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Forrest Kim

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Articles by Forrest Kim

AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes

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By Jens Luebeck, Ted Liefeld, Edwin Huang, Forrest Kim, Bhargavi Dameracharla, Michael Chan, Kyra Fetter, Dhruv Khatri, Kaiyuan Zhu, Thorin Tabor, Daniel Schreyer, Gino Prasad, Aditi Gnanasekar, Siavash Raeisi Dehkordi, Simone Spandau, Rishaan Kenkre, Soyeon Kim, Hoon Kim, Peter Bailey, Roel G. W. Verhaak, Viraj Deshpande, Michael Reich, Paul S. Mischel, Jill P. Mesirov, Vineet Bafna, Rohil Ahuja, Michał Adamaszek, Tushar Agashe, Devika Torvi
| Nature Verified
Abstract Here we present AmpliconSuite, a toolkit for focal amplification analysis from cancer whole-genome sequencing that identifies extrachromosomal DNA (ecDNA), breakage–fusion–bridges and other amplification modes. Its ecContext module categorizes ecDNA structures to understand formation mechanisms. Validation across 175 metaphase fluorescence in situ hybridization-probed genes in 72 models demonstrated accurate predictions.
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AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes

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By Jens Luebeck, Edwin Huang, Forrest Kim, Ted Liefeld
| BioRxiv
Abstract Focal amplifications in the cancer genome, particularly extrachromosomal DNA (ecDNA) amplifications, are emerging as a pivotal event in cancer progression across diverse cancer contexts, presenting a paradigm shift in our understanding of tumor dynamics. Simultaneously, identification of the various modes of focal amplifications is bioinformatically challenging.
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Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis

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By Michael Reich, Forrest Kim, Thorin Tabor, Ted Liefeld
| BioRxiv
New Results doi: https://doi.org/10.1101/2023.04.04.535621 Abstract We present Genomics to Notebook (g2nb), an environment that combines the JupyterLab notebook system with widely-used bioinformatics platforms. Galaxy, GenePattern, and the JavaScript versions of IGV and Cytoscape are currently available within g2nb.
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