Systems Biology Journal Club Recommended Papers

I encourage members of my lab to recommend papers and post them into our electronic lab notebook. This list is a selection of those papers. Journal club students can pick from this list or find other papers that fit the overall topic and their area of research interests. I’ve put these into categories of introductory reviews, analytical methods, computational methods, and applications.

Introductory Reviews
Training in metabolomics research. I. Designing the experiment, collecting and extracting samples and generating metabolomics data.

Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future

Analytical Methods

Combining DI-ESI-MS and NMR datasets for metabolic profiling.

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions.

Getting Your Peaks in Line: A Review of Alignment Methods for NMR Spectral Data

Knowns and unknowns in metabolomics identified by multidimensional NMR and hybrid MS/NMR methods.

Computational Methods

Molecular Networking as a Dereplication Strategy

Increasing rigor in NMR-based metabolomics through validated and open source tools.

Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics

Power Analysis and Sample Size Determination in Metabolic Phenotyping 

Applications

Genetic Basis of Metabolome Variation in Yeast

The Pentose Phosphate Pathway Regulates the Circadian Clock

Human gut microbes impact host serum metabolome and insulin sensitivity

Interspecies Systems Biology Uncovers Metabolites Affecting C. elegans Gene Expression and Life History Traits

Glucose or Altered Ceramide Biosynthesis Mediate Oxygen Deprivation Sensitivity Through Novel Pathways Revealed by Transcriptome Analysis in Caenorhabditis elegans.

The Caenorhabditis elegans lipidome: A primer for lipid analysis in Caenorhabditis elegans

The mutational structure of metabolism in Caenorhabditis elegans.