Author

Adam A. Margolin

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Biology Disciplines

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Bioinformatics· 3 Genomics· 1

Signature Assays, Organisms & Methods

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Organism:human· 3 Approach:statistical model· 3 Research Focus:benchmarking· 2 Assay:whole-genome sequencing· 2 Research Focus:batch correction / integration· 1 Assay:bulk RNA-seq· 1 Research Focus:database / resource· 1 Approach:simulation· 1

Frequent Co-Authors

Kyle EllrottiD· 3 shared Adam D. EwingiD· 2 shared Cristian Caloian· 2 shared J Christopher BareiD· 2 shared Joshua M. StuartiD· 2 shared Kathleen E. HoulahaniD· 2 shared Paul Christopher BoutrosiD· 2 shared Takafumi N. YamaguchiiD· 2 shared

Activity by Year

2018-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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3 shared papersBioinformatics

Kyle EllrottORCID

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Author profile →

4 papers

Recent·Most cited

An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences

Burcu Gurun, Wesley R. Horton, Dhaarini Murugan, Biqing Zhu, Patrick Leyshock, Sushil Kumar, Katelyn T. Byrne, Robert H. Vonderheide, Adam A. Margolin, Motomi Mori, Paul T. Spellman, Lisa M. Coussens, Terence Paul Speed

The paper presents a cost-effective, non-commercial protocol for normalizing TCRβ CDR3 sequencing data to correct amplification bias in bulk TCR repertoire profiling.

BMC Genomics · Jun 26, 2023Peer-reviewedBioinformatics

A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants

Alex Handler Wagner, Brian Walsh, Georgia Mayfield, David Tamborero, Dmitriy Sonkin, Kilannin Krysiak, Jordi Deu-Pons, Ryan P. Duren, Jianjiong Gao, Julie A. McMurry, Sara E. Patterson, Catherine Del Vecchio Fitz, Beth A. Pitel, Osman Uğur Sezerman, Kyle Ellrott, , Adam A. Margolin

The paper harmonizes clinical interpretations of cancer genomic variants across six knowledgebases, improving overlap and matching with patient cohorts.

Nature Genetics · Apr 1, 2020Peer-reviewedBioinformatics

Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic structural variant detection

Anna Y. Lee, Adam D. Ewing, Kyle Ellrott, Yin Hu, Kathleen E. Houlahan, J Christopher Bare, Shadrielle M. G. Espiritu, Vincent Huang, Kristen Dang, Zechen Chong, Cristian Caloian, Takafumi N. Yamaguchi, ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Michael Kellen, Ken Chen, , Paul Christopher Boutros

The paper benchmarks somatic structural variant detection methods using synthetic tumors and crowd-sourced submissions, finding that ensembles do not always outperform individual methods.

Genome biology · Nov 6, 2018Peer-reviewedBioinformatics

Germline Contamination and Leakage in Whole Genome Somatic Single Nucleotide Variant Detection

Dorota H.S. Sendorek, Cristian Caloian, Kyle Ellrott, J Christopher Bare, Takafumi N. Yamaguchi, Adam D. Ewing, Kathleen E. Houlahan, Thea Norman, Adam A. Margolin, Joshua M. Stuart, Paul Christopher Boutros

The paper quantifies germline leakage in somatic SNV detection across 259 datasets and introduces a tool to correct it, finding low leakage rates that can be further reduced with pre-filtering.

BMC Bioinformatics · Jan 31, 2018Peer-reviewedGenomics