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Taxonomic and diversity profiling of the microbiome - 16S rRNA gene amplicon sequence data

1 minute read


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. Read more

Quantitative proteomics: label-free quantitation of proteins

2 minute read


Liquid chromatography (LC) coupled with mass spectrometry (MS) has been widely used for protein expression quantification. Protein quantification by tandem-MS (MS/MS) uses integrated peak intensity from the parent-ion mass (MS1) or features from fragment-ions (MS2). MS1 methods use the iBAQ (intensity Based Absolute Quantification) algorithm (a protein’s total non-normalised intensities are divided by the number of measurable tryptic peptides). Untargeted label-free quantitation (LFQ) of proteins, aims to determine the relative amount of proteins in two or more biological samples. Read more

Genomic variants from RNA-Seq data

1 minute read


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. Read more

eQTL analysis of RNA-Seq data

less than 1 minute read


Genetic locus that affects gene expression is often referred to as expression quantitative trait locus (eQTL). eQTL mapping studies assesses the association of SNPs with genome-wide expression levels. Read more

Quality control for GWAS studies

1 minute read


An important step in the analysis of genome-wide association studies (GWAS) is to identify problematic subjects and markers. Quality control (QC) in GWAS removes markers and individuals, and greatly increases the accuracy of findings. Read more


Chromosomal distributuin of copy number variations

Copy number variation (CNV), generated through duplication or deletion events that affect one or more loci, is widespread in the human genomes and is often associated with functional consequences that may include changes in gene expression levels or fusion of genes.
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Analysis of inflammatory and lipid metabolic networks across RAW264.7 and thioglycolate-elicited macrophages.

Published in Journal of Lipid Research, 2013

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Recommended citation: Maurya MR, Gupta S, Li X, Fahy E, Dinasarapu AR, Sud M, Brown HA, Glass CK, Murphy RC, Russell DW, Dennis EA, Subramaniam S. (2013). "Analysis of inflammatory and lipid metabolic networks across RAW264.7 and thioglycolate-elicited macrophages." J Lipid Res. 54(9):2525-42.