Alex Pollen
@brainevodevo.bsky.social
Studying specializations and vulnerabilities of human brain development
Our new manuscript, led by Emily Corrigan, examines inhibitory neuron diversity across approximately 160 million years of evolutionary divergence, as part of BRAIN Initiative Cell Atlas Network (BICAN) developing brain atlas package: www.nature.com/articles/s41...
Conservation and alteration of mammalian striatal interneurons - Nature
An analysis of cell-type diversity in brain samples from a variety of mammalian species, both during development and in adult animals, reveals that the TAC3 initial class of striatal interneurons is c...
www.nature.com
November 7, 2025 at 6:06 PM
Our new manuscript, led by Emily Corrigan, examines inhibitory neuron diversity across approximately 160 million years of evolutionary divergence, as part of BRAIN Initiative Cell Atlas Network (BICAN) developing brain atlas package: www.nature.com/articles/s41...
Reposted by Alex Pollen
🧠🌟🐭 Excited to share some of my postdoc work on the evolution of dexterity!
We compared deer mice evolved in forest vs prairie habitats. We found that forest mice have:
(1) more corticospinal neurons (CSNs)
(2) better hand dexterity
(3) more dexterous climbing, which is linked to CSN number🧵
We compared deer mice evolved in forest vs prairie habitats. We found that forest mice have:
(1) more corticospinal neurons (CSNs)
(2) better hand dexterity
(3) more dexterous climbing, which is linked to CSN number🧵
October 22, 2025 at 8:41 PM
🧠🌟🐭 Excited to share some of my postdoc work on the evolution of dexterity!
We compared deer mice evolved in forest vs prairie habitats. We found that forest mice have:
(1) more corticospinal neurons (CSNs)
(2) better hand dexterity
(3) more dexterous climbing, which is linked to CSN number🧵
We compared deer mice evolved in forest vs prairie habitats. We found that forest mice have:
(1) more corticospinal neurons (CSNs)
(2) better hand dexterity
(3) more dexterous climbing, which is linked to CSN number🧵
Reposted by Alex Pollen
I am thrilled to share our latest work: we identified a population of central amygdala neurons that promote the earliest and perhaps most important social behavior: pup suckling!... We also developed new tools for pup neuroscience
Work by @Jeff Moore now at USC, a collaboration with @Sam Pfaff lab
Work by @Jeff Moore now at USC, a collaboration with @Sam Pfaff lab
October 21, 2025 at 10:18 AM
I am thrilled to share our latest work: we identified a population of central amygdala neurons that promote the earliest and perhaps most important social behavior: pup suckling!... We also developed new tools for pup neuroscience
Work by @Jeff Moore now at USC, a collaboration with @Sam Pfaff lab
Work by @Jeff Moore now at USC, a collaboration with @Sam Pfaff lab
Reposted by Alex Pollen
“Intraspecific sequence variation and complete genomes refine the identification of rapidly evolved regions in humans”
New work on HAQERs, by
@rimangan.bsky.social Yanting Luo Craig Lowe @debbysilver.bsky.social @manoliskellis.bsky.social & colleagues
🧪🧬
www.biorxiv.org/content/10.1...
New work on HAQERs, by
@rimangan.bsky.social Yanting Luo Craig Lowe @debbysilver.bsky.social @manoliskellis.bsky.social & colleagues
🧪🧬
www.biorxiv.org/content/10.1...
Intraspecific sequence variation and complete genomes refine the identification of rapidly evolved regions in humans
Humans exhibit significant phenotypic differences from other great apes, yet pinpointing the underlying genetic changes has been limited by incomplete reference genomes and a reliance on single assemb...
www.biorxiv.org
October 21, 2025 at 10:14 AM
“Intraspecific sequence variation and complete genomes refine the identification of rapidly evolved regions in humans”
New work on HAQERs, by
@rimangan.bsky.social Yanting Luo Craig Lowe @debbysilver.bsky.social @manoliskellis.bsky.social & colleagues
🧪🧬
www.biorxiv.org/content/10.1...
New work on HAQERs, by
@rimangan.bsky.social Yanting Luo Craig Lowe @debbysilver.bsky.social @manoliskellis.bsky.social & colleagues
🧪🧬
www.biorxiv.org/content/10.1...
Reposted by Alex Pollen
We’re excited to host @nkschaefer.bsky.social from the Pollen Lab @brainevodevo.bsky.social, UCSF!
He’ll present Cellbouncer, a new bioinformatic tool for pooled single-cell processing that yields insights into hominid evolution 🧬
More about the lab 👉 www.pollenlab.org
He’ll present Cellbouncer, a new bioinformatic tool for pooled single-cell processing that yields insights into hominid evolution 🧬
More about the lab 👉 www.pollenlab.org
September 19, 2025 at 11:32 AM
We’re excited to host @nkschaefer.bsky.social from the Pollen Lab @brainevodevo.bsky.social, UCSF!
He’ll present Cellbouncer, a new bioinformatic tool for pooled single-cell processing that yields insights into hominid evolution 🧬
More about the lab 👉 www.pollenlab.org
He’ll present Cellbouncer, a new bioinformatic tool for pooled single-cell processing that yields insights into hominid evolution 🧬
More about the lab 👉 www.pollenlab.org
Reposted by Alex Pollen
"Sources said the administration is specifically considering a full termination of federal grant funding for the University of California and California State University systems."
Pure vandalism.
This could never happen in a country with functioning checks and balances.
Pure vandalism.
This could never happen in a country with functioning checks and balances.
Trump preparing large-scale cancellation of federal funding for California, sources say | CNN Politics
The Trump administration is preparing to cancel a large swath of federal funding to California, an effort which could begin as soon as Friday, according to multiple sources.
www.cnn.com
June 6, 2025 at 8:01 PM
"Sources said the administration is specifically considering a full termination of federal grant funding for the University of California and California State University systems."
Pure vandalism.
This could never happen in a country with functioning checks and balances.
Pure vandalism.
This could never happen in a country with functioning checks and balances.
Reposted by Alex Pollen
EMBOMtg Paris May 6-9
@aydoganlab.bsky.social @jamesbriscoe.bsky.social @brunetlab.bsky.social @ebisuyamiki.bsky.social @mwdorr.bsky.social @beyerlab.bsky.social @franckp.bsky.social @janereznick.bsky.social @olmedo-lab.bsky.social @perez-carrasco.bsky.social
meetings.embo.org/event/25-dev...
@aydoganlab.bsky.social @jamesbriscoe.bsky.social @brunetlab.bsky.social @ebisuyamiki.bsky.social @mwdorr.bsky.social @beyerlab.bsky.social @franckp.bsky.social @janereznick.bsky.social @olmedo-lab.bsky.social @perez-carrasco.bsky.social
meetings.embo.org/event/25-dev...
Developmental timing across species: From mechanisms to evolutionary insights
Like choreography, development consists of a highly ordered suite of steps and transitions. Modifying developmental tempo can affect final size and composition of tissues, as well as their plasticity…
meetings.embo.org
March 29, 2025 at 3:00 PM
Congratulations to Nathan for conceiving and designing this unified demultiplexing toolkit!
Picture this: you are running a single cell sequencing experiment and want to incorporate cells from different species, individuals, and maybe even perturbations. You process everything together to save time while reducing batch artifacts. You collect data. What do you do now?
a man in a green shirt is carrying a pink bag
ALT: a man in a green shirt is carrying a pink bag
media.tenor.com
March 24, 2025 at 10:12 PM
Congratulations to Nathan for conceiving and designing this unified demultiplexing toolkit!
We put CellBouncer to the test with a challenging demultiplexing problem of assigning 24 hominid tetraploid composite cell lines generated by Bryan Pavlovic to both individuals-of-origin and identifying the mitochondrial haplotypes present.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
March 24, 2025 at 10:07 PM
We put CellBouncer to the test with a challenging demultiplexing problem of assigning 24 hominid tetraploid composite cell lines generated by Bryan Pavlovic to both individuals-of-origin and identifying the mitochondrial haplotypes present.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Introducing CellBouncer, a unified demultiplexing toolkit built by nkschaefer.bsky.social to check IDs and keep the riff raff out of single cell genomics datasets, including by using genetic variation as an external ground-truth for ambient RNA removal:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
March 24, 2025 at 9:48 PM
Introducing CellBouncer, a unified demultiplexing toolkit built by nkschaefer.bsky.social to check IDs and keep the riff raff out of single cell genomics datasets, including by using genetic variation as an external ground-truth for ambient RNA removal:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Alex Pollen
Excellent preprint by @bhadurilab.bsky.social, offering a metabolic atlas of the early human cortex, & revealing how shifts in metabolic processes regulate cell fate transitions. Very valuable resource to address evolutionary questions 🧪🧠🧫
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Metabolic Atlas of Early Human Cortex Identifies Regulators of Cell Fate Transitions
Characterization of cell type emergence during human cortical development, which enables unique human cognition, has focused primarily on anatomical and transcriptional characterizations. Metabolic pr...
www.biorxiv.org
March 12, 2025 at 12:56 PM
Excellent preprint by @bhadurilab.bsky.social, offering a metabolic atlas of the early human cortex, & revealing how shifts in metabolic processes regulate cell fate transitions. Very valuable resource to address evolutionary questions 🧪🧠🧫
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Alex Pollen
Francis Collins, the NIH Director for 12 years, led the Human Genome Project and other NIH efforts for 32 years, resigned today. Key words from his resignation letter
www.nytimes.com/2025/03/01/u...
www.nytimes.com/2025/03/01/u...
March 1, 2025 at 6:07 PM
Francis Collins, the NIH Director for 12 years, led the Human Genome Project and other NIH efforts for 32 years, resigned today. Key words from his resignation letter
www.nytimes.com/2025/03/01/u...
www.nytimes.com/2025/03/01/u...
Reposted by Alex Pollen
By @katherinejwu.com
"The NIH... supported 99 percent of the drugs approved in the U.S. from 2010 to 2019. The agency has had a hand in “nearly all of our major medical breakthroughs over the past several decades,”
The NIH is in a struggle for its (and our) lives. This is existential to America:
"The NIH... supported 99 percent of the drugs approved in the U.S. from 2010 to 2019. The agency has had a hand in “nearly all of our major medical breakthroughs over the past several decades,”
The NIH is in a struggle for its (and our) lives. This is existential to America:
Inside the Collapse at NIH
Administration officials pressured NIH to avoid clear advice from the agency’s own lawyers to restart grant funding now.
www.theatlantic.com
February 27, 2025 at 5:29 PM
By @katherinejwu.com
"The NIH... supported 99 percent of the drugs approved in the U.S. from 2010 to 2019. The agency has had a hand in “nearly all of our major medical breakthroughs over the past several decades,”
The NIH is in a struggle for its (and our) lives. This is existential to America:
"The NIH... supported 99 percent of the drugs approved in the U.S. from 2010 to 2019. The agency has had a hand in “nearly all of our major medical breakthroughs over the past several decades,”
The NIH is in a struggle for its (and our) lives. This is existential to America:
Reposted by Alex Pollen
Check out our new preprint describing CiFi - a method that couples 3C and PacBio HiFi sequencing with low input requirements. We apply it to human GM12878 to better characterize chromatin across repetitive regions, as well as single insect samples (a mosquito and a Mediterranean fruit fly).
CiFi: Accurate long-read chromatin conformation capture with low-input requirements https://www.biorxiv.org/content/10.1101/2025.01.31.635566v1
February 5, 2025 at 11:49 PM
Check out our new preprint describing CiFi - a method that couples 3C and PacBio HiFi sequencing with low input requirements. We apply it to human GM12878 to better characterize chromatin across repetitive regions, as well as single insect samples (a mosquito and a Mediterranean fruit fly).
Pleasure to co-edit this issue of Current Opinion on human genetic origins with @steinlab.bsky.social:
www.sciencedirect.com/special-issu...
www.sciencedirect.com/special-issu...
Current Opinion in Genetics & Development | Genetics of Human Origin (2024) | ScienceDirect.com by ElsevierScienceDirect
Identification of the genetic variants underlying distinctive human traits provides a new perspective on human origins. However, complete descriptions of genetic variants under selective pressure alon...
www.sciencedirect.com
February 27, 2025 at 5:56 PM
Pleasure to co-edit this issue of Current Opinion on human genetic origins with @steinlab.bsky.social:
www.sciencedirect.com/special-issu...
www.sciencedirect.com/special-issu...
Reposted by Alex Pollen
A new story about our recent paper came out today in the Science section of Forbes! Check it out! www.forbes.com/sites/grrlsc...
Super Enzyme Regulates Testosterone Levels In Male Ruffs
A single gene in the shorebird species known as ruffs controls the levels of testosterone in males, and this in turn affects their appearance and mating strategies.
www.forbes.com
February 15, 2025 at 1:35 PM
A new story about our recent paper came out today in the Science section of Forbes! Check it out! www.forbes.com/sites/grrlsc...
Reposted by Alex Pollen
New preprint 📣! Excited to share the result of several years of work, led by @ellylewerissa.bsky.social & @olivieroleonardi.bsky.social, in collaboration with friends @naelnadifkasri-lab.bsky.social & Giuseppe Testa. On CHD2, a chromatin remodeller, its role in evolution & development [🧵]
🧪🧠🧫🧬
🧪🧠🧫🧬
January 22, 2025 at 10:38 AM
New preprint 📣! Excited to share the result of several years of work, led by @ellylewerissa.bsky.social & @olivieroleonardi.bsky.social, in collaboration with friends @naelnadifkasri-lab.bsky.social & Giuseppe Testa. On CHD2, a chromatin remodeller, its role in evolution & development [🧵]
🧪🧠🧫🧬
🧪🧠🧫🧬
Reposted by Alex Pollen
First post on this platform 👋. Glad to reconnect with old friends, and also learn from new contacts. Will post about intersecting themes: human evolution, genetics (esp. aDNA), neuroscience & cognition. Currently focusing on brain organoids and early developmental changes that may have had an impact
![cortical organoid [image credit: O. Leonardi, who is leading this collaborative project]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:ljcyk7tem65k7epgu5pkwuuh/bafkreico75nbiyo5zg6kzzahk5kxmcpcajygslloxkndmry2tnzr5q72pu@jpeg)
November 16, 2024 at 7:16 AM
First post on this platform 👋. Glad to reconnect with old friends, and also learn from new contacts. Will post about intersecting themes: human evolution, genetics (esp. aDNA), neuroscience & cognition. Currently focusing on brain organoids and early developmental changes that may have had an impact
Reposted by Alex Pollen
Happy to be on Bluesky! Our lab is fascinated by how the brain develops, how this goes awry in disease, and this is co-opted in evolution. A major focus is dynamic spatial and temporal #RNA control in the developing brain.
Please see our new review on evolution!
www.sciencedirect.com/science/arti...
Please see our new review on evolution!
www.sciencedirect.com/science/arti...
How our brains are built: emerging approaches to understand human-specific features
Understanding what makes us uniquely human is a long-standing question permeating fields from genomics, neuroscience, and developmental biology to med…
www.sciencedirect.com
November 16, 2024 at 7:36 PM
Happy to be on Bluesky! Our lab is fascinated by how the brain develops, how this goes awry in disease, and this is co-opted in evolution. A major focus is dynamic spatial and temporal #RNA control in the developing brain.
Please see our new review on evolution!
www.sciencedirect.com/science/arti...
Please see our new review on evolution!
www.sciencedirect.com/science/arti...
Reposted by Alex Pollen
1st preprint recommendation here (proud @biorxivpreprint.bsky.social affiliate): @brainevodevo.bsky.social & his team do great, creative work and I like their phylogeny-in-a-dish approach to examine gene regulatory evolution. Here they focus on dopaminergic neurons
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Interspecies Organoids Reveal Human-Specific Molecular Features of Dopaminergic Neuron Development and Vulnerability
The disproportionate expansion of telencephalic structures during human evolution involved tradeoffs that imposed greater connectivity and metabolic demands on midbrain dopaminergic neurons. Despite t...
www.biorxiv.org
November 16, 2024 at 4:30 PM
1st preprint recommendation here (proud @biorxivpreprint.bsky.social affiliate): @brainevodevo.bsky.social & his team do great, creative work and I like their phylogeny-in-a-dish approach to examine gene regulatory evolution. Here they focus on dopaminergic neurons
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Alex Pollen
Check out this awesome paper!
The latest from our group, led by Megan Ostrowski and @martyyang.bsky.social, is now published in final form (www.cell.com/cell/fulltex...! Many thanks to our excellent peer reviewers for suggesting several experiments (including CAF-1 perturbation) to really improve the study =) #epigenetics
The single-molecule accessibility landscape of newly replicated mammalian chromatin
By developing a long-read sequencing method to simultaneously map replication status
and protein-DNA contacts in cells, Ostrowski, Yang, et al. show that newly replicated
chromatin is enriched for unw...
www.cell.com
November 15, 2024 at 8:13 PM
Check out this awesome paper!
@jenellewallace.bsky.social
led a preview of two outstanding papers from the labs of Cecile Charrier, Pierre Vanderhaeghen, and @franckp.bsky.social that connect regulation of the tempo of synaptogenesis by the human-specific gene SRGAP2C to ASD-linked genes: authors.elsevier.com/a/1k3583BtfH...
led a preview of two outstanding papers from the labs of Cecile Charrier, Pierre Vanderhaeghen, and @franckp.bsky.social that connect regulation of the tempo of synaptogenesis by the human-specific gene SRGAP2C to ASD-linked genes: authors.elsevier.com/a/1k3583BtfH...
November 12, 2024 at 10:35 PM
@jenellewallace.bsky.social
led a preview of two outstanding papers from the labs of Cecile Charrier, Pierre Vanderhaeghen, and @franckp.bsky.social that connect regulation of the tempo of synaptogenesis by the human-specific gene SRGAP2C to ASD-linked genes: authors.elsevier.com/a/1k3583BtfH...
led a preview of two outstanding papers from the labs of Cecile Charrier, Pierre Vanderhaeghen, and @franckp.bsky.social that connect regulation of the tempo of synaptogenesis by the human-specific gene SRGAP2C to ASD-linked genes: authors.elsevier.com/a/1k3583BtfH...
Building on our recent review, Tyler Fair performed CRISPRi-based genetic screens to assign human-specific deletions to molecular and cellular phenotypes:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 29, 2023 at 6:49 PM
Building on our recent review, Tyler Fair performed CRISPRi-based genetic screens to assign human-specific deletions to molecular and cellular phenotypes:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
I learned so much from writing this review led by @jenellewallace.bsky.social . Protracted neuronal maturation is a hallmark feature of human cortex with unknown origins. We are excited that many groups are now making the mechanisms of species differences in timing experimentally tractable:
I'm thrilled to announce that the review I wrote with
@brainevodevo.bsky.social
is now online @Nature Review Neuroscience: www.nature.com/articles/s41... We cover mechanisms of prolonged human neuronal maturation, integrating lessons from model organisms with studies on species differences.
@brainevodevo.bsky.social
is now online @Nature Review Neuroscience: www.nature.com/articles/s41... We cover mechanisms of prolonged human neuronal maturation, integrating lessons from model organisms with studies on species differences.
Human neuronal maturation comes of age: cellular mechanisms and species differences - Nature Reviews...
Human cortical neurons undergo a protracted period of postmitotic maturation compared with those of other species. Wallace and Pollen review the cell-intrinsic and cell-extrinsic mechanisms that gover...
www.nature.com
December 14, 2023 at 9:35 PM
I learned so much from writing this review led by @jenellewallace.bsky.social . Protracted neuronal maturation is a hallmark feature of human cortex with unknown origins. We are excited that many groups are now making the mechanisms of species differences in timing experimentally tractable: