The DNA methylome is an incredibly rich signature of cell identity and gene regulation. But what if we're missing half the story? Our new preprint shows that, for neurons, 5-methyl-cytosine (5mC) is only the tip of the methylberg... 🧵

bioRxivpreprint@biorxivpreprint.bsky.social · 6mo ago

Postnatal conversion of methylcytosine to hydroxymethylcytosine reconfigures the human neuronal epigenome https://www.biorxiv.org/content/10.64898/2026.02.18.706675v1

Exciting to see a package of brain development studies (mainly from mouse) from the NIH (not on bsky!?) #BRAINInitiative . Congrats to the authors, and I'm looking forward to digging into the findings/data. www.nature.com/collections/...

BICAN: A cell census of the developing human brain

Building on their landmark efforts to create cell-type atlases of adult brains using single-cell and spatial genomics technologies, researchers in the BRAIN ...

nature.com

What do you get when you cross a joke with a rhetorical question?

I have been trying to get this published as an op-ed, but I am going to post it here since I think it is timely in light of the "consent" extortion events. Deafening Quiet from the Scientific Establishment jeremymberg.github.io/jeremyberg.g... 1/14

🧪 And House appropriators say: no cuts to NIH budget! House subcommittee version just came out (link below). Holds NIH flat at $48 billion. To be clear: this is far from over. But a good sign that science still matters across both sides of aisle. YOUR VOICE MATTERS!!

Dr. David Miller 🏳️‍🌈@davidimiller.bsky.social · last yr.

🧪 Senate appropriators say: NIH's budget gets a... boost! Rather than 40% cut, NIH gets a $400M *increase* in the Senate committee bill for FY26 (about +1%). "Congress has your back," said @murray.senate.gov. ADVOCACY MATTERS! There's still a long road (esp in the House), so keep up pressure.

I always enjoyed visiting DC for neuroscience conferences, but now that they've sent in the storm troopers I'm sure the criminal violations of statistical best practices will finally end

Can universities go on strike by withholding licensing of all their patents by any US govt agency (incl military)? Seems like the only leverage they have and better than just giving their lunch money to the bullies

Interesting to see Nature retracting a study based on apparent over-clustering of single cell sequencing data www.thetransmitter.org/cell-types/n...

Nature retracts paper on novel brain cell type

A 2022 paper was retracted after an independent team of researchers reanalyzed the data and questioned its validity.

thetransmitter.org

A reanalysis of data published in a 2024 Nature paper highlights a “thorny problem” in genetics research: how to balance curiosity and caution when searching for gene candidates. By Katie Moisse #neuroskyence www.thetransmitter.org/statistics/m...

Memory study sparks debate over statistical methods

The study used data filtering and statistical approaches that can yield spurious findings, but more rigorous methods can result in missed leads.

thetransmitter.org

Cool work, Marcelo et al!

Marcelo Mattar@marcelomattar.bsky.social · last yr.

Thrilled to see our TinyRNN paper in @nature! We show how tiny RNNs predict choices of individual subjects accurately while staying fully interpretable. This approach can transform how we model cognitive processes in both healthy and disordered decisions. doi.org/10.1038/s415...

I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...

Reply to: Reply to: False positives in the study of memory-related gene expression

In the Nature paper “Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory” published on March 14th, 2024, authors Sun et al. claimed to identify cell-type specifi…

liorpachter.wordpress.com

Great to see attention being paid to rigor in neuroscience methods.

The Transmitter @thetransmitter.bsky.social · last yr.

A statistical error known as pseudoreplication appears in more than half of recent mouse studies on neurological disorders, according to a new study. Peter Kind and Constantino Elfetheriou tell Lauren Schenkman why researchers should pay attention. www.thetransmitter.org/pseudoreplic...

My statement on what's unfolding in Los Angeles.

Always pseudobulk, always correct for multiple comparisons, and always consult with a biostatistian. www.nature.com/articles/s41...

False positives in study of memory-related gene expression - Nature

Nature - False positives in study of memory-related gene expression

nature.com

www.nature.com/articles/s41... The engram is still out there, waiting to be rigorously discovered!

False positives in study of memory-related gene expression - Nature

Nature - False positives in study of memory-related gene expression

nature.com

Very happy to see our comment about scRNAseq methods and rigor finally published. Now more than ever, science must be an example of integrity and self-examination. If we abandon rigor, we will be even more isolated and vulnerable.

Lior Pachter@lpachter.bsky.social · last yr.

As @neurome.bsky.social and Yu point out, #methodsmatter. They are spot on here: www.nature.com/articles/s41...

Hard to process the news about Harvard and international students. Other universities should stand in solidarity with our colleagues who are being persecuted.

Francis Crick speculated that DNA modifications might be key to memory.... but synaptic molecules are specific to individual neural connections

Quanta Magazine@quantamagazine.org · last yr.

A classic test of a molecule’s importance is to block it and see what breaks. A team of researchers are using this approach to sort out why some memories stick around for a lifetime.

Genuine question: what will all the talented US and international people who would have gone into science do instead? Real estate?

"A report by economists at American University in Washington DC estimates that a 50% reduction in federal science funding would reduce the US gross domestic product by approximately 7.6%." Science is an amazing engine of economic activity and progress for the US ... or at least it was.

Nature@nature.com · last yr.

Staff members at the US National Science Foundation (NSF) were told on 30 April to “stop awarding all funding actions until further notice,” according to an email seen by Nature. https://go.nature.com/44Ugf9V

First they came for the data, and I did not speak out... because I was not data Then they came for the models, and I did not speak... because I was not a model. Then they came for the scientists, and there was no one left to speak for me.

Science not Silence. (Kudos to the students on my hallway who put these up)

I signed and urge others to sign as well.

Surya Ganguli@suryaganguli.bsky.social · last yr.

I signed. Please consider signing.

I'm ashamed of my country

So who is leading the resistance? We have no time to lose.

Spent today hearing inspiring and exciting science from fellow members of an NIH Consortium studying HIV and opioid effects on the 🧠. A reminder of what we have to lose if the US abandons our scientific enterprise.

So when we "buy" Greenland, will we call it Trumpistan? Donaldland? Maganesia? The Panama Canal will be called Trump's Trickle.

My awesome colleague @seantrott.bsky.social quoted on understanding the nature of our new robot overlords in @nytimes.com www.nytimes.com/2024/12/16/o...

Opinion | How Does A.I. Think? Here’s One Theory.

It may employ a kind of reasoning humans use all the time — but you’ve probably never heard of it.

nytimes.com

Low tide in La Jolla today

Calcium imaging of Climbing Fiber complex spikes in mice performing skilled movements... Ahh this brings back fond memories for me :). Very cool.

Surya Ganguli@suryaganguli.bsky.social · 2y ago

The Kumamoto model is great! It came in a handy in modeling motor synchronization at movement onset: www.sciencedirect.com/science/arti... And in grid cell remapping in altered virtual reality: www.nature.com/articles/s41...