Michael M. Reich

The paper introduces g2nb, a notebook environment integrating bioinformatics platforms into a unified interface for genomics analysis.

AmpliconSuite identifies focal amplifications in cancer genomes, showing ecDNA has higher copy numbers and stronger oncogene enrichment compared to other amplification types.

The paper introduces computational tools for NMF analysis of single-cell RNA-seq data, demonstrating their use in quantifying cell state transitions in pancreatic cancer.

This paper introduces REVEALER 2.0, an improved algorithm for identifying genomic alterations associated with functional profiles, showing increased speed and resolution for analyzing cancer genomic data.

NMFClustering provides GPU-accelerated non-negative matrix factorization for efficient clustering of large RNA-Seq and scRNA-seq datasets.

The paper analyzes transcriptomics data availability and reusability between microarray and RNA-seq experiments published between 2009 and 2013, and provides recommendations to improve RNA-seq data sharing.

The paper introduces Tangent and Pseudo-Tangent pipelines for copy-number inference from cancer genome data, improving noise reduction and accuracy in SNP array and WES analyses.