Devika Torvi YOU? Author Swipe

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Open Invitation to Help Curate This Field & Enhance Impact .ORG

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

Jens Luebeck, E.-S. Huang, Forrest Kim, Ted Liefeld, Bhargavi Dameracharla , et al. · 2024

Computer science Biology

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 …

matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2 Open

Cheng Ye, Bryan Thornlow, Angie S. Hinrichs, Alexander Krämer, Cade Michandani , et al. · 2022

Computer science Biology Medicine

This is the 100K-sample tree and 1M-sample tree used for benchmarking matOptimize and TNT.

matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2 Open

Cheng Ye, Bryan Thornlow, Angie S. Hinrichs, Alexander Krämer, Cade Mirchandani , et al. · 2022

Computer science Biology Mathematics

Motivation Phylogenetic tree optimization is necessary for precise analysis of evolutionary and transmission dynamics, but existing tools are inadequate for handling the scale and pace of data produced during the coronavirus disease 2019 (…

matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2 Open

Ye Cheng, Bryan Thornlow, Angie S. Hinrichs, Devika Torvi, Robert Lanfear , et al. · 2022

Computer science Biology Mathematics

Phylogenetic tree optimization is necessary for precise analysis of evolutionary and transmission dynamics, but existing tools are inadequate for handling the scale and pace of data produced during the COVID-19 pandemic. One transformative…

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