A guide to conquer the biological network era using graph theory
Networks are one of the most common ways to represent biological systems as complex sets
of binary interactions or relations between different bioentities. In this article, we discuss the …
of binary interactions or relations between different bioentities. In this article, we discuss the …
HERB: a high-throughput experiment-and reference-guided database of traditional Chinese medicine
Pharmacotranscriptomics has become a powerful approach for evaluating the therapeutic
efficacy of drugs and discovering new drug targets. Recently, studies of traditional Chinese …
efficacy of drugs and discovering new drug targets. Recently, studies of traditional Chinese …
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 …
Pervasive chromosomal instability and karyotype order in tumour evolution
Chromosomal instability in cancer consists of dynamic changes to the number and structure
of chromosomes,. The resulting diversity in somatic copy number alterations (SCNAs) may …
of chromosomes,. The resulting diversity in somatic copy number alterations (SCNAs) may …
How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?
RNA-seq is now the technology of choice for genome-wide differential gene expression
experiments, but it is not clear how many biological replicates are needed to ensure valid …
experiments, but it is not clear how many biological replicates are needed to ensure valid …
[HTML][HTML] Dynamics in transcriptomics: advancements in RNA-seq time course and downstream analysis
D Spies, C Ciaudo - Computational and structural biotechnology journal, 2015 - Elsevier
Abstract Analysis of gene expression has contributed to a plethora of biological and medical
research studies. Microarrays have been intensively used for the profiling of gene …
research studies. Microarrays have been intensively used for the profiling of gene …
[HTML][HTML] Transcriptional alterations in dorsolateral prefrontal cortex and nucleus accumbens implicate neuroinflammation and synaptic remodeling in opioid use …
Background Prevalence rates of opioid use disorder (OUD) have increased dramatically,
accompanied by a surge of overdose deaths. While opioid dependence has been …
accompanied by a surge of overdose deaths. While opioid dependence has been …
Combining multiple tools outperforms individual methods in gene set enrichment analyses
M Alhamdoosh, M Ng, NJ Wilson, JM Sheridan… - …, 2017 - academic.oup.com
Motivation Gene set enrichment (GSE) analysis allows researchers to efficiently extract
biological insight from long lists of differentially expressed genes by interrogating them at a …
biological insight from long lists of differentially expressed genes by interrogating them at a …
Application of human liver organoids as a patient-derived primary model for HBV infection and related hepatocellular carcinoma
The molecular events that drive hepatitis B virus (HBV)-mediated transformation and
tumorigenesis have remained largely unclear, due to the absence of a relevant primary …
tumorigenesis have remained largely unclear, due to the absence of a relevant primary …
Smyd3 is a transcriptional potentiator of multiple cancer-promoting genes and required for liver and colon cancer development
ME Sarris, P Moulos, A Haroniti, A Giakountis… - Cancer cell, 2016 - cell.com
Smyd3 is a protein methyltransferase implicated in cancer development. Here we show that
Smyd3 expression in mice is required for chemically induced liver and colon cancer …
Smyd3 expression in mice is required for chemically induced liver and colon cancer …