Is this you? As a journalist, you can create a free Muck Rack account to customize your profile, list your contact preferences, and upload a portfolio of your best work.
Claim your profile
Articles by Ted Liefeld
AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes
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.
Profiling ranked list enrichment scoring in sparse data elucidates algorithmic tradeoffs
Abstract Gene Set Enrichment Analysis (GSEA) is a method for quantifying pathway and process activation in groups of samples, and its single sample version (ssGSEA) scores activation using mRNA abundance in a single sample. GSEA and ssGSEA were developed for bulk samples rather than individual cell technologies such as microarrays and bulk RNA-sequencing (RNA-seq) data.
AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes
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.
NMFClustering: Accessible NMF-based clustering utilizing GPU acceleration
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
NMFClustering: Accessible NMF-based clustering utilizing GPU acceleration
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis
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.
Show More
loading
Actions
Is this you?
As a journalist, you can create a free Muck Rack account to customize your profile, list your contact preferences, and upload a portfolio of your best work.Get in touch with Ted
Contact Ted, search articles and posts on X, monitor coverage, and track replies from one place.
Learn more about Muck Rack