Zizhen Yao

PIANO: Probabilistic Inference Autoencoder Networks for multi-Omics enables robust generative modeling of gene expression and scales single-cell integration to 100 million cells

PIANO integrates single-cell data across species and modalities, models gene expression, and scales to 100 million cells for drug perturbation analysis.

Multimodal characterization of variation in neuronal types in the mouse basal ganglia

This study uses multimodal Patch-seq data to show that gene expression gradients in mouse basal ganglia neurons correlate with spatial location, physiology, and morphology.

Conserved Cell Type Signatures Across the Brainstem and Spinal Cord in the Mouse Central Nervous System

The paper maps conserved cell type signatures in the adult mouse brainstem and spinal cord using multi-omics data, revealing shared and region-specific features.

Genome-scale functional mapping of the mammalian whole brain with in vivo Perturb-seq

The paper maps gene expression responses to loss of 1,947 disease-associated genes across the mouse brain using Perturb-seq, revealing cell-type-specific essentiality and transcriptional programs.

MapMyCells: High-performance mapping of unlabeled cell-by-gene data to reference brain taxonomies

MapMyCells maps unlabeled single-cell datasets to reference brain taxonomies, enabling cross-study integration and reproducible cell-type annotation.

A consensus spinal cord cell type atlas across mouse, macaque, and human

The paper creates a cross-species spinal cord cell type atlas integrating data from mouse, macaque, and human, identifying conserved and species-specific features.

Cross-species consensus atlas of the primate basal ganglia

The paper creates a cross-species consensus atlas of primate basal ganglia cell types using multiomic data from human, macaque, and marmoset, identifying 61 conserved cell types and a novel hybrid medium spiny neuron type.

Fast Optimization of Robust Transcriptomics Embeddings using Probabilistic Inference Autoencoder Networks for multi-Omics

The paper introduces PIANO, a variational autoencoder for multi-omics integration, showing improved performance on single-species and multi-atlas datasets.

The transcriptomic and spatial organization of telencephalic GABAergic neuronal types

The paper analyzes the transcriptomic and spatial organization of GABAergic neurons in the mouse telencephalon, revealing complex developmental and spatial relationships across multiple brain regions.

Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque

The paper identifies enhancers for spinal motor neurons and develops AAV vectors to target these cells in rodents and macaques, enabling functional studies and potential therapeutic applications.

Integrated Classification of Cortical Cells and Quantitative Projectomic Mapping Unveil Organizational Principles of Brain-Wide Connectomes at Single Cell Level

This study integrates molecular and morphological data to classify cortical neurons and map their connectomes, revealing organizational principles of brain-wide networks at the single-cell level.

Continuous cell type diversification throughout the embryonic and postnatal mouse visual cortex development

The paper constructs a high-resolution transcriptomic and epigenomic atlas of the developing mouse visual cortex, revealing continuous cell type diversification across embryonic and postnatal stages.

Spontaneously regenerative corticospinal neurons in mice

The paper identifies a class of spontaneously regenerative corticospinal neurons in mice that project ipsilaterally and share molecular features with embryonic-like regenerating neurons.

A molecularly defined and spatially resolved cell atlas of the whole mouse brain

MERFISH profiling of >1,100 genes in ~8 million cells spanning the whole mouse brain, integrated with scRNA-seq, maps >5,000 clusters into the Allen Common Coordinate Framework.

Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain

The paper generates a single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain, identifying methylation patterns and regulatory networks across cell types and brain regions.

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

This paper creates a high-resolution transcriptomic and spatial cell type atlas of the whole adult mouse brain, revealing spatial organization and transcription factor codes for cell types.

Morpho-electric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex

The paper identifies transcriptomic and morpho-electric diversity in human neocortical layer 1 interneurons, revealing greater subclass distinction compared to mouse.

Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species

The paper develops AAV-based genetic tools to specifically target astrocytes and oligodendrocytes across species, revealing functional roles in reward-dependent acetylcholine responses.

Cell-type specific molecular signatures of aging revealed in a brain-wide transcriptomic cell-type atlas

The paper identifies cell-type-specific molecular signatures of aging in a brain-wide transcriptomic atlas of mice, revealing key changes in non-neuronal cells and specific regions like the hypothalamic third ventricle.

Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes

The paper identifies gene-CRE pairs in mouse brain cells by integrating single-cell transcriptomes and epigenomes, controlling for gene co-expression.

Brain-wide Correspondence Between Neuronal Epigenomics and Long-Distance Projections

The paper links single-cell epigenomes and projection patterns of 33,034 mouse neurons to identify transcriptomic and epigenomic properties of projection cell types.

The BRAIN Initiative Cell Census Data Ecosystem: A User's Guide

The paper provides a guide to the BRAIN Initiative Cell Census Network (BICCN) data ecosystem, its tools, and resources for analyzing brain cell types across species.

Single-neuron models linking electrophysiology, morphology and transcriptomics across cortical cell types

The paper generates and evaluates over 130 million single-neuron models with active conductances to link electrophysiology, morphology, and transcriptomics across cortical cell types.

Dense Functional and Molecular Readout of a Circuit Hub in Sensory Cortex

The paper combines calcium imaging and spatial transcriptomics to study functional and molecular properties of neuronal subclasses in the somatosensory cortex during a tactile working memory task.

Isoform cell type specificity in the mouse primary motor cortex

The paper uses full-length single-cell RNA-seq to identify isoform-specific markers in mouse primary motor cortex cells, revealing isoform shifts masked at the gene level.

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

The paper compares cellular diversity in the primary motor cortex across human, marmoset, and mouse using single-nucleus transcriptomics and epigenomics, finding conserved cell types and species-specific adaptations.

A multimodal cell census and atlas of the mammalian primary motor cortex

The paper generates a multimodal cell census and atlas of the mammalian primary motor cortex, revealing a unified molecular genetic landscape and cross-species taxonomy of cell types.

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

The paper creates a comprehensive atlas of mouse primary motor cortex cell types using integrated transcriptomic and epigenomic data from over 600,000 samples.

Single-cell RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates and humans

The paper uses single-cell RNA-seq to analyze relay neurons in the dLGN across species, finding subtle transcriptomic differences compared to morphological and functional distinctions.

A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

This study defines a comprehensive transcriptomic cell type taxonomy of the adult mouse isocortex and hippocampal formation using single-cell RNA-sequencing.