Author

Jessie Huang

Yale University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Same name, identified by ORCID

Biology Disciplines

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Bioinformatics· 2 Neuroscience· 2 Systems Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 5 Approach:statistical model· 5 Research Focus:clustering· 3 Research Focus:differential expression· 3 Approach:machine learning (classical)· 2 Assay:scRNA-seq· 2 Assay:ATAC-seq· 1 Research Focus:benchmarking· 1

Frequent Co-Authors

Guy WolfiD· 4 shared Smita KrishnaswamyiD· 4 shared Jean‐Christophe GrenieriD· 2 shared Julie HussiniD· 2 shared Manik Razdan KuchrooiD· 2 shared Scott GiganteiD· 2 shared Abhinav Godavarthi· 1 shared Achille NazaretiD· 1 shared

Activity by Year

2020-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 26 mutual co-author links

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4 shared papersNeuroscience

Guy WolfORCID

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

Spatiotemporal Single-Cell Analysis Reveals T Cell Clonal Dynamics and Phenotypic Plasticity in Human Graft-versus-Host Disease

Lingting Shi, Ajna Uzuni, Ximi Kevin Wang, Michael Pressler, David W Harle, Shami Chakrabarti, Rodney Macedo, Kirubel Belay, Christian A. Gordillo, Erik Raps, Jia Yi Zhang, Achille Nazaret, Joy Linyue Fan, Yinuo Jin, Xin Shen, , Ran Reshef

This study uses spatiotemporal single-cell analysis to track T cell clonal dynamics and phenotypic plasticity in GVHD, revealing links between TCR features, clonal expansion, and disease severity.

bioRxiv · May 24, 2025 · PreprintSystems Biology

Multi-view manifold learning of human brain statetrajectories

Erica L. Busch, Jessie Huang, Andrew Benz, Tom Wallenstein, Guillaume Lajoie, Guy Wolf, Smita Krishnaswamy, Nicholas B. Turk‐Browne

This paper introduces T-PHATE, a nonlinear manifold learning algorithm for time-series data like fMRI, showing improvements in visualization, classification, and segmentation.

Nature Computational Science · Mar 27, 2023Peer-reviewedNeuroscience

Data-driven approaches for genetic characterization of SARS-CoV-2 lineages

Fatima Mostefai, Isabel Gamache, Jessie Huang, Arnaud N’Guessan, Justin Pelletier, Ahmad Pesaranghader, David J. Hamelin, Carmen Lía Murall, Raphaël Poujol, Jean‐Christophe Grenier, Martin A. Smith, Étienne Caron, Morgan Craig, B. Jesse Shapiro, Guy Wolf, , Julie Hussin

The paper presents computational tools for analyzing SARS-CoV-2 genetic data, showing that haplotype networks and unsupervised learning can reveal lineage emergence and population dynamics.

bioRxiv · Sep 28, 2021 · PreprintBioinformatics

Topological analysis of single-cell data reveals shared glial landscape of macular degeneration and neurodegenerative diseases

Manik Razdan Kuchroo, Marcello DiStasio, Eda Calapkulu, Maryam Ige, Le Zhang, Amar H. Sheth, Madhvi Menon, Yu Xing, Scott Gigante, Jessie Huang, Rahul M. Dhodapkar, Bastian Rieck, Guy Wolf, Smita Krishnaswamy, Brian P. Hafler

A topological machine learning approach applied to single-nucleus RNA sequencing identifies shared glial activation states in AMD, AD, and MS.

bioRxiv · Jan 19, 2021 · PreprintNeuroscience

Multiscale PHATE Exploration of SARS-CoV-2 Data Reveals Multimodal Signatures of Disease

Manik Razdan Kuchroo, Jessie Huang, Patrick Wong, Jean‐Christophe Grenier, Dennis Legen Shung, Alexander Tong, Carolina Gonçalves de Oliveira Lucas, Jon Klein, Daniel B. Burkhardt, Scott Gigante, Abhinav Godavarthi, Benjamin Israelow, Tianyang Mao, Ji Eun Oh, Júlio Dos Santos Silva, , Smita Krishnaswamy

The paper introduces Multiscale PHATE, a method for exploring high-dimensional biomedical data, and applies it to identify immune cell signatures associated with severe COVID-19 outcomes.

bioRxiv · Nov 15, 2020 · PreprintBioinformatics