Anish Bhaswanth Chakka
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View article: MET alterations are enriched in lung adenocarcinoma brain metastases, defining a distinct biologic subtype
MET alterations are enriched in lung adenocarcinoma brain metastases, defining a distinct biologic subtype Open
Non-small cell lung cancer (NSCLC) exhibits the highest rates of brain metastases (BM) among all solid tumors and presents a significant clinical challenge. The development of novel therapeutic strategies targeting BM is clearly needed. We…
View article: Multimodal Atlas of Caudate Head Reveals Impact of pTau Burden on Resident Glial Cells
Multimodal Atlas of Caudate Head Reveals Impact of pTau Burden on Resident Glial Cells Open
Background Dysfunction of the Basal Ganglia is implicated in several neurodegenerative diseases such as Parkinson’s and Huntington’s. A substructure of the Basal Ganglia, the caudate nucleus, is observed to have diffuse amyloid plaques in …
View article: An integrated, multiregional, and multimodal cell atlas of Alzheimer’s disease
An integrated, multiregional, and multimodal cell atlas of Alzheimer’s disease Open
Background Alzheimer’s disease (AD) is clinically characterized by a progressive cognitive decline associated with stereotyped accumulation of amyloid‐beta (Aβ) plaques and hyperphosphorylated Tau (pTau) tangles across brain regions. While…
View article: Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque
Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque Open
Experimental access to cell types within the mammalian spinal cord is severely limited by the availability of genetic tools. To enable access to spinal motor neurons (SMNs) and SMN subtypes, we generated single-cell multiome datasets from …
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: Technical and biological sources of noise confound multiplexed enhancer AAV screening
Technical and biological sources of noise confound multiplexed enhancer AAV screening Open
Cis -acting regulatory enhancer elements are valuable tools for gaining cell type-specific genetic access. Leveraging large chromatin accessibility atlases, putative enhancer sequences can be identified and deployed in adeno-associated vir…
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: Continuous cell type diversification throughout the embryonic and postnatal mouse visual cortex development
Continuous cell type diversification throughout the embryonic and postnatal mouse visual cortex development Open
The mammalian cortex is composed of a highly diverse set of cell types and develops through a series of temporally regulated events that build out the cell type and circuit foundation for cortical function. The mechanisms underlying the de…
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: Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque
Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque Open
Summary Experimental access to cell types within the mammalian spinal cord is severely limited by the availability of genetic tools. To enable access to lower motor neurons (LMNs) and LMN subtypes, we generated single cell multiome dataset…
View article: The transcriptomic and spatial organization of telencephalic GABAergic neuronal types
The transcriptomic and spatial organization of telencephalic GABAergic neuronal types Open
The telencephalon of the mammalian brain comprises multiple regions and circuit pathways that play adaptive and integrative roles in a variety of brain functions. There is a wide array of GABAergic neurons in the telencephalon; they play a…
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: Uveal melanoma immunogenomics predict immunotherapy resistance and susceptibility
Uveal melanoma immunogenomics predict immunotherapy resistance and susceptibility Open
Immune checkpoint inhibition has shown success in treating metastatic cutaneous melanoma but has limited efficacy against metastatic uveal melanoma, a rare variant arising from the immune privileged eye. To better understand this resistanc…
View article: A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain Open
The mammalian brain consists of millions to billions of cells that are organized into many cell types with specific spatial distribution patterns and structural and functional properties 1–3 . Here we report a comprehensive and high-resolu…
View article: Multimodal and multiregional atlas of Alzheimer’s disease changes
Multimodal and multiregional atlas of Alzheimer’s disease changes Open
Background Alzheimer’s disease (AD) is the most common form of dementia. The progression of AD throughout the brain follows a stereotypical pattern that can be described by the quantification of histopathological changes in several brain r…
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: A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain Open
The mammalian brain is composed of millions to billions of cells that are organized into numerous cell types with specific spatial distribution patterns and structural and functional properties. An essential step towards understanding brai…
View article: Differential gene expression in peripheral blood mononuclear cells from children immunized with inactivated influenza vaccine
Differential gene expression in peripheral blood mononuclear cells from children immunized with inactivated influenza vaccine Open
The human immune response to inactivated influenza vaccine is dynamic and impacted by age and preexisting immunity. Our goal was to identify postvaccination transcriptomic changes in peripheral blood mononuclear cells from children. Blood …
View article: A Novel Small Molecule Targets Androgen Receptor and Its Splice Variants in Castration-Resistant Prostate Cancer
A Novel Small Molecule Targets Androgen Receptor and Its Splice Variants in Castration-Resistant Prostate Cancer Open
Reactivation of androgen receptor (AR) appears to be the major mechanism driving the resistance of castration-resistant prostate cancer (CRPC) to second-generation antiandrogens and involves AR overexpression, AR mutation, and/or expressio…
View article: Immunogenomic correlates of response to cetuximab monotherapy in head and neck squamous cell carcinoma
Immunogenomic correlates of response to cetuximab monotherapy in head and neck squamous cell carcinoma Open
Background Mechanisms of resistance to immune‐modulating cancer treatments are poorly understood. Using a novel cohort of patients with head and neck squamous cell carcinoma (HNSCC), we investigated mechanisms of immune escape from epiderm…
View article: IL-33-mediated IL-13 secretion by ST2+ Treg controls inflammation after lung injury
IL-33-mediated IL-13 secretion by ST2+ Treg controls inflammation after lung injury Open
Acute respiratory distress syndrome is an often fatal disease that develops after acute lung injury and trauma. How released tissue damage signals, or alarmins, orchestrate early inflammatory events is poorly understood. Herein we reveal t…
View article: TCGA Expedition: A Data Acquisition and Management System for TCGA Data
TCGA Expedition: A Data Acquisition and Management System for TCGA Data Open
Our open-source, freely available TCGA Expedition software can be used to create a local collaborative infrastructure for acquiring, managing, and analyzing TCGA data and other large public datasets.
View article: Publicly available NGS datasets used for analysis (<i>Current Users</i>).
Publicly available NGS datasets used for analysis (<i>Current Users</i>). Open
Publicly available NGS datasets used for analysis (Current Users).
View article: Research Resource: The Dexamethasone Transcriptome in Hypothalamic Embryonic Neural Stem Cells
Research Resource: The Dexamethasone Transcriptome in Hypothalamic Embryonic Neural Stem Cells Open
Exposure to excess glucocorticoids during fetal development has long-lasting physiological and behavioral consequences, although the mechanisms are poorly understood. The impact of prenatal glucocorticoids exposure on stress responses in j…
View article: Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center
Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center Open
Next Generation Sequencing (NGS) methods are driving profound changes in biomedical research, with a growing impact on patient care. Many academic medical centers are evaluating potential models to prepare for the rapid increase in NGS inf…