Deciphering cell–cell interactions and communication from gene expression
E Armingol, A Officer, O Harismendy… - Nature Reviews …, 2021 - nature.com
Cell–cell interactions orchestrate organismal development, homeostasis and single-cell
functions. When cells do not properly interact or improperly decode molecular messages …
functions. When cells do not properly interact or improperly decode molecular messages …
Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols
In recent years, RNA-sequencing (RNA-seq) has emerged as a powerful technology for
transcriptome profiling. For a given gene, the number of mapped reads is not only …
transcriptome profiling. For a given gene, the number of mapped reads is not only …
Zinc cyclic di-AMP nanoparticles target and suppress tumours via endothelial STING activation and tumour-associated macrophage reinvigoration
The clinical utility of stimulator of interferon genes (STING) agonists has been limited due to
poor tumour-targeting and unwanted toxicity following systemic delivery. Here we describe a …
poor tumour-targeting and unwanted toxicity following systemic delivery. Here we describe a …
Exaggerated false positives by popular differential expression methods when analyzing human population samples
When identifying differentially expressed genes between two conditions using human
population RNA-seq samples, we found a phenomenon by permutation analysis: two …
population RNA-seq samples, we found a phenomenon by permutation analysis: two …
Three differential expression analysis methods for RNA sequencing: limma, EdgeR, DESeq2
S Liu, Z Wang, R Zhu, F Wang, Y Cheng… - JoVE (Journal of Visualized …, 2021 - jove.com
RNA sequencing (RNA-seq) is one of the most widely used technologies in transcriptomics
as it can reveal the relationship between the genetic alteration and complex biological …
as it can reveal the relationship between the genetic alteration and complex biological …
Integrated omics: tools, advances and future approaches
With the rapid adoption of high-throughput omic approaches to analyze biological samples
such as genomics, transcriptomics, proteomics, and metabolomics, each analysis can …
such as genomics, transcriptomics, proteomics, and metabolomics, each analysis can …
Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis
LA Corchete, EA Rojas, D Alonso-López… - Scientific reports, 2020 - nature.com
RNA-seq is currently considered the most powerful, robust and adaptable technique for
measuring gene expression and transcription activation at genome-wide level. As the …
measuring gene expression and transcription activation at genome-wide level. As the …
A multi-omics machine learning framework in predicting the survival of colorectal cancer patients
M Yang, H Yang, L Ji, X Hu, G Tian, B Wang… - Computers in biology and …, 2022 - Elsevier
Background Colorectal cancer (CRC), the 3rd most universal cancer globally, accounts for
approximately 10% of newly diagnosed cancer incidences each year. Identifying biomarkers …
approximately 10% of newly diagnosed cancer incidences each year. Identifying biomarkers …
A microbial sea of possibilities: current knowledge and prospects for an improved understanding of the fish microbiome
The mucosal surfaces of fish represent an important barrier that supports and regulates a
diverse array of microbial assemblages and contributes to the overall health and fitness of …
diverse array of microbial assemblages and contributes to the overall health and fitness of …
Artificial intelligence and machine learning approaches using gene expression and variant data for personalized medicine
S Vadapalli, H Abdelhalim, S Zeeshan… - Briefings in …, 2022 - academic.oup.com
Precision medicine uses genetic, environmental and lifestyle factors to more accurately
diagnose and treat disease in specific groups of patients, and it is considered one of the …
diagnose and treat disease in specific groups of patients, and it is considered one of the …