Manik Kuchroo
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View article: in vivo CRISPR screen identifies novel regulators of microglia state in Alzheimer’s disease 9094
in vivo CRISPR screen identifies novel regulators of microglia state in Alzheimer’s disease 9094 Open
Description Genome-wide association studies (GWAS) in Alzheimer’s disease (AD) have identified over 200 diseased-associated genes that are predominantly expressed in microglia. While these studies implicate microglia in AD pathogenesis, th…
View article: Author response: Exploring neurodevelopment via spatiotemporal collation of anatomical networks with NeuroSC
Author response: Exploring neurodevelopment via spatiotemporal collation of anatomical networks with NeuroSC Open
View article: Exploring neurodevelopment via spatiotemporal collation of anatomical networks with NeuroSC
Exploring neurodevelopment via spatiotemporal collation of anatomical networks with NeuroSC Open
Volume electron microscopy (vEM) datasets such as those generated for connectome studies allow nanoscale quantifications and comparisons of the cell biological features underpinning circuit architectures. Quantifying cell biological relati…
View article: Author response: NeuroSC: Exploring Neurodevelopment via Spatiotemporal Collation of Anatomical Networks
Author response: NeuroSC: Exploring Neurodevelopment via Spatiotemporal Collation of Anatomical Networks Open
View article: NeuroSC: Exploring Neurodevelopment via Spatiotemporal Collation of Anatomical Networks
NeuroSC: Exploring Neurodevelopment via Spatiotemporal Collation of Anatomical Networks Open
Volume electron microscopy (vEM) datasets such as those generated for connectome studies allow nanoscale quantifications and comparisons of the cell biological features underpinning circuit architectures. Quantifying cell biological relati…
View article: Exploring neurodevelopment via spatiotemporal collation of anatomical networks with NeuroSC
Exploring neurodevelopment via spatiotemporal collation of anatomical networks with NeuroSC Open
Volume electron microscopy (vEM) datasets such as those generated for connectome studies allow nanoscale quantifications and comparisons of the cell biological features underpinning circuit architectures. Quantifying cell biological relati…
View article: NeuroSCAN: Exploring Neurodevelopment via Spatiotemporal Collation of Anatomical Networks
NeuroSCAN: Exploring Neurodevelopment via Spatiotemporal Collation of Anatomical Networks Open
Volume electron microscopy (vEM) datasets such as those generated for connectome studies allow nanoscale quantifications and comparisons of the cell biological features underpinning circuit architectures. Quantifications of cell biological…
View article: NeuroSC: Exploring Neurodevelopment via Spatiotemporal Collation of Anatomical Networks
NeuroSC: Exploring Neurodevelopment via Spatiotemporal Collation of Anatomical Networks Open
Volume electron microscopy (vEM) datasets such as those generated for connectome studies allow nanoscale quantifications and comparisons of the cell biological features underpinning circuit architectures. Quantifying cell biological relati…
View article: Revealing dynamic temporal regulatory networks driving cancer cell state plasticity with neural ODE-based optimal transport
Revealing dynamic temporal regulatory networks driving cancer cell state plasticity with neural ODE-based optimal transport Open
Despite advances in single-cell technologies and temporal sampling, the seamless connection of cell states over time and the inference of gene-gene relationships driving cancer cell state remains a formidable challenge. We present Cflows ,…
View article: Time-Inhomogeneous Diffusion Geometry and Topology
Time-Inhomogeneous Diffusion Geometry and Topology Open
.Diffusion condensation is a dynamic process that yields a sequence of multiscale data representations that aim to encode meaningful abstractions. It has proven effective for manifold learning, denoising, clustering, and visualization of h…
View article: Single-cell analysis reveals inflammatory interactions driving macular degeneration
Single-cell analysis reveals inflammatory interactions driving macular degeneration Open
View article: linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells
linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells Open
Thousands of long intergenic non-coding RNAs (lincRNAs) are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open-reading frames and are speculated…
View article: Revealing dynamic temporal trajectories and underlying regulatory networks with <i>Cflows</i>
Revealing dynamic temporal trajectories and underlying regulatory networks with <i>Cflows</i> Open
While single-cell technologies provide snapshots of tumor states, building continuous trajectories and uncovering causative gene regulatory networks remains a significant challenge. We present Cflows , an AI framework that combines neural …
View article: Author response: linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells
Author response: linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells Open
Full text Figures and data Side by side Abstract Editor's evaluation Introduction Results Discussion gMaterials and methods Appendix 1 Data availability References Decision letter Author response Article and author information Metrics Abst…
View article: Manifold Interpolating Optimal-Transport Flows for Trajectory Inference.
Manifold Interpolating Optimal-Transport Flows for Trajectory Inference. Open
We present a method called Manifold Interpolating Optimal-Transport Flow (MIOFlow) that learns stochastic, continuous population dynamics from static snapshot samples taken at sporadic timepoints. MIOFlow combines dynamic models, manifold …
View article: spARC recovers human glioma spatial signaling networks with graph filtering
spARC recovers human glioma spatial signaling networks with graph filtering Open
Biological networks operate within architectural frameworks that influence the state and function of cells through niche-specific factors such as exposure to nutrients and metabolites, soluble signaling molecules, and direct cognate cell-c…
View article: Immune cells and their inflammatory mediators modify β cells and cause checkpoint inhibitor–induced diabetes
Immune cells and their inflammatory mediators modify β cells and cause checkpoint inhibitor–induced diabetes Open
Checkpoint inhibitors (CPIs) targeting programmed death 1 (PD-1)/programmed death ligand 1 (PD-L1) and cytotoxic T lymphocyte antigen 4 (CTLA-4) have revolutionized cancer treatment but can trigger autoimmune complications, including CPI-i…
View article: <i>linc-mipep</i> and <i>linc-wrb</i> encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells
<i>linc-mipep</i> and <i>linc-wrb</i> encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells Open
Thousands of long intergenic non-coding RNAs (lincRNAs) are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains has recently been found to contain cryptic open reading frames and are speculated …
View article: Manifold Interpolating Optimal-Transport Flows for Trajectory Inference
Manifold Interpolating Optimal-Transport Flows for Trajectory Inference Open
We present a method called Manifold Interpolating Optimal-Transport Flow (MIOFlow) that learns stochastic, continuous population dynamics from static snapshot samples taken at sporadic timepoints. MIOFlow combines dynamic models, manifold …
View article: Embedding Signals on Graphs with Unbalanced Diffusion Earth Mover’s Distance
Embedding Signals on Graphs with Unbalanced Diffusion Earth Mover’s Distance Open
In modern relational machine learning it is common to encounter large graphs that arise via interactions or similarities between observations in many domains. Further, in many cases the target entities for analysis are actually signals on …
View article: Time-inhomogeneous diffusion geometry and topology
Time-inhomogeneous diffusion geometry and topology Open
Diffusion condensation is a dynamic process that yields a sequence of multiscale data representations that aim to encode meaningful abstractions. It has proven effective for manifold learning, denoising, clustering, and visualization of hi…
View article: Multiscale PHATE identifies multimodal signatures of COVID-19
Multiscale PHATE identifies multimodal signatures of COVID-19 Open
View article: Multimodal Data Visualization and Denoising with Integrated Diffusion
Multimodal Data Visualization and Denoising with Integrated Diffusion Open
We propose a method called integrated diffusion for combining multimodal data, gathered via different sensors on the same system, to create a integrated data diffusion operator. As real world data suffers from both local and global noise, …
View article: A reservoir of stem-like CD8 <sup>+</sup> T cells in the tumor-draining lymph node preserves the ongoing antitumor immune response
A reservoir of stem-like CD8 <sup>+</sup> T cells in the tumor-draining lymph node preserves the ongoing antitumor immune response Open
Tumor-specific CD8 + T cells in stable tumor-draining lymph node reservoir are clonally and developmentally related to those in tumors.
View article: Embedding Signals on Knowledge Graphs with Unbalanced Diffusion Earth Mover's Distance
Embedding Signals on Knowledge Graphs with Unbalanced Diffusion Earth Mover's Distance Open
In modern relational machine learning it is common to encounter large graphs that arise via interactions or similarities between observations in many domains. Further, in many cases the target entities for analysis are actually signals on …
View article: Multiscale PHATE Exploration of SARS-CoV-2 Data Reveals Multimodal Signatures of Disease
Multiscale PHATE Exploration of SARS-CoV-2 Data Reveals Multimodal Signatures of Disease Open
The biomedical community is producing increasingly high dimensional datasets, integrated from hundreds of patient samples, which current computational techniques struggle to explore. To uncover biological meaning from these complex dataset…
View article: Diffusion Earth Mover's Distance and Distribution Embeddings
Diffusion Earth Mover's Distance and Distribution Embeddings Open
We propose a new fast method of measuring distances between large numbers of related high dimensional datasets called the Diffusion Earth Mover's Distance (EMD). We model the datasets as distributions supported on common data graph that is…
View article: Structural and developmental principles of neuropil assembly in C. elegans
Structural and developmental principles of neuropil assembly in C. elegans Open
View article: Multimodal data visualization, denoising and clustering with integrated diffusion.
Multimodal data visualization, denoising and clustering with integrated diffusion. Open
We propose a method called integrated diffusion for combining multimodal datasets, or data gathered via several different measurements on the same system, to create a joint data diffusion operator. As real world data suffers from both loca…
View article: Multimodal Data Visualization and Denoising with Integrated Diffusion
Multimodal Data Visualization and Denoising with Integrated Diffusion Open
We propose a method called integrated diffusion for combining multimodal datasets, or data gathered via several different measurements on the same system, to create a joint data diffusion operator. As real world data suffers from both loca…