Nils Gehlenborg

The paper introduces the SenNet Portal, a resource for senescent cell data and tools, and discusses its usage and future developments.

SpatialQuery identifies multicellular spatial patterns and characterizes their molecular programs in spatial omics data, revealing cross-germ-layer signaling and disease-specific niches.

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

The paper develops a machine learning model to prioritize genes for newborn sequencing programs based on factors like evidence of disease natural history and treatment efficacy.

The paper defines the chromatin landscape of healthy and injured kidney cells using multi-omics data, identifying regulatory elements and transcription factor networks involved in injury response.

This paper describes OME-Zarr, a cloud-optimized bioimaging file format developed through community collaboration to improve scalability and data access.

The paper introduces MAMS, a metadata standard for single-cell data matrices and analysis workflows, to improve reproducibility and interoperability across datasets.

The paper introduces the 4DN Data Portal, a resource for searching and visualizing curated nucleomics data, including Hi-C and other chromosome architecture datasets.

PO_SCPLOWEAXC_SCPLOW enables interactive visual pattern search in sequential data using unsupervised deep representation learning, outperforming existing techniques in retrieving similar patterns.

Halyos is a visual EHR interface that helps patients understand their health risks through interactive visualizations of longitudinal data and risk scores.

This paper introduces Scalable Insets, a technique for exploring annotated patterns in multiscale visualizations, improving search speed and comparison accuracy.

HiGlass, a web-based, containerized viewer, enables continuous multiscale navigation of Hi-C contact maps alongside genomic tracks using composable views linked by location and zoom.

Lineage is a visual analysis tool that maps multifactorial disease analysis to multivariate graph visualization using genealogical, clinical, and genetic data.

SATORI provides an ontology-guided visual exploration tool for biomedical data repositories, enabling seamless search and semantic querying through interconnected visualizations.

The paper introduces a method for visualizing and refining cluster assignments in biological data, improving the differentiation of genotypes and phenotypes.

HiPiler is an interactive visualization tool for exploring large genome interaction matrices, enabling users to define and analyze regions of interest through thumbnails and linked exploration.

UpSetR provides a scalable matrix-based visualization for intersecting sets and their properties, offering an alternative to Venn and Euler diagrams.

UBiT2 is a client-side web application for analyzing RNA-seq and qPCR data, offering offline analysis and visualization with interactive tools and exportable figures.

The paper introduces an adaptive provenance visualization method for complex data workflows, enabling users to explore and communicate multi-step analyses through interest-driven graph expansion.

The paper introduces AVOCADO, a visualization tool for data provenance in biomedical research, enabling adaptive and scalable exploration of complex analysis workflows.