Author

Desiree Hernandez

Broad Institute

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

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Bioinformatics· 4

Signature Assays, Organisms & Methods

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Assay:imaging· 4 Approach:experimental assay· 3 Research Focus:benchmarking· 2 Organism:human· 2 Research Focus:batch correction / integration· 1 Approach:benchmark study· 1 Research Focus:cell type annotation· 1 Research Focus:database / resource· 1

Frequent Co-Authors

Amy B. GoodaleiD· 4 shared Anne Elizabeth CarpenteriD· 4 shared Beth A. CiminiiD· 4 shared Briana Fritchman· 4 shared Lisa MilleriD· 4 shared Maria Kost‐AlimovaiD· 4 shared Shantanu SinghiD· 4 shared Srinivas Niranj ChandrasekaraniD· 4 shared

Activity by Year

2023-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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4 shared papersBioinformatics

Amy B. GoodaleORCID

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4 papers

Recent·Most cited

Morphological map of under- and over-expression of genes in human cells

Srinivas Niranj Chandrasekaran, Eric Alix, John Arévalo, Adriana Borowa, Patrick J. Byrne, William G Charles, Zitong Chen, Beth A. Cimini, Boxiong Deng, John G. Doench, Jessica Ewald, Briana Fritchman, Colin J. Fuller, Jedidiah Gaetz, Amy B. Goodale, , Anne Elizabeth Carpenter

The paper presents a comprehensive genetic perturbation dataset using Cell Painting to analyze gene expression effects in human cells, revealing novel gene clusters and functional relationships.

Nature Methods · Aug 1, 2025Peer-reviewedBioinformatics

Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations

Srinivas Niranj Chandrasekaran, Beth A. Cimini, Amy B. Goodale, Lisa Miller, Maria Kost‐Alimova, Nasim Jamali, John G. Doench, Briana Fritchman, Adam P. Skepner, Michelle Melanson, Alexandr A. Kalinin, John Arévalo, Marzieh Haghighi, Juan C. Caicedo, Daniel Kühn, , Anne Elizabeth Carpenter

The paper introduces a dataset of cell morphology images treated with matched chemical and genetic perturbations and evaluates methods for identifying perturbation similarities.

Nature Methods · Apr 9, 2024Peer-reviewedBioinformatics

Optimizing the Cell Painting assay for image-based profiling

Beth A. Cimini, Srinivas Niranj Chandrasekaran, Maria Kost‐Alimova, Lisa Miller, Amy B. Goodale, Briana Fritchman, Patrick J. Byrne, Sakshi Garg, Nasim Jamali, David J. Logan, John B. Concannon, Charles-Hugues Lardeau, Elizabeth Mouchet, Shantanu Singh, Hamdah Shafqat Abbasi, , Anne Elizabeth Carpenter

The paper updates the Cell Painting assay protocol to improve morphological profiling, finding that simplified steps and reduced stain concentrations maintain robust outputs.

Nature Protocols · Jun 21, 2023Peer-reviewedBioinformatics

JUMP Cell Painting chemical dataset: Morphological map of 115,796 compounds in human cells

Srinivas Niranj Chandrasekaran, Jeanelle Ackerman, Eric Alix, Dale Michael Ando, John Arévalo, Melissa Bennion, Nicolas Boisseau, Adriana Borowa, Justin D. Boyd, Laurent Brino, Patrick J. Byrne, Hugo Ceulemans, Carolyn Ch’ng, Beth A. Cimini, Djork-Arné Clevert, , Anne Elizabeth Carpenter

Cell Painting images and profiles for 115,796 compounds in U2OS cells from 12 laboratories; 15.2% of analyzed compounds are phenotypically active, and cross-laboratory replicates cut reference-compound activity by 34%.

bioRxiv · Mar 23, 2023 · PreprintBioinformatics✦ In-depth digest