Author

Spencer Farrell

Dalhousie University

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

Biology Disciplines

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Systems Biology· 2 Bioinformatics· 1 Developmental Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 3 Approach:statistical model· 3 Research Focus:trajectory inference· 3 Assay:scRNA-seq· 2 Research Focus:clustering· 1 Research Focus:database / resource· 1 Approach:deep learning· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Andrew D. RutenbergiD· 2 shared Sidhartha GoyaliD· 2 shared Alice E. KaneiD· 1 shared Amy P. WongiD· 1 shared Andrei L. TurinskyiD· 1 shared Arnold MitnitskiiD· 1 shared Brian Thomas KalishiD· 1 shared Christine E. BeariD· 1 shared

Activity by Year

2020-2024 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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2 shared papersSystems Biology

Andrew D. RutenbergORCID

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Author profile →

4 papers

Recent·Most cited

Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity.

Henry Quach, Spencer Farrell, Ming Jia Michael Wu, Kayshani R. Kanagarajah, Joseph Wai-Hin Leung, Xiaoqiao Xu, Prajkta S. Kallurkar, Andrei L. Turinsky, Christine E. Bear, Felix A. Ratjen, Brian Thomas Kalish, Sidhartha Goyal, Theo J. Moraes, Amy P. Wong

This study creates a single-cell atlas of human fetal lung development, revealing epithelial cell plasticity and lineage hierarchies through scRNA-seq and spatial transcriptomics.

Nature Communications · Jul 13, 2024Peer-reviewedDevelopmental Biology

Inferring single-cell transcriptomic dynamics with structured latent gene expression dynamics

Spencer Farrell, Madhav Mani, Sidhartha Goyal

This paper introduces LatentVelo, a method that improves trajectory inference in single-cell RNA-seq by modeling gene dynamics with neural ODEs and a variational autoencoder, enabling lineage-specific dynamics and batch correction.

Cell Reports Methods · Sep 1, 2023Peer-reviewedBioinformatics

Measurements of damage and repair in aging mice and humans reveals that robustness and resilience decrease with age, operate over broad timescales, and are affected differently by interventions

Spencer Farrell, Alice E. Kane, Elise S. Bisset, Susan Ellen Howlett, Andrew D. Rutenberg

The paper measures damage and repair rates in aging mice and humans, finding that robustness and resilience decline with age, with robustness having a greater impact on damage accumulation.

eLife · Nov 21, 2022Peer-reviewedSystems Biology

Generating synthetic aging trajectories with a weighted network model using cross-sectional data

Spencer Farrell, Arnold Mitnitski, Kenneth J. Rockwood, Andrew D. Rutenberg

This paper develops a weighted network model to generate synthetic aging trajectories from cross-sectional health data, showing good agreement with observed mortality and health characteristics.

Scientific Reports · Nov 16, 2020Peer-reviewedSystems Biology