Alex A. Pollen

A foundation model for brain organoid network dynamics uncovers intrinsic computation and convergent disease phenotypes

PULSE, a foundation model trained on neural recordings, reveals how disease variants affect network development and how circuits encode information in brain organoids.

Single-cell transcriptomic atlas of frontoinsular cortex reveals molecular correlates of selective neuronal vulnerability in FTD

The paper identifies molecular subtypes of neurons in the frontoinsular cortex and links specific gene expression patterns to neuronal vulnerability in FTD.

Developmental signaling reveals functionally enriched human-specific gene regulation in telencephalic progenitors

The paper identifies human-specific gene regulation in telencephalic progenitors by analyzing morphogen-dependent gene expression responses across human, chimpanzee, and orangutan species.

CellBouncer, A Unified Toolkit for Single-Cell Demultiplexing and Ambient RNA Analysis, Reveals Hominid Mitochondrial Incompatibilities

CellBouncer demultiplexes and analyzes pooled single-cell data, revealing mitochondrial incompatibilities between humans and chimpanzees.

A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos

This study presents a pan-pangenome of humans, chimpanzees, and bonobos, revealing structural variation, selection patterns, and adaptations related to immunity and malaria resistance.

Dissecting Gene Regulatory Networks Governing Human Cortical Cell Fate

The paper identifies transcription factors and effector genes involved in human cortical neurogenesis using CRISPRi screening in a primary culture system.

NPEPPS segmental duplication drives position effect expression of TBC1D3 in the human brain

The paper identifies a segmental duplication that drives position effect expression of TBC1D3 in the human brain, explaining its high structural heterozygosity.

Mapping cis- and trans-regulatory target genes of human-specific deletions

The paper identifies human-specific deletions that affect gene expression by using CRISPRi screening in chimpanzee stem cells.

Interrogating the Regulatory Function of HAQERs during Human Cortical Development

The paper identifies HAQERs in human cortical development, showing their role in gene regulation through CpG gains and links them to neurological disorders.

Conservation, alteration, and redistribution of mammalian striatal interneurons

The paper analyzes the conservation and evolution of striatal interneurons across mammals, finding that TAC3 interneurons are conserved and that neuronal types evolve through redistribution and refinement.

ANTIPODE Provides a Global View of Cell Type Homology and Transcriptomic Divergence in the Developing Mammalian Brain

ANTIPODE integrates single-cell data across species to identify homologous cell types and reveal gene regulatory divergence in developing mammalian brains.

Accelerated Tempo of Cortical Neurogenesis in Down Syndrome

This study shows that TS21 accelerates radial glia lineage progression, leading to premature production of inhibitory neurons and oligodendrocytes in Down syndrome.

Fate plasticity of interneuron specification

This study shows that the identity of MGE-derived cortical interneurons can be dynamically influenced by their environment, with human 3D models promoting Pvalb expression over Sst.

Interspecies Organoids Reveal Human-Specific Molecular Features of Dopaminergic Neuron Development and Vulnerability

Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex

The paper identifies 46,802 enhancers and 164 psychiatric disorder variants with regulatory effects in the developing cortex and organoids using massively parallel reporter assays and deep learning.

Structurally divergent and recurrently mutated regions of primate genomes

The paper identifies structurally divergent regions in primate genomes and quantifies the impact of structural variants across multiple species.

A cross-species proteomic map reveals neoteny of human synapse development

This study creates a cross-species proteomic map of synapse development in human, macaque, and mouse neocortex, revealing slower human PSD maturation and its potential link to neoteny.

Light-weight Electrophysiology Hardware and Software Platform for Cloud-Based Neural Recording Experiments

The paper introduces Piphys, an open-source platform for neural recording that enables remote control and scalability through cloud-based software and low-cost hardware.

UCSC Cell Browser: Visualize Your Single-Cell Data

The UCSC Cell Browser allows visualization of gene expression and metadata in single-cell datasets through a web interface and Python package.

Tropism of SARS-CoV-2 for Developing Human Cortical Astrocytes

In primary human cortical tissue and stem cell-derived organoids, SARS-CoV-2 infects astrocytes almost exclusively, apparently through DPP4 rather than ACE2, leaving them reactive and stressed.

3D Epigenomic Characterization Reveals Insights Into Gene Regulation and Lineage Specification During Corticogenesis

This study characterizes 3D epigenomic landscapes during human corticogenesis, revealing chromatin looping and super interactive promoters involved in lineage-specific gene regulation.

Optimization and scaling of patient-derived brain organoids uncovers deep phenotypes of disease

This paper develops an automated system to scale patient-derived brain organoids, revealing consistent donor and batch effects and demonstrating reproducible disease phenotypes in tuberous sclerosis models.

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution

The paper uses chimpanzee cerebral organoids to identify human-specific genes in cortical development and finds increased PI3K/AKT/mTOR activation in human outer radial glia.

Regulation of Cell-Type-Specific Transcriptomes by miRNA Networks During Human Brain Development

The paper investigates how miRNA-mRNA networks regulate cell-type-specific transcriptomes during human brain development using AGO2-HITS-CLIP, single-cell profiling, and bipartite network analysis.

Human-specific NOTCH-like genes in a region linked to neurodevelopmental disorders affect cortical neurogenesis

The paper identifies human-specific NOTCH2NL genes linked to neurodevelopmental disorders and shows they affect cortical neurogenesis through Notch signaling.

Saturating Single-Cell Datasets

The paper investigates the relationship between cell number and transcriptional heterogeneity in single-cell datasets, finding that 50,000 cells can capture most biologically meaningful insights from 1.3 million cells.