B. Alver
YOU?
Author Swipe
View article: An integrated view of the structure and function of the human 4D nucleome
An integrated view of the structure and function of the human 4D nucleome Open
The dynamic three-dimensional (3D) organization of the human genome (the 4D nucleome) is linked to genome function. Here we describe efforts by the 4D Nucleome Project 1 to map and analyse the 4D nucleome in widely used H1 human embryonic …
View article: An integrated view of the structure and function of the human 4D nucleome
An integrated view of the structure and function of the human 4D nucleome Open
The dynamic three-dimensional (3D) organization of the human genome (the “4D Nucleome”) is closely linked to genome function. Here, we integrate a wide variety of genomic data generated by the 4D Nucleome Project to provide a detailed view…
View article: Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs
Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs Open
Summary As the amount of 3D chromosomal interaction data continues to increase, storing and accessing such data efficiently becomes paramount. We introduce Pairs, a block-compressed text file format for storing paired genomic coordinates f…
View article: Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications
Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications Open
For quality, interpretation, reproducibility and sharing value, microscopy images should be accompanied by detailed descriptions of the conditions that were used to produce them. Micro-Meta App is an intuitive, highly interoperable, open-s…
View article: The 4D Nucleome Data Portal: a resource for searching and visualizing curated nucleomics data
The 4D Nucleome Data Portal: a resource for searching and visualizing curated nucleomics data Open
The 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in the nucleus and the impact of their disruption in disease biology. We present the 4DN Data Portal ( https://data.4dnucleome.org/ ), a …
View article: Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs
Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs Open
Summary As the amount of three-dimensional chromosomal interaction data continues to increase, storing and accessing such data efficiently becomes paramount. We introduce Pairs, a block-compressed text file format for storing paired genomi…
View article: Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications
Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications Open
For the information content of microscopy images to be appropriately interpreted, reproduced, and meet FAIR (Findable Accessible Interoperable and Reusable) principles, they should be accompanied by detailed descriptions of microscope hard…
View article: WU-BIMAC/MicroMetaApp-React: 1.2.2-b1-1 stable beta (4DN v5 Integration - VII)
WU-BIMAC/MicroMetaApp-React: 1.2.2-b1-1 stable beta (4DN v5 Integration - VII) Open
This is the latest stable beta release of the React implementation of the Micro-Meta App. This version of the Micro-Meta App is based on the Core and Basic extension of the v2.01 of the 4DN-BINA-OME Microscopy Metadata specifications which…
View article: WU-BIMAC/MicroMetaApp-Electron: 1.2.2-b1-1 stable beta
WU-BIMAC/MicroMetaApp-Electron: 1.2.2-b1-1 stable beta Open
This is the latest stable beta release of the Micro-Meta App. This version of the Micro-Meta App is based on the Core and Basic extension of the v2.01 of the 4DN-BINA-OME Microscopy Metadata specifications which allow documenting transmitt…
View article: Comparative analysis of metazoan chromatin organization
Comparative analysis of metazoan chromatin organization Open
Genome function is dynamically regulated in part by chromatin, which consists of the histones, non-histone proteins and RNA molecules that package DNA. Studies in Caenorhabditis elegans and Drosoph ...
View article: HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data
HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data Open
Hi-C is a common technique for assessing 3D chromatin conformation. Recent studies have shown that long-range interaction information in Hi-C data can be used to generate chromosome-length genome assemblies and identify large-scale structu…
View article: The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae
The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae Open
Spn1/Iws1 is a conserved protein involved in transcription and chromatin dynamics, yet its general in vivo requirement for these functions is unknown. Using a Spn1 depletion system in Saccharomyces cerevisiae, we demonstrate that Spn1 broa…
View article: The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in<i>Saccharomyces cerevisiae</i>
The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in<i>Saccharomyces cerevisiae</i> Open
Spn1/Iws1 is a conserved protein involved in transcription and chromatin dynamics, yet its general in vivo requirement for these functions is unknown. Using a Spn1 depletion system in S. cerevisiae, we demonstrate that Spn1 broadly influen…
View article: The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae
The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae Open
All data analyses supporting our preprint "The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae". Reproduce the figures of the paper starting from raw da…
View article: HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data
HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data Open
Hi-C is a common technique for assessing three-dimensional chromatin conformation. Recent studies have shown that long-range interaction information in Hi-C data can be used to generate chromosome-length genome assemblies and identify larg…
View article: GiniQC: a measure for quantifying noise in single-cell Hi-C data
GiniQC: a measure for quantifying noise in single-cell Hi-C data Open
Summary Single-cell Hi-C (scHi-C) allows the study of cell-to-cell variability in chromatin structure and dynamics. However, the high level of noise inherent in current scHi-C protocols necessitates careful assessment of data quality befor…
View article: HiNT: a computational method for detecting copy number variations and translocations from Hi-C data
HiNT: a computational method for detecting copy number variations and translocations from Hi-C data Open
The three-dimensional conformation of a genome can be profiled using Hi-C, a technique that combines chromatin conformation capture with high-throughput sequencing. However, structural variations (SV) often yield features that can be mista…
View article: Tibanna: software for scalable execution of portable pipelines on the cloud
Tibanna: software for scalable execution of portable pipelines on the cloud Open
Summary We introduce Tibanna, an open-source software tool for automated execution of bioinformatics pipelines on Amazon Web Services (AWS). Tibanna accepts reproducible and portable pipeline standards including Common Workflow Language (C…
View article: Tibanna: software for scalable execution of portable pipelines on the cloud
Tibanna: software for scalable execution of portable pipelines on the cloud Open
Summary We introduce Tibanna, an open-source software tool for automated execution of bioinformatics pipelines on Amazon Web Services (AWS). Tibanna accepts reproducible and portable pipeline standards including Common Workflow Language (C…
View article: HiGlass: web-based visual exploration and analysis of genome interaction maps
HiGlass: web-based visual exploration and analysis of genome interaction maps Open
We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D genomic tracks, allowing users to combine variou…