Best practices for single-cell analysis across modalities
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …
The gene ontology knowledgebase in 2023
Abstract The Gene Ontology (GO) knowledgebase (http://geneontology. org) is a
comprehensive resource concerning the functions of genes and gene products (proteins …
comprehensive resource concerning the functions of genes and gene products (proteins …
Large language models generate functional protein sequences across diverse families
Deep-learning language models have shown promise in various biotechnological
applications, including protein design and engineering. Here we describe ProGen, a …
applications, including protein design and engineering. Here we describe ProGen, a …
An integrated cell atlas of the lung in health and disease
Single-cell technologies have transformed our understanding of human tissues. Yet, studies
typically capture only a limited number of donors and disagree on cell type definitions …
typically capture only a limited number of donors and disagree on cell type definitions …
g: Profiler—interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update)
Abstract g: Profiler is a reliable and up-to-date functional enrichment analysis tool that
supports various evidence types, identifier types and organisms. The toolset integrates many …
supports various evidence types, identifier types and organisms. The toolset integrates many …
[PDF][PDF] The gene ontology knowledgebase in 2023
Abstract The Gene Ontology (GO) knowledgebase (http://geneontology. org) is a
comprehensive resource concerning the functions of genes and gene products (proteins …
comprehensive resource concerning the functions of genes and gene products (proteins …
CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data
C Hu, T Li, Y Xu, X Zhang, F Li, J Bai… - Nucleic acids …, 2023 - academic.oup.com
Abstract CellMarker 2.0 (http://bio-bigdata. hrbmu. edu. cn/CellMarker or http://117.50.
127.228/CellMarker/) is an updated database that provides a manually curated collection of …
127.228/CellMarker/) is an updated database that provides a manually curated collection of …
Deep bidirectional language-knowledge graph pretraining
Pretraining a language model (LM) on text has been shown to help various downstream
NLP tasks. Recent works show that a knowledge graph (KG) can complement text data …
NLP tasks. Recent works show that a knowledge graph (KG) can complement text data …
Obtaining genetics insights from deep learning via explainable artificial intelligence
Artificial intelligence (AI) models based on deep learning now represent the state of the art
for making functional predictions in genomics research. However, the underlying basis on …
for making functional predictions in genomics research. However, the underlying basis on …
FlyBase: a guided tour of highlighted features
LS Gramates, J Agapite, H Attrill, BR Calvi… - Genetics, 2022 - academic.oup.com
FlyBase provides a centralized resource for the genetic and genomic data of Drosophila
melanogaster. As FlyBase enters our fourth decade of service to the research community …
melanogaster. As FlyBase enters our fourth decade of service to the research community …