Biology subjects

Purushotham, D.

Publications and source records attributed to Purushotham, D..

5 recordsLinked to original sources

bioRxiv2022

Comparing Genomic and Epigenomic Features across Species Using the WashU Comparative Epigenome Browser

Genome browsers have become an intuitive and critical tool to visualize and analyze genomic features and data. Conventional genome browsers display data/annotations on a single reference genome/assembly; there are also genomic alignment viewer/browsers that help users visualize alignment, mismatch, and rearrangement between syntenic regions. However, there is a growing need for a comparative epigenome browser that can display genomic and epigenomic datasets across different species and enable users to compare them between syntenic regions. Here, we present the WashU Comparative Epigenome Browser (http://comparativegateway.wustl.edu). It allows users to load functional genomic datasets/annotations mapped to different genomes and display them over syntenic regions simultaneously. The browser also displays genetic differences between the genomes from single nucleotide variants (SNVs) to structural variants (SVs) to visualize the association between epigenomic differences and genetic differences. Instead of anchoring all datasets to the reference genome coordinates, it creates independent coordinates of different genome assemblies to faithfully present features and data mapped to different genomes. It uses a simple, intuitive genome-align track to illustrate the syntenic relationship between different species. It extends the widely used WashU Epigenome Browser infrastructure and can be expanded to support multiple species. This new browser function will greatly facilitate comparative genomic/epigenomic research, as well as support the recent growing needs to directly compare and benchmark the T2T CHM13 assembly and other human genome assemblies.

genomics↗

bioRxiv2022

Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser

Biological functions are not only encoded by the genomes sequence but also regulated by its three-dimensional (3D) structure. More and more studies have revealed the importance of 3D chromatin structures in development and diseases; therefore, visualizing the connections between genome sequence, epigenomic dynamics (1D) and the 3D genome becomes a pressing need. The WashU Epigenome Browser introduces a new 3D visualization module to integrate visualization of 1D (such as sequence features, epigenomic data) and 2D data (such as chromosome conformation capture data) with 3D genome structure. Genomic coordinates are encoded in 3D models of the chromosomes; thus, all genomic information displayed on a 1D genome browser can be visualized on a 3D model, supported by genome browser utilities and facilitating interpretation of genomic data. Biological information that is difficult to illustrate in 1D becomes more intuitive when displayed in 3D, providing novel and powerful tools for investigators to hypothesize and understand the connections between biological functions and 3D genome structures.

bioinformatics↗

bioRxiv2020

The qBED track: a novel genome browser visualization for point processes

SummaryTransposon calling cards is a genomic assay for identifying transcription factor binding sites in both bulk and single cell experiments. Here we describe the qBED format, an open, text-based standard for encoding and analyzing calling card data. In parallel, we introduce the qBED track on the WashU Epigenome Browser, a novel visualization that enables researchers to inspect calling card data in their genomic context. Finally, through examples, we demonstrate that qBED files can be used to visualize non-calling card datasets, such as CADD scores and GWAS/eQTL hits, and may have broad utility to the genomics community. Availability and ImplementationThe qBED track is available on the WashU Epigenome Browser (http://epigenomegateway.wustl.edu/browser), beginning with version 46. Source code for the WashU Epigenome Browser with qBED support is available on GitHub (http://github.com/arnavm/eg-react and http://github.com/lidaof/eg-react). We have also released a tutorial on how to upload qBED data to the browser (dx.doi.org/10.17504/protocols.io.bca8ishw).

bioinformatics↗

bioRxiv2020

Exploring the coronavirus epidemic using the new WashU Virus Genome Browser

Since its debut in mid-December, 2019, the novel coronavirus (2019-nCoV) has rapidly spread from its origin in Wuhan, China, to several countries across the globe, leading to a global health crisis. As of February 7, 2020, 44 strains of the virus have been sequenced and uploaded to NCBIs GenBank [1], providing insight into the viruss evolutionary history and pathogenesis. Here, we present the WashU Virus Genome Browser, a web-based portal for viewing virus genomic data. The browser is home to 16 complete 2019-nCoV genome sequences, together with hundreds of related viral sequences including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and Ebola virus. In addition, the browser features unique customizability, supporting user-provided upload of novel viral sequences in various formats. Sequences can be viewed in both a track-based representation as well as a phylogenetic tree-based view, allowing the user to easily compare sequence features across multiple strains. The WashU Virus Genome Browser inherited many features and track types from the WashU Epigenome Browser, and additionally incorporated a new type of SNV track to address the specific needs of viral research. Our Virus Browser portal can be accessed at https://virusgateway.wustl.edu, and documentation is available at https://virusgateway.readthedocs.io/.

genomics↗

bioRxiv2017

Chromatin interaction data visualization in the WashU Epigenome Browser

MotivationLong-range chromatin interactions are critical for gene regulations and genome maintenance. HiC and Cool are the two most common data formats used by the community, including the 4D Nucleome Consortium (4DN), to represent chromatin interaction data from a variety of chromatin conformation capture experiments, and specialized tools were developed for their analysis, visualization, and conversion. However, there does not exist a tool that can support visualization of both data formats simultaneously.\n\nResultsThe WashU Epigenome Browser has integrated both HiC and Cool data formats into its visualization platform. Investigators can seamlessly explore chromatin interaction data regardless of their underlying data format. For developers it is straightforward to benchmark the differences in rendering speed and computational resource usage between the two data formats.\n\nAvailabilityhttp://epigenomegateway.wustl.edu/browser/.

bioinformatics↗