View article: Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update Open
Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of …
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The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets Open
Cellular life depends on a complex web of functional associations between biomolecules. Among these associations, protein–protein interactions are particularly important due to their versatility, specificity and adaptability. The STRING da…
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DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update) Open
DAVID is a popular bioinformatics resource system including a web server and web service for functional annotation and enrichment analyses of gene lists. It consists of a comprehensive knowledgebase and a set of functional analysis tools. …
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g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) Open
Biological data analysis often deals with lists of genes arising from various studies. The g:Profiler toolset is widely used for finding biological categories enriched in gene lists, conversions between gene identifiers and mappings to the…
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GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis Open
Introduced in 2017, the GEPIA (Gene Expression Profiling Interactive Analysis) web server has been a valuable and highly cited resource for gene expression analysis based on tumor and normal samples from the TCGA and the GTEx databases. He…
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WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs Open
WebGestalt is a popular tool for the interpretation of gene lists derived from large scale -omics studies. In the 2019 update, WebGestalt supports 12 organisms, 342 gene identifiers and 155 175 functional categories, as well as user-upload…
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Heatmapper: web-enabled heat mapping for all Open
Heatmapper is a freely available web server that allows users to interactively visualize their data in the form of heat maps through an easy-to-use graphical interface. Unlike existing non-commercial heat map packages, which either lack gr…
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The reactome pathway knowledgebase Open
The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations in a single consist…
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PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements Open
This FAIRsharing record describes: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and …
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PDBsum: Structural summaries of PDB entries Open
PDBsum is a web server providing structural information on the entries in the Protein Data Bank (PDB). The analyses are primarily image‐based and include protein secondary structure, protein‐ligand and protein‐DNA interactions, PROCHECK an…
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CellMarker: a manually curated resource of cell markers in human and mouse Open
One of the most fundamental questions in biology is what types of cells form different tissues and organs in a functionally coordinated fashion. Larger-scale single-cell sequencing and biology experiment studies are now rapidly opening up …
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The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins Open
Genomics, epigenomics, transcriptomics, proteomics and metabolomics efforts rapidly generate a plethora of data on the activity and levels of biomolecules within mammalian cells. At the same time, curation projects that organize knowledge …
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WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit Open
Functional enrichment analysis has played a key role in the biological interpretation of high-throughput omics data. As a long-standing and widely used web application for functional enrichment analysis, WebGestalt has been constantly upda…
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Sangerbox: A comprehensive, interaction‐friendly clinical bioinformatics analysis platform Open
In recent decades, with the continuous development of high‐throughput sequencing technology, data volume in medical research has increased, at the same time, almost all clinical researchers have their own independent omics data, which prov…
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<i>checkCIF</i> validation ALERTS: what they mean and how to respond Open
Authors of a paper that includes a new crystal-structure determination are expected to not only report the structural results of interest and their interpretation, but are also expected to archive in computer-readable CIF format the experi…
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BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins Open
Interest in secondary metabolites such as RiPPs (ribosomally synthesized and posttranslationally modified peptides) is increasing worldwide. To facilitate the research in this field we have updated our mining web server. BAGEL4 is faster t…
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Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees Open
Evolview is an interactive tree visualization tool designed to help researchers in visualizing phylogenetic trees and in annotating these with additional information. It offers the user with a platform to upload trees in most common tree f…
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Common pitfalls and recommendations for using machine learning to detect and prognosticate for COVID-19 using chest radiographs and CT scans Open
Machine learning methods offer great promise for fast and accurate detection and prognostication of coronavirus disease 2019 (COVID-19) from standard-of-care chest radiographs (CXR) and chest computed tomography (CT) images. Many articles …
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Microreact: visualizing and sharing data for genomic epidemiology and phylogeography Open
Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides a framework onto which associated data (geographical, temp…
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A Survey of Wearable Devices and Challenges Open
As smartphone penetration saturates, we are witnessing a new trend in personal mobile devices-wearable mobile devices or simply wearables as it is often called. Wearables come in many different forms and flavors targeting different accesso…
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jPOSTrepo: an international standard data repository for proteomes Open
Major advancements have recently been made in mass spectrometry-based proteomics, yielding an increasing number of datasets from various proteomics projects worldwide. In order to facilitate the sharing and reuse of promising datasets, it …
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A multi-decade record of high-quality <i>f</i> CO <sub>2</sub> data in version 3 of the Surface Ocean CO <sub>2</sub> Atlas (SOCAT) Open
The Surface Ocean CO2 Atlas (SOCAT) is a synthesis of quality-controlled fCO2 (fugacity of carbon dioxide) values for the global surface oceans and coastal seas with regular updates. Version 3 of SOCAT has 14.7 million fCO2 values from 364…
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Federated Learning: A Survey on Enabling Technologies, Protocols, and Applications Open
This paper provides a comprehensive study of Federated Learning (FL) with an emphasis on enabling software and hardware platforms, protocols, real-life applications and use-cases. FL can be applicable to multiple domains but applying it to…
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PubChem BioAssay: 2017 update Open
PubChem's BioAssay database (https://pubchem.ncbi.nlm.nih.gov) has served as a public repository for small-molecule and RNAi screening data since 2004 providing open access of its data content to the community. PubChem accepts data submiss…
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OncoLnc: linking TCGA survival data to mRNAs, miRNAs, and lncRNAs Open
OncoLnc is a tool for interactively exploring survival correlations, and for downloading clinical data coupled to expression data for mRNAs, miRNAs, or long noncoding RNAs (lncRNAs). OncoLnc contains survival data for 8,647 patients from 2…
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Communication-Efficient Federated Deep Learning With Layerwise Asynchronous Model Update and Temporally Weighted Aggregation Open
Federated learning obtains a central model on the server by aggregating models trained locally on clients. As a result, federated learning does not require clients to upload their data to the server, thereby preserving the data privacy of …
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Federated Learning: Collaborative Machine Learning withoutCentralized Training Data Open
Federated learning (also known as collaborative learning) is a machine learning technique that trains an algorithm without transferring data samples across numerous decentralized edge devices or servers. This strategy differs from standard…
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Anti-Social Media: How Facebook Disconnects Us and Undermines Democracy Open
Social media, and Facebook in particular, have become such a ubiquitous and deeply imbedded part of culture that few would bother to mark their existence with more than a casual shrug. People use social media to fulfill all manner of tasks…
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OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs Open
OrthoDB is a comprehensive catalog of orthologs, genes inherited by extant species from a single gene in their last common ancestor. In 2016 OrthoDB reached its 9th release, growing to over 22 million genes from over 5000 species, now addi…
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15 years of GDR: New data and functionality in the Genome Database for Rosaceae Open
The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding data and data-mining tools to facilitate basic, …