Author

Serena Hughes

University of California, Los Angeles

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

Biology Disciplines

Click to filter author papers

Systems Biology· 2

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:benchmarking· 2 Assay:ATAC-seq· 1 Assay:bulk RNA-seq· 1 Research Focus:clustering· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Research Focus:dimensionality reduction· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Eric J. DeedsiD· 2 shared Timothy HamiltoniD· 2 shared Breanne SpartaiD· 1 shared Gunalan Natesan· 1 shared Juan V. Najar· 1 shared Tom Kolokotrones· 1 shared

Activity by Year

2022-2025 · peak 1/yr

Co-Author Collaboration Network

6 top collaborators · 12 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

2 shared papersSystems Biology

Eric J. DeedsORCID

Mutual co-authors in cluster

Author profile →

2 papers

Recent·Most cited

DeepAtlas: a tool for effective manifold learning

Serena Hughes, Timothy Hamilton, Tom Kolokotrones, Eric J. Deeds

DeepAtlas generates local manifold embeddings and assesses the manifold hypothesis, finding that many datasets, including single-cell RNA-sequencing, do not conform to it.

bioRxiv · Aug 26, 2025 · PreprintSystems Biology

A lack of distinct cell identities in single-cell measurements: revisiting Waddingtons landscape

Breanne Sparta, Timothy Hamilton, Juan V. Najar, Serena Hughes, Gunalan Natesan, Eric J. Deeds

This paper challenges the idea that distinct cell types correspond to attractors in gene expression space by showing cells of different types occupy the same regions in epigenetic space.

bioRxiv · Jun 3, 2022 · PreprintSystems Biology