Lightnews — Scholar-powered news

Eran Mukamel @neurome.bsky.social · 1d

Thank you for clearly articulating what's needed. Scientists need to have the courage to defend what they know to be right.

Reposted by Eran Mukamel

Jeremy Berg @jeremymberg.bsky.social · 2d

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...

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jeremymberg.github.io

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Eran Mukamel @neurome.bsky.social · 12d

I would bust out a slide rule for that one

Reposted by Eran Mukamel

Dr. David Miller 🏳️‍🌈 @davidimiller.bsky.social · Sep 1

🧪 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!!

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Eran Mukamel @neurome.bsky.social · Aug 24

I thought this was super cool too! Amazing that they can infer allele specific effects in these kind of data. But in the end I'm not sure it uncovers a ton more parent of origin effects than were previously known?

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Eran Mukamel @neurome.bsky.social · Aug 12

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

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Eran Mukamel @neurome.bsky.social · Aug 7

Wow

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Eran Mukamel @neurome.bsky.social · Jul 24

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

Eran Mukamel @neurome.bsky.social · Jul 14

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A 2022 paper was retracted after an independent team of researchers reanalyzed the data and questioned its validity.

www.thetransmitter.org

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Reposted by Eran Mukamel

The Transmitter @thetransmitter.bsky.social · Jul 2

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.

www.thetransmitter.org

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Eran Mukamel @neurome.bsky.social · Jul 3

Cool work, Marcelo et al!

Marcelo Mattar @marcelomattar.bsky.social · Jul 2

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...

Discovering cognitive strategies with tiny recurrent neural networks - Nature

Modelling biological decision-making with tiny recurrent neural networks enables more accurate predictions of animal choices than classical cognitive models and offers insights into the underlying cog...

doi.org

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Eran Mukamel @neurome.bsky.social · Jun 17

Thanks for this thoughtful and lucid exposition of an important issue that (alas) goes well beyond a single paper or group of authors. Neurogenomics deserves rigorous standards, so we don't squander the potential of large-scale sequencing for answering fundamental questions about the brain.

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Reposted by Eran Mukamel

Lior Pachter @lpachter.bsky.social · Jun 16

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

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Eran Mukamel @neurome.bsky.social · Jun 13

I guess it really was a Stanford thing...

Here's to Good Friends

stanfordmag.org

Eran Mukamel @neurome.bsky.social · Jun 13

Ofc the guy bringing EANABS to the party is not going to be the most popular one there, but I guess someone has to help the field avoid a hangover

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Eran Mukamel @neurome.bsky.social · Jun 13

I remember when I was in grad school the Stanford ugrads were partying too much, so the Univ mandated all gatherings had to have EANABS-- equally attractive non alcoholic beverages.

We need EANABS for stats--methods that are powerful and insightful but without cutting corners in rigor.

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Eran Mukamel @neurome.bsky.social · Jun 12

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

The Transmitter @thetransmitter.bsky.social · Jun 12

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...

Sounding the alarm on pseudoreplication: Q&A with Constantinos Eleftheriou and Peter Kind

Most studies of neurological disorders in mice erroneously treat multiple samples from a single animal as independent replicates, according to a new analysis. But scientists and journals can take…

www.thetransmitter.org

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Reposted by Eran Mukamel

Kamala Harris @kamalaharris.com · Jun 8

My statement on what's unfolding in Los Angeles.

A statement from Kamala D. Harris:

Los Angeles is my home. And like so many Americans, I am appalled at what we are witnessing on the streets of our city. Deploying the National Guard is a dangerous escalation meant to provoke chaos. In addition to the recent ICE raids in Southern California and across our nation, it is part of the Trump Administration’s cruel, calculated agenda to spread panic and division.

This Administration’s actions are not about public safety —they’re about stoking fear. Fear of a community demanding dignity and due process.

Protest is a powerful tool — essential in the fight for justice. And as the LAPD, Mayor, and Governor have noted, demonstrations in defense of our immigrant neighbors have been overwhelmingly peaceful.

I continue to support the millions of Americans who are standing up to protect our most fundamental rights and freedoms.

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Reposted by Eran Mukamel

Michael Totty @mictott.bsky.social · Jun 4

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

www.nature.com

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Eran Mukamel @neurome.bsky.social · Jun 5

Is Multiome OMG a new kit from 10x? :)

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Eran Mukamel @neurome.bsky.social · Jun 5

Aww thanks Jessica, your encouragement helped me shake the feeling that I must be crazy.

I guess this topic is not going away anytime soon.

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Eran Mukamel @neurome.bsky.social · Jun 5

Collaboration is great! An good computational collaborator can come up with many interesting and powerful ways of looking at data that don't require cutting corners on rigor.

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Eran Mukamel @neurome.bsky.social · Jun 5

Indeed. I think the topic of sex differences is rife with shoddy stats. I even wrote a similar thing about it in the context of brain sex differences. I guess the temptation to ignore pesky statistical standards is just irresistible.

www.biologicalpsychiatryjournal.com/article/S000...

Multiple Comparisons and Inappropriate Statistical Testing Lead to Spurious Sex Differences in Gene Expression

The substantial differences in the incidence and symptoms of stress, depression, and addiction between males and females have motivated studies of sex differences in the brain’s molecular responses to...

www.biologicalpsychiatryjournal.com

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Eran Mukamel @neurome.bsky.social · Jun 5

This is simply double dipping. If you use the condition labels to filter the genes you will enrich for genes with an apparent difference between conditions.

The common practice of filtering out nonexpressed genes is not double dipping because it doesn't use the condition labels.

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Eran Mukamel @neurome.bsky.social · Jun 5

They did not make that argument in the original paper. They presented the omics data as straightforward evidence of an effect.

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