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Reposted by Brandon Logeman

Anshul Kundaje @anshulkundaje.bsky.social · 20h

Friendly reminder that there is only one official release of ChromBPNet at our lab GitHub github.com/kundajelab/chr…

There are other versions floating around eg. in the CRESTED package that are NOT anywhere close to the official implementation. 1/

https://github.com/kundajelab/chr…

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Reposted by Brandon Logeman

bioRxiv Genomics @biorxiv-genomic.bsky.social · 1d

Direct In-Sample Sequencing of the 3' Transcriptome Expands the Capabilities of Optical Pooled Screens https://www.biorxiv.org/content/10.1101/2025.10.11.681797v1

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Reposted by Brandon Logeman

Victor Tatarskiy @greenrat.bsky.social · 13d

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

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.

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Reposted by Brandon Logeman

bioRxiv Genomics @biorxiv-genomic.bsky.social · 12d

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

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Reposted by Brandon Logeman

Ding Liu @dingliu.bsky.social · 12d

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!

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Reposted by Brandon Logeman

Laura White @laurakwhite.bsky.social · 16d

Every single one of these leaves is a bug.

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.

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Reposted by Brandon Logeman

Oded Rechavi @odedrechavi.bsky.social · 19d

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!

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Brandon Logeman @blogeman.bsky.social · 22d

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.

bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 26d

Sequence-Independent RNA Sensing in Living Mammalian Cells https://www.biorxiv.org/content/10.1101/2025.09.18.677213v1

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Reposted by Brandon Logeman

Michael Baym @baym.lol · 22d

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

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Reposted by Brandon Logeman

Anshul Kundaje @anshulkundaje.bsky.social · 23d

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/

Yun S. Song @yun-s-song.bsky.social · 23d

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)

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Reposted by Brandon Logeman

Anders Sejr Hansen @andersshansen.bsky.social · 24d

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...

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Reposted by Brandon Logeman

Danielle Navarro @djnavarro.net · 24d

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

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

blog.djnavarro.net

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Brandon Logeman @blogeman.bsky.social · 25d

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

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Reposted by Brandon Logeman

Anders Sejr Hansen @andersshansen.bsky.social · 26d

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/...

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Brandon Logeman @blogeman.bsky.social · 26d

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

Brandon Logeman @blogeman.bsky.social · 26d

"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)"

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Brandon Logeman @blogeman.bsky.social · 26d

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/...

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...

www.science.org

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Reposted by Brandon Logeman

Jesse Engreitz @jengreitz.bsky.social · 26d

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

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Brandon Logeman @blogeman.bsky.social · 28d

Congrats Chad! Exciting to see this spatially defined

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Brandon Logeman @blogeman.bsky.social · 28d

Got it, thanks for the help 💯

Brandon Logeman @blogeman.bsky.social · 29d

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

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Brandon Logeman @blogeman.bsky.social · 29d

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.

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Brandon Logeman @blogeman.bsky.social · 29d

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.

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Brandon Logeman @blogeman.bsky.social · 29d

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/...

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Brandon Logeman @blogeman.bsky.social · 29d

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...

Linking disease associations with regulatory information in the human genome

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

genome.cshlp.org

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