Jill P. Mesirov

The Multi-scale Copula Index (MCI): a new information-theoretic measure of association and its applications in functional cancer genomics

The paper introduces the Multi-scale Copula Index (MCI), an information-theoretic measure of association, and demonstrates its utility in cancer genomics for capturing contextual associations in complex datasets.

Preservation and Clonal Behavior of Extrachromosomal DNA in Patient-Derived Xenograft Models of Childhood Cancers

This study compares ecDNA prevalence, conservation, and clonal dynamics in PDX models and primary tumors of childhood cancers, finding high sequence conservation and selective growth advantage of ecDNA-positive clones.

igv-reports: Embedding interactive genomic visualizations in HTML reports to aid variant review

igv-reports creates standalone HTML reports with interactive genomic visualizations to aid in variant inspection without requiring input data files.

Interferon Restores Antigen Presentation and Sensitizes Medulloblastoma to T Cell Killing

This study shows that interferon gamma restores antigen presentation in medulloblastoma and enhances T cell-mediated tumor killing in a mouse model.

Inactivation of histone chaperone HIRA unmasks a link between normal embryonic development of melanoblasts and maintenance of adult melanocyte stem cells

This study shows that inactivating HIRA during embryonic development affects melanoblasts and leads to aging-related defects in melanocyte stem cells, but not in postnatal melanocytes.

Single Nuclei-Derived Molecular Subtypes of Gastrointestinal Stromal Tumors Correlate with Clinicopathologic Features and Predict Clinical Outcomes

The paper identifies six molecular subtypes of GIST using single nucleus RNA sequencing and correlates them with clinicopathologic features and clinical outcomes.

MICAL2 Is a Super Enhancer Associated Gene that Promotes Pancreatic Cancer Growth and Metastasis

This study identifies MICAL2 as a super enhancer-associated gene that promotes pancreatic cancer growth and metastasis through multiple molecular mechanisms.

Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis

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

Data driven refinement of gene expression signatures for enrichment analysis

The paper refines gene expression signatures using multi-omics data to improve enrichment analysis by addressing lack of coordinate expression in gene sets.

Profiling ranked list enrichment scoring in sparse data elucidates algorithmic tradeoffs

The paper evaluates ssGSEA's performance on scRNA-seq data, finds it unreliable due to sparsity, and identifies UCell as more robust for pseudobulk analysis.

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

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

Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R, and GenePattern Notebook implementations of CoGAPS

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.

Deciphering the Functional Roles of Individual Cancer Alleles Across Comprehensive Cancer Genomic Studies

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: Accessible NMF-based clustering utilizing GPU acceleration

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

igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV)

igv.js provides a web-based, embeddable version of the Integrative Genomics Viewer with no external dependencies or backend requirements.

The Molecular Signatures Database Revisited: Extending Support for Mouse Data

The paper extends the Molecular Signatures Database to support mouse gene data by adding mouse-specific gene sets and improved orthology mapping resources.

What does your cell really do? Model-based assessment of mammalian cells metabolic functionalities using omics data

The paper introduces a framework to predict how changes in omics data affect metabolic functions in mammalian cells using curated metabolic tasks and genome-scale networks.

GeNets: A unified web platform for network-based analyses of genomic data

GeNets provides a platform to compare genomic networks using machine learning and allows analysis of genetic and RNA sequencing data.

Juicebox.js provides a cloud-based visualization system for Hi-C data

Juicebox.js is a cloud-based tool for visualizing Hi-C data, enabling users to explore and share 3D genome structures through an intuitive interface.