Author

Andrew Nutter-Upham

Whitehead Institute for Biomedical Research

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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Cell Biology· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Research Focus:gene regulatory network inference· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Research Focus:drug response / drug discovery· 1 Approach:experimental assay· 1

Frequent Co-Authors

Alexa Mallar· 1 shared Alexander Henderson· 1 shared Ana Karla Cepeda DiaziD· 1 shared Antony A. CooperiD· 1 shared Autumn Rose MorrowiD· 1 shared Camila A. ZanellaiD· 1 shared Clemens R. ScherzeriD· 1 shared Daniel H. GeschwindiD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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1 shared paperCell Biology

Alexa Mallar

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Author profile →

2 papers

Recent·Most cited

Brieflow: An Integrated Computational Pipeline for High-Throughput Analysis of Optical Pooled Screening Data

Matteo Di Bernardo, Roshan Kern, Ana Karla Cepeda Diaz, Alexa Mallar, Samuel J. Choi, Andrew Nutter-Upham, Sebastian Lourido, Paul C. Blainey, Iain M. Cheeseman

Brieflow is a computational pipeline for analyzing optical pooled screening data, demonstrating its ability to recover biological modules missed by existing methods.

Nature Communications · May 30, 2026Peer-reviewedCell Biology

Deep sequencing of proteotoxicity modifier genes uncovers a Presenilin-2/beta-amyloid-actin genetic risk module shared among alpha-synucleinopathies

Sumaiya Nazeen, Xinyuan Wang, Dina Zielinski, Isabel Lam, Erinc Hallacli, Ping Xu, Elizabeth Ethier, Ronya Strom, Camila A. Zanella, Vanitha Nithianandam, Dylan Ritter, Alexander Henderson, Nathalie G. Saurat, Jalwa Afroz, Andrew Nutter-Upham, , Vikram Khurana

The paper identifies a shared genetic risk module involving PSEN2 and actin regulation across alpha-synucleinopathies, linking them to Alzheimer's disease mechanisms.

bioRxiv · Mar 3, 2024 · PreprintGenomics