Brandon Logeman

On the left - western blot of B16F10 cells wt and KO for CDK8. Our in house produced antibodies give a lot of unspecific bands. On the right same probes with antibodies preincubated with fixed CDK8 KO cells - there is a specific band and faint unspecific bands, which can be probably eliminated with increase of amount of KO cells.

Neat trick if you polycolonal ab's suck. Incubate them with fixed cells with a KO of your protein of interest, then spin. Protocol here: www.med.upenn.edu/markslab/ass...
I was amazed how well it worked on first try (I'm sure that I can completely eliminate unspecific bands)
#WesternBlot #cellsky

Persistent hindrances to data re-use in single-cell genomics https://www.biorxiv.org/content/10.1101/2025.10.02.680150v1

My Own Lab at Westlake University is OPEN! We are recruiting cool people at all levels NOW!
By tinkering behaviors and neural circuits in distinct animal species (mouse, sugar glider, etc), we are exploring new ways of doing social neuroscience in vivo, in silico and at home!

It’s a display case containing 20 or so bugs that look like leaves, at the Montreal Insectarium. Most of the bigs are brown, but some are light teal. The glass is labeled “Just like a bug” in English and French.

Zoom in on a whole bunch of brown not-leaves arranged naturalistically on a branch.

Every single one of these leaves is a bug.

It's probably the deterioration of social media (I hope) but i'm exposed to a lot less cool science. It used to feel like a new cool study is being preprinted/published every week, and lately it's rare (at least so it seems). Share a recent study that's worth knowing!

mRNA-based sensors are now more modular, but still rely on overexpression of ADAR1 which interferes with endogenous biology. Seems to be a situation where enzyme engineering to make a bio-orthogonal ADAR-like protein that only deaminates the reporter should be within reach.

The great thing about Rosh Hashanah and Fat Bear Week starting the same day is apples and honey is completely appropriate for both

This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/

Asking BlueSky for help: For a review, I am trying to accurately credit the first paper that measured pairwise 3D distances between 2 pieces of DNA on the same chromosome (or cosmid). Is Trask 1989 the first?
I know of earlier single-locus papers (1982).
www.sciencedirect.com/science/arti...

Some notes on probability judgement – Notes from a data witch For the love of fuck, literally nobody thinks that 20% of the population is transgender. Please stop sharing that ridiculous YouGov statistic

Against my better instincts, I have written some notes on how human probability judgements work and what you should expect from surveys that ask people to guess what proportion of the population is transgender. I hope never to speak of this matter again

This is a great story and exciting to think about the possibilities genome wide, congrats!

Jamie Drayton and I were fortunate to contribute some RCMC analyses to this beautiful paper from Eder, Moene...van Steensel that systematically maps the relationship between enhancer location and gene expression (and nice to see RCMC predict expression in Fig 2H-I):
www.science.org/doi/10.1126/...

Speaks to the peculiar fact that postmitotic neurons have some of the most long-range enhancers 🧐

"For elements separated by 10 s of megabases, the average search time (2 to 10 days) is estimated to be longer than the cell cycle length...extreme long-range cis regulation (79–82) may require substantially longer cell cycles (or be postmitotic)"

Kinetic organization of the genome revealed by ultraresolution multiscale live imaging Genome function requires regulated genome motion. However, tools to directly observe this motion in vivo have been limited in coverage and resolution. Here we introduce an approach to tile mammalian c...

Very interesting paper from the group of Alistair Boettiger examining DNA contact using long-term live cell imaging. Generated ~75TB of data!

www.science.org/doi/10.1126/...

bioRxiv - An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq

New preprint from our lab!

What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?

Find out here: www.biorxiv.org/content/10.1...

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Congrats Chad! Exciting to see this spatially defined

Got it, thanks for the help 💯

Tried to tag @sashagusevposts.bsky.social in the first post but the link got disrupted.

Thanks Tuuli. 🙏 When writing grants do you have any favorite key reference(s) that you like to use? Asking as neuroscientist who is new to genetics work.

Any thoughts on the current estimate for how many causal GWAS variants are coding vs regulatory? What references am I missing? Any help appreciated. End thread.

Likewise, another 2012 paper places calculates non-coding variants to be ~95%. However, this is examining lead variants, with ~41% of variants present in introns...which could be in LD with coding variants. 🧵
www-science-org.ezp-prod1.hul.harvard.edu/doi/10.1126/...

Fig.2 from the 2012 paper that @anshulkundaje.bsky.social worked on shows 95% of lead variants are non-coding, but functional annotation adjustment places that number closer to 84% 🧵
genome.cshlp.org/content/22/9...

🚨 Request for functional genomics / GWAS folks. I repeatedly see claims that “… 90% of GWAS identified variants lie in regulatory regions…” from reviews, but have had a hard time tracking down where this number comes from. 🧵@sashagusevposts.bsky.social @jkpritch.bsky.social @tuuliel.bsky.social

Second that you can do this through bonsai. Also in my experience the folks at neurophotometrics are super helpful.

Next-generation hybridization chain reaction tools with enhanced sensitivities to detect challenging targets https://www.biorxiv.org/content/10.1101/2025.09.09.675218v1

Too many late nights in the lab uncovering fundamental synaptic properties🤣🤣🤣…..Melon Collie (both CDs) is what did it for me

One of the greatest alt rock bands, conjures up memories for me as well!

Brain control of energy homeostasis: Implications for anti-obesity pharmacotherapy Advances in mapping how the brain regulates energy homeostasis, together with progress in peptide-based pharmacotherapy, highlight emerging opportunities for obesity treatment with the potential to su...

@clemmensenc.bsky.social you have a very nice 🧵 on this great review over at the other site. Would love to have something similar here

www.cell.com/cell/fulltex...

AI-generated MLH1 small binder improves prime editing efficiency A compact, AI-generated suppressor of DNA mismatch repair can enhance prime editing in vivo and in vitro and can be integrated into a variety of prime editing architectures.

Utilizing in silico designed protein binders to inhibit mismatch repair and increase editing efficiency of Cas9-mediated Prime Editing

www.cell.com/cell/fulltex...