Published:
Quantitative proteomics is a cutting-edge approach for measuring protein levels in complex biological samples. One innovative method in this field is aptamer-based protein quantification. Aptamers, which are short, single-stranded DNA or RNA molecules, are engineered to specifically bind to target proteins with high precision.
Published:
The Kaplan-Meier curve is a powerful tool in survival analysis, commonly used to estimate the probability of an event—such as survival—at different time intervals. It provides a visual representation of the time it takes for an event to occur across a patient population. This method is especially useful in medical studies where understanding survival rates is key.
Published:
Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.
Published:
Quantification of proteins using isobaric labeling (tandem mass tag or TMT) starts with the reduction of disulfide bonds in proteins with Dithiothreitol (DTT).
Published:
Updated on September 13, 2021
Published:
Running spaceranger as cluster mode that uses Sun Grid Engine (SGE) as queuing.
Published:
ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput Sequencing) is a next-generation sequencing approach for the analysis of open chromatin regions to assess the genome-wise chromatin accessibility.
Published:
Updated on November 28, 2023
Published:
The 16S ribosomal RNA (rRNA) gene of Bacteria codes for the RNA component of the 30S subunit. Different bacterial species have one to multiple copies of the 16S rRNA gene, and each with 9 hypervariable regions, V1-V9. High-throughput sequencing of 16S rRNA gene (a “marker gene”) amplicons has become a widely used method to study bacterial phylogeny and species classification.
Published:
This workflow consists of taxonomic and functional profiling of shotgun metagenomics sequencing (MGS) reads using MetaPhlAn2 and HUMAnN2, respectively. To perform taxonomic (phyla, genera or species level) profiling of the MGS data, the MetaPhlAn2 pipeline was run on a high performance multicore cluster computing environment.
Published:
A simple RNA-Seq differential expression analysis using High Performance Computing (HPC).
Published:
RNA-Seq allows the detection and quantification of known and rare RNA transcripts within a sample. In addition to differential expression and detection of novel transcripts, RNA-seq also supports the detection of genomic variation in expressed regions.
Published:
Understanding how genetic variations impact gene expression is crucial for uncovering the underlying mechanisms of complex traits and diseases. One powerful tool for this investigation is the expression quantitative trait locus (eQTL) analysis, which examines the relationship between genetic variants and genome-wide expression levels.
Published:
A crucial step in analyzing genome-wide association studies (GWAS) is identifying problematic subjects and markers. Quality control (QC) in GWAS involves removing unreliable markers and individuals, significantly enhancing the accuracy of results.
Published:
The human complement activation takes place through one or more of the well-established pathways consisting of plasma and membrane-bound proteins.
Published:
Copy number variations (CNVs) are genomic alterations that involve the gain or loss of specific regions of DNA. These variations can be inherited from parents or can arise de novo, and they play a significant role in neuropsychiatric disorders and cancers.