the stats in Figs 4J and 6B? When you have three biological replicates you should use N=3, not N=193, regardless of how many measurements you take. It's unclear to me from the figures if these results are actually significant.
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Barmada Lab
Barmada Lab@BarmadaLab·
Also, Sami will be giving a talk on MTMR5 and neuronal autophagy at 4:53pm in the "Mechanisms of Autophagic and Endolysosomal Trafficking in Neuronal Function and Neurodegeneration" subgroup tomorrow! #CellBio2022
Barmada Lab@BarmadaLab

Check out our lab's posters at #CellBio2022 tomorrow (Monday Dec 5)! - Genesis Rodriguez on VPS13A function in mitochondria/ER (P2106/B430) - Josephine Wu on calcium and calmodulin-dependent Matrin3 homeostasis (P2076/B399) - Sumin Kim on neuronal NPC biogenesis (P2019/B339)

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Barmada Lab
Barmada Lab@BarmadaLab·
Check out our lab's posters at #CellBio2022 tomorrow (Monday Dec 5)! - Genesis Rodriguez on VPS13A function in mitochondria/ER (P2106/B430) - Josephine Wu on calcium and calmodulin-dependent Matrin3 homeostasis (P2076/B399) - Sumin Kim on neuronal NPC biogenesis (P2019/B339)
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Barmada Lab
Barmada Lab@BarmadaLab·
Congratulations to Mike on a fantastic thesis defense today! Mike’s work on m6A and TDP43 opened up many new avenues for the lab to pursue, and he has been pivotal in introducing the lab to science memes. Great job and many congratulations, Dr. McMillan!
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