CCPA: cloud-based, self-learning modules for consensus pathway analysis using GO, KEGG and Reactome
This manuscript describes the development of a resource module that is part of a learning
platform named 'NIGMS Sandbox for Cloud-based Learning'(https://github …
platform named 'NIGMS Sandbox for Cloud-based Learning'(https://github …
Alleviating batch effects in cell type deconvolution with SCCAF-D
S Feng, L Huang, AV Pournara, Z Huang… - Nature …, 2024 - nature.com
Cell type deconvolution methods can impute cell proportions from bulk transcriptomics data,
revealing changes in disease progression or organ development. But benchmarking studies …
revealing changes in disease progression or organ development. But benchmarking studies …
DeSide: A unified deep learning approach for cellular deconvolution of tumor microenvironment
X ** human brain through computational modeling
The human brain's distinctive folding pattern has attracted the attention of researchers from
different fields. Neuroscientists have provided insights into the role of four fundamental cell …
different fields. Neuroscientists have provided insights into the role of four fundamental cell …
Identifying representative sequences of protein families using submodular optimization
Identifying representative sequences for groups of functionally similar proteins and enzymes
poses significant computational challenges. In this study, we applied submodular …
poses significant computational challenges. In this study, we applied submodular …
A protocol for loading Calcein-AM into extracellular vesicles from mammalian cells for clear visualization with a fluorescence microscope coupled to a deconvolution …
Extracellular vesicles (EVs) are membrane-bound structures produced and released into the
extracellular space by all types of cells. Due to their characteristics, EVs play crucial roles in …
extracellular space by all types of cells. Due to their characteristics, EVs play crucial roles in …
Benchmarking second-generation methods for cell-type deconvolution of transcriptomic data
In silico cell-type deconvolution from bulk transcriptomics data is a powerful technique to
gain insights into the cellular composition of complex tissues. While first-generation methods …
gain insights into the cellular composition of complex tissues. While first-generation methods …
[HTML][HTML] Epigenomic, cistromic, and transcriptomic profiling of primary kidney tubular cells
Z Liu, L Zhang, Y Chen - Journal of Biological Methods, 2024 - pmc.ncbi.nlm.nih.gov
Spatiotemporal regulation of gene expression is essential for maintaining cellular
homeostasis throughout kidney development and disease progression. Transcription factors …
homeostasis throughout kidney development and disease progression. Transcription factors …
DECOMICS, a shiny application for unsupervised cell type deconvolution and biological interpretation of bulk omic data
Unsupervised deconvolution algorithms are often used to estimate cell composition from
bulk tissue samples. However, applying cell-type deconvolution and interpreting the results …
bulk tissue samples. However, applying cell-type deconvolution and interpreting the results …