B. Alver

An integrated view of the structure and function of the human 4D nucleome

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 4D Nucleome Data Portal: a resource for searching and visualizing curated nucleomics data

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

Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs

The paper introduces Pairs, a compressed file format for Hi-C read pairs, and Pairix, a tool for indexing and querying these files, along with a quality control tool.

Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications

Micro-Meta App is an open-source tool that helps collect and organize microscopy metadata according to community standards, improving reproducibility and data sharing.

HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data

HiTea uses Hi-C data to detect non-reference transposable element insertions, outperforming whole genome sequencing-based methods in human cell lines.

HiNT: a computational method for detecting copy number variations and translocations from Hi-C data

HiNT detects copy number variations and translocations from Hi-C data with single base-pair resolution, outperforming existing methods on simulated and real data.

Tibanna: software for scalable execution of portable pipelines on the cloud

Tibanna automates bioinformatics pipeline execution on AWS using CWL, WDL, and Docker, supporting large-scale and variable computational needs.

HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction Maps

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.