Alex Pollen

1/ Our new study, led by Jingwen Ding, examines the role of transcription factors during human neurogenesis to identify gene regulatory networks influencing cell fate, maturation, and subtype specification www.nature.com/articles/s41...

9/ We hope our study will provide a framework for functionally studying how disease and evolution shape human cortical development.

1/ Our new study, led by Jingwen Ding, examines the role of transcription factors during human neurogenesis to identify gene regulatory networks influencing cell fate, maturation, and subtype specification www.nature.com/articles/s41...

7/ We found a postmitotic role for ARX in safeguarding interneuron identity. Without ARX, the cells display “ectopic" subtype identity, characterized by LMO1 upregulation.

1/ Our new study, led by Jingwen Ding, examines the role of transcription factors during human neurogenesis to identify gene regulatory networks influencing cell fate, maturation, and subtype specification www.nature.com/articles/s41...

5/ We also identified NR2E1 and ARX that have opposing roles in regulating the balance of excitatory versus inhibitory neurogenesis. By combining single cell lineage tracing with Perturb-seq, we discovered their roles in balancing RG lineage plasticity and progression.

1/ Our new study, led by Jingwen Ding, examines the role of transcription factors during human neurogenesis to identify gene regulatory networks influencing cell fate, maturation, and subtype specification www.nature.com/articles/s41...

3/ We used CRISPRi to repress 44 transcription factors in human radial glia and then measured the consequences on neurogenesis using single cell RNA sequencing.

1/ Our new study, led by Jingwen Ding, examines the role of transcription factors during human neurogenesis to identify gene regulatory networks influencing cell fate, maturation, and subtype specification www.nature.com/articles/s41...

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...

Collectively, the broad pattern of inhibitory neuron conservation suggests that, on the mammalian timescale, evolution modifies the brain by ‘teaching old cells new tricks’, rather than inventing novel cell types early in 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...

In adult mouse, we identified a rare subpopulation of Th interneurons which expresses residual Tac2 (TAC3). Using the Allen institute’s Merscope data, we find this rare Tac2-expressing population is spatially restricted to the ventromedial striatum.

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...

Surprisingly, we find that the population was hiding in plain sight, but disguised by the loss of TAC3 (called Tac2 in mouse) and gain of Th expression, indicating an unappreciated homology between rodent Th and mammalian TAC3 striatal interneurons.

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...

Although the TAC3 initial class is conserved to marsupials (opossum and sugar glider), we observe turnover of signaling pathway genes across multiple timescales, and an additional migratory destination in Laurasiatherian (pig and ferret) cortex

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...

We begin by performing cross-species analysis of developing initial classes of both striatal and cortical inhibitory neuron populations by integrating single cell sequencing data from 8 mammals, spanning from primates to marsupials.

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...

Surprisingly, cells with mitochondria from two hominids show evidence for apoptotic pathway induction, reduced mRNA expression, and less efficient processing of polycistronic mitochondrial transcripts, revealing recently evolved incompatibilities in the hominid lineage.

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...

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...

For full details on how the tools work, see: bsky.app/profile/nksc...

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...

CellBouncer assigns sgRNAs and other perturbation tags to cell-of-origin, accounting for low coverage and increased tag background

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...

Importantly, CellBouncer uses sequence variation as an external ground-truth for ambient RNA determination, improving individual-of-origin assignments and enabling cell level corrections, while providing insights into the nature and sources of ambient RNA.

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...

Individual-of-origin assignments for cells that account for deep population structure, scale across large SNP sets, and are robust to ambient RNA

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...

Pooled processing or culture of cells provides a promising avenue to connect human genetics and single cell genomics but creates new bioinformatic challenges.. CellBouncer provides 7 integrated tools to accelerate pooled experiments, including:

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...