Brandon Logeman

BRAIN Initiative K99/R00 Awardee || Studying hormonal control of neuronal circuits at the single cell level || 🐷 former pig farmer 🐷 #FirstGenCollege

[Rahul Satija @satijalab]

Excited to share VIPerturb-seq!

New tech from my lab which aims to improve the cost, data quality, and efficiency of single-cell CRISPR screens so that they are accessible to any lab - even at genome-wide scale

Preprint and 🧵 (1/): https://t.co/m8nleniSUD

[Vega Shah @dr_alphalyrae]

The latest issue of COB describes how AI infrastructure can create value for biotechnology beyond finding new drug candidates. Highly recommend reading if you work at the intersection of tech and life sciences

[Brandon Logeman @brandon_logeman]

@LaramieDuncan @PGCgenetics @SashaGusevPosts @dgmacarthur @tuuliel @hailianghuang Thanks @LaramieDuncan , I'll look up those works. BTW I'm very excited to dig into your recent paper on cell-type associations in complex brain phenotypes...its next on my list!

[Brandon Logeman @brandon_logeman]

Naive population genetics question: in multi-ancestry GWAS, are ancestry-specific associations common? For example, the recent BD analysis from @PGCgenetics found EAS specific associations. Rule or exception?

@SashaGusevPosts @dgmacarthur @tuuliel

https://t.co/grKwq1WMdY

[Brandon Logeman @brandon_logeman]

@doctorveera @sanogenetics Gotcha, thanks @doctorveera for the explanation that what is being observed is more statistical, rather than biological, in nature.

[Brandon Logeman @brandon_logeman]

@SashaGusevPosts @PGCgenetics @dgmacarthur @tuuliel “…apparent cross-population differences in genetic effects may be largely explained by differences in allele frequencies or linkage disequilibrium with “tagging” variants rather than differences in the underlying effect sizes.”

Thanks for the great write up @SashaGusevPosts

[Brandon Logeman @brandon_logeman]

Excellent write up by @doctorveera found here:https://t.co/A4xc1gYfzw

[Brandon Logeman @brandon_logeman]

A new paper has identified an answer to this question, in which a structural variant causes the de novo creation of a cardiomyocyte-specific enhancer, leading to ectopic expression of a potassium channel and heart disease.

[Brandon Logeman @brandon_logeman]

I’m looking for examples where a gene is normally expressed in cell type A but a GWAS/QTL hit contains a variant that causes ectopic expression in cell type B. All examples welcome, plz RT! @jkpritch @doctorveera @SashaGusevPosts @dgmacarthur @tuuliel @anshulkundaje

[Fusion Conferences @Fusion_Conf]

A big congratulations to our #GWAS24 Poster Winners, Luis Eichelmann (@LuisEichelmann) from @UniLuebeck & Brandon Logeman (@brandon_logeman) from @Harvard 🎉👏

[Brandon Logeman @brandon_logeman]

@TonyZador Others have discussed grant funding as a weighted lottery (i.e. better study section score gives you more ping pong balls in the ticket tumbler)....could something similar happen for publications?

[Brandon Logeman @brandon_logeman]

@TonyZador Their solution was to inject noise into the ordering of draft picks; a lottery that is weighted by the teams number of wins. It overall allocates resources (draft picks) where they belong but due to individual randomness keeps teams from gaming the system and losing on purpose

[Brandon Logeman @brandon_logeman]

@GeneticsMike7 @BritMartinez Dependent on one's definition of beauty, pretty sure Alaska can give Hawaii a run for its money

[Brandon Logeman @brandon_logeman]

@Jeff_Mold Agreed. I sometimes catch myself thinking the same thing.

[Brandon Logeman @brandon_logeman]

@OstuniLab @MolecularCell @pioneerfactors Thanks for highlighting this discussion which has a core topic (advantages / disadvantages of in vitro / in vivo studies) that is relevant beyond pioneer factors and permeates much of biology. Well written on both sides.

[Brandon Logeman @brandon_logeman]

@Vale_Tornini Congrats Valerie! 🎉

[Brandon Logeman @brandon_logeman]

@GeneticsMike7 @doctorveera @Nature @mnelsonxy @NatureGenet Conceptually the important genes = low effect sizes seems measurable. Practically I'm not sure how it would be done; perhaps some kind of meta study across multiple traits comparing effect size with PhyloP scores or dN/dS...something like that. Anyone tried this?

[Brandon Logeman @brandon_logeman]

New GWAS study examines when a baby takes their first steps 🧬 ➡️ 🚼 ➡️ 🚶‍♀️

SNP based heritability, a lower bound of heritability calculated using only common variants, shows up at ~25%, much higher than I would have guessed.

Work led by @annagui86

[PGC Consortium @PGCgenetics]

This recent GWAS preprint is the first to explore genetic influences on the age at onset of walking 🚶‍♀️🚶, a milestone that may indicate broader (neuro)developmental delays.

Find out more⤵️
https://t.co/MkzgEtKodl

[Brandon Logeman @brandon_logeman]

@doctorveera @Nature @mnelsonxy @NatureGenet I’m sure folks smarter than me have pondered over this before, if anyone has any thoughts please share; would love to learn more

[Brandon Logeman @brandon_logeman]

@doctorveera @Nature @mnelsonxy @NatureGenet But on the other hand I could image a set of coding mutations that very slightly decrease their function but is not enough to be completely eliminated from the population…..in this case perhaps these low effect GWAS genes would be enriched for rare variants in disease cases