Author

Alex Buchanan

Oregon Health & Science University

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· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Assay:whole-genome sequencing· 2 Approach:benchmark study· 1 Organism:human· 1 Approach:simulation· 1 Approach:statistical model· 1 Research Focus:variant calling· 1 Assay:whole-exome sequencing· 1

Frequent Co-Authors

Kyle EllrottiD· 3 shared Adriana SalcedoiD· 2 shared Amit G. DeshwariD· 2 shared David C. WedgeiD· 2 shared Dimitris AnastassiouiD· 2 shared Hongjiu ZhangiD· 2 shared Ignaty LeshchineriD· 2 shared Imaad Umar· 2 shared

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2017-2022 · peak 1/yr

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10 top collaborators · 45 mutual co-author links

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3 shared papersBioinformatics

Kyle EllrottORCID

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Author profile →

3 papers

Recent·Most cited

Crowd-sourced benchmarking of single-sample tumour subclonal reconstruction

Adriana Salcedo, Maxime Tarabichi, Alex Buchanan, Shadrielle M. G. Espiritu, Hongjiu Zhang, Kaiyi Zhu, Tai-Hsien Ou Yang, Ignaty Leshchiner, Dimitris Anastassiou, Yuanfang Guan, Gun Ho Jang, Kerstin Haase, Amit G. Deshwar, William Zou, Imaad Umar, , Paul Christopher Boutros

The paper benchmarks 31 subclonal reconstruction algorithms on simulated tumours, finding that algorithm choice significantly impacts performance and no single algorithm excels across all tasks.

bioRxiv · Jun 14, 2022 · PreprintBioinformatics

Creating Standards for Evaluating Tumour Subclonal Reconstruction

DREAM SMC-Het Participants, Adriana Salcedo, Maxime Tarabichi, Shadrielle M. G. Espiritu, Amit G. Deshwar, Matei David, Nathan M. Wilson, Stefan C. Dentro, Jeff A. Wintersinger, Lydia Liu, Minjeong Ko, Srinivasan Sivanandan, Hongjiu Zhang, Kaiyi Zhu, Tai-Hsien Ou Yang, , Paul Christopher Boutros

This study develops quantitative metrics and simulated datasets to evaluate subclonal reconstruction methods in tumours.

Nature Biotechnology · Jan 1, 2020Peer-reviewedBioinformatics

Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments

Christina K. Yung, Brian D. O’Connor, Sergei Yakneen, Junjun Zhang, Kyle Ellrott, Kortine Kleinheinz, Naoki Miyoshi, Keiran M. Raine, Romina Royo, Gordon Saksena, Matthias Schlesner, Solomon I. Shorser, Miguel Vazquez, Joachim Weischenfeldt, Denis Yuen, , Charles L. Short

The paper describes the PCAWG project's large-scale analysis of cancer whole genomes across multiple computing environments, producing validated consensus variants for downstream research.

bioRxiv · Jul 10, 2017 · PreprintGenomics