Author

Allison Brookhart

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· 1 Cancer Biology· 1 Genetics· 1

Signature Assays, Organisms & Methods

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Organism:human· 3 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Approach:experimental assay· 2 Research Focus:gene regulatory network inference· 2 Assay:long-read sequencing· 2 Research Focus:cell-cell communication· 1 Research Focus:database / resource· 1

Frequent Co-Authors

Akanksha KhorgadeiD· 2 shared Aziz M. Al’KhafajiiD· 2 shared Brian J. HaasiD· 2 shared Christophe H. GeorgescuiD· 2 shared Ghamdan Al‐EryaniiD· 2 shared Houlin YuiD· 2 shared Victoria PopiciD· 2 shared Aaron S. MeyeriD· 1 shared

Activity by Year

2026-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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2 shared papersGenetics

Akanksha KhorgadeORCID

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Author profile →

3 papers

Recent·Most cited

Scalable single-cell isoform profiling with sequencing-by-expansion

Christophe H. Georgescu, Ghamdan Al‐Eryani, Allison Brookhart, Jagdeesh Chandrasekar, Stephanie J. Yaung, Megan Rogers-Peckham, Megan Freer, Michael E. Kartje, Houlin Yu, Akanksha Khorgade, Charlotte Yang, Lacey McGee, Kendall Berg, Cynthia Cech, Salka Barrett, , Aziz M. Al’Khafaji

This paper introduces a high-throughput single-cell RNA isoform sequencing method using sequencing-by-expansion (SBX) and the CUDLL algorithm, achieving high accuracy and enabling isoform-level analysis across cell types.

bioRxiv · Jul 28, 2026 · PreprintGenetics

Systems serology of responses against tumor antigens in ovarian cancer reveal disrupted Fc-mediated immunity

Michelle Loui, Meera Trisal, Laura B. James‐Allan, Scott D. Taylor, Het Desai, Gabriella DiBernardo, Allison Brookhart, Yun-Rong Ting, Jessica Gebraeel, Neda A. Moatamed, Pamela K. Kreeger, Sanaz Memarzadeh, Aaron S. Meyer

This study identifies tumor-binding autoantibodies in ovarian cancer patients that fail to engage Fc{gamma}RIIIa, impairing antibody-dependent cellular cytotoxicity.

bioRxiv · Apr 29, 2026 · PreprintCancer Biology

Accurate strand-specific long-read transcript isoform discovery and quantification at bulk, single-cell, and single-nucleus resolution

Houlin Yu, Christophe H. Georgescu, Akanksha Khorgade, Ghamdan Al‐Eryani, Daniel A. Bartlett, Allison Brookhart, Can Koçkan, James T. Webber, Asa Shin, Emily White, Xylena Reed, Fangle Hu, Sarah Bromberek, Sandra Ndayambaje, Sandeep Aryal, , Aziz M. Al’Khafaji

The paper introduces LRAA, a framework for accurate isoform discovery and quantification in long-read RNA-seq data, outperforming existing methods across multiple benchmarks.

bioRxiv · Feb 12, 2026 · PreprintBioinformatics