Multiscale PHATE identifies multimodal signatures of COVID-19

M Kuchroo, J Huang, P Wong, JC Grenier… - Nature …, 2022 - nature.com
As the biomedical community produces datasets that are increasingly complex and high
dimensional, there is a need for more sophisticated computational tools to extract biological …

Single-cell analysis reveals inflammatory interactions driving macular degeneration

M Kuchroo, M DiStasio, E Song, E Calapkulu… - Nature …, 2023 - nature.com
Due to commonalities in pathophysiology, age-related macular degeneration (AMD)
represents a uniquely accessible model to investigate therapies for neurodegenerative …

Mapping phenotypic plasticity upon the cancer cell state landscape using manifold learning

DB Burkhardt, BP San Juan, JG Lock, S Krishnaswamy… - Cancer discovery, 2022 - AACR
Phenotypic plasticity describes the ability of cancer cells to undergo dynamic, nongenetic
cell state changes that amplify cancer heterogeneity to promote metastasis and therapy …

Building and analyzing metacells in single-cell genomics data

M Bilous, L Hérault, AAG Gabriel… - Molecular Systems …, 2024 - embopress.org
The advent of high-throughput single-cell genomics technologies has fundamentally
transformed biological sciences. Currently, millions of cells from complex biological tissues …

Structural and developmental principles of neuropil assembly in C. elegans

MW Moyle, KM Barnes, M Kuchroo, A Gonopolskiy… - Nature, 2021 - nature.com
Neuropil is a fundamental form of tissue organization within the brain, in which densely
packed neurons synaptically interconnect into precise circuit architecture,. However, the …

Taxonomy of benchmarks in graph representation learning

R Liu, S Cantürk, F Wenkel, S McGuire… - Learning on Graphs …, 2022 - proceedings.mlr.press
Abstract Graph Neural Networks (GNNs) extend the success of neural networks to graph-
structured data by accounting for their intrinsic geometry. While extensive research has been …

Multiscale geometric and topological analyses for characterizing and predicting immune responses from single cell data

A Venkat, D Bhaskar, S Krishnaswamy - Trends in Immunology, 2023 - cell.com
Single cell genomics has revolutionized our ability to map immune heterogeneity and
responses. With the influx of large-scale data sets from diverse modalities, the resolution …

[PDF][PDF] Cuts: A deep learning and topological framework for multigranular unsupervised medical image segmentation

C Liu, M Amodio, LL Shen, F Gao, A Avesta… - … on Medical Image …, 2024 - openreview.net
Segmenting medical images is critical to facilitating both patient diagnoses and quantitative
research. A major limiting factor is the lack of labeled data, as obtaining expert annotations …

Multiscale PHATE exploration of SARS-CoV-2 data reveals multimodal signatures of disease

M Kuchroo, J Huang, P Wong, JC Grenier, D Shung… - BioRxiv, 2020 - biorxiv.org
The biomedical community is producing increasingly high dimensional datasets, integrated
from hundreds of patient samples, which current computational techniques struggle to …

[PDF][PDF] Cuts: A framework for multigranular unsupervised medical image segmentation

C Liu, M Amodio, L Shen, F Gao, A Avesta… - arXiv preprint arXiv …, 2022 - researchgate.net
Segmenting medical images is critical to facilitating both patient diagnoses and quantitative
research. A major limiting factor is the lack of labeled data, as obtaining expert annotations …