Author

Hamdah Shafqat Abbasi

Broad InstituteORCID 0000-0003-0237-0323Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Assay:imaging· 2 Approach:benchmark study· 1 Research Focus:differential expression· 1 Approach:experimental assay· 1 Assay:spatial transcriptomics· 1 Approach:statistical model· 1

Frequent Co-Authors

Anne Elizabeth CarpenteriD· 3 shared Shantanu SinghiD· 3 shared Adam P. SkepneriD· 2 shared Amy B. GoodaleiD· 2 shared Beth A. CiminiiD· 2 shared Briana Fritchman· 2 shared Desiree Hernandez· 2 shared Lisa MilleriD· 2 shared

Activity by Year

2019-2024 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersBioinformatics

Anne Elizabeth CarpenterORCID

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Author profile →

3 papers

Recent·Most cited

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

Capturing single-cell heterogeneity via data fusion improves image-based profiling

Mohammad Hossein Rohban, Hamdah Shafqat Abbasi, Shantanu Singh, Anne Elizabeth Carpenter

The paper improves image-based profiling by fusing data to capture cell heterogeneity, enhancing prediction of compound mechanisms of action and gene pathways by ~20%.

Nature Communications · May 7, 2019Peer-reviewedBioinformatics