Author

Adam Officer

Broad Institute

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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Bioinformatics· 2 Genomics· 2 Systems Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 5 Organism:human· 4 Assay:proteomics· 3 Research Focus:benchmarking· 2 Assay:spatial transcriptomics· 2 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Research Focus:cell-cell communication· 1

Frequent Co-Authors

Alexander D. BorowskyiD· 2 shared Brendan MacLeaniD· 2 shared Daniela NachmansoniD· 2 shared Farnaz Hasteh· 2 shared Gillian L. HirstiD· 2 shared Huazhen Yao· 2 shared Jacob D. JaffeiD· 2 shared Joseph Steward· 2 shared

Activity by Year

2018-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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2 shared papersGenomics

Alexander D. BorowskyORCID

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Author profile →

5 papers

Recent·Most cited

spatiAlytica: Viewer-Grounded Multimodal Agentic System for Interactive Spatial Omics Analysis

Arun Das, Kexun Zhang, Jifeng Song, Meiru Han, Angela Chen, Wen Meng, Hugh Galloway, Po-Yuan Chen, Sumin Jo, Zhentao Liu, Md Musaddaqul Hasib, Adam Officer, Harsh Sinha, Yu‐Chiao Chiu, Shou‐Jiang Gao, , Yufei Huang

spatiAlytica enables non-programmer biologists to perform interactive spatial omics analysis using natural language and a viewer-centric agentic system.

bioRxiv · May 4, 2026 · PreprintBioinformatics

The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ

Daniela Nachmanson, Adam Officer, Hidetoshi Mori, Jonathan Gordon, Mark Francis Evans, Joseph Steward, Huazhen Yao, Thomas J. O’Keefe, Farnaz Hasteh, Gary Stephen Stein, Kristen Jepsen, Donald L. Weaver, Gillian L. Hirst, Brian L. Sprague, Laura J. Esserman, , Olivier Harismendy

The paper creates a breast pre-cancer atlas by analyzing multiple micro-dissected regions from DCIS cases, revealing molecular and micro-environmental diversity and immune states associated with progression risk.

npj Breast Cancer · Jan 13, 2022Peer-reviewedGenomics

Mutational profiling of micro-dissected pre-malignant lesions from archived specimens

Daniela Nachmanson, Joseph Steward, Huazhen Yao, Adam Officer, Eliza Jeong, Thomas J. O’Keefe, Farnaz Hasteh, Kristen Jepsen, Gillian L. Hirst, Laura J. Esserman, Alexander D. Borowsky, Olivier Harismendy

This paper develops a method to improve mutational profiling of pre-malignant lesions using degraded FFPE DNA, achieving better coverage and variant calling accuracy.

BMC Medical Genomics · Nov 18, 2020Peer-reviewedGenomics

Avant-garde: An automated data-driven DIA data curation tool.

Alvaro Sebastian Vaca Jácome, Ryan Peckner, Nicholas Shulman, Karsten Krug, Katherine C. DeRuff, Adam Officer, Karen E. Christianson, Brendan MacLean, Michael J. MacCoss, Steven A. Carr, Jacob D. Jaffe

Avant-garde improves DIA data analysis by refining signals, reducing interference, and controlling false discovery rates through a data-driven approach.

Nature Methods · Nov 16, 2020Peer-reviewedBioinformatics

A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations

Lev Litichevskiy, Ryan Peckner, Jennifer G. Abelin, Jacob K. Asiedu, Amanda L. Creech, John F. Davis, Desiree Davison, Caitlin M. Dunning, Jarrett D. Egertson, Shawn B. Egri, Joshua Gould, Tak Ko, Sarah Johnson, David L. Lahr, Daniel Lam, , Jacob D. Jaffe

The paper creates a proteomic resource profiling 90 drugs in six cell lines, revealing cell-specific responses and enabling integration with transcriptional data to identify therapeutic opportunities.

Cell Systems · Apr 1, 2018Peer-reviewedSystems Biology