Author

John A. Smolka

University of California, BerkeleyORCID 0000-0002-4697-8835Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Cell Biology· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 3 Organism:human· 3 Research Focus:cell type annotation· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:differential expression· 1 Assay:imaging· 1 Approach:machine learning (classical)· 1

Frequent Co-Authors

Adam BegemaniD· 1 shared Ahmad ShamiiD· 1 shared Frederic L. ChediniD· 1 shared Lionel A. SanziD· 1 shared Samantha C. LewisiD· 1 shared Stella R. HartonoiD· 1 shared Tejashree Pradip WaingankariD· 1 shared

Activity by Year

2021-2025 · peak 2/yr

Co-Author Collaboration Network

7 top collaborators · 9 mutual co-author links

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1 shared paperCell Biology

Adam BegemanORCID

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Author profile →

3 papers

Recent·Most cited

Integrating process, proximity, and prediction implicates novel protein and RNA interactions in human Origin Recognition Complex function

The paper identifies novel protein and RNA interactions involving ORC subunits by integrating CRISPR screens, proximity labeling, proteomics, and structural predictions.

bioRxiv · May 28, 2025 · PreprintBioinformatics

A spatial atlas of mitochondrial gene expression reveals dynamic translation hubs and remodeling in stress

Adam Begeman, John A. Smolka, Ahmad Shami, Tejashree Pradip Waingankar, Samantha C. Lewis

This study reveals spatial organization of mitochondrial RNA translation and remodeling under stress in human cells.

Science Advances · Apr 18, 2025Peer-reviewedCell Biology

Recognition of cellular RNAs by the S9.6 antibody creates pervasive artefacts when imaging RNA:DNA hybrids

John A. Smolka, Lionel A. Sanz, Stella R. Hartono, Frederic L. Chedin

This study shows that the S9.6 antibody binds RNA rather than RNA:DNA hybrids in fixed cells, leading to unreliable imaging data.

The Journal of Cell Biology · Mar 11, 2021Peer-reviewedMolecular Biology