Using clusterProfiler to characterize multiomics data

S Xu, E Hu, Y Cai, Z **e, X Luo, L Zhan, W Tang… - Nature protocols, 2024 - nature.com
With the advent of multiomics, software capable of multidimensional enrichment analysis
has become increasingly crucial for uncovering gene set variations in biological processes …

Network pharmacology approaches for research of Traditional Chinese Medicines

LI **ang, LIU Ziqi, L Jie, C Qian, LU **aoyan… - Chinese Journal of …, 2023 - Elsevier
Pharmacodynamics material basis and effective mechanisms are the two main issues to
decipher the mechnisms of action of Traditional Chinese medicines (TCMs) for the treatment …

Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data

D Dimitrov, D Türei, M Garrido-Rodriguez… - Nature …, 2022 - nature.com
The growing availability of single-cell data, especially transcriptomics, has sparked an
increased interest in the inference of cell-cell communication. Many computational tools …

Integrating artificial intelligence for drug discovery in the context of revolutionizing drug delivery

AI Visan, I Negut - Life, 2024 - mdpi.com
Drug development is expensive, time-consuming, and has a high failure rate. In recent
years, artificial intelligence (AI) has emerged as a transformative tool in drug discovery …

Network pharmacology prediction and molecular docking-based strategy to explore the potential mechanism of Huanglian Jiedu Decoction against sepsis

X Li, S Wei, S Niu, X Ma, H Li, M **g, Y Zhao - Computers in biology and …, 2022 - Elsevier
Abstract Background Huanglian Jiedu Decoction (HLJDD) is a classical herbal formula with
potential efficacy in the treatment of sepsis. However, the main components and potential …

Artificial intelligence to deep learning: machine intelligence approach for drug discovery

R Gupta, D Srivastava, M Sahu, S Tiwari, RK Ambasta… - Molecular …, 2021 - Springer
Drug designing and development is an important area of research for pharmaceutical
companies and chemical scientists. However, low efficacy, off-target delivery, time …

The DisGeNET knowledge platform for disease genomics: 2019 update

J Piñero, JM Ramírez-Anguita… - Nucleic acids …, 2020 - academic.oup.com
One of the most pressing challenges in genomic medicine is to understand the role played
by genetic variation in health and disease. Thanks to the exploration of genomic variants at …

[HTML][HTML] Dual proteome-scale networks reveal cell-specific remodeling of the human interactome

EL Huttlin, RJ Bruckner, J Navarrete-Perea, JR Cannon… - Cell, 2021 - cell.com
Thousands of interactions assemble proteins into modules that impart spatial and functional
organization to the cellular proteome. Through affinity-purification mass spectrometry, we …

g: Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

U Raudvere, L Kolberg, I Kuzmin, T Arak… - Nucleic acids …, 2019 - academic.oup.com
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 …

EZH2 noncanonically binds cMyc and p300 through a cryptic transactivation domain to mediate gene activation and promote oncogenesis

J Wang, X Yu, W Gong, X Liu, KS Park, A Ma… - Nature cell …, 2022 - nature.com
Canonically, EZH2 serves as the catalytic subunit of PRC2, which mediates H3K27me3
deposition and transcriptional repression. Here, we report that in acute leukaemias, EZH2 …