Amanda Gary
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View article: MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics
MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics Open
Image-based spatial transcriptomics platforms are powerful tools often used to identify cell populations and describe gene expression in intact tissue. Spatial experiments return large, high-dimensional datasets and several open-source sof…
View article: Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species
Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species Open
Proper brain function requires the assembly and function of diverse populations of neurons and glia. Single cell gene expression studies have mostly focused on characterization of neuronal cell diversity; however, recent studies have also …
View article: Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species
Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species Open
Proper brain function requires the assembly and function of diverse populations of neurons and glia. Single cell gene expression studies have mostly focused on characterization of neuronal cell diversity; however, recent studies have also …
View article: Success of GDNF-based treatment of Hirschsprung disease depends on NCAM1 signaling and various subtypes of enteric neural progenitors
Success of GDNF-based treatment of Hirschsprung disease depends on NCAM1 signaling and various subtypes of enteric neural progenitors Open
Hirschsprung disease (HSCR) is a deadly congenital disorder where the enteric nervous system (ENS) is absent from the distal bowel. Current surgical treatment is generally life-saving but is often accompanied by long-term bowel problems an…
View article: A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types
A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Open
The mammalian cortex is comprised of cells classified into types according to shared properties. Defining the contribution of each cell type to the processes guided by the cortex is essential for understanding its function in health and di…
View article: MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics
MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics Open
Image-based spatial transcriptomics platforms are powerful tools often used to identify cell populations and describe gene expression in intact tissue. Spatial experiments return large, high-dimensional datasets and several open-source sof…
View article: MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics
MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics Open
Image-based spatial transcriptomics platforms are powerful tools often used to identify cell populations and describe gene expression in intact tissue. Spatial experiments return large, high-dimension datasets and several open-source softw…
View article: Brain-wide cell-type-specific transcriptomic signatures of healthy ageing in mice
Brain-wide cell-type-specific transcriptomic signatures of healthy ageing in mice Open
Biological ageing can be defined as a gradual loss of homeostasis across various aspects of molecular and cellular function1,2. Mammalian brains consist of thousands of cell types3, which may be differentially susceptible or resilient to a…
View article: MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics
MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics Open
Image-based spatial transcriptomics platforms are powerful tools often used to identify cell populations and describe gene expression in intact tissue. Spatial experiments return large, high-dimensional datasets and several open-source sof…
View article: Integrated multimodal cell atlas of Alzheimer’s disease
Integrated multimodal cell atlas of Alzheimer’s disease Open
Alzheimer’s disease (AD) is the leading cause of dementia in older adults. Although AD progression is characterized by stereotyped accumulation of proteinopathies, the affected cellular populations remain understudied. Here we use multiomi…
View article: Enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits
Enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits Open
We present an enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits. Best-in-class vectors were curated for accessing major striatal neuron populations including medium spiny neurons (MSNs), direct and indirect…
View article: A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types
A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Open
Summary The mammalian cortex is comprised of cells classified into types according to shared properties. Defining the contribution of each cell type to the processes guided by the cortex is essential for understanding its function in healt…
View article: Connecting single-cell transcriptomes to projectomes in mouse visual cortex
Connecting single-cell transcriptomes to projectomes in mouse visual cortex Open
The mammalian brain is composed of diverse neuron types that play different functional roles. Recent single-cell RNA sequencing approaches have led to a whole brain taxonomy of transcriptomically-defined cell types, yet cell type definitio…
View article: Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex
Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex Open
Human cortex transcriptomic studies have revealed a hierarchical organization of γ-aminobutyric acid–producing (GABAergic) neurons from subclasses to a high diversity of more granular types. Rapid GABAergic neuron viral genetic labeling pl…
View article: Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex
Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex Open
Neocortical layer 1 (L1) is a site of convergence between pyramidal-neuron dendrites and feedback axons where local inhibitory signaling can profoundly shape cortical processing. Evolutionary expansion of human neocortex is marked by disti…
View article: Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species
Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species Open
Proper brain function requires the assembly and function of diverse populations of neurons and glia. Single cell gene expression studies have mostly focused on characterization of neuronal cell diversity; however, recent studies have also …
View article: Cell-type specific molecular signatures of aging revealed in a brain-wide transcriptomic cell-type atlas
Cell-type specific molecular signatures of aging revealed in a brain-wide transcriptomic cell-type atlas Open
Biological aging can be defined as a gradual loss of homeostasis across various aspects of molecular and cellular function. Aging is a complex and dynamic process which influences distinct cell types in a myriad of ways. The cellular archi…
View article: Integrated multimodal cell atlas of Alzheimer’s disease
Integrated multimodal cell atlas of Alzheimer’s disease Open
Alzheimer’s disease (AD) is the most common cause of dementia in older adults. Neuropathological and imaging studies have demonstrated a progressive and stereotyped accumulation of protein aggregates, but the underlying molecular and cellu…
View article: Signature morpho-electric properties of diverse GABAergic interneurons in the human neocortex
Signature morpho-electric properties of diverse GABAergic interneurons in the human neocortex Open
Human cortical interneurons have been challenging to study due to high diversity and lack of mature brain tissue platforms and genetic targeting tools. We employed rapid GABAergic neuron viral labeling plus unbiased Patch-seq sampling in b…
View article: Morpho-electric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex
Morpho-electric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex Open
Neocortical layer 1 (L1) is a site of convergence between pyramidal neuron dendrites and feedback axons where local inhibitory signaling can profoundly shape cortical processing. Evolutionary expansion of human neocortex is marked by disti…
View article: Local connectivity and synaptic dynamics in mouse and human neocortex
Local connectivity and synaptic dynamics in mouse and human neocortex Open
We present a unique, extensive, and open synaptic physiology analysis platform and dataset. Through its application, we reveal principles that relate cell type to synaptic properties and intralaminar circuit organization in the mouse and h…
View article: A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex
A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex Open
Identification of the structural connections between neurons is a prerequisite to understanding brain function. We developed a pipeline to systematically map brain-wide monosynaptic inputs to specific neuronal populations using Cre-driver …
View article: A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex
A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex Open
Identification of the structural connections between neurons is a prerequisite to understanding brain function. We developed a pipeline to systematically map brain-wide monosynaptic inputs to specific neuronal populations using Cre-driver …
View article: Human cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neurons
Human cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neurons Open
The neocortex is disproportionately expanded in human compared to mouse, both in its total volume relative to subcortical structures and in the proportion occupied by supragranular layers that selectively make connections within the cortex…