Best practices for single-cell analysis across modalities

L Heumos, AC Schaar, C Lance, A Litinetskaya… - Nature Reviews …, 2023‏ - nature.com
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

[HTML][HTML] Revolutionizing medicinal chemistry: the application of artificial intelligence (AI) in early drug discovery

R Han, H Yoon, G Kim, H Lee, Y Lee - Pharmaceuticals, 2023‏ - mdpi.com
Artificial intelligence (AI) has permeated various sectors, including the pharmaceutical
industry and research, where it has been utilized to efficiently identify new chemical entities …

g: Profiler—interoperable web service for functional enrichment analysis and gene identifier map** (2023 update)

L Kolberg, U Raudvere, I Kuzmin, P Adler… - Nucleic acids …, 2023‏ - academic.oup.com
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 …

Persistent complement dysregulation with signs of thromboinflammation in active Long Covid

C Cervia-Hasler, SC Brüningk, T Hoch, B Fan, G Muzio… - Science, 2024‏ - science.org
Long Covid is a debilitating condition of unknown etiology. We performed multimodal
proteomics analyses of blood serum from COVID-19 patients followed up to 12 months after …

The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest

D Szklarczyk, R Kirsch, M Koutrouli… - Nucleic acids …, 2023‏ - academic.oup.com
Much of the complexity within cells arises from functional and regulatory interactions among
proteins. The core of these interactions is increasingly known, but novel interactions …

Spatially resolved multiomics of human cardiac niches

K Kanemaru, J Cranley, D Muraro, AMA Miranda… - Nature, 2023‏ - nature.com
The function of a cell is defined by its intrinsic characteristics and its niche: the tissue
microenvironment in which it dwells. Here we combine single-cell and spatial …

JBrowse 2: a modular genome browser with views of synteny and structural variation

C Diesh, GJ Stevens, P **e, T De Jesus Martinez… - Genome biology, 2023‏ - Springer
We present JBrowse 2, a general-purpose genome annotation browser offering enhanced
visualization of complex structural variation and evolutionary relationships. It retains core …

The reactome pathway knowledgebase 2024

M Milacic, D Beavers, P Conley, C Gong… - Nucleic acids …, 2024‏ - academic.oup.com
Abstract The Reactome Knowledgebase (https://reactome. org), an Elixir and GCBR core
biological data resource, provides manually curated molecular details of a broad range of …

The IUPHAR/BPS guide to PHARMACOLOGY in 2024

SD Harding, JF Armstrong, E Faccenda… - Nucleic acids …, 2024‏ - academic.oup.com
Abstract The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb; https://www.
guidetopharmacology. org) is an open-access, expert-curated, online database that …

LIPID MAPS: update to databases and tools for the lipidomics community

MJ Conroy, RM Andrews, S Andrews… - Nucleic Acids …, 2024‏ - academic.oup.com
Abstract LIPID MAPS (LIPID Metabolites and Pathways Strategy), www. lipidmaps. org,
provides a systematic and standardized approach to organizing lipid structural and …